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1,346 results on '"Greninger, Alexander L."'

1. The harms of promoting the lab leak hypothesis for SARS-CoV-2 origins without evidence.

Author

Alwine, James, Goodrum, Felicia, Banfield, Bruce, Bloom, David, Britt, William J, Broadbent, Andrew J, Campos, Samuel K, Casadevall, Arturo, Chan, Gary C, Cliffe, Anna R, Dermody, Terence, Duprex, Paul, Enquist, Lynn W, Frueh, Klaus, Geballe, Adam P, Gaglia, Marta, Goldstein, Stephen, Greninger, Alexander L, Gronvall, Gigi Kwick, Jung, Jae U, Kamil, Jeremy P, Lakdawala, Seema, Liu, Shan-Lu, Luftig, Micah, Moore, John P, Moscona, Anne, Neuman, Benjamin W, Nikolich, Janko Ž, O'Connor, Christine, Pekosz, Andrew, Permar, Sallie, Pfeiffer, Julie, Purdy, John, Rasmussen, Angela, Semler, Bert, Smith, Gregory A, Stein, David A, Van Doorslaer, Koenraad, Weller, Sandra K, Whelan, Sean PJ, and Yurochko, Andrew

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Biomedical and Clinical Sciences, Emerging Infectious Diseases, Coronaviruses, Infectious Diseases, Life on Land, COVID-19, SARS-CoV-2, anti-science, lab leak, origin, pandemic, science advocacy, science policy, spillover, zoonosis, Agricultural and Veterinary Sciences, Medical and Health Sciences, Virology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract

Science is humanity's best insurance against threats from nature, but it is a fragile enterprise that must be nourished and protected. The preponderance of scientific evidence indicates a natural origin for SARS-CoV-2. Yet, the theory that SARS-CoV-2 was engineered in and escaped from a lab dominates media attention, even in the absence of strong evidence. We discuss how the resulting anti-science movement puts the research community, scientific research, and pandemic preparedness at risk.

Published
2024

2. Clinical and Genomic Epidemiology of Coxsackievirus A21 and Enterovirus D68 in Homeless Shelters, King County, Washington, USA, 2019-2021. (SYNOPSIS)

Author

Cox, Sarah N., Casto, Amanda M., Franko, Nicholas M., Chow, Eric J., Han, Peter D., Gamboa, Luis, Pfau, Brian, Xie, Hong, Kong, Kevin, Sereewit, Jaydee, Rolfes, Melissa A., Mosites, Emily, Uyeki, Timothy M., Greninger, Alexander L., Carone, Marco, Shim, M. Mia, Bedford, Trevor, Shendure, Jay, Boeckh, Michael, Englund, Janet A., Starita, Lea M., Roychoudhury, Pavitra, and Chu, Helen Y.

Subjects
United States. Centers for Disease Control and Prevention, Nucleotide sequencing, Coxsackievirus infections, Epidemics, Communicable diseases, Genomics, DNA sequencing, Genomes, Adults, Epidemiology, Homeless shelters, Health
Abstract

Enteroviruses are responsible for [approximately equal to] 10-15 million symptomatic illnesses in the United States annually; however, epidemiologic surveillance and genetic characterization of many enterovirus subspecies is limited (1-3). Coxsackievirus [...]

Published
2024
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4. Virology—the path forward

Author

Rasmussen, Angela L, Gronvall, Gigi K, Lowen, Anice C, Goodrum, Felicia, Alwine, James, Andersen, Kristian G, Anthony, Simon J, Baines, Joel, Banerjee, Arinjay, Broadbent, Andrew J, Brooke, Christopher B, Campos, Samuel K, Caposio, Patrizia, Casadevall, Arturo, Chan, Gary C, Cliffe, Anna R, Collins-McMillen, Donna, Connell, Nancy, Damania, Blossom, Daugherty, Matthew D, Debbink, Kari, Dermody, Terence S, DiMaio, Daniel, Duprex, W Paul, Emerman, Michael, Galloway, Denise A, Garry, Robert F, Goldstein, Stephen A, Greninger, Alexander L, Hartman, Amy L, Hogue, Brenda G, Horner, Stacy M, Hotez, Peter J, Jung, Jae U, Kamil, Jeremy P, Karst, Stephanie M, Laimins, Lou, Lakdawala, Seema S, Landais, Igor, Letko, Michael, Lindenbach, Brett, Liu, Shan-Lu, Luftig, Micah, McFadden, Grant, Mehle, Andrew, Morrison, Juliet, Moscona, Anne, Mühlberger, Elke, Munger, Joshua, Münger, Karl, Murphy, Eain, Neufeldt, Christopher J, Nikolich, Janko Z, O'Connor, Christine M, Pekosz, Andrew, Permar, Sallie R, Pfeiffer, Julie K, Popescu, Saskia V, Purdy, John G, Racaniello, Vincent R, Rice, Charles M, Runstