176 results on '"David A. O'Connor"'
Search Results
2. Genetic Diversity and Evolutionary Convergence of Cryptic SARS-CoV-2 Lineages Detected Via Wastewater Sequencing
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Devon A. Gregory, Monica Trujillo, Clayton Rushford, Anna Flury, Sherin Kannoly, Kaung Myat San, Dustin Lyfoung, Roger W. Wiseman, Karen Bromert, Ming-Yi Zhou, Ellen Kesler, Nathan Bivens, Jay Hoskins, Chung-Ho Lin, David H. O’Connor, Chris Wieberg, Jeff Wenzel, Rose S. Kantor, John J. Dennehy, and Marc C. Johnson
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SARS-CoV-2 ,Virology ,Immunology ,Genetics ,Animals ,Humans ,COVID-19 ,Genetic Variation ,Parasitology ,Wastewater ,Molecular Biology ,Microbiology - Abstract
Wastewater-based epidemiology (WBE) is an effective way of tracking the appearance and spread of SARS-COV-2 lineages through communities. Beginning in early 2021, we implemented a targeted approach to amplify and sequence the receptor binding domain (RBD) of SARS-COV-2 to characterize viral lineages present in sewersheds. Over the course of 2021, we reproducibly detected multiple SARS-COV-2 RBD lineages that have never been observed in patient samples in 9 sewersheds located in 3 states in the USA. These cryptic lineages contained between 4 to 24 amino acid substitutions in the RBD and were observed intermittently in the sewersheds in which they were found for as long as 14 months. Many of the amino acid substitutions in these lineages occurred at residues also mutated in the Omicron variant of concern (VOC), often with the same substitution. One of the sewersheds contained a lineage that appeared to be derived from the Alpha VOC, but the majority of the lineages appeared to be derived from pre-VOC SARS-COV-2 lineages. Specifically, several of the cryptic lineages from New York City appeared to be derived from a common ancestor that most likely diverged in early 2020. While the source of these cryptic lineages has not been resolved, it seems increasingly likely that they were derived from immunocompromised patients or animal reservoirs. Our findings demonstrate that SARS-COV-2 genetic diversity is greater than what is commonly observed through routine SARS-CoV-2 surveillance. Wastewater sampling may more fully capture SARS-CoV-2 genetic diversity than patient sampling and could reveal new VOCs before they emerge in the wider human population.Author SummaryDuring the COVID-19 pandemic, wastewater-based epidemiology has become an effective public health tool. Because many infected individuals shed SARS-CoV-2 in feces, wastewater has been monitored to reveal infection trends in the sewersheds from which the samples were derived. Here we report novel SARS-CoV-2 lineages in wastewater samples obtained from 3 different states in the USA. These lineages appeared in specific sewersheds intermittently over periods of up to 14 months, but generally have not been detected beyond the sewersheds in which they were initially found. Many of these lineages may have diverged in early 2020. Although these lineages share considerable overlap with each other, they have never been observed in patients anywhere in the world. While the wastewater lineages have similarities with lineages observed in long-term infections of immunocompromised patients, animal reservoirs cannot be ruled out as a potential source.
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- 2022
3. Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual
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Peter J Halfmann, Nicholas R Minor, Luis A Haddock III, Robert Maddox, Gage K Moreno, Katarina M Braun, David A Baker, Kasen K Riemersa, Ankur Prasad, Kirsten J Alman, Matthew C Lambert, Kelsey Florek, Allen Bateman, Ryan Westergaard, Nasia Safdar, David R Andes, Yoshihiro Kawaoka, Madiha Fida, Joseph D Yao, Thomas C Friedrich, and David H O’Connor
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Virology ,Microbiology - Abstract
Prolonged infections in immunocompromised individuals may be a source for novel SARS-CoV-2 variants, particularly when both the immune system and antiviral therapy fail to clear the infection and enable within-host evolution. Here we describe a 486-day case of SARS-CoV-2 infection in an immunocompromised individual. Following monotherapy with the monoclonal antibody Bamlanivimab, the individual’s virus acquired resistance, likely via the earliest known occurrence of Spike amino acid variant E484T. Recently, E484T has arisen again as a derivative of E484A in the Omicron Variant of Concern, supporting the hypothesis that prolonged infections can give rise to novel variants long before they become prevalent in the human population.
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- 2022
4. Frequent first-trimester pregnancy loss in rhesus macaques infected with African-lineage Zika virus
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Jenna R. Rosinski, Lauren E. Raasch, Patrick Barros Tiburcio, Meghan E. Breitbach, Phoenix M. Shepherd, Keisuke Yamamoto, Elaina Razo, Nicholas P. Krabbe, Mason I. Bliss, Alexander D. Richardson, Morgan A. Einwalter, Andrea M. Weiler, Emily L. Sneed, Kerri B. Fuchs, Xiankun Zeng, Kevin K. Noguchi, Terry K. Morgan, Alexandra J. Alberts, Kathleen M. Antony, Sabrina Kabakov, Karla K. Ausderau, Ellie K. Bohm, Julia C. Pritchard, Rachel V. Spanton, James N. Ver Hoove, Charlene B. Y. Kim, T. Michael Nork, Alex W. Katz, Carol A. Rasmussen, Amy Hartman, Andres Mejia, Puja Basu, Heather A. Simmons, Jens C. Eickhoff, Thomas C. Friedrich, Matthew T. Aliota, Emma L. Mohr, Dawn M. Dudley, David H. O’Connor, and Christina M. Newman
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Virology ,Immunology ,Genetics ,Parasitology ,Molecular Biology ,Microbiology - Abstract
In the 2016 Zika virus (ZIKV) pandemic, a previously unrecognized risk of birth defects surfaced in babies whose mothers were infected with Asian-lineage ZIKV during pregnancy. Less is known about the impacts of gestational African-lineage ZIKV infections. Given high human immunodeficiency virus (HIV) burdens in regions where African-lineage ZIKV circulates, we evaluated whether pregnant rhesus macaques infected with simian immunodeficiency virus (SIV) have a higher risk of African-lineage ZIKV-associated birth defects. Remarkably, in both SIV+ and SIV-animals, ZIKV infection early in the first trimester caused a high incidence (78%) of spontaneous pregnancy loss within 20 days. These findings suggest a significant risk for early pregnancy loss associated with African-lineage ZIKV infection and provide the first consistent ZIKV-associated phenotype in macaques for testing medical countermeasures.
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- 2023
5. Antiretroviral therapy reveals triphasic decay of intact SIV genomes and persistence of ancestral variants
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Emily J. Fray, Fengting Wu, Francesco R. Simonetti, Carolin Zitzmann, Narmada Sambaturu, Carmen Molina-Paris, Alexandra M. Bender, Po-Ting Liu, John D. Ventura, Roger W. Wiseman, David H. O’Connor, Romas Geleziunas, Thomas Leitner, Ruy M. Ribeiro, Alan S. Perelson, Dan H. Barouch, Janet D. Siliciano, and Robert F. Siliciano
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Virology ,Parasitology ,Microbiology - Published
- 2023
6. Spondweni virus causes fetal harm in Ifnar1 mice and is transmitted by Aedes aegypti mosquitoes
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Shelby L. O’Connor, Anna S. Jaeger, Matthew T. Aliota, Davis M. Seelig, Andrea M. Weiler, Michael K. Fritsch, Thomas C. Friedrich, David H. O’Connor, Sierra Rybarczyk, and Ryan V. Moriarty
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Placental histopathology ,Mosquito Vectors ,Receptor, Interferon alpha-beta ,Aedes aegypti ,medicine.disease_cause ,Article ,Flavivirus Infections ,Zika virus ,Mice ,03 medical and health sciences ,Aedes ,Virology ,parasitic diseases ,medicine ,Animals ,Humans ,Congenital zika syndrome ,030304 developmental biology ,Mice, Knockout ,Arbovirus ,Spondweni virus ,0303 health sciences ,Fetus ,biology ,Flavivirus ,fungi ,030302 biochemistry & molecular biology ,virus diseases ,biology.organism_classification ,Culex quinquefasciatus ,Mice, Inbred C57BL ,Disease Models, Animal ,Female ,Vector competence - Abstract
Spondweni virus (SPONV) is the most closely related known flavivirus to Zika virus (ZIKV). Its pathogenic potential and vector specificity have not been well defined. SPONV has been found predominantly in Africa, but was recently detected in a pool of Culex quinquefasciatus mosquitoes in Haiti. Here we show that SPONV can cause significant fetal harm, including demise, comparable to ZIKV, in a mouse model of vertical transmission. Following maternal inoculation, we detected infectious SPONV in placentas and fetuses, along with significant fetal and placental histopathology, together suggesting vertical transmission. To test vector competence, we exposed Aedes aegypti and Culex quinquefasciatus mosquitoes to SPONV-infected bloodmeals. Aedes aegypti could efficiently transmit SPONV, whereas Culex quinquefasciatus could not. Our results suggest that SPONV has the same features that made ZIKV a public health risk.
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- 2020
7. Shedding of infectious SARS-CoV-2 despite vaccination
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Kasen K. Riemersma, Luis A. Haddock, Nancy A. Wilson, Nicholas Minor, Jens Eickhoff, Brittany E. Grogan, Amanda Kita-Yarbro, Peter J. Halfmann, Hannah E. Segaloff, Anna Kocharian, Kelsey R. Florek, Ryan Westergaard, Allen Bateman, Gunnar E. Jeppson, Yoshihiro Kawaoka, David H. O’Connor, Thomas C. Friedrich, and Katarina M. Grande
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Delta ,Cycle threshold ,COVID-19 Vaccines ,business.industry ,SARS-CoV-2 ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Immunology ,Vaccination ,Immune escape ,Outbreak ,COVID-19 ,Viral Vaccines ,Microbiology ,Virology ,Immunization ,Genetics ,Medicine ,Humans ,Parasitology ,business ,Molecular Biology ,Viral load - Abstract
The SARS-CoV-2 Delta Variant of Concern is highly transmissible and contains mutations that confer partial immune escape. The emergence of Delta in North America caused the first surge in COVID-19 cases after SARS-CoV-2 vaccines became widely available. To determine whether individuals infected despite vaccination might be capable of transmitting SARS-CoV-2, we compared RT-PCR cycle threshold (Ct) data from 20,431 test-positive anterior nasal swab specimens from fully vaccinated (n = 9,347) or unvaccinated (n=11,084) individuals tested at a single commercial laboratory during the interval 28 June – 1 December 2021 when Delta variants were predominant. We observed no significant effect of vaccine status alone on Ct value, nor when controlling for vaccine product or sex. Testing a subset of low-Ct (
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- 2021
8. Neonatal Development in Prenatally Zika Virus-Exposed Infant Macaques with Dengue Immunity
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Natalie Dulaney, Kathleen M. Antony, Saverio Capuano, Cristhian Salas-Quinchucua, Mason Bliss, Andres Mejia, Sabrina A. Kabakov, Thomas C. Friedrich, Chelsea M. Crooks, Matthew T. Aliota, Jens C. Eickhoff, Heather A. Simmons, David H. O’Connor, Thaddeus G. Golos, Ann Mitzey, Logan T Keding, Lex G. Medina-Magües, Andrea M. Weiler, Mary L. Schneider, Emma L. Mohr, Kathryn M. Bach, Elaina Razo, Karla Ausderau, and Terry K. Morgan
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Offspring ,viruses ,prenatal ZIKV exposure ,Dengue virus ,Motor Activity ,medicine.disease_cause ,Antibodies, Viral ,Microbiology ,Macaque ,Nervous System ,Virus ,Article ,Dengue fever ,Zika virus ,Dengue ,Fetal Development ,Immunity ,Pregnancy ,Virology ,biology.animal ,Orientation ,Medicine ,Animals ,Pregnancy Complications, Infectious ,biology ,neurodevelopment ,business.industry ,Zika Virus Infection ,virus diseases ,Zika Virus ,biochemical phenomena, metabolism, and nutrition ,Dengue Virus ,medicine.disease ,biology.organism_classification ,Macaca mulatta ,QR1-502 ,maternal DENV infection ,macaque model ,Disease Models, Animal ,Infectious Diseases ,Animals, Newborn ,Prenatal Exposure Delayed Effects ,Immunology ,Female ,business - Abstract
Infants exposed to Zika virus (ZIKV) prenatally may develop birth defects, developmental deficits, or remain asymptomatic. It is unclear why some infants are more affected than others, although enhancement of maternal ZIKV infection via immunity to an antigenically similar virus, dengue virus (DENV), may play a role. We hypothesized that DENV immunity may worsen prenatal ZIKV infection and developmental deficits in offspring. We utilized a translational macaque model to examine how maternal DENV immunity influences ZIKV-exposed infant macaque neurodevelopment in the first month of life. We inoculated eight macaques with prior DENV infection with ZIKV, five macaques with ZIKV, and four macaques with saline. DENV/ZIKV-exposed infants had significantly worse visual orientation skills than ZIKV-exposed infants whose mothers were DENV-naive, with no differences in motor, sensory or state control development. ZIKV infection characteristics and pregnancy outcomes did not individually differ between dams with and without DENV immunity, but when multiple factors were combined in a multivariate model, maternal DENV immunity combined with ZIKV infection characteristics and pregnancy parameters predicted select developmental outcomes. We demonstrate that maternal DENV immunity exacerbates visual orientation and tracking deficits in ZIKV-exposed infant macaques, suggesting that human studies should evaluate how maternal DENV immunity impacts long-term neurodevelopment.
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- 2021
9. Previous exposure to dengue virus is associated with increased Zika virus burden at the maternal-fetal interface in rhesus macaques
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Dawn M. Dudley, David H. O’Connor, Thaddeus G. Golos, Leah C. Katzelnick, Terry K. Morgan, Eric Peterson, Elizabeth A. Brown, Andrea M. Weiler, Keisuke Yamamoto, Eva Harris, Chelsea M. Crooks, Anna S. Jaeger, Megan E. Murphy, Angel Balmaseda, Thomas C. Friedrich, Amber Possell, Sierra Rybarczyk, Katarina M. Braun, Jens C. Eickhoff, Kara Weaver, Heather A. Simmons, Christina M. Newman, Elaina Razo, Mason Bliss, Phoenix M. Shepherd, Nancy Schultz-Darken, Ann Mitzey, Kathleen M. Antony, Andres Mejia, Jennifer M. Hayes, Emma L. Mohr, Matthew T. Aliota, and Michael K. Fritsch
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0301 basic medicine ,RNA viruses ,Viral Diseases ,Embryology ,Physiology ,viruses ,Placenta ,Maternal Health ,RC955-962 ,Dengue virus ,Monkeys ,medicine.disease_cause ,Pathology and Laboratory Medicine ,Antibodies, Viral ,Virus Replication ,Macaque ,Biochemistry ,Zika virus ,Dengue ,0302 clinical medicine ,Medical Conditions ,Pregnancy ,Arctic medicine. Tropical medicine ,Immune Physiology ,Medicine and Health Sciences ,Medicine ,030212 general & internal medicine ,Antigens, Viral ,Maternal-Fetal Exchange ,Mammals ,Immune System Proteins ,biology ,Zika Virus Infection ,virus diseases ,Eukaryota ,Obstetrics and Gynecology ,Infectious Diseases ,Medical Microbiology ,Viral Pathogens ,Vertebrates ,Viruses ,RNA, Viral ,Female ,Antibody ,Public aspects of medicine ,RA1-1270 ,Pathogens ,Anatomy ,Viral load ,Research Article ,Primates ,Immunology ,Viremia ,Microbiology ,Antibodies ,03 medical and health sciences ,Immunity ,biology.animal ,Old World monkeys ,Animals ,Microbial Pathogens ,Biology and life sciences ,Flaviviruses ,business.industry ,Public Health, Environmental and Occupational Health ,Organisms ,Reproductive System ,Proteins ,Zika Virus ,biochemical phenomena, metabolism, and nutrition ,Dengue Virus ,biology.organism_classification ,medicine.disease ,Virology ,Infectious Disease Transmission, Vertical ,030104 developmental biology ,Viral replication ,Amniotes ,biology.protein ,Women's Health ,business ,Zoology ,Developmental Biology - Abstract
Concerns have arisen that pre-existing immunity to dengue virus (DENV) could enhance Zika virus (ZIKV) disease, due to the homology between ZIKV and DENV and the observation of antibody-dependent enhancement (ADE) among DENV serotypes. To date, no study has examined the impact of pre-existing DENV immunity on ZIKV pathogenesis during pregnancy in a translational non-human primate model. Here we show that macaques with a prior DENV-2 exposure had a higher burden of ZIKV vRNA in maternal-fetal interface tissues as compared to DENV-naive macaques. However, pre-existing DENV immunity had no detectable impact on ZIKV replication kinetics in maternal plasma, and all pregnancies progressed to term without adverse outcomes or gross fetal abnormalities detectable at delivery. Understanding the risks of ADE to pregnant women worldwide is critical as vaccines against DENV and ZIKV are developed and licensed and as DENV and ZIKV continue to circulate., Author summary Zika virus (ZIKV) gained global attention during an explosive outbreak in the Americas in 2015–16 when it was causally associated with the constellation of birth defects now termed congenital Zika syndrome (CZS). However, a substantial proportion of gestational ZIKV infections result in babies without apparent birth defects. Could there be other factors that influence ZIKV pathogenicity? For example, it is well-established that pre-existing immunity to one dengue virus (DENV) serotype can enhance the severity of a secondary DENV infection. ZIKV is antigenically closely related to DENV, but whether DENV-specific antibodies enhance the severity of ZIKV infection is unclear. To answer this question, we used our non-human primate model of ZIKV to assess the impact of pre-existing immunity to DENV on ZIKV pathogenesis during pregnancy. We did not observe any difference in ZIKV replication in plasma between macaques that were immune to DENV and those that were not. However, there was more ZIKV vRNA detected in the placenta of macaques immune to DENV, suggesting DENV immunity could enhance ZIKV infection of the placenta. As vaccines to both DENV and ZIKV are developed, it remains critical to understand the risks of DENV immunity for pregnant women exposed to ZIKV.
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- 2021
10. Characterization of a new SARS-CoV-2 variant that emerged in Brazil
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Hiroaki Mitsuya, Tadashi Maemura, Ichiro Nakachi, Rie Baba, Riccardo Valdez, Hiroyuki Nagai, Hideaki Nakajima, Tetsuya Suzuki, Michiko Koga, Junichi Ochi, Tadaki Suzuki, Aubree Gordon, Samantha Loeber, Kensuke Fujita, Kenji Maeda, Maki Kiso, Carmen Gherasim, David A. Baker, Norio Sugaya, Makoto Saito, Noriko Nakajima, Yoshihiro Kawaoka, Takayuki Ogura, John J. Baczenas, Moe Okuda, Hideaki Kato, Kiyoko Iwatsuki-Horimoto, Shuetsu Fukushi, Hiroshi Ueki, Tiago J. S. Lopes, Yudai Kuroda, Shiho Chiba, Tokiko Watanabe, Makoto Kuroda, Norio Ohmagari, Tsuguto Fujimoto, Masaki Imai, Osamu Akasaka, Peter Halfmann, Masato Hatta, Michiko Ujie, Eisuke Adachi, Ken Maeda, Shelby L. O’Connor, Hiroshi Yotsuyanagi, Atsuhiro Yasuhara, Shinya Yamamoto, Amie J. Eisfeld, Yusuke Miyazato, Kenta Takahashi, Keiko Mitamura, Yuko Sakai-Tagawa, Mutsumi Ito, Shin ichiro Hattori, Morio Nakamura, Yuri Furusawa, David H. O’Connor, Seiya Yamayoshi, and Kazuma Yagi
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0106 biological sciences ,0301 basic medicine ,Letter ,viruses ,Virus Replication ,Microbiology ,01 natural sciences ,Neutralization ,reinfection ,Mice ,03 medical and health sciences ,Immunogenicity, Vaccine ,Immune system ,Antigen ,Cricetinae ,Animals ,Humans ,skin and connective tissue diseases ,Lung ,Infectivity ,Multidisciplinary ,Mesocricetus ,biology ,SARS-CoV-2 ,fungi ,virus diseases ,COVID-19 ,convalescent human plasma ,X-Ray Microtomography ,Biological Sciences ,biology.organism_classification ,Antibodies, Neutralizing ,Virology ,body regions ,Titer ,030104 developmental biology ,P.1 variant ,Viral replication ,Spike Glycoprotein, Coronavirus ,biology.protein ,Antibody ,Syrian hamsters ,010606 plant biology & botany - Abstract
Significance Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are of concern, with the P.1 variants dominating in Brazil. Brazil is now seeing a record number of deaths. Here, we report that the pathogenicity in hamsters of a P.1 variant is similar to that of nonvariant SARS-CoV-2. However, it has an expanded host range as shown by its replication in mice. Prior infection with nonvariant SARS-CoV-2 strains efficiently prevented replication of the P.1 variant in the lower respiratory tract of hamsters upon reinfection. Convalescent sera from patients infected with nonvariants or sera from messenger RNA vaccinees showed comparable neutralization titers among the P.1 and previously circulating strains. These results suggest that previous SARS-CoV-2 infection and vaccines based on the original SARS-CoV-2 will provide some protection against P.1 infection., The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a key role in viral infectivity. It is also the major antigen stimulating the host's protective immune response, specifically, the production of neutralizing antibodies. Recently, a new variant of SARS-CoV-2 possessing multiple mutations in the S protein, designated P.1, emerged in Brazil. Here, we characterized a P.1 variant isolated in Japan by using Syrian hamsters, a well-established small animal model for the study of SARS-CoV-2 disease (COVID-19). In hamsters, the variant showed replicative abilities and pathogenicity similar to those of early and contemporary strains (i.e., SARS-CoV-2 bearing aspartic acid [D] or glycine [G] at position 614 of the S protein). Sera and/or plasma from convalescent patients and BNT162b2 messenger RNA vaccinees showed comparable neutralization titers across the P.1 variant, S-614D, and S-614G strains. In contrast, the S-614D and S-614G strains were less well recognized than the P.1 variant by serum from a P.1-infected patient. Prior infection with S-614D or S-614G strains efficiently prevented the replication of the P.1 variant in the lower respiratory tract of hamsters upon reinfection. In addition, passive transfer of neutralizing antibodies to hamsters infected with the P.1 variant or the S-614G strain led to reduced virus replication in the lower respiratory tract. However, the effect was less pronounced against the P.1 variant than the S-614G strain. These findings suggest that the P.1 variant may be somewhat antigenically different from the early and contemporary strains of SARS-CoV-2.
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- 2021
11. Development and Characterization of a cDNA-Launch Recombinant Simian Hemorrhagic Fever Virus Expressing Enhanced Green Fluorescent Protein: ORF 2b’ Is Not Required for In Vitro Virus Replication
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Courtney L. Finch, Jens H. Kuhn, Ying Fang, Shuiqing Yu, Michael Lauck, Thomas C. Friedrich, David H. O’Connor, Yanhua Li, Peter B. Jahrling, Laura Bollinger, Reed F. Johnson, Gustavo Palacios, Elena Postnikova, Sheli R. Radoshitzky, Yíngyún Caì, Tony L. Goldberg, and Steven Mazur
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0301 basic medicine ,Nidovirales ,Simian hemorrhagic fever virus ,DNA, Complementary ,Arterivirus ,viruses ,030106 microbiology ,Green Fluorescent Proteins ,Clone (cell biology) ,lcsh:QR1-502 ,Rodentia ,Virus Replication ,Proof of Concept Study ,Article ,Arteriviridae ,lcsh:Microbiology ,Cell Line ,03 medical and health sciences ,Open Reading Frames ,reverse genetics ,Plasmid ,Virology ,Complementary DNA ,Chiroptera ,SHFV ,Animals ,Humans ,Simarterivirinae ,Tropism ,Recombination, Genetic ,biology ,cell tropism ,infectious clone ,Hominidae ,biology.organism_classification ,simarterivirin ,simian hemorrhagic fever virus ,Open reading frame ,030104 developmental biology ,Infectious Diseases ,Viral replication ,RNA, Viral ,simarterivirus ,Plasmids - Abstract
Simian hemorrhagic fever virus (SHFV) causes acute, lethal disease in macaques. We developed a single-plasmid cDNA-launch infectious clone of SHFV (rSHFV) and modified the clone to rescue an enhanced green fluorescent protein-expressing rSHFV-eGFP that can be used for rapid and quantitative detection of infection. SHFV has a narrow cell tropism in vitro, with only the grivet MA-104 cell line and a few other grivet cell lines being susceptible to virion entry and permissive to infection. Using rSHFV-eGFP, we demonstrate that one cricetid rodent cell line and three ape cell lines also fully support SHFV replication, whereas 55 human cell lines, 11 bat cell lines, and three rodent cells do not. Interestingly, some human and other mammalian cell lines apparently resistant to SHFV infection are permissive after transfection with the rSHFV-eGFP cDNA-launch plasmid. To further demonstrate the investigative potential of the infectious clone system, we introduced stop codons into eight viral open reading frames (ORFs). This approach suggested that at least one ORF, ORF 2b’, is dispensable for SHFV in vitro replication. Our proof-of-principle experiments indicated that rSHFV-eGFP is a useful tool for illuminating the understudied molecular biology of SHFV.
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- 2021
12. A cellular trafficking signal in the SIV envelope protein cytoplasmic domain is strongly selected for in pathogenic infection
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Scott P. Lawrence, Samra E. Elser, Workineh Torben, Robert V. Blair, Bapi Pahar, Pyone P. Aye, Faith Schiro, Dawn Szeltner, Lara A. Doyle-Meyers, Beth S. Haggarty, Andrea P. O. Jordan, Josephine Romano, George J. Leslie, Xavier Alvarez, David H. O’Connor, Roger W. Wiseman, Christine M. Fennessey, Yuan Li, Michael Piatak, Jeffrey D. Lifson, Celia C. LaBranche, Andrew A. Lackner, Brandon F. Keele, Nicholas J. Maness, Mark Marsh, and James A. Hoxie
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Virology ,Immunology ,Simian Acquired Immunodeficiency Syndrome ,Genetics ,Animals ,Gene Products, env ,Simian Immunodeficiency Virus ,Parasitology ,Macaca nemestrina ,Macaca mulatta ,Molecular Biology ,Microbiology ,Endocytosis - Abstract
The HIV/SIV envelope glycoprotein (Env) cytoplasmic domain contains a highly conserved Tyr-based trafficking signal that mediates both clathrin-dependent endocytosis and polarized sorting. Despite extensive analysis, the role of these functions in viral infection and pathogenesis is unclear. An SIV molecular clone (SIVmac239) in which this signal is inactivated by deletion of Gly-720 and Tyr-721 (SIVmac239ΔGY), replicates acutely to high levels in pigtail macaques (PTM) but is rapidly controlled. However, we previously reported that rhesus macaques and PTM can progress to AIDS following SIVmac239ΔGY infection in association with novel amino acid changes in the Env cytoplasmic domain. These included an R722G flanking the ΔGY deletion and a nine nucleotide deletion encoding amino acids 734–736 (ΔQTH) that overlaps therevandtatopen reading frames. We show that molecular clones containing these mutations reconstitute signals for both endocytosis and polarized sorting. In one PTM, a novel genotype was selected that generated a new signal for polarized sorting but not endocytosis. This genotype, together with the ΔGY mutation, was conserved in association with high viral loads for several months when introduced into naïve PTMs. For the first time, our findings reveal strong selection pressure for Env endocytosis and particularly for polarized sorting during pathogenic SIV infectionin vivo.
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- 2022
13. A tyrosine-based trafficking signal in the simian immunodeficiency virus envelope cytoplasmic domain is strongly selected for in pathogenic SIV infection
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Faith Schiro, Robert V Blair, Mark Marsh, Bapi Pahar, Celia C. LaBranche, David H. O’Connor, Beth S. Haggarty, Christine M. Fennessey, Dawn M. Szeltner, Yuxing Li, Nicholas J. Maness, James A. Hoxie, Workineh Torben, Xavier Alvarez, Brandon F. Keele, Josephine Romano, Jeffrey D. Lifson, Scott P. Lawrence, Lara A. Doyle-Meyers, Samra E. Elser, Michael Piatak, Roger W. Wiseman, Andrea P. O. Jordan, Pyone P. Aye, and Andrew A. Lackner
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chemistry.chemical_classification ,Mutation ,Clone (cell biology) ,Pigtail macaque ,Simian immunodeficiency virus ,Biology ,Endocytosis ,medicine.disease_cause ,biology.organism_classification ,Virology ,Open reading frame ,chemistry ,medicine ,Tyrosine ,Glycoprotein - Abstract
SUMMARYThe HIV/SIV envelope glycoprotein (Env) cytoplasmic domain contains a highly conserved Tyr-dependent trafficking signal that mediates both clathrin-dependent endocytosis and polarized sorting of Env. Despite extensive characterization, the role of these functions in viral infection and pathogenesis is unclear. An SIV molecular clone (SIVmac239) in which the Tyr-based signal is inactivated by deletion of Gly-720 and Tyr-721 (SIVmac239ΔGY) replicates to high levels acutely in pigtail macaques (PTM) but is rapidly controlled. We previously reported that rhesus macaques and PTM can progress to AIDS following SIVmac239ΔGY infection in association with novel amino acid changes in the Env cytoplasmic domain. These included an R722G flanking the ΔGY deletion and a nine nucleotide deletion that encodes amino acids 734-736 (ΔQTH) and overlaps with the rev and tat open reading frames. We show that molecular clones containing these mutations reconstitute signals for both endocytosis and polarized sorting. In one PTM, a novel genotype was selected, which generated a new signal for polarized sorting but not endocytosis. This mutation by itself was sufficient to maintain high viral loads for several months when introduced into naïve PTMs. These findings reveal, for the first time, strong selection pressure for Env endocytosis and, in particular, for polarized sorting during pathogenic SIV infection in vivo.
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- 2021
14. Initial evaluation of a mobile SARS-CoV-2 RT-LAMP testing strategy
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Miranda R Stauss, Elizabeth D Somsen, Olivia E Harwood, Roger W. Wiseman, Matthew R. Reynolds, Hailey E. Bussan, Cecilia G. Shortreed, Corrie B. Burmeister, Ryan V. Moriarty, Laurel M. Stewart, William M. Rehrauer, Thomas C. Friedrich, Katrina N Fauser, Christina M. Newman, Mason Bliss, Julie A. Karl, Amelia K. Haj, Kristi L Hall, David H. O’Connor, Andrea M. Weiler, Anna S. Heffron, Dawn M. Dudley, Chelsea M. Crooks, Shelby L. O’Connor, Trent M. Prall, Matthew T. McLaughlin, Luis A. Haddock, Robert J Maddox, Mitchell D. Ramuta, Emma K. Neumann, and Molly A. Accola
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Test strategy ,Saliva ,Concordance ,Loop-mediated isothermal amplification ,Asymptomatic ,Sensitivity and Specificity ,Article ,law.invention ,COVID-19 Testing ,law ,Medicine ,Humans ,Molecular Biology ,Polymerase chain reaction ,business.industry ,SARS-CoV-2 ,RNA ,COVID-19 ,Articles ,Virology ,Reverse transcriptase ,Molecular Diagnostic Techniques ,RNA, Viral ,medicine.symptom ,business ,Nucleic Acid Amplification Techniques - Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) control in the United States remains hampered, in part, by testing limitations. We evaluated a simple, outdoor, mobile, colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay workflow where self-collected saliva is tested for SARS-CoV-2 RNA. From July 16 to November 19, 2020, 4,704 surveillance samples were collected from volunteers and tested for SARS-CoV-2 at 5 sites. A total of 21 samples tested positive for SARS-CoV-2 by RT-LAMP; 12 were confirmed positive by subsequent quantitative reverse-transcription polymerase chain reaction (qRT-PCR) testing, while 8 were negative for SARS-CoV-2 RNA, and 1 could not be confirmed because the donor did not consent to further molecular testing. We estimated the RT-LAMP assay’s false-negative rate from July 16 to September 17, 2020 by pooling residual heat-inactivated saliva that was unambiguously negative by RT-LAMP into groups of 6 or less and testing for SARS-CoV-2 RNA by qRT-PCR. We observed a 98.8% concordance between the RT-LAMP and qRT-PCR assays, with only 5 of 421 RT-LAMP negative pools (2,493 samples) testing positive in the more sensitive qRT-PCR assay. Overall, we demonstrate a rapid testing method that can be implemented outside the traditional laboratory setting by individuals with basic molecular biology skills and can effectively identify asymptomatic individuals who would not typically meet the criteria for symptom-based testing modalities.
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- 2021
15. Prior dengue immunity enhances Zika virus infection of the maternal-fetal interface in rhesus macaques
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Michael K. Fritsch, Elaina Razo, Dawn M. Dudley, Megan E. Murphy, Andres Mejia, Elizabeth A. Brown, Thomas C. Friedrich, Amber Possell, Thaddeus G. Golos, Andrea M. Weiler, David H. O’Connor, Sierra Rybarczyk, Keisuke Yamamoto, Matthew T. Aliota, Terry K. Morgan, Kara Weaver, Eva Harris, Leah C. Katzelnick, Phoenix M. Shepherd, Emma L. Mohr, Chelsea M. Crooks, Jens C. Eickhoff, Christina M. Newman, Angel Balmaseda, Ann Mitzey, Anna S. Jaeger, Kathleen M. Antony, Eric J. Peterson, Mason Bliss, Nancy Schultz-Darken, Katarina M. Braun, Heather A. Simmons, and Jennifer M. Hayes
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Pregnancy ,biology ,Adverse outcomes ,business.industry ,viruses ,virus diseases ,Disease ,biochemical phenomena, metabolism, and nutrition ,Dengue virus ,biology.organism_classification ,medicine.disease ,medicine.disease_cause ,Virology ,Zika virus ,Dengue fever ,Immunity ,Medicine ,Maternal fetal ,business - Abstract
Concerns have arisen that pre-existing immunity to dengue virus (DENV) could enhance Zika virus (ZIKV) disease, due to the homology between ZIKV and DENV and the observation of antibody-dependent enhancement (ADE) among DENV serotypes. To date, no study has examined the impact of pre-existing DENV immunity on ZIKV pathogenesis during pregnancy in a translational non-human primate model. Here we show that prior DENV-2 exposure enhanced ZIKV infection of maternal-fetal interface tissues in macaques. However, pre-existing DENV immunity had no detectable impact on ZIKV replication kinetics in maternal plasma, and all pregnancies progressed to term without adverse outcomes or gross fetal abnormalities detectable at delivery. Understanding the risks of ADE to pregnant women worldwide is critical as vaccines against DENV and ZIKV are developed and licensed and as DENV and ZIKV continue to circulate.
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- 2021
16. Ribonuclease zymogen induces cytotoxicity upon HIV-1 infection
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Ian W. Windsor, Dawn M. Dudley, Ronald T. Raines, and David H. O’Connor
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Models, Molecular ,RNase P ,medicine.medical_treatment ,HIV Infections ,Ribonucleases ,Virology ,Zymogen ,medicine ,Cytotoxic T cell ,Animals ,Humans ,Pharmacology (medical) ,Ribonuclease ,chemistry.chemical_classification ,Enzyme Precursors ,Protease ,biology ,business.industry ,Research ,RNA ,RC581-607 ,Amino acid ,Enzyme ,Biochemistry ,chemistry ,biology.protein ,HIV-1 ,Molecular Medicine ,Immunologic diseases. Allergy ,business - Abstract
BackgroundTargeting RNA is a promising yet underdeveloped modality for the selective killing of cells infected with HIV-1. The secretory ribonucleases (RNases) found in vertebrates have cytotoxic ribonucleolytic activity that is kept in check by a cytosolic ribonuclease inhibitor protein, RI.MethodsWe engineered amino acid substitutions that enable human RNase 1 to evade RI upon its cyclization into a zymogen that is activated by the HIV-1 protease. In effect, the zymogen has an HIV-1 protease cleavage site between the termini of the wild-type enzyme, thereby positioning a cleavable linker over the active site that blocks access to a substrate.ResultsThe amino acid substitutions in RNase 1 diminish its affinity for RI by 106-fold and confer high toxicity for T-cell leukemia cells. Pretreating these cells with the zymogen leads to a substantial drop in their viability upon HIV-1 infection, indicating specific toxicity toward infected cells.ConclusionsThese data demonstrate the utility of ribonuclease zymogens as biologic prodrugs.
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- 2021
17. Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck
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Katarina M. Braun, Tadashi Maemura, Gage K. Moreno, Yoshihiro Kawaoka, Emma B. Hodcroft, Andrea M. Weiler, Masato Hatta, Shiho Chiba, Amelia K. Haj, Peter Halfmann, Thomas C. Friedrich, Emma C. Boehm, David A. Baker, David H. O’Connor, and Katia Koelle
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RNA viruses ,Evolutionary Genetics ,Pulmonology ,Coronaviruses ,Adaptation, Biological ,Cat Diseases ,law.invention ,Negative selection ,0302 clinical medicine ,Medical Conditions ,law ,030212 general & internal medicine ,Biology (General) ,610 Medicine & health ,Phylogeny ,Pathology and laboratory medicine ,Mammals ,COVID-19 ,Genetic drift ,Domestic animals ,Mammalian genomics ,Viral transmission and infection ,SARS CoV 2 ,Respiratory infections ,Viral evolution ,Cats ,0303 health sciences ,CATS ,Eukaryota ,Medical microbiology ,Biological Evolution ,Fixation (population genetics) ,Transmission (mechanics) ,Infectious Diseases ,Viruses ,Vertebrates ,Pathogens ,360 Social problems & social services ,Research Article ,Evolutionary Processes ,SARS coronavirus ,QH301-705.5 ,Immunology ,Biology ,Microbiology ,Bottleneck ,Article ,Viral Evolution ,Evolution, Molecular ,03 medical and health sciences ,Respiratory Disorders ,Virology ,Genetic variation ,Genetics ,Humans ,Animals ,Selection, Genetic ,Molecular Biology ,Selection (genetic algorithm) ,030304 developmental biology ,Medicine and health sciences ,Evolutionary Biology ,Biology and life sciences ,Population Biology ,SARS-CoV-2 ,Genetic Drift ,Organisms ,Viral pathogens ,Genetic Variation ,RNA virus ,RC581-607 ,biology.organism_classification ,Organismal Evolution ,Microbial pathogens ,Evolutionary biology ,Amniotes ,Microbial Evolution ,Respiratory Infections ,Parasitology ,Adaptation ,Immunologic diseases. Allergy ,Zoology ,Population Genetics ,Viral Transmission and Infection - Abstract
The evolutionary mechanisms by which SARS-CoV-2 viruses adapt to mammalian hosts and, potentially, undergo antigenic evolution depend on the ways genetic variation is generated and selected within and between individual hosts. Using domestic cats as a model, we show that SARS-CoV-2 consensus sequences remain largely unchanged over time within hosts, while dynamic sub-consensus diversity reveals processes of genetic drift and weak purifying selection. We further identify a notable variant at amino acid position 655 in Spike (H655Y), which was previously shown to confer escape from human monoclonal antibodies. This variant arises rapidly and persists at intermediate frequencies in index cats. It also becomes fixed following transmission in two of three pairs. These dynamics suggest this site may be under positive selection in this system and illustrate how a variant can quickly arise and become fixed in parallel across multiple transmission pairs. Transmission of SARS-CoV-2 in cats involved a narrow bottleneck, with new infections founded by fewer than ten viruses. In RNA virus evolution, stochastic processes like narrow transmission bottlenecks and genetic drift typically act to constrain the overall pace of adaptive evolution. Our data suggest that here, positive selection in index cats followed by a narrow transmission bottleneck may have instead accelerated the fixation of S H655Y, a potentially beneficial SARS-CoV-2 variant. Overall, our study suggests species- and context-specific adaptations are likely to continue to emerge. This underscores the importance of continued genomic surveillance for new SARS-CoV-2 variants as well as heightened scrutiny for signatures of SARS-CoV-2 positive selection in humans and mammalian model systems., Author summary Through ongoing human adaptation, spill-back events from other animal intermediates, or with the distribution of vaccines and therapeutics, the landscape of SARS-CoV-2 genetic variation is certain to change. The evolutionary mechanisms by which SARS-CoV-2 will continue to adapt to mammalian hosts depend on genetic variation generated within and between hosts. Here, using domestic cats as a model, we show that within-host SARS-CoV-2 genetic variation is predominantly influenced by genetic drift and purifying selection. Transmission of SARS-CoV-2 between hosts is defined by a narrow transmission bottleneck, involving 2–5 viruses. We further identify a notable variant at amino acid position 655 in Spike (H655Y), which arises rapidly and is transmitted in cats. Spike H655Y has been previously shown to confer escape from human monoclonal antibodies and is currently found in over 1,000 human sequences. Overall, our study suggests species- and context-specific adaptations are likely to continue to emerge, underscoring the importance of continued genomic surveillance in humans and non-human mammalian hosts.
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- 2021
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18. African-lineage Zika virus replication dynamics and maternal-fetal interface infection in pregnant rhesus macaques
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Andres Mejia, Andrea M. Weiler, David H. O’Connor, Jennifer M. Hayes, Elaina Razo, Thaddeus G. Golos, Kathleen M. Antony, Phoenix M. Shepherd, Kara Weaver, Jens C. Eickhoff, Anna S. Jaeger, Katarina M. Braun, Terry K. Morgan, Dawn M. Dudley, Ann Mitzey, Amber Possell, Heather A. Simmons, Matthew T. Aliota, Keisuke Yamamoto, Chelsea M. Crooks, Elizabeth A. Brown, Thomas C. Friedrich, Michael K. Fritsch, Mason Bliss, Nancy Schultz-Darken, Emma L. Mohr, Eric Peterson, Megan E. Murphy, and Sierra Rybarczyk
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Pregnancy ,Microcephaly ,medicine.medical_specialty ,Lineage (genetic) ,Outbreak ,Biology ,medicine.disease ,biology.organism_classification ,Virology ,Zika virus ,Titer ,Viral replication ,Epidemiology ,medicine - Abstract
Following the Zika virus (ZIKV) outbreak in the Americas, ZIKV was causally associated with microcephaly and a range of neurological and developmental symptoms, termed congenital Zika syndrome (CZS). The isolates responsible for this outbreak belonged to the Asian lineage of ZIKV. However, in-vitro and in-vivo studies assessing the pathogenesis of African-lineage ZIKV demonstrated that African-lineage isolates often replicated to high titer and caused more severe pathology than Asian-lineage isolates. To date, the pathogenesis of African-lineage ZIKV in a translational model, particularly during pregnancy, has not been rigorously characterized. Here we infected four pregnant rhesus macaques with a low-passage strain of African-lineage ZIKV and compared its pathogenesis to a cohort of four pregnant rhesus macaques infected with an Asian-lineage isolate and a cohort of mock-infected controls. Viral replication kinetics were not significantly different between the two experimental groups and both groups developed robust neutralizing antibody titers above levels considered to be protective. There was no evidence of significant fetal head growth restriction or gross fetal harm at delivery in either group. However, a significantly higher burden of ZIKV vRNA was found in maternal-fetal interface tissues in the macaques exposed to an African-lineage isolate. Our findings suggest that ZIKV isolates of any genetic lineage pose a threat to women and their infants.IMPORTANCEZIKV was first identified over 70 years ago in Africa, but most of our knowledge of ZIKV is based on studies of the distinct Asian genetic lineage, which caused the outbreak in the Americas in 2015-16. In its most recent update, the WHO stated that improved understanding of African-lineage pathogenesis during pregnancy must be a priority. Recent detection of African-lineage isolates in Brazil underscores the need to understand the impact of these viruses. Here we provide the first comprehensive assessment of African-lineage ZIKV infection during pregnancy in a translational non-human primate model. We show African-lineage isolates replicate with similar kinetics to Asian-lineage isolates and are capable of infecting the placenta. However, there was no evidence of more severe outcomes with African-lineage isolates. Our results highlight both the threat that African-lineage ZIKV poses to women and their infants and the need for future epidemiological and translational in-vivo studies with African-lineage ZIKV.
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- 2020
19. The landscape of antibody binding to SARS-CoV-2
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David A. Baker, Ajay K. Sethi, Anna S. Heffron, David H. O’Connor, Peter Halfmann, Yoshihiro Kawaoka, Maya F. Amjadi, Sean J. McIlwain, Ann C. Palmenberg, Miriam A. Shelef, Irene M. Ong, Tammy Armbrust, and Saniya Khullar
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RNA viruses ,0301 basic medicine ,Viral Diseases ,Proteome ,Coronaviruses ,Physiology ,Proteomes ,viruses ,Peptide ,Antibodies, Viral ,medicine.disease_cause ,Severity of Illness Index ,Biochemistry ,Cross-reactivity ,Immunoglobulin G ,Epitope ,Medical Conditions ,0302 clinical medicine ,Immune Physiology ,Medicine and Health Sciences ,030212 general & internal medicine ,Biology (General) ,Enzyme-Linked Immunoassays ,skin and connective tissue diseases ,Pathology and laboratory medicine ,Cross Reactivity ,Coronavirus ,chemistry.chemical_classification ,education.field_of_study ,Immune System Proteins ,biology ,General Neuroscience ,virus diseases ,Medical microbiology ,Infectious Diseases ,Viruses ,Epitopes, B-Lymphocyte ,Peptide microarray ,SARS CoV 2 ,Pathogens ,Antibody ,General Agricultural and Biological Sciences ,Research Article ,SARS coronavirus ,QH301-705.5 ,Immunology ,Population ,Cross Reactions ,Research and Analysis Methods ,Microbiology ,Antibodies ,General Biochemistry, Genetics and Molecular Biology ,Article ,Viral Proteins ,03 medical and health sciences ,Homologous chromosome ,medicine ,Humans ,Immunoassays ,education ,SARS ,Biology and life sciences ,General Immunology and Microbiology ,Immunodominant Epitopes ,SARS-CoV-2 ,fungi ,Organisms ,Viral pathogens ,COVID-19 ,Proteins ,Covid 19 ,biochemical phenomena, metabolism, and nutrition ,Virology ,Microbial pathogens ,respiratory tract diseases ,030104 developmental biology ,chemistry ,Immunologic Techniques ,biology.protein - Abstract
The search for potential antibody-based diagnostics, vaccines, and therapeutics for pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has focused almost exclusively on the spike (S) and nucleocapsid (N) proteins. Coronavirus membrane (M), ORF3a, and ORF8 proteins are humoral immunogens in other coronaviruses (CoVs) but remain largely uninvestigated for SARS-CoV-2. Here, we use ultradense peptide microarray mapping to show that SARS-CoV-2 infection induces robust antibody responses to epitopes throughout the SARS-CoV-2 proteome, particularly in M, in which 1 epitope achieved excellent diagnostic accuracy. We map 79 B cell epitopes throughout the SARS-CoV-2 proteome and demonstrate that antibodies that develop in response to SARS-CoV-2 infection bind homologous peptide sequences in the 6 other known human CoVs. We also confirm reactivity against 4 of our top-ranking epitopes by enzyme-linked immunosorbent assay (ELISA). Illness severity correlated with increased reactivity to 9 SARS-CoV-2 epitopes in S, M, N, and ORF3a in our population. Our results demonstrate previously unknown, highly reactive B cell epitopes throughout the full proteome of SARS-CoV-2 and other CoV proteins., Profiling of antibody binding from naïve and COVID-19 convalescent human sera to the entire proteome of SARS-CoV-2 and other human, bat and pangolin coronaviruses identifies 79 B cell epitopes throughout the SARS-CoV-2 proteome, finding that the most sensitive and specific binding occurred in the membrane (M) protein, and revealing cross-reactivity patterns.
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- 2020
20. #20: Modeling Zika virus tissue tropism in rhesus macaques to define the risk of donor derived transmission
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Emma L. Mohr, Christina M. Newman, Mason Bliss, Taylor A Treadway, Keisuke Yamamoto, Michele L Schotzko, Elaina Razo, Heather A. Simmons, Dawn M. Dudley, Sierra Rybarczyk, Matthew R Semler, Phoenix M. Shepherd, David H. O’Connor, Andrea M. Weiler, Michelle R Koenig, Andres Mejia, Thaddeus G. Golos, Thomas C. Friedrich, Laurel M. Stewart, Eric C. Peterson, Ann Mitzey, and Meghan E. Breitbach
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biology ,business.industry ,Transmission (medicine) ,viruses ,Viremia ,General Medicine ,biology.organism_classification ,medicine.disease ,Virology ,Zika virus ,Transplantation ,Infectious Diseases ,Pediatrics, Perinatology and Child Health ,Tissue tropism ,Medicine ,Donor derived ,Organ donation ,business ,Tropism - Abstract
Background Almost 115,000 people in the United States are currently on a transplant waitlist, which vastly exceeds the number of organ donors every year. This discrepancy emphasizes the need for retention of all possible donors. Those who have recently traveled to an area with an active outbreak of Zika virus (ZIKV) are often disqualified as a donor because immunosuppressed recipients would be at risk of a donor-derived ZIKV infection. Therefore, we define ZIKV tissue tropism and the risk of donor derived transmission. Methods We subcutaneously inoculated 15 Indian-origin rhesus macaques (RM) with a Puerto Rican isolate of ZIKV (PRVABC59). All RMs were inoculated in mid to early gestation.We inoculated during pregnancy because plasma viremia is typically prolonged in pregnancy and we wanted to model tissue tropism for donor derived transmission in the worst scenario of prolonged viremia. At 30, 65, and 105 days post-infection (dpi), the animals were euthanized and comprehensive necropsies were performed, which evaluated a minimum of 60 tissues per animal. ZIKV RNA was quantified in tissues via qRT-PCR. Results Plasma viremia duration was >10 days in 13 of 15 RMs. ZIKV RNA was most commonly detected in lymph nodes, with 19/45 lymph nodes that were vRNA positive in 5 RMs at 30 dpi. There were 15/45 vRNA positive lymph nodes at 60 dpi and 8/38 at 105 dpi. Reproductive and maternal fetal-interface (MFI) tissues were the second most commonly positive tissues. Twenty-five MFI tissues, including the amniotic/chorionic membrane, decidua, placenta, uterus, and placental bed, were positive, with 10/53 positive at 30 dpi, 14/24 positive at 60 dpi and 1/47 positive at 105 dpi. Other vRNA positive tissues included the primary bronchus, femoral vein, kidney, thyroid, lung, colon, mammary gland, pericardium, hand nerve, and sciatic nerve in 1–2 RMs at one of the three timepoints. Conclusions We found ZIKV RNA most frequently within lymph nodes. Lymph nodes are included in lung and small bowel transplants, indicating that these transplants could pose a risk of donor-derived ZIKV transmission. Virus detection within other commonly transplanted tissues, such as the kidney and blood vessels was much less common. We did not determine what fraction of vRNA comes from replication-competent virus in each tissue; some tissues with vRNA might not contain virions that could initiate new infections. Donor-derived Zika virus transmission from other commonly transplanted organs, such as liver, seems unlikely since no viral RNA was detected in this organ.
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- 2021
21. Optimizing direct RT-LAMP to detect transmissible SARS-CoV-2 from primary nasopharyngeal swab samples
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Cecilia G. Shortreed, Dawn M. Dudley, Thomas C. Friedrich, David H. O’Connor, Andrea M. Weiler, William M. Rehrauer, Anna S. Heffron, Molly A. Accola, Christina M. Newman, and Mitchell D. Ramuta
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0301 basic medicine ,RNA viruses ,Coronaviruses ,Molecular biology ,Physiology ,Biochemistry ,0302 clinical medicine ,Limit of Detection ,Nasopharynx ,Nucleic Acids ,Medicine ,030212 general & internal medicine ,Pathology and laboratory medicine ,Virus Testing ,Multidisciplinary ,Medical microbiology ,Viral Load ,RNA isolation ,Molecular Diagnostic Techniques ,COVID-19 Nucleic Acid Testing ,Viruses ,RNA, Viral ,RNA extraction ,SARS CoV 2 ,Pathogens ,Viral load ,Nucleic Acid Amplification Techniques ,Research Article ,Lysis (Medicine) ,SARS coronavirus ,Science ,Loop-mediated isothermal amplification ,Biomolecular isolation ,Microbiology ,03 medical and health sciences ,Extraction techniques ,Diagnostic Medicine ,Virology ,Lysis buffer ,Tissue Repair ,Humans ,DNA Primers ,Detection limit ,Medicine and health sciences ,Biology and life sciences ,business.industry ,SARS-CoV-2 ,Organisms ,Viral pathogens ,RNA ,COVID-19 ,Nucleic acid amplification technique ,Viral Replication ,Microbial pathogens ,Research and analysis methods ,030104 developmental biology ,Molecular biology techniques ,Nucleic acid ,business ,Physiological Processes ,Viral Transmission and Infection - Abstract
SARS-CoV-2 testing is crucial to controlling the spread of this virus, yet shortages of nucleic acid extraction supplies and other key reagents have hindered the response to COVID-19 in the US. Several groups have described loop-mediated isothermal amplification (LAMP) assays for SARS-CoV-2, including testing directly from nasopharyngeal swabs and eliminating the need for reagents in short supply. Frequent surveillance of individuals attending work or school is currently unavailable to most people but will likely be necessary to reduce the ~50% of transmission that occurs when individuals are nonsymptomatic. Here we describe a fluorescence-based RT-LAMP test using direct nasopharyngeal swab samples and show consistent detection in clinically confirmed primary samples with a limit of detection (LOD) of ~625 copies/μl, approximately 100-fold lower sensitivity than qRT-PCR. While less sensitive than extraction-based molecular methods, RT-LAMP without RNA extraction is fast and inexpensive. Here we also demonstrate that adding a lysis buffer directly into the RT-LAMP reaction improves the sensitivity of some samples by approximately 10-fold. Furthermore, purified RNA in this assay achieves a similar LOD to qRT-PCR. These results indicate that high-throughput RT-LAMP testing could augment qRT-PCR in SARS-CoV-2 surveillance programs, especially while the availability of qRT-PCR testing and RNA extraction reagents is constrained.
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- 2020
22. Optimizing direct RT-LAMP to detect transmissible SARS-CoV-2 from primary nasopharyngeal swab and saliva patient samples
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Thomas C. Friedrich, Andrea M. Weiler, Ceclia G. Shortreed, Dawn M. Dudley, Anna S. Heffron, Molly A. Accola, Mitchell D. Ramuta, Christina M. Newman, David H. O’Connor, and William M. Rehrauer
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Detection limit ,Saliva ,Chemistry ,Lysis buffer ,Nucleic acid ,Loop-mediated isothermal amplification ,RNA ,RNA extraction ,Virology ,Virus - Abstract
SARS-CoV-2 testing is crucial to controlling the spread of this virus, yet shortages of nucleic acid extraction supplies and other key reagents have hindered the response to COVID-19 in the US. Several groups have described loop-mediated isothermal amplification (LAMP) assays for SARS-CoV-2, including testing directly from nasopharyngeal swabs and eliminating the need for reagents in short supply. Here we describe a fluorescence-based RT-LAMP test using direct nasopharyngeal swab samples and show consistent detection in clinically confirmed samples, albeit with approximately 100-fold lower sensitivity than qRT-PCR. We demonstrate that adding lysis buffer directly into the RT-LAMP reaction improves the sensitivity of some samples by approximately 10-fold. Overall, the limit of detection (LOD) of RT-LAMP using direct nasopharyngeal swab or saliva samples without RNA extraction is 1×105-1×106 copies/ml. This LOD is sufficient to detect samples from which infectious virus can be cultured. Therefore, samples that test positive in this assay contain levels of virus that are most likely to perpetuate transmission. Furthermore, purified RNA in this assay achieves a similar LOD to qRT-PCR and we provide a revised method to work directly with saliva as starting material. These results indicate that high-throughput RT-LAMP testing could augment qRT-PCR in SARS-CoV-2 screening programs, especially while the availability of qRT-PCR testing and RNA extraction reagents is constrained.
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- 2020
23. Discovery of a Novel Simian Pegivirus in Common Marmosets (Callithrix jacchus) with Lymphocytic Enterocolitis
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David H. O’Connor, Saverio Capuano, Elizabeth D Somsen, Elizabeth Townsend, Andres Mejia, Michael Lauck, Adam L. Bailey, Jens C. Eickhoff, Christina M. Newman, Megan E. Sosa, Jens H. Kuhn, Heather A. Simmons, and Anna S. Heffron
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0301 basic medicine ,Microbiology (medical) ,endocrine system ,animal structures ,040301 veterinary sciences ,Pegivirus ,Simian ,Microbiology ,Article ,common marmoset ,lymphocytic enterocolitis ,0403 veterinary science ,03 medical and health sciences ,flavivirus ,Virology ,biology.animal ,Callithrix jacchus ,Aotus trivirgatus ,medicine ,Primate ,lcsh:QH301-705.5 ,novel virus discovery ,Enterocolitis ,biology ,Night monkey ,pegivirus ,Marmoset ,04 agricultural and veterinary sciences ,biology.organism_classification ,Callithrix ,body regions ,030104 developmental biology ,lcsh:Biology (General) ,Novel virus ,next-generation sequencing ,medicine.symptom - Abstract
From 2010 to 2015, 73 common marmosets (Callithrix jacchus) housed at the Wisconsin National Primate Research Center (WNPRC) were diagnosed postmortem with lymphocytic enterocolitis. We used unbiased deep-sequencing to screen the blood of deceased enterocolitis-positive marmosets for the presence of RNA viruses. In five out of eight marmosets with lymphocytic enterocolitis, we discovered a novel pegivirus that was not present in ten subsequently deep-sequenced matched, clinically-normal common marmosets with no evidence of lymphocytic enterocolitis. The novel virus, which we have named Southwest bike trail virus (SOBV), is most closely related (68% nucleotide identity) to a strain of simian pegivirus A that was previously isolated from a three-striped night monkey (Aotus trivirgatus). To determine the prevalence of this novel virus within the WNPRC marmoset colony, we screened 146 living animals and found an overall prevalence of 34% (50/146). Over the next four years, 85 of the 146 screened marmosets died or were euthanized and were examined histologically for lymphocytic enterocolitis. Out of these 85 animals, 27 SOBV-positive common marmosets had developed lymphocytic enterocolitis, compared to 42 SOBV-negative common marmosets, indicating no evidence of an association between this virus and development of enterocolitis in this cohort (p=0.0798). The novel pegivirus was also found in two of 32 (6%) clinically-normal common marmosets screened while in quarantine during the transfer from the New England Primate Research Center to the WNPRC, suggesting SOBV has different prevalence at different centers and could exert confounding influences on the comparison of marmoset studies from multiple centers.ImportanceCommon marmosets (Callithrix jacchus) are a valuable model species. We discovered two variants of a novel simian pegivirus, which we named the Southwest bike trail virus (SOBV), in common marmosets which had postmortem histologic diagnosis of lymphocytic enterocolitis. The virus was not present in ten matched, clinically-normal controls. We screened 146 live healthy common marmosets in the Wisconsin National Primate Research Center colony and found 34% (50/146) of the animals were SOBV-positive. SOBV was also present in two of 32 (6%) clinically-normal common marmosets from the New England Primate Research Center. These findings could have confounding effects in animal studies, especially those in which infection-free animals are desired, and they demonstrate the need for further investigations into SOBV transmission, the length of time of SOBV persistence, and SOBV prevalence at other primate centers, in order to increase understanding of the effects of SOBV and of this viral genus.
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- 2020
24. Using barcoded Zika virus to assess virus population structure in vitro and in Aedes aegypti mosquitoes
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David H. O’Connor, Gregory D. Ebel, Thomas C. Friedrich, Selene M. Garcia, Claudia Rückert, Alex D. Byas, Shelby L. O’Connor, Matthew T. Aliota, and James Weger-Lucarelli
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0301 basic medicine ,viruses ,Population ,Aedes aegypti ,Genome ,Arbovirus ,Deep sequencing ,Article ,Virus ,Cell Line ,Zika virus ,Flaviviridae ,03 medical and health sciences ,Aedes ,Virology ,medicine ,Animals ,education ,Genetics ,education.field_of_study ,biology ,Genetic Variation ,Haplorhini ,Zika Virus ,biology.organism_classification ,medicine.disease ,Flavivirus ,030104 developmental biology ,Viral evolution - Abstract
Arboviruses such as Zika virus (ZIKV, Flaviviridae; Flavivirus) replicate in both mammalian and insect hosts where they encounter a variety of distinct host defenses. To overcome these pressures, arboviruses exist as diverse populations of distinct genomes. However, transmission between hosts and replication within hosts can involve genetic bottlenecks, during which population size and viral diversity may be significantly reduced, potentially resulting in large fitness losses. Understanding the points at which bottlenecks exist during arbovirus transmission is critical to identifying targets for preventing transmission. To study these bottleneck effects, we constructed 4 “barcoded” ZIKV clones - 2 with an 8-base-pair degenerate insertion in the 3’ UTR and 2 with 8 or 9 degenerate synonymous changes in the coding sequence, theoretically containing thousands of variants each. We passaged these viruses 3 times each in 2 mammalian and 2 mosquito cell lines and characterized selection of the “barcode” populations using deep sequencing. Additionally, the viruses were used to feed three recently field-caught populations of Aedes aegypti mosquitoes to assess bottlenecks in a natural host. The barcoded viruses replicated well in multiple cell lines in vitro and in vivo in mosquitoes and could be characterized using next-generation sequencing. The stochastic nature of mosquito transmission was clearly shown by tracking individual barcodes in Ae. aegypti mosquitoes. Barcoded viruses provide an efficient method to examine bottlenecks during virus infection.AUTHOR SUMMARYIn general, mosquito-borne viruses like ZIKV must replicate in two very different host environments: an insect and a mammalian host. RNA viruses such as ZIKV must maintain genetic diversity in order to adapt to these changing conditions. During this transmission cycle, several barriers exist which can severely restrict viral genetic diversity, causing bottlenecks in the virus population. It is critical to understand these bottlenecks during virus transmission as this will provide important insights into the selective forces shaping arbovirus evolution within and between hots. Here, we employ a set of barcoded ZIKV constructs containing a degenerate stretch of nucleotides that can be tracked using next-generation sequencing. We found that the insertion site in the genome was an important determinant of the resulting diversity of the genetic barcode. We also found that bottlenecks varied between different mosquito populations and patterns of genetic diversity were distinct among individual mosquitoes within a single population, highlighting the randomness of virus dissemination in mosquitoes. Our study characterizes a new tool for tracking bottlenecks during virus transmission in vivo and highlights the importance of both viral and host factors on the maintenance of viral diversity.
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- 2018
25. Long-Term Protection of Rhesus Macaques from Zika Virus Reinfection
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Logan J Vosler, Sierra Rybarczyk, Andrea M. Weiler, Gage K. Moreno, Kim L. Weisgrau, Eva G. Rakasz, Thomas C. Friedrich, Nancy Schultz-Darken, David H. O’Connor, Michelle R Koenig, Mariel S. Mohns, Christina M. Newman, Nicholas Pomplun, and Dawn M. Dudley
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Immunology ,Viremia ,Antibodies, Viral ,Microbiology ,Arbovirus ,Herd immunity ,Zika virus ,Disease Outbreaks ,03 medical and health sciences ,0302 clinical medicine ,Immune system ,Immunity ,Virology ,medicine ,Animals ,030212 general & internal medicine ,030304 developmental biology ,0303 health sciences ,biology ,Zika Virus Infection ,Outbreak ,Zika Virus ,medicine.disease ,biology.organism_classification ,Antibodies, Neutralizing ,Macaca mulatta ,Flavivirus ,Disease Models, Animal ,Insect Science ,Cytokines ,Pathogenesis and Immunity - Abstract
By the end of the 2016 Zika virus (ZIKV) outbreak, it is estimated that there were up to 100 million infections in the Americas. In approximately one in seven infants born to mothers infected during pregnancy, ZIKV has been linked to microcephaly, developmental delays, or other congenital disorders collectively known as congenital Zika syndrome, as well as Guillain-Barré syndrome, in ZIKV-infected adults. It is a global health priority to develop a vaccine against ZIKV that elicits long-lasting immunity; however, the durability of immunity to ZIKV is unknown. Previous studies in mice and nonhuman primates have been crucial in vaccine development but have not defined the duration of immunity generated by ZIKV infection. In this study, we rechallenged five rhesus macaques with ZIKV 22 to 28 months after a primary ZIKV infection. We show that primary ZIKV infection generates high titers of neutralizing antibodies that protect from detectable plasma viremia following rechallenge and persist for at least 22 to 28 months. While additional longitudinal studies are necessary with longer time frames, this study establishes a new experimentally defined minimal length of protective ZIKV immunity. IMPORTANCE ZIKV emerged as a vector-borne pathogen capable of causing illness in infected adults and congenital birth defects in infants born to mothers infected during pregnancy. Despite the decrease in ZIKV cases since the 2015-2016 epidemic, questions concerning the prevalence and longevity of protective immunity have left vulnerable communities fearful that they may become the center of next ZIKV outbreak. Although preexisting herd immunity in regions of past outbreaks may dampen the potential for future outbreaks to occur, we currently do not know the longevity of protective immunity to ZIKV after a person becomes infected. Here, we establish a new experimentally defined minimal length of protective ZIKV immunity. We show that five rhesus macaques initially infected with ZIKV 22 to 28 months prior to rechallenge elicit a durable immune response that protected from detectable plasma viremia. This study establishes a new minimal length of protective immunity.
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- 2019
26. Diversity of Influenza A(H5N1) Viruses in Infected Humans, Northern Vietnam, 2004–2010
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David H. O’Connor, Michael Lauck, Gabriele Neumann, Yuko Sakai-Tagawa, Andrew J. Thompson, Thomas C. Friedrich, Ryan McBride, Hirotaka Imai, Louise H. Moncla, Yoshihiro Kawaoka, Shinya Yamada, Julie Eggenberger, Wenjie Peng, Anthony Hanson, James C. Paulson, Tiago J. S. Lopes, Gongxun Zhong, Jorge M. Dinis, Yasuo Suzuki, Masato Hatta, and Mai thi Q. Le
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0301 basic medicine ,Microbiology (medical) ,H5N1 subtype ,Genes, Viral ,Epidemiology ,lcsh:Medicine ,Hemagglutinin Glycoproteins, Influenza Virus ,adaptation ,medicine.disease_cause ,History, 21st Century ,influenza virus ,Virus ,lcsh:Infectious and parasitic diseases ,Cell Line ,respiratory infections ,03 medical and health sciences ,Interferon ,Influenza, Human ,medicine ,Animals ,Humans ,lcsh:RC109-216 ,viruses ,Gene ,Phylogeny ,Polymerase ,Diversity of Influenza A(H5N1) Viruses in Infected Humans, Northern Vietnam, 2004–2010 ,Genetic diversity ,Influenza A Virus, H5N1 Subtype ,biology ,Host (biology) ,Research ,lcsh:R ,Genetic Variation ,virus diseases ,genetic diversity ,Virology ,Influenza A virus subtype H5N1 ,3. Good health ,Molecular Typing ,Viral Tropism ,030104 developmental biology ,Infectious Diseases ,Vietnam ,Population Surveillance ,biology.protein ,Adaptation ,influenza ,medicine.drug - Abstract
Influenza viruses exist in each host as a collection of genetically diverse variants, which might enhance their adaptive potential. To assess the genetic and functional diversity of highly pathogenic avian influenza A(H5N1) viruses within infected humans, we used deep-sequencing methods to characterize samples obtained from infected patients in northern Vietnam during 2004–2010 on different days after infection, from different anatomic sites, or both. We detected changes in virus genes that affected receptor binding, polymerase activity, or interferon antagonism, suggesting that these factors could play roles in influenza virus adaptation to humans. However, the frequency of most of these mutations remained low in the samples tested, implying that they were not efficiently selected within these hosts. Our data suggest that adaptation of influenza A(H5N1) viruses is probably stepwise and depends on accumulating combinations of mutations that alter function while maintaining fitness.
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- 2018
27. Spondweni virus causes fetal harm in a mouse model of vertical transmission and is transmitted by Aedes aegypti mosquitoes
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Thomas C. Friedrich, Andrea M. Weiler, Ryan V. Moriarty, David H. O’Connor, Anna S. Jaeger, Sierra Rybarczyk, Michael K. Fritsch, Shelby L. O’Connor, Matthew T. Aliota, and Davis M. Seelig
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Spondweni virus ,0303 health sciences ,Fetus ,biology ,Placental histopathology ,030231 tropical medicine ,fungi ,virus diseases ,Aedes aegypti ,biology.organism_classification ,medicine.disease_cause ,Virology ,Culex quinquefasciatus ,3. Good health ,Zika virus ,03 medical and health sciences ,Flavivirus ,0302 clinical medicine ,parasitic diseases ,medicine ,030304 developmental biology - Abstract
Spondweni virus (SPONV) is the most closely related known flavivirus to Zika virus (ZIKV). Its pathogenic potential and vector specificity have not been well defined. SPONV has been found predominantly in Africa, but was recently detected in a pool ofCulex quinquefasciatusmosquitoes in Haiti. Here we show that SPONV can cause significant fetal harm, including demise, comparable to ZIKV, in a mouse model of vertical transmission. Following maternal inoculation, we detected infectious SPONV in placentas and fetuses, along with significant fetal and placental histopathology, together indicating vertical transmission. To test vector competence, we exposedAedes aegyptiandCulex quinquefasciatusmosquitoes to SPONV-infected bloodmeals.Aedes aegypticould efficiently transmit SPONV, whereasCulex quinquefasciatuscould not. Our results suggest that SPONV has the same features that made ZIKV a public health risk.
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- 2019
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28. Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks
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David H. O’Connor, Thomas C. Friedrich, David A. Baker, Gage K. Moreno, Cassia Wagner, Trevor Bedford, Molly A. Accola, Louise H. Moncla, Katia Koelle, William M. Rehrauer, and Katarina M. Braun
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RNA viruses ,Time Factors ,Pulmonology ,Coronaviruses ,Genome ,law.invention ,Database and Informatics Methods ,Medical Conditions ,law ,Biology (General) ,Phylogeny ,Pathology and laboratory medicine ,Data Management ,Immune escape ,Phylogenetic Analysis ,Genomics ,Medical microbiology ,Phylogenetics ,Infectious Diseases ,Transmission (mechanics) ,Acute Disease ,Viruses ,SARS CoV 2 ,Pathogens ,Research Article ,Computer and Information Sciences ,Evolutionary Immunology ,SARS coronavirus ,Bioinformatics ,QH301-705.5 ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Immunology ,Genome, Viral ,Biology ,Research and Analysis Methods ,Microbiology ,Viral Evolution ,Evolution, Molecular ,Respiratory Disorders ,Virology ,Genetic variation ,Genetics ,Humans ,Evolutionary Systematics ,Molecular Biology ,Taxonomy ,Medicine and health sciences ,Evolutionary Biology ,Biology and life sciences ,SARS-CoV-2 ,Host (biology) ,Organisms ,Viral pathogens ,COVID-19 ,Genetic Variation ,RC581-607 ,Organismal Evolution ,Microbial pathogens ,Evolutionary biology ,Microbial Evolution ,Respiratory Infections ,Parasitology ,Immunologic diseases. Allergy ,Diversity (business) - Abstract
The emergence of divergent SARS-CoV-2 lineages has raised concern that novel variants eliciting immune escape or the ability to displace circulating lineages could emerge within individual hosts. Though growing evidence suggests that novel variants arise during prolonged infections, most infections are acute. Understanding how efficiently variants emerge and transmit among acutely-infected hosts is therefore critical for predicting the pace of long-term SARS-CoV-2 evolution. To characterize how within-host diversity is generated and propagated, we combine extensive laboratory and bioinformatic controls with metrics of within- and between-host diversity to 133 SARS-CoV-2 genomes from acutely-infected individuals. We find that within-host diversity is low and transmission bottlenecks are narrow, with very few viruses founding most infections. Within-host variants are rarely transmitted, even among individuals within the same household, and are rarely detected along phylogenetically linked infections in the broader community. These findings suggest that most variation generated within-host is lost during transmission., Author summary RNA viruses generate diversity within individual, infected hosts. This genetic diversity can be used to trace how viruses evolve during the course of infection within individuals, and transmission between them. To investigate how SARS-CoV-2 diversity is generated and propagated, we deep sequenced 133 SARS-CoV-2 genomes isolated from acutely infected individuals in Wisconsin. We capitalize on a large dataset of consensus genomes from Wisconsin to investigate how variants are transmitted within the surrounding community, and use a unique household dataset to estimate the number of viruses that are transmitted between epidemiologically linked individuals. We find that most SARS-CoV-2 infections are characterized by limited within-host diversity, and that the vast majority of intra-host single nucleotide variants (iSNVs) are lost during transmission. We do not find evidence that variation is frequently propagated along phylogenetically linked infections, and estimate that most infections are founded by very few unique virions. The combination of limited within-host diversity and tight transmission bottlenecks may slow the pace of SARS-CoV-2 evolution in the future, and suggests that extensive within-host evolution is likely rare.
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- 2021
29. Zika in the Americas, year 2: What have we learned? What gaps remain? A report from the Global Virus Network
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Matthew T. Aliota, Nikos Vasilakis, Edward McSweegan, Leda Bassit, Michael J. Ricciardi, Thomas C. Friedrich, Guilherme S. Ribeiro, Natalia Mercer, Geraldine Schott-Lerner, George R. Saade, Thaddeus G. Golos, Shelton S. Bradrick, Diane E. Griffin, Mariano A. Garcia-Blanco, Lisa F. P. Ng, Pei Yong Shi, Diogo M. Magnani, Bryan Cox, Christina Gavegnano, Marc Lecuit, Chao Shan, Caroline Marrs, Andrew D. Haddow, David I. Watkins, Jorge E. Osorio, Scott C. Weaver, Raymond F. Schinazi, David H. O’Connor, Esper G. Kallas, Shannan L. Rossi, Uriel Kitron, University of Wisconsin-Madison, Emory University [Atlanta, GA], The University of Texas Medical Branch (UTMB), Global Virus Network, University of South Florida [Tampa] (USF), Johns Hopkins Bloomberg School of Public Health [Baltimore], Johns Hopkins University (JHU), U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Universidade de São Paulo = University of São Paulo (USP), Biologie des Infections - Biology of Infection, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), University of Miami Leonard M. Miller School of Medicine (UMMSM), Agency for science, technology and research [Singapore] (A*STAR), Universidade Federal da Bahia (UFBA), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP), Work from the authors’ laboratories was funded by in part by U.S. National Institutes of Health grants: R01NS087539-S1 (to DEG), R21AI129607 (to RFS), and R24AI120942, R01AI121452 (to SCW) R01 AI107157-01A1 (to TGG), R01AI116382-01A1S1 (to DHO), U01AI115577 (to NV) and P51 OD011106 (to the WNPRC)., U.S. Army Medical Research Institute of Infectious Diseases, University of São Paulo (USP), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des Maladies Génétiques Imagine [Paris], Fundação Oswaldo Cruz (FIOCRUZ), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)
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0301 basic medicine ,Gerontology ,medicine.medical_specialty ,Asia ,Sexual transmission ,MALFORMAÇÕES ,[SDV]Life Sciences [q-bio] ,Disease ,Antiviral therapy ,Nervous System Malformations ,Arbovirus ,Article ,Zika virus ,03 medical and health sciences ,[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases ,Virology ,Drug Discovery ,Pandemic ,Disease Transmission, Infectious ,medicine ,Animals ,Maternal-fetal transmission ,Pharmacology ,Vaccines ,[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,biology ,Diagnostic Tests, Routine ,Zika Virus Infection ,business.industry ,Transmission (medicine) ,Public health ,Outbreak ,medicine.disease ,biology.organism_classification ,Infectious Disease Transmission, Vertical ,3. Good health ,Congenital manifestations ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,030104 developmental biology ,Family medicine ,Africa ,Communicable Disease Control ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Americas ,business ,[SDV.MHEP]Life Sciences [q-bio]/Human health and pathology - Abstract
International audience; In response to the outbreak of Zika virus (ZIKV) infection in the Western Hemisphere and the recognition of a causal association with fetal malformations, the Global Virus Network (GVN) assembled an international taskforce of virologists to promote basic research, recommend public health measures and encourage the rapid development of vaccines, antiviral therapies and new diagnostic tests. In this article, taskforce members and other experts review what has been learned about ZIKV-induced disease in humans, its modes of transmission and the cause and nature of associated congenital manifestations. After describing the make-up of the taskforce, we summarize the emergence of ZIKV in the Americas, Africa and Asia, its spread by mosquitoes, and current control measures. We then review the spectrum of primary ZIKV-induced disease in adults and children, sites of persistent infection and sexual transmission, then examine what has been learned about maternal-fetal transmission and the congenital Zika syndrome, including knowledge obtained from studies in laboratory animals. Subsequent sections focus on vaccine development, antiviral therapeutics and new diagnostic tests. After reviewing current understanding of the mechanisms of emergence of Zika virus, we consider the likely future of the pandemic.
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- 2017
30. Long-term protection of rhesus macaques from Zika virus reinfection
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Nancy Schultz-Darken, David H. O’Connor, Christina M. Newman, Andrea M. Weiler, Thomas C. Friedrich, Gage K. Moreno, Logan J Vosler, Eva G. Rakasz, Nicholas Pomplun, Michelle R Koenig, Sierra Rybarczyk, Mariel S. Mohns, and Dawn M. Dudley
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Pregnancy ,biology ,business.industry ,Outbreak ,Viremia ,medicine.disease ,biology.organism_classification ,Virology ,Herd immunity ,Zika virus ,Immune system ,Immunity ,biology.protein ,Medicine ,Antibody ,business - Abstract
By the end of the 2016 Zika virus (ZIKV) outbreak, it is estimated that there were up to 100 million infections in the Americas. In approximately one in seven infants born to mothers infected during pregnancy, ZIKV has been linked to microcephaly, developmental delays, or other congenital disorders collectively known as congenital Zika syndrome (CZS). Guillain-Barré syndrome (GBS) in ZIKV infected adults. It is a global health priority to develop a vaccine against ZIKV that elicits long-lasting immunity, however, the durability of immunity to ZIKV is unknown. Previous studies in mice and nonhuman primates have been crucial in vaccine development but have not defined the duration of immunity generated by ZIKV infection. In this study, we rechallenged five rhesus macaques with ZIKV two years after a primary ZIKV infection. We show that primary ZIKV infection generates high titers of neutralizing antibodies (nAbs) that protect from detectable plasma viremia following rechallenge and persist for at least 27 months. While additional longitudinal studies are necessary with longer time frames, this study establishes a new experimentally defined minimal length of protective ZIKV immunity.Author SummaryZIKV emerged as a vector-borne pathogen capable of causing illness in infected adults and congenital birth defects in infants born to mothers infected during pregnancy. Despite the drop in ZIKV cases since the 2015-16 epidemic, questions concerning the prevalence and longevity of protective immunity have left vulnerable communities fearful that they may become the center of next ZIKV outbreak. While pre-existing herd immunity in regions of past outbreaks may dampen the potential for future outbreaks to occur, we currently do not know the longevity of protective immunity to ZIKV after a person becomes infected. Here, we establish a new experimentally defined minimal length of protective ZIKV immunity. We show that five rhesus macaques initially infected with ZIKV two years prior to rechallenge elicit a durable immune response that protected from detectable plasma viremia. While this work establishes a new minimal length of protective immunity, additional studies are necessary to define the maximum length of protective immunity following ZIKV infection.
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- 2019
31. Using Macaques to Address Critical Questions in Zika Virus Research
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David H. O’Connor, Dawn M. Dudley, Thaddeus G. Golos, Thomas C. Friedrich, Christina M. Newman, Matthew T. Aliota, and Emma L. Mohr
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Macaque ,Arbovirus ,Virus ,Article ,Zika virus ,03 medical and health sciences ,0302 clinical medicine ,Pregnancy ,Virology ,biology.animal ,medicine ,Animals ,Humans ,030212 general & internal medicine ,030304 developmental biology ,0303 health sciences ,biology ,Zika Virus Infection ,Zika Virus ,biology.organism_classification ,medicine.disease ,Macaca mulatta ,Pregnancy Complications ,Rhesus macaque ,Flavivirus ,Disease Models, Animal ,Female - Abstract
Zika virus (ZIKV) and nonhuman primates have been inextricably linked since the virus was first discovered in a sentinel rhesus macaque in Uganda in 1947. Soon after ZIKV was epidemiologically associated with birth defects in Brazil late in 2015, researchers capitalized on the fact that rhesus macaques are commonly used to model viral immunity and pathogenesis, quickly establishing macaque models for ZIKV infection. Within months, the susceptibility of pregnant macaques to experimental ZIKV challenge and ZIKV-associated abnormalities in fetuses was confirmed. This review discusses key unanswered questions in ZIKV immunity and in the pathogenesis of thecongenital Zika virus syndrome. We focus on those questions that can be best addressed in pregnant nonhuman primates and lessons learned from developing macaque models for ZIKV amid an active epidemic.
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- 2019
32. Primary infection with dengue or Zika virus does not affect the severity of heterologous secondary infection in macaques
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Laurel M. Stewart, Wendy Newton, Hansi Dean, Dawn M. Dudley, Phoenix M. Shepherd, Saverio Capuano, Andrea M. Weiler, Gabrielle L. Barry, Ginger Young, Eric Peterson, Thomas C. Friedrich, Jens Eichkoff, Michelle R Koenig, David H. O’Connor, Holly Heimsath, Chelsea M. Crooks, Keisuke Yamamoto, Christina M. Newman, Sallie R. Permar, Nancy Schultz-Darken, Emma L. Mohr, Meghan E. Breitbach, Matthew T. Aliota, Jorge E. Osorio, and Matthew R Semler
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Male ,RNA viruses ,Serotype ,Physiology ,viruses ,Monkeys ,Dengue virus ,Antibodies, Viral ,Pathology and Laboratory Medicine ,medicine.disease_cause ,Macaque ,Biochemistry ,Dengue fever ,Zika virus ,Dengue ,Immune Physiology ,Medicine and Health Sciences ,Biology (General) ,Enzyme-Linked Immunoassays ,Mammals ,0303 health sciences ,Immune System Proteins ,biology ,Coinfection ,Zika Virus Infection ,030302 biochemistry & molecular biology ,Eukaryota ,virus diseases ,Animal Models ,Viral Load ,Body Fluids ,3. Good health ,Flavivirus ,Blood ,Experimental Organism Systems ,Medical Microbiology ,Viral Pathogens ,Vertebrates ,Viruses ,Female ,Pathogens ,Anatomy ,Viral load ,Research Article ,Primates ,QH301-705.5 ,Secondary infection ,Immunology ,Cross Reactions ,Research and Analysis Methods ,Microbiology ,Antibodies ,Blood Plasma ,Virus ,03 medical and health sciences ,Immunity ,biology.animal ,Virology ,Old World monkeys ,Genetics ,medicine ,Animals ,Immunoassays ,Molecular Biology ,Microbial Pathogens ,030304 developmental biology ,Biology and life sciences ,Flaviviruses ,Rhesus Monkeys ,030306 microbiology ,Organisms ,Proteins ,Zika Virus ,RC581-607 ,Dengue Virus ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,medicine.disease ,Antibodies, Neutralizing ,Macaca mulatta ,Amniotes ,Animal Studies ,Immunologic Techniques ,Parasitology ,Immunologic diseases. Allergy ,Viral Transmission and Infection - Abstract
Zika virus (ZIKV) and dengue virus (DENV) are genetically and antigenically related flaviviruses that now co-circulate in much of the tropical and subtropical world. The rapid emergence of ZIKV in the Americas in 2015 and 2016, and its recent associations with Guillain-Barré syndrome, birth defects, and fetal loss have led to the hypothesis that DENV infection induces cross-reactive antibodies that influence the severity of secondary ZIKV infections. It has also been proposed that pre-existing ZIKV immunity could affect DENV pathogenesis. We examined outcomes of secondary ZIKV infections in three rhesus and fifteen cynomolgus macaques, as well as secondary DENV-2 infections in three additional rhesus macaques up to a year post-primary ZIKV infection. Although cross-binding antibodies were detected prior to secondary infection for all animals and cross-neutralizing antibodies were detected for some animals, previous DENV or ZIKV infection had no apparent effect on the clinical course of heterotypic secondary infections in these animals. All animals had asymptomatic infections and, when compared to controls, did not have significantly perturbed hematological parameters. Rhesus macaques infected with DENV-2 approximately one year after primary ZIKV infection had higher vRNA loads in plasma when compared with serum vRNA loads from ZIKV-naive animals infected with DENV-2, but a differential effect of sample type could not be ruled out. In cynomolgus macaques, the serotype of primary DENV infection did not affect the outcome of secondary ZIKV infection., Author summary Pre-existing immunity to one of the four DENV serotypes is known to increase the risk of severe disease upon secondary infection with a different serotype. Due to the antigenic similarities between ZIKV and DENV, it has been proposed that these viruses could interact in a similar fashion. Data from in vitro experiments and murine models suggests that pre-existing immunity to one virus could either enhance or protect against infection with the other. These somewhat contradictory findings highlight the need for immune competent animal models for understanding the role of cross-reactive antibodies in flavivirus pathogenesis. We examined secondary ZIKV or DENV infections in rhesus and cynomolgus macaques that had previously been infected with the other virus. We assessed the outcomes of secondary ZIKV or DENV infections by quantifying vRNA loads, clinical and laboratory parameters, body temperature, and weight for each cohort of animals and compared them with control animals. These comparisons demonstrated that within a year of primary infection, secondary infections with either ZIKV or DENV were similar to primary infections and were not associated with enhancement or reduction in severity of disease based on the outcomes that we assessed.
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- 2019
33. Human, Nonhuman Primate, and Bat Cells Are Broadly Susceptible to Tibrovirus Particle Cell Entry
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Courtney L. Finch, Michael Lauck, Elena Postnikova, Shuǐqìng Yú, Rohit K. Jangra, David H. O’Connor, Yíngyún Caì, Gustavo Palacios, Charles Y. Chiu, Sean P. J. Whelan, Jens H. Kuhn, Sheli R. Radoshitzky, Kartik Chandran, Michael R. Wiley, Robert B. Tesh, and Jiro Wada
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Microbiology (medical) ,Bas-Congo virus ,food.ingredient ,viruses ,lcsh:QR1-502 ,Biology ,Microbiology ,Genome ,lcsh:Microbiology ,Virus ,Viral hemorrhagic fever ,03 medical and health sciences ,food ,tibrovirus ,medicine ,viral hemorrhagic fever ,Mononegavirales ,Pathogen ,Original Research ,030304 developmental biology ,0303 health sciences ,mononegavirus ,030306 microbiology ,tropism ,Tibrovirus ,Rhabdoviridae ,medicine.disease ,biology.organism_classification ,Virology ,3. Good health ,Boa constrictor ,Human Virus ,Vesiculovirus ,rhabdovirus - Abstract
In 2012, the genome of a novel rhabdovirus, Bas-Congo virus, was discovered in the acute-phase serum of a Congolese patient with presumed viral hemorrhagic fever. In the absence of a replicating virus isolate, fulfilling Koch's postulates to determine whether Bas-Congo virus is indeed a human virus and/or pathogen has been impossible. However, experiments with vesiculoviral particles pseudotyped with Bas-Congo glycoprotein suggested that Bas-Congo virus particles can enter cells from multiple animals, including humans. In 2015, genomes of two related viruses, Ekpoma virus 1 and Ekpoma virus 2, were detected in human sera in Nigeria. Isolates could not be obtained. Phylogenetic analyses led to the classification of Bas-Congo virus, Ekpoma virus 1, and Ekpoma virus 2 in the same genus, Tibrovirus, together with five biting midge-borne rhabdoviruses (i.e., Beatrice Hill virus, Bivens Arm virus, Coastal Plains virus, Sweetwater Branch virus, and Tibrogargan virus) not known to infect humans. Using individual recombinant vesiculoviruses expressing the glycoproteins of all eight known tibroviruses and more than 75 cell lines representing different animal species, we demonstrate that the glycoproteins of all tibroviruses can mediate vesiculovirus particle entry into human, bat, nonhuman primate, cotton rat, boa constrictor, and Asian tiger mosquito cells. Using four of five isolated authentic tibroviruses (i.e., Bivens Arm virus, Coastal Plains virus, Sweetwater Branch virus, and Tibrogargan virus), our experiments indicate that many cell types may be partially resistant to tibrovirus replication after virion cell entry. Consequently, experimental data solely obtained from experiments using tibrovirus surrogate systems (e.g., vesiculoviral pseudotypes, recombinant vesiculoviruses) cannot be used to predict whether Bas-Congo virus, or any other tibrovirus, infects humans.
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- 2018
34. Subclinical Infection of Macaques and Baboons with A Baboon Simarterivirus
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Kathy Brasky, Connor R. Buechler, David H. O’Connor, Reed F. Johnson, Jens H. Kuhn, Deborah Chavez, Matthew R Semler, Robert E. Lanford, Christina M. Newman, Adam L. Bailey, Bernadette Guerra, David A. Baker, and Joseph P. Cornish
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Male ,0301 basic medicine ,Simian hemorrhagic fever virus ,SWBV-1 ,lcsh:QR1-502 ,Viremia ,Genome, Viral ,Antibodies, Viral ,Virus Replication ,Arteriviridae ,Article ,Epitope ,lcsh:Microbiology ,Pathogenesis ,03 medical and health sciences ,RNA Virus Infections ,Viral Envelope Proteins ,Virology ,biology.animal ,SHFV ,medicine ,Animals ,Asymptomatic Infections ,Subclinical infection ,Immunity, Cellular ,biology ,southwest baboon virus 1 ,Viral Load ,biology.organism_classification ,medicine.disease ,Macaca mulatta ,3. Good health ,simian hemorrhagic fever virus ,Titer ,030104 developmental biology ,Infectious Diseases ,Mutation ,biology.protein ,Antibody ,simarterivirus ,Papio ,Baboon - Abstract
Simarteriviruses (Arteriviridae: Simarterivirinae) are commonly found at high titers in the blood of African monkeys but do not cause overt disease in these hosts. In contrast, simarteriviruses cause severe disease in Asian macaques upon accidental or experimental transmission. Here, we sought to better understand the host-dependent drivers of simarterivirus pathogenesis by infecting olive baboons (n = 4) and rhesus monkeys (n = 4) with the simarterivirus Southwest baboon virus 1 (SWBV-1). Surprisingly, none of the animals in our study showed signs of disease following SWBV-1 inoculation. Three animals (two rhesus monkeys and one olive baboon) became infected and sustained high levels of SWBV-1 viremia for the duration of the study. The course of SWBV-1 infection was highly predictable: plasma viremia peaked between 1 ×, 107 and 1 ×, 108 vRNA copies/mL at 3&ndash, 10 days post-inoculation, which was followed by a relative nadir and then establishment of a stable set-point between 1 ×, 106 and 1 ×, 107 vRNA copies/mL for the remainder of the study (56 days). We characterized cellular and antibody responses to SWBV-1 infection in these animals, demonstrating that macaques and baboons mount similar responses to SWBV-1 infection, yet these responses are ineffective at clearing SWBV-1 infection. SWBV-1 sequencing revealed the accumulation of non-synonymous mutations in a region of the genome that corresponds to an immunodominant epitope in the simarterivirus major envelope glycoprotein GP5, which likely contribute to viral persistence by enabling escape from host antibodies.
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- 2018
35. Clinical Characterization of Host Response to Simian Hemorrhagic Fever Virus Infection in Permissive and Refractory Hosts: A Model for Determining Mechanisms of VHF Pathogenesis
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Monica Paneru, Peter B. Jahrling, Mahnaz Minai, Steven Mazur, James Pettitt, Reed F. Johnson, Jens H. Kuhn, Donna L. Perry, Ian N. Moore, Adam L. Bailey, Joseph P. Cornish, David H. O’Connor, Connor R. Buechler, Katie R Hagan, John G. Bernbaum, Abigail Lara, Dominique Promeneur, Kimmo Virtaneva, and Kurt Cooper
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Male ,Simian hemorrhagic fever virus ,Hemorrhagic Fevers, Viral ,Cercopithecinae ,lcsh:QR1-502 ,Antibodies, Viral ,Virus Replication ,Macaque ,Virus ,Article ,Arteriviridae ,lcsh:Microbiology ,Viral hemorrhagic fever ,Arterivirus ,Patas monkey ,Virology ,biology.animal ,arterivirus ,SHFV ,medicine ,Animals ,host response ,viral hemorrhagic fever ,Erythrocebus ,Subclinical infection ,patas monkey ,biology ,Arterivirus Infections ,Macrophages ,pathogenesis ,Erythrocebus patas ,Monkey Diseases ,macaque ,biology.organism_classification ,medicine.disease ,Infectious Diseases ,Host-Pathogen Interactions ,Cytokines ,Macaca ,RNA, Viral ,Female ,simian hemorrhagic fever ,simarterivirus - Abstract
Simian hemorrhagic fever virus (SHFV) causes a fulminant and typically lethal viral hemorrhagic fever (VHF) in macaques (Cercopithecinae: Macaca spp.) but causes subclinical infections in patas monkeys (Cercopithecinae: Erythrocebus patas). This difference in disease course offers a unique opportunity to compare host responses to infection by a VHF-causing virus in biologically similar susceptible and refractory animals. Patas and rhesus monkeys were inoculated side-by-side with SHFV. Unlike the severe disease observed in rhesus monkeys, patas monkeys developed a limited clinical disease characterized by changes in complete blood counts, serum chemistries, and development of lymphadenopathy. Viral RNA was measurable in circulating blood 2 days after exposure, and its duration varied by species. Infectious virus was detected in terminal tissues of both patas and rhesus monkeys. Varying degrees of overlap in changes in serum concentrations of interferon (IFN)-&gamma, monocyte chemoattractant protein (MCP)-1, and interleukin (IL)-6 were observed between patas and rhesus monkeys, suggesting the presence of common and species-specific cytokine responses to infection. Similarly, quantitative immunohistochemistry of livers from terminal monkeys and whole blood flow cytometry revealed varying degrees of overlap in changes in macrophages, natural killer cells, and T-cells. The unexpected degree of overlap in host response suggests that relatively small subsets of a host&rsquo, s response to infection may be responsible for driving hemorrhagic fever pathogenesis. Furthermore, comparative SHFV infection in patas and rhesus monkeys offers an experimental model to characterize host&ndash, response mechanisms associated with viral hemorrhagic fever and evaluate pan-viral hemorrhagic fever countermeasures.
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- 2018
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36. #79: Modeling Zika Virus Tissue Tropism in Rhesus Macaques to Define the Risk of Donor-derived Transmission
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Matthew R Semler, Michele L Schotzko, Taylor A Treadway, Eric C. Peterson, David H. O’Connor, Andrea M. Weiler, Sierra Rybarczyk, Ann Mitzey, Thaddeus G. Golos, Heather A. Simmons, Andres Mejia, Emma L. Mohr, Laurel M. Stewart, Mason Bliss, Thomas C. Friedrich, Elaina Razo, Dawn M. Dudley, Phoenix M. Shepherd, Michelle R Koenig, Meghan E. Breitbach, Christina M. Newman, and Keisuke Yamamoto
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biology ,Transmission (medicine) ,business.industry ,viruses ,Viremia ,General Medicine ,medicine.disease ,biology.organism_classification ,Virology ,Zika virus ,Transplantation ,Infectious Diseases ,Pediatrics, Perinatology and Child Health ,Tissue tropism ,medicine ,Donor derived ,Organ donation ,business ,Tropism - Abstract
Background Almost 115,000 people in the United States are currently on a transplant waitlist, which vastly exceeds the number of organ donors every year. This discrepancy emphasizes the need for retention of all possible donors. Those who have recently traveled to an area with an active outbreak of Zika virus (ZIKV) are often disqualified as a donor because immunosuppressed recipients would be at risk of a donor-derived ZIKV infection. Therefore, we define ZIKV tissue tropism and the risk of donor-derived transmission. Methods We subcutaneously inoculated 15 Indian-origin rhesus macaques (RM) with a Puerto Rican isolate of ZIKV (PRVABC59). All RMs were inoculated in mid to early gestation. We inoculated during pregnancy because plasma viremia is typically prolonged in pregnancy and we wanted to model tissue tropism for donor-derived transmission in the worst scenario of prolonged viremia. At 30, 65, and 105 days post-infection (dpi), the animals were euthanized and comprehensive necropsies were performed, which evaluated a minimum of 60 tissues per animal. ZIKV RNA was quantified in tissues via qRT-PCR. Results Plasma viremia duration was >10 days in 13 of 15 RMs. ZIKV RNA was most commonly detected in lymph nodes, with 19/45 lymph nodes that were vRNA positive in 5 RMs at 30 dpi. There were 15/45 vRNA positive lymph nodes at 60 dpi and 8/38 at 105 dpi. Reproductive and maternal fetal-interface (MFI) tissues were the second most commonly positive tissues. Twenty-five MFI tissues, including the amniotic/chorionic membrane, decidua, placenta, uterus, and placental bed, were positive, with 10/53 positive at 30 dpi, 14/24 positive at 60 dpi and 1/47 positive at 105 dpi. Other vRNA positive tissues included the primary bronchus, femoral vein, kidney, thyroid, lung, colon, mammary gland, pericardium, hand nerve, and sciatic nerve in 1–2 RMs at one of the three timepoints. Conclusions We found ZIKV RNA most frequently within lymph nodes. Lymph nodes are included in lung and small bowel transplants, indicating that these transplants could pose a risk of donor-derived ZIKV transmission. Virus detection within other commonly transplanted tissues, such as the kidney and blood vessels was much less common. We did not determine what fraction of vRNA comes from replication-competent virus in each tissue; some tissues with vRNA might not contain virions that could initiate new infections. Donor-derived Zika virus transmission from other commonly transplanted organs, such as the liver, seems unlikely since no viral RNA was detected in this organ.
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- 2021
37. Discovery of Lanama Virus, a Distinct Member of Species Kunsagivirus C (Picornavirales: Picornaviridae), in Wild Vervet Monkeys (Chlorocebus pygerythrus)
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Matthew G. Lackemeyer, Nick J. Knowles, Kim Valenta, Michael Lauck, Tony L. Goldberg, Samuel D. Sibley, Peter B. Jahrling, David H. O’Connor, Joshua C. Johnson, Patrick A. Omeja, Colin A. Chapman, Cristine Campos Lawson, and Jens H. Kuhn
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0301 basic medicine ,LNMV ,030106 microbiology ,lcsh:QR1-502 ,Picornaviridae ,Kunsagivirus ,nonhuman primate ,lcsh:Microbiology ,Virus ,03 medical and health sciences ,vervet ,Genus ,Virology ,parasitic diseases ,Chlorocebus pygerythrus ,biology ,Phylogenetic tree ,kunsagivirus ,biology.organism_classification ,lanama virus ,030104 developmental biology ,Infectious Diseases ,Novel virus ,Picornavirales - Abstract
We report the discovery and sequence-based molecular characterization of a novel virus, lanama virus (LNMV), in blood samples obtained from two wild vervet monkeys (Chlorocebus pygerythrus), sampled near Lake Nabugabo, Masaka District, Uganda. Sequencing of the complete viral genomes and subsequent phylogenetic analysis identified LNMV as a distinct member of species Kunsagivirus C, in the undercharacterized picornavirid genus Kunsagivirus.
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- 2020
38. A Multicomponent Animal Virus Isolated from Mosquitoes
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David Hyeroba, Albert J. Auguste, Karla Prieto, Jose R. Loaiza, Brett Beitzel, Marie C. Gestole, Lisa H. Cazares, Gillian Eastwood, Michael R. Wiley, Robert B. Tesh, Fanny Castro-Llanos, Michael D. Ward, Alan P. Dupuis, Daniel Reyes, Tara Kenny, Matthew T. Aliota, Vsevolod L. Popov, David H. O’Connor, Laura D. Kramer, Jason T. Ladner, Bailey White, David Kimmel, Thomas C. Friedrich, Michael Lauck, Michael E. Lindquist, Tadeusz J. Kochel, Hilda Guzman, Ernst E. Brueggemann, Krishna P. Kota, Scott C. Weaver, Samuel D. Sibley, Gustavo Palacios, David P Fetterer, Tony L. Goldberg, and Lena St. John
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0301 basic medicine ,Culex ,viruses ,030106 microbiology ,Colobus ,Microbiology ,Genome ,Article ,Virus ,03 medical and health sciences ,Flaviviridae ,Virology ,Animals ,RNA Viruses ,Clade ,Phylogeny ,Genetics ,biology ,RNA ,RNA virus ,Animal virus ,biology.organism_classification ,Biological Evolution ,Culicidae ,030104 developmental biology ,Microscopy, Fluorescence ,Viruses ,Parasitology - Abstract
RNA viruses exhibit a variety of genome organization strategies, including multicomponent genomes in which each segment is packaged separately. Although multicomponent genomes are common among viruses infecting plants and fungi, their prevalence among those infecting animals remains unclear. We characterize a multicomponent RNA virus isolated from mosquitoes, designated Guaico Culex virus (GCXV). GCXV belongs to a diverse clade of segmented viruses (Jingmenvirus) related to the prototypically unsegmented Flaviviridae. The GCXV genome comprises five segments, each of which appears to be separately packaged. The smallest segment is not required for replication, and its presence is variable in natural infections. We also describe a variant of Jingmen tick virus, another Jingmenvirus, sequenced from a Ugandan red colobus monkey, thus expanding the host range of this segmented and likely multicomponent virus group. Collectively, this study provides evidence for the existence of multicomponent animal viruses and their potential relevance for animal and human health.
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- 2016
39. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components
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David H. O’Connor, Lee Gehrke, James J. Collins, Keith Pardee, Nina M. Donghia, Melissa K. Takahashi, Melina Fan, Dawn M. Dudley, Alexander A. Green, Duo Ma, Tom Ferrante, Irene Bosch, Nichole M. Daringer, Guillaume Lambert, Jeong Wook Lee, Dana Braff, Institute for Medical Engineering and Science, Harvard University--MIT Division of Health Sciences and Technology, Collins, James, Takahashi, Melissa Kimie, Braff, Dana, Lee, Jeongwook, Daringer, Nichole Marie, Bosch, Irene, Gehrke, Lee, and Collins, James J.
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0301 basic medicine ,02 engineering and technology ,Dengue virus ,medicine.disease_cause ,Genome ,General Biochemistry, Genetics and Molecular Biology ,Zika virus ,Dengue fever ,Dengue ,03 medical and health sciences ,Synthetic biology ,medicine ,Animals ,CRISPR ,Clustered Regularly Interspaced Short Palindromic Repeats ,Computer Simulation ,biology ,Zika Virus Infection ,Cas9 ,Zika Virus ,021001 nanoscience & nanotechnology ,biology.organism_classification ,medicine.disease ,Molecular diagnostics ,Macaca mulatta ,Virology ,Blood ,030104 developmental biology ,Genetic Techniques ,Molecular Diagnostic Techniques ,RNA, Viral ,0210 nano-technology - Abstract
The recent Zika virus outbreak highlights the need for low-cost diagnostics that can be rapidly developed for distribution and use in pandemic regions. Here, we report a pipeline for the rapid design, assembly, and validation of cell-free, paper-based sensors for the detection of the Zika virus RNA genome. By linking isothermal RNA amplification to toehold switch RNA sensors, we detect clinically relevant concentrations of Zika virus sequences and demonstrate specificity against closely related Dengue virus sequences. When coupled with a novel CRISPR/Cas9-based module, our sensors can discriminate between viral strains with single-base resolution. We successfully demonstrate a simple, field-ready sample-processing workflow and detect Zika virus from the plasma of a viremic macaque. Our freeze-dried biomolecular platform resolves important practical limitations to the deployment of molecular diagnostics in the field and demonstrates how synthetic biology can be used to develop diagnostic tools for confronting global health crises., Defense Threat Reduction Agency (DTRA) (HDTRA1-14-1-0006), United States. National Institutes of Health (NIH AI100190)
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- 2016
40. The TB-specific CD4+ T cell immune repertoire in both cynomolgus and rhesus macaques largely overlap with humans
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Nadia A. Golden, Thomas J. Scriba, Patrick S. Bohn, David H. O’Connor, Myles B.C. Dillon, Trey Gilpin, Roger W. Wiseman, Taylor W. Foreman, Cecilia S. Lindestam Arlehamn, Deepak Kaushal, Bianca R. Mothé, Alessandro Sette, JoAnne L. Flynn, Mark Rodgers, Courtney Dow, Julie A. Karl, and Smriti Mehra
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CD4-Positive T-Lymphocytes ,Microbiology (medical) ,Enzyme-Linked Immunospot Assay ,T cell ,Immunology ,Macaque ,Microbiology ,Epitope ,Article ,Immune system ,Antigen ,Species Specificity ,biology.animal ,Immunopathology ,medicine ,Animals ,Humans ,Tuberculosis ,Primate ,Antigens, Bacterial ,biology ,Immunodominant Epitopes ,Histocompatibility Antigens Class II ,Mycobacterium tuberculosis ,Virology ,Macaca mulatta ,Disease Models, Animal ,Macaca fascicularis ,Epitope mapping ,medicine.anatomical_structure ,Infectious Diseases ,Host-Pathogen Interactions ,BCG Vaccine ,Epitope Mapping ,Interferon-gamma Release Tests - Abstract
Non-human primate (NHP) models of tuberculosis (TB) immunity and pathogenesis, especially rhesus and cynomolgus macaques, are particularly attractive because of the high similarity of the human and macaque immune systems. However, little is known about the MHC class II epitopes recognized in macaques, thus hindering the establishment of immune correlates of immunopathology and protective vaccination. We characterized immune responses in rhesus macaques vaccinated against and/or infected with Mycobacterium tuberculosis (Mtb), to a panel of antigens currently in human vaccine trials. We defined 54 new immunodominant CD4(+) T cell epitopes, and noted that antigens immunodominant in humans are also immunodominant in rhesus macaques, including Rv3875 (ESAT-6) and Rv3874 (CFP10). Pedigree and inferred restriction analysis demonstrated that this phenomenon was not due to common ancestry or inbreeding, but rather presentation by common alleles, as well as, promiscuous binding. Experiments using a second cohort of rhesus macaques demonstrated that a pool of epitopes defined in the previous experiments can be used to detect T cell responses in over 75% of individual monkeys. Additionally, 100% of cynomolgus macaques, irrespective of their latent or active TB status, responded to rhesus and human defined epitope pools. Thus, these findings reveal an unexpected general repertoire overlap between MHC class II epitopes recognized in both species of macaques and in humans, showing that epitope pools defined in humans can also be used to characterize macaque responses, despite differences in species and antigen exposure. The results have general implications for the evaluation of new vaccines and diagnostics in NHPs, and immediate applicability in the setting of macaque models of TB.
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- 2015
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41. Reorganization and expansion of the nidoviral family Arteriviridae
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Lark L. Coffey, B. A. Lapin, Nathan D. Wolfe, Elena Postnikova, Jean Michel Takuo, Joseph Le Doux Diffo, Jeffrey Rogers, Eric Delwart, Magdalena Dunowska, Tatyana V. Vishnevskaya, Zinaida V. Shevtsova, Ubald Tamoufe, Laura Bollinger, Matthew G. Lackemeyer, Bradley S. Schneider, Deriabin Pg, S. V. Alkhovsky, Michael Lauck, Matthew LeBreton, Peter B. Jahrling, Terry Fei Fan Ng, Amethyst Gillis, Nikola O. Kondov, Shchetinin Am, Anna N. Clawson, Adam L. Bailey, Yīmíng Bào, Jens H. Kuhn, David H. O’Connor, Jiro Wada, Tony L. Goldberg, Thomas C. Friedrich, Sheli R. Radoshitzky, and Gustavo Palacios
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0301 basic medicine ,Simian hemorrhagic fever virus ,040301 veterinary sciences ,viruses ,Sequence Homology ,Genome, Viral ,Arteriviridae ,Article ,Virus ,0403 veterinary science ,Arterivirus ,Open Reading Frames ,03 medical and health sciences ,RNA Virus Infections ,Genus ,Terminology as Topic ,Virology ,Cluster Analysis ,Nomenclature ,Phylogeny ,Virus classification ,biology ,04 agricultural and veterinary sciences ,General Medicine ,Porcine reproductive and respiratory syndrome virus ,biology.organism_classification ,3. Good health ,030104 developmental biology ,RNA, Viral ,Taxonomy (biology) - Abstract
The family Arteriviridae presently includes a single genus Arterivirus. This genus includes four species as the taxonomic homes for equine arteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV), porcine respiratory and reproductive syndrome virus (PRRSV), and simian hemorrhagic fever virus (SHFV), respectively. A revision of this classification is urgently needed to accommodate the recent description of eleven highly divergent simian arteriviruses in diverse African nonhuman primates, one novel arterivirus in an African forest giant pouched rat, and a novel arterivirus in common brushtails in New Zealand. In addition, the current arterivirus nomenclature is not in accordance with the most recent version of the International Code of Virus Classification and Nomenclature. Here we outline an updated, amended, and improved arterivirus taxonomy based on current data. Taxon-specific sequence cut-offs are established relying on a newly established open reading frame 1b phylogeny and pairwise sequence comparison (PASC) of coding-complete arterivirus genomes. As a result, the current genus Arterivirus is replaced by five genera: Equartevirus (for EAV), Rodartevirus (LDV + PRRSV), Simartevirus (SHFV + simian arteriviruses), Nesartevirus (for the arterivirus from forest giant pouched rats), and Dipartevirus (common brushtail arterivirus). The current species Porcine reproductive and respiratory syndrome virus is divided into two species to accommodate the clear divergence of the European and American “types” of PRRSV, both of which now receive virus status. The current species Simian hemorrhagic fever virus is divided into nine species to accommodate the twelve known simian arteriviruses. Non-Latinized binomial species names are introduced to replace all current species names to clearly differentiate them from virus names, which remain largely unchanged.
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- 2015
42. Zoonotic Potential of Simian Arteriviruses
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David H. O’Connor, Michael Lauck, Thomas C. Friedrich, Adam L. Bailey, Samuel D. Sibley, Anna J. Jasinska, Tony L. Goldberg, Jens H. Kuhn, Jeffrey Rogers, Cristian Apetrei, Nelson B. Freimer, Clifford J. Jolly, Jane E. Phillips-Conroy, Preston A. Marx, and Pierson, TC
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0301 basic medicine ,Simian hemorrhagic fever virus ,Arterivirus ,viruses ,Immunology ,Viremia ,Simian ,Medical and Health Sciences ,Microbiology ,Macaque ,Viral hemorrhagic fever ,Vaccine Related ,03 medical and health sciences ,Arterivirus Infections ,Zoonoses ,Virology ,biology.animal ,Genetics ,medicine ,Animals ,Humans ,2.2 Factors relating to the physical environment ,Aetiology ,Agricultural and Veterinary Sciences ,biology ,Transmission (medicine) ,Prevention ,Primate Diseases ,Haplorhini ,Biological Sciences ,medicine.disease ,biology.organism_classification ,Vector-Borne Diseases ,Infectious Diseases ,Emerging Infectious Diseases ,030104 developmental biology ,Insect Science ,Minireview ,Infection - Abstract
Wild nonhuman primates are immediate sources and long-term reservoirs of human pathogens. However, ethical and technical challenges have hampered the identification of novel blood-borne pathogens in these animals. We recently examined RNA viruses in plasma from wild African monkeys and discovered several novel, highly divergent viruses belonging to the family Arteriviridae . Close relatives of these viruses, including simian hemorrhagic fever virus, have caused sporadic outbreaks of viral hemorrhagic fever in captive macaque monkeys since the 1960s. However, arterivirus infection in wild nonhuman primates had not been described prior to 2011. The arteriviruses recently identified in wild monkeys have high sequence and host species diversity, maintain high viremia, and are prevalent in affected populations. Taken together, these features suggest that the simian arteriviruses may be “preemergent” zoonotic pathogens. If not, this would imply that biological characteristics of RNA viruses thought to facilitate zoonotic transmission may not, by themselves, be sufficient for such transmission to occur.
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- 2015
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43. Subclinical infection of macaques and baboons with a baboon simartevirus
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Bernadette Guerra, David H. O’Connor, Robert E. Lanford, Christina M. Newman, David A. Baker, Kathy Brasky, Matthew R Semler, Adam L. Bailey, Deborah Chavez, Connor R. Buechler, Reed F. Johnson, Joseph P. Cornish, and Jens H. Kuhn
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0303 health sciences ,biology ,Transmission (medicine) ,030231 tropical medicine ,Viremia ,medicine.disease ,Virology ,Epitope ,3. Good health ,Pathogenesis ,03 medical and health sciences ,Titer ,0302 clinical medicine ,biology.animal ,medicine ,biology.protein ,Antibody ,030304 developmental biology ,Subclinical infection ,Baboon - Abstract
Simarteviruses (Arteriviridae:Simartevirus) are commonly found at high titers in the blood of African monkeys but do not cause overt disease in these hosts. In contrast, simarteviruses cause severe disease in Asian macaques upon accidental or experimental transmission. Here, we sought to better understand the host-dependent drivers of simartevirus pathogenesis by infecting olive baboons (n=4) and rhesus macaques (n=4) with the simartevirus Southwest baboon virus 1 (SWBV-1). Surprisingly, none of the animals in our study showed signs of disease following SWBV-1 inoculation. Three animals (two rhesus monkeys and one olive baboon) became infected and sustained high levels of SWBV-1 viremia for the duration of the study. The course of SWBV-1 infection was highly predictable: plasma viremia peaked between 1×107and 1×108vRNA copies/ml at 3–10 days post-inoculation, which was followed by a relative nadir and then establishment of a stable set-point between 1×106and 1×107vRNA copies/ml for the remainder of the study (56 days). We characterized cellular and antibody responses to SWBV-1 infection in these animals, demonstrating that macaques and baboons mount similar responses to SWBV-1 infection, yet these responses are ineffective at clearing SWBV-1 infection. SWBV-1 sequencing revealed the accumulation of non-synonymous mutations in a region of the genome that corresponds to an immunodominant epitope in the simartevirus major envelope glycoprotein GP5, which likely contribute to viral persistence by enabling escape from host antibodies.One Sentence SummarySimartevirus infection has multiple disease manifestations following cross-species transmission.Accessible Summary/ImportanceSimarteviruses are known to infect African monkeys, such as olive baboons, without causing overt disease. In contrast, accidental infection of Asian monkeys, such as rhesus monkeys, has resulted in severe and often fatal disease. We used a simartevirus found circulating among captive olive baboons (Southwest baboon virus 1; SWBV-1) to experimentally infect both olive baboons and rhesus monkeys to model infection with the same virus in both natural and non-natural hosts. Surprisingly, neither baboons nor macaques displayed any laboratory abnormalities or signs of disease over the course of infection, despite robust SWBV-1 replication. In the accompanying study by Cornish et al., a similar experimental approach was undertaken: African patas monkeys and rhesus monkeys were infected with the simartevirus simian hemorrhagic fever virus (SHFV). In contrast to our study, SHFV caused disease in both of these hosts, albeit with much more severe disease developing in the macaques. Interestingly, we observed similar levels of immune cell activation in simartevirus-infected animals across both studies, suggesting that finer nuances of the host response, and perhaps properties of each individual simartevirus, may influences pathogenicity of these viruses in primates. Taken together, our collective findings highlight the wide clinical spectrum of simartevirus infection, ranging from highly-lethal hemorrhagic disease to persistent infection without any overt signs of disease, even in non-natural primate hosts.
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- 2018
44. Antibody responses to Zika virus proteins in pregnant and non-pregnant macaques
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Hanying Li, Adam L. Bailey, David H. O’Connor, Erica Beckman, Laurel M. Stewart, Mustafa N Rasheed, Anna S. Heffron, Michelle R Koenig, Jens C. Eickhoff, Meghan E. Breitbach, Mariel S. Mohns, Christina M. Newman, Dawn M. Dudley, Emma L. Mohr, Jigar Patel, Connor R. Buechler, David Baker, John C. Tan, Amelia K. Haj, and Richard S. Pinapati
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Male ,RNA viruses ,0301 basic medicine ,Serotype ,Physiology ,Microarrays ,RC955-962 ,Antibody Response ,Viral Nonstructural Proteins ,Monkeys ,Dengue virus ,Antibodies, Viral ,Pathology and Laboratory Medicine ,medicine.disease_cause ,Biochemistry ,Cross-reactivity ,Macaque ,Epitope ,Zika virus ,Epitopes ,0302 clinical medicine ,Pregnancy ,Seroepidemiologic Studies ,Immune Physiology ,Arctic medicine. Tropical medicine ,Medicine and Health Sciences ,Immune Response ,Cross Reactivity ,Mammals ,0303 health sciences ,Immune System Proteins ,biology ,Zika Virus Infection ,Eukaryota ,3. Good health ,Bioassays and Physiological Analysis ,Infectious Diseases ,Medical Microbiology ,Viral Pathogens ,Viruses ,Vertebrates ,Female ,Pathogens ,Public aspects of medicine ,RA1-1270 ,Antibody ,Research Article ,Primates ,Immunology ,030106 microbiology ,Cross Reactions ,Research and Analysis Methods ,Microbiology ,Antibodies ,03 medical and health sciences ,Antigen ,Immunity ,biology.animal ,Old World monkeys ,medicine ,Animals ,Humans ,Microbial Pathogens ,030304 developmental biology ,Biology and life sciences ,Flaviviruses ,Linear epitope ,Organisms ,Public Health, Environmental and Occupational Health ,Proteins ,Zika Virus ,Dengue Virus ,biology.organism_classification ,Virology ,Pregnancy Complications ,030104 developmental biology ,Antibody Formation ,Amniotes ,biology.protein ,Macaca ,Epitope Mapping ,Arboviruses ,030217 neurology & neurosurgery - Abstract
The specificity of the antibody response against Zika virus (ZIKV) is not well-characterized. This is due, in part, to the antigenic similarity between ZIKV and closely related dengue virus (DENV) serotypes. Since these and other similar viruses co-circulate, are spread by the same mosquito species, and can cause similar acute clinical syndromes, it is difficult to disentangle ZIKV-specific antibody responses from responses to closely-related arboviruses in humans. Here we use high-density peptide microarrays to profile anti-ZIKV antibody reactivity in pregnant and non-pregnant macaque monkeys with known exposure histories and compare these results to reactivity following DENV infection. We also compare cross-reactive binding of ZIKV-immune sera to the full proteomes of 28 arboviruses. We independently confirm a purported ZIKV-specific IgG antibody response targeting ZIKV nonstructural protein 2B (NS2B) that was recently reported in ZIKV-infected people and we show that antibody reactivity in pregnant animals can be detected as late as 127 days post-infection (dpi). However, we also show that these responses wane over time, sometimes rapidly, and in one case the response was elicited following DENV infection in a previously ZIKV-exposed animal. These results suggest epidemiologic studies assessing seroprevalence of ZIKV immunity using linear epitope-based strategies will remain challenging to interpret due to susceptibility to false positive results. However, the method used here demonstrates the potential for rapid profiling of proteome-wide antibody responses to a myriad of neglected diseases simultaneously and may be especially useful for distinguishing antibody reactivity among closely related pathogens., Author summary ZIKV has emerged as a vector-borne pathogen capable of causing serious illness in infected adults and congenital birth defects. The vulnerability of communities to future ZIKV outbreaks will depend, in part, on the prevalence and longevity of protective immunity, thought to be mediated principally by antibodies. We currently lack diagnostic assays able to differentiate ZIKV-specific antibodies from antibodies produced following infection with closely related DENV, and we do not know how long anti-ZIKV responses are detectable. Here we profile antibodies recognizing linear epitopes throughout the entire ZIKV polyprotein, and we profile cross-reactivity with the proteomes of other co-endemic arboviruses. We show that while ZIKV-specific antibody binding can be detected, these responses are generally weak and ephemeral, and false positives may arise through DENV infection. This may complicate efforts to discern ZIKV infection and to determine ZIKV seroprevalence using linear epitope-based assays. The method used in this study, however, has promise as a tool for profiling antibody responses for a broad array of neglected tropical diseases and other pathogens and in distinguishing serology of closely-related viruses.
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- 2018
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45. The role of MHC-E in T Cell immunity is conserved among humans, rhesus macaques, and cynomolgus macaques
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David H. O’Connor, Lina Gao, Alfred W. Legasse, Justin M. Greene, Byung Park, Fidel Ferrer, Roger W. Wiseman, Simon Brackenridge, Katherine B. Hammond, Nicholas J. Maness, Scott G. Hansen, Benjamin N. Bimber, Benjamin J. Burwitz, Michael K. Axthelm, Jason S. Reed, Shaheed A. Abdulhaqq, Andrew J. McMichael, Helen L. Wu, Louis J. Picker, Jonah B. Sacha, Colette M. Hughes, and Gabriela M. Webb
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CD4-Positive T-Lymphocytes ,0301 basic medicine ,T cell ,Immunology ,Antigen presentation ,Simian Acquired Immunodeficiency Syndrome ,chemical and pharmacologic phenomena ,Human leukocyte antigen ,CD8-Positive T-Lymphocytes ,Biology ,Major histocompatibility complex ,Article ,03 medical and health sciences ,Antigen ,Histocompatibility Antigens ,MHC class I ,medicine ,Animals ,Humans ,Immunology and Allergy ,Antigens, Viral ,Cells, Cultured ,Conserved Sequence ,Antigen Presentation ,Histocompatibility Antigens Class I ,Acquired immune system ,Macaca mulatta ,Virology ,Killer Cells, Natural ,Macaca fascicularis ,030104 developmental biology ,medicine.anatomical_structure ,Models, Animal ,biology.protein ,Simian Immunodeficiency Virus ,Peptides ,CD8 - Abstract
MHC-E is a highly conserved nonclassical MHC class Ib molecule that predominantly binds and presents MHC class Ia leader sequence-derived peptides for NK cell regulation. However, MHC-E also binds pathogen-derived peptide Ags for presentation to CD8+ T cells. Given this role in adaptive immunity and its highly monomorphic nature in the human population, HLA-E is an attractive target for novel vaccine and immunotherapeutic modalities. Development of HLA-E–targeted therapies will require a physiologically relevant animal model that recapitulates HLA-E–restricted T cell biology. In this study, we investigated MHC-E immunobiology in two common nonhuman primate species, Indian-origin rhesus macaques (RM) and Mauritian-origin cynomolgus macaques (MCM). Compared to humans and MCM, RM expressed a greater number of MHC-E alleles at both the population and individual level. Despite this difference, human, RM, and MCM MHC-E molecules were expressed at similar levels across immune cell subsets, equivalently upregulated by viral pathogens, and bound and presented identical peptides to CD8+ T cells. Indeed, SIV-specific, Mamu-E–restricted CD8+ T cells from RM recognized antigenic peptides presented by all MHC-E molecules tested, including cross-species recognition of human and MCM SIV-infected CD4+ T cells. Thus, MHC-E is functionally conserved among humans, RM, and MCM, and both RM and MCM represent physiologically relevant animal models of HLA-E–restricted T cell immunobiology.
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- 2018
46. Infection via mosquito bite alters Zika virus tissue tropism and replication kinetics in rhesus macaques
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Jorge E. Osorio, Matthew R Semler, Shelby L. O’Connor, Matthew T. Aliota, Emma L. Mohr, Lalli J, Saverio Capuano, David H. O’Connor, Katie Zarbock, Thomas C. Friedrich, Andrea M. Weiler, Michelle R Koenig, Laurel M. Stewart, Mariel S. Mohns, Dawn M. Dudley, Gabrielle L. Barry, Eric Peterson, Wendy Newton, Meghan E. Breitbach, Christina M. Newman, and Nancy Schultz-Darken
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0301 basic medicine ,Male ,Science ,030231 tropical medicine ,General Physics and Astronomy ,Disease ,Mosquito Vectors ,Biology ,Virus Replication ,General Biochemistry, Genetics and Molecular Biology ,Deep sequencing ,Virus ,Article ,Zika virus ,03 medical and health sciences ,0302 clinical medicine ,Aedes ,parasitic diseases ,Chlorocebus aethiops ,Animals ,Humans ,lcsh:Science ,Vero Cells ,Multidisciplinary ,Zika Virus Infection ,fungi ,Primate Diseases ,General Chemistry ,Zika Virus ,Viral Load ,biology.organism_classification ,Virology ,Macaca mulatta ,3. Good health ,Kinetics ,Viral Tropism ,030104 developmental biology ,Viral replication ,Tissue tropism ,Vero cell ,lcsh:Q ,Female ,Viral load - Abstract
Mouse and nonhuman primate models now serve as useful platforms to study Zika virus (ZIKV) pathogenesis, candidate therapies, and vaccines, but they rely on needle inoculation of virus: the effects of mosquito-borne infection on disease outcome have not been explored in these models. Here we show that infection via mosquito bite delays ZIKV replication to peak viral loads in rhesus macaques. Importantly, in mosquito-infected animals ZIKV tissue distribution was limited to hemolymphatic tissues, female reproductive tract tissues, kidney, and liver, potentially emulating key features of human ZIKV infections, most of which are characterized by mild or asymptomatic disease. Furthermore, deep sequencing analysis reveals that ZIKV populations in mosquito-infected monkeys show greater sequence heterogeneity and lower overall diversity than in needle-inoculated animals. This newly developed system will be valuable for studying ZIKV disease because it more closely mimics human infection by mosquito bite than needle-based inoculations., Vector saliva can affect infectivity and pathogenesis of vector-borne viruses, but this hasn’t been studied for Zika virus infection. Here, Dudley et al. show that mosquito-mediated Zika infection of macaques results in altered replication kinetics and greater sequence heterogeneity.
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- 2017
47. Molecularly barcoded Zika virus libraries to probe in vivo evolutionary dynamics
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Gregory D. Ebel, Gabrielle L. Barry, Michele L Schotzko, David H. O’Connor, Amelia K. Haj, Heather A. Simmons, Meghan E. Breitbach, Wendy Newton, Andrea M. Weiler, Jennifer M. Hayes, Dawn M. Dudley, Laruel M Stewart, Eric Peterson, Thomas C. Friedrich, Miles P. Davenport, Saverio Capuano, Katie Zarbock, Christina M. Newman, Mariel S. Mohns, Ryan V. Moriarty, Vanessa Venturi, Michelle R Koenig, Nancy Schultz-Darken, Emma L. Mohr, Shelby L. O’Connor, James Weger-Lucarelli, Matthew T. Aliota, Andres Mejia, and Matthew R Semler
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0301 basic medicine ,Male ,RNA viruses ,Physiology ,Artificial Gene Amplification and Extension ,Monkeys ,Disease Vectors ,Pathology and Laboratory Medicine ,Macaque ,Polymerase Chain Reaction ,Mosquitoes ,Zika virus ,Sequencing techniques ,Medicine and Health Sciences ,Biology (General) ,lcsh:QH301-705.5 ,Mammals ,education.field_of_study ,biology ,Zika Virus Infection ,High-Throughput Nucleotide Sequencing ,Eukaryota ,RNA sequencing ,Viral Load ,Biological Evolution ,3. Good health ,Body Fluids ,Insects ,Blood ,Infectious Diseases ,Medical Microbiology ,Viral Pathogens ,Vertebrates ,Viruses ,Female ,Pathogens ,Anatomy ,Viral load ,Research Article ,lcsh:Immunologic diseases. Allergy ,Primates ,Arthropoda ,QH301-705.5 ,030106 microbiology ,Immunology ,Population ,Viremia ,Mosquito Vectors ,Research and Analysis Methods ,Microbiology ,Deep sequencing ,Virus ,Blood Plasma ,03 medical and health sciences ,biology.animal ,Virology ,Old World monkeys ,Genetics ,medicine ,Animals ,education ,Molecular Biology Techniques ,Microbial Pathogens ,Molecular Biology ,Gene Library ,Biology and life sciences ,Flaviviruses ,Organisms ,Zika Virus ,RC581-607 ,biology.organism_classification ,medicine.disease ,Macaca mulatta ,Invertebrates ,Infectious Disease Transmission, Vertical ,Viral Replication ,Insect Vectors ,Species Interactions ,030104 developmental biology ,lcsh:Biology (General) ,Viral replication ,Amniotes ,Parasitology ,Immunologic diseases. Allergy ,lcsh:RC581-607 ,Viral Transmission and Infection - Abstract
Defining the complex dynamics of Zika virus (ZIKV) infection in pregnancy and during transmission between vertebrate hosts and mosquito vectors is critical for a thorough understanding of viral transmission, pathogenesis, immune evasion, and potential reservoir establishment. Within-host viral diversity in ZIKV infection is low, which makes it difficult to evaluate infection dynamics. To overcome this biological hurdle, we constructed a molecularly barcoded ZIKV. This virus stock consists of a “synthetic swarm” whose members are genetically identical except for a run of eight consecutive degenerate codons, which creates approximately 64,000 theoretical nucleotide combinations that all encode the same amino acids. Deep sequencing this region of the ZIKV genome enables counting of individual barcodes to quantify the number and relative proportions of viral lineages present within a host. Here we used these molecularly barcoded ZIKV variants to study the dynamics of ZIKV infection in pregnant and non-pregnant macaques as well as during mosquito infection/transmission. The barcoded virus had no discernible fitness defects in vivo, and the proportions of individual barcoded virus templates remained stable throughout the duration of acute plasma viremia. ZIKV RNA also was detected in maternal plasma from a pregnant animal infected with barcoded virus for 67 days. The complexity of the virus population declined precipitously 8 days following infection of the dam, consistent with the timing of typical resolution of ZIKV in non-pregnant macaques and remained low for the subsequent duration of viremia. Our approach showed that synthetic swarm viruses can be used to probe the composition of ZIKV populations over time in vivo to understand vertical transmission, persistent reservoirs, bottlenecks, and evolutionary dynamics., Author summary Understanding the complex dynamics of Zika virus (ZIKV) infection during pregnancy and during transmission to and from vertebrate host and mosquito vector is critical for a thorough understanding of viral transmission, pathogenesis, immune evasion, and reservoir establishment. We sought to develop a virus model system for use in nonhuman primates and mosquitoes that allows for the genetic discrimination of molecularly cloned viruses. This “synthetic swarm” of viruses incorporates a molecular barcode that allows for tracking and monitoring individual viral lineages during infection. Here we infected rhesus macaques with this virus to study the dynamics of ZIKV infection in nonhuman primates as well as during mosquito infection/transmission. We found that the proportions of individual barcoded viruses remained relatively stable during acute infection in pregnant and nonpregnant animals. However, in a pregnant animal, the complexity of the virus population declined precipitously 8 days following infection, consistent with the timing of typical resolution of ZIKV in non-pregnant macaques and remained low for the subsequent duration of viremia.
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- 2017
48. Molecularly barcoded Zika virus libraries to probe in vivo evolutionary dynamics
- Author
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Heather A. Simmons, Dawn M. Dudley, Michele L Schotzko, Gregory D. Ebel, Andrea M. Weiler, Gabrielle L. Barry, Saverio Capuano, Katie Zarbock, Mariel S. Mohns, Meghan E. Breitbach, David H. O’Connor, Vanessa Venturi, Matthew R Semler, Christina M. Newman, Michelle R Koenig, Eric Peterson, Thomas C. Friedrich, Jennifer M. Hayes, Andres Mejia, Miles P. Davenport, Emma L. Mohr, Shelby L. O’Connor, Wendy Newton, Matthew T. Aliota, James Weger-Lucarelli, Nancy Schultz-Darken, and Laruel M Stewart
- Subjects
education.field_of_study ,Population ,RNA ,Viremia ,Biology ,medicine.disease ,biology.organism_classification ,Virology ,Genome ,Deep sequencing ,Virus ,Zika virus ,medicine ,Evolutionary dynamics ,education - Abstract
Defining the complex dynamics of Zika virus (ZIKV) infection in pregnancy and during transmission between vertebrate hosts and mosquito vectors is critical for a thorough understanding of viral transmission, pathogenesis, immune evasion, and potential reservoir establishment. Within-host viral diversity in ZIKV infection is low, which makes it difficult to evaluate infection dynamics. To overcome this biological hurdle, we constructed a molecularly barcoded ZIKV. This virus stock consists of a “synthetic swarm” whose members are genetically identical except for a run of eight consecutive degenerate codons, which creates approximately 64,000 theoretical nucleotide combinations that all encode the same amino acids. Deep sequencing this region of the ZIKV genome enables counting of individual barcode clonotypes to quantify the number and relative proportions of viral lineages present within a host. Here we used these molecularly barcoded ZIKV variants to study the dynamics of ZIKV infection in pregnant and non-pregnant macaques as well as during mosquito infection/transmission. The barcoded virus had no discernible fitness defectsin vivo, and the proportions of individual barcoded virus templates remained stable throughout the duration of acute plasma viremia. ZIKV RNA also was detected in maternal plasma from a pregnant animal infected with barcoded virus for 64 days. The complexity of the virus population declined precipitously 8 days following infection of the dam, consistent with the timing of typical resolution of ZIKV in non-pregnant macaques, and remained low for the subsequent duration of viremia. Our approach showed that synthetic swarm viruses can be used to probe the composition of ZIKV populations over timein vivoto understand vertical transmission, persistent reservoirs, bottlenecks, and evolutionary dynamics.Author summaryUnderstanding the complex dynamics of Zika virus (ZIKV) infection during pregnancy and during transmission to and from vertebrate host and mosquito vector is critical for a thorough understanding of viral transmission, pathogenesis, immune evasion, and reservoir establishment. We sought to develop a virus model system for use in nonhuman primates and mosquitoes that allows for the genetic discrimination of molecularly cloned viruses. This “synthetic swarm” of viruses incorporates a molecular barcode that allows for tracking and monitoring individual viral lineages during infection. Here we infected rhesus macaques with this virus to study the dynamics of ZIKV infection in nonhuman primates as well as during mosquito infection/transmission. We found that the proportions of individual barcoded viruses remained relatively stable during acute infection in pregnant and nonpregnant animals. However, in a pregnant animal, the complexity of the virus population declined precipitously 8 days following infection, consistent with the timing of typical resolution of ZIKV in non-pregnant macaques, and remained low for the subsequent duration of viremia.
- Published
- 2017
- Full Text
- View/download PDF
49. Pegivirus avoids immune recognition but does not attenuate acute-phase disease in a macaque model of HIV infection
- Author
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Saverio Capuano, Kevin Brunner, Christina M. Newman, Adam J. Ericsen, Eric J. Peterson, Mariel S. Mohns, John C. Tan, Emma L. Mohr, Michelle R Koenig, Daniel R. Matson, Heather A. Simmons, Laurel M. Stewart, David T. Yang, Meghan E. Breitbach, Adam L. Bailey, David H. O’Connor, and Connor R. Buechler
- Subjects
RNA viruses ,0301 basic medicine ,Physiology ,animal diseases ,viruses ,Simian Acquired Immunodeficiency Syndrome ,Monkeys ,Pathology and Laboratory Medicine ,medicine.disease_cause ,Biochemistry ,White Blood Cells ,0302 clinical medicine ,Immunodeficiency Viruses ,Animal Cells ,Immune Physiology ,Medicine and Health Sciences ,030212 general & internal medicine ,Immune Response ,lcsh:QH301-705.5 ,Mammals ,Immune System Proteins ,biology ,Coinfection ,T Cells ,Eukaryota ,virus diseases ,Flaviviridae Infections ,Viral Load ,3. Good health ,SIV ,Medical Microbiology ,Viral Pathogens ,Vertebrates ,Viruses ,Infectious diseases ,Simian Immunodeficiency Virus ,Pathogens ,Cellular Types ,Antibody ,Viral load ,Macaque ,Research Article ,HIV infections ,Primates ,lcsh:Immunologic diseases. Allergy ,Immune Cells ,Pegivirus ,Immunology ,GB virus C ,Viral diseases ,Research and Analysis Methods ,Microbiology ,Antibodies ,Virus ,03 medical and health sciences ,Immune system ,Virology ,Old World monkeys ,Retroviruses ,Genetics ,medicine ,Animals ,Microbial Pathogens ,Immunohistochemistry Techniques ,Molecular Biology ,Blood Cells ,Biology and life sciences ,Lentivirus ,Organisms ,Proteins ,Cell Biology ,Simian immunodeficiency virus ,medicine.disease ,biology.organism_classification ,Histochemistry and Cytochemistry Techniques ,Disease Models, Animal ,Macaca fascicularis ,030104 developmental biology ,lcsh:Biology (General) ,Amniotes ,Immunologic Techniques ,biology.protein ,Parasitology ,lcsh:RC581-607 ,Viral Transmission and Infection - Abstract
Human pegivirus (HPgV) protects HIV+ people from HIV-associated disease, but the mechanism of this protective effect remains poorly understood. We sequentially infected cynomolgus macaques with simian pegivirus (SPgV) and simian immunodeficiency virus (SIV) to model HIV+HPgV co-infection. SPgV had no effect on acute-phase SIV pathogenesis–as measured by SIV viral load, CD4+ T cell destruction, immune activation, or adaptive immune responses–suggesting that HPgV’s protective effect is exerted primarily during the chronic phase of HIV infection. We also examined the immune response to SPgV in unprecedented detail, and found that this virus elicits virtually no activation of the immune system despite persistently high titers in the blood over long periods of time. Overall, this study expands our understanding of the pegiviruses–an understudied group of viruses with a high prevalence in the global human population–and suggests that the protective effect observed in HIV+HPgV co-infected people occurs primarily during the chronic phase of HIV infection., Author summary People infected with HIV live longer, healthier lives when they are co-infected with the human pegivirus (HPgV)–an understudied virus with a high prevalence in the global human population. To better understand how HPgV protects people with HIV from HIV-associated disease, we infected macaques with simian versions of these two viruses (SPgV and SIV). We found that SPgV had no impact on SIV-associated disease early during the course of SIV infection–a time when SIV and HIV are known to cause irreversible damage to the immune system. Oddly, we found that the immune system did not recognize SPgV; a finding that warrants further investigation. Overall, this study greatly expands on our understanding of the pegiviruses and their interaction with the immune system.
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- 2017
50. Historical Outbreaks of Simian Hemorrhagic Fever in Captive Macaques Were Caused by Distinct Arteriviruses
- Author
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Adam L. Bailey, Jiro Wada, Tatyana V. Vishnevskaya, Peter B. Jahrling, Steven Mazur, Michael Lauck, Shchetinin Am, Thomas C. Friedrich, Matthew G. Lackemeyer, Tony L. Goldberg, Sheli R. Radoshitzky, Elena Postnikova, S. V. Alkhovsky, Yīmíng Bào, Zinaida V. Shevtsova, David H. O’Connor, B. A. Lapin, Jens H. Kuhn, and Deriabin Pg
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Hemorrhagic Fevers, Viral ,Simian hemorrhagic fever virus ,Arterivirus ,viruses ,Molecular Sequence Data ,Immunology ,Simian ,Microbiology ,Virus ,Serology ,Evolution, Molecular ,Viral Proteins ,Arterivirus Infections ,Virology ,Animals ,Humans ,Amino Acid Sequence ,Phylogeny ,Sequence Homology, Amino Acid ,biology ,Primate Diseases ,Outbreak ,History, 20th Century ,biology.organism_classification ,Hemorrhagic Fevers ,Genetic Diversity and Evolution ,Insect Science ,Macaca - Abstract
Simian hemorrhagic fever (SHF) is lethal for macaques. Based on clinical presentation and serological diagnosis, all reported SHF outbreaks were thought to be caused by different strains of the same virus, simian hemorrhagic fever virus (SHFV; Arteriviridae ). Here we show that the SHF outbreaks in Sukhumi in 1964 and in Alamogordo in 1989 were caused not by SHFV but by two novel divergent arteriviruses. Our results indicate that multiple divergent simian arteriviruses can cause SHF.
- Published
- 2015
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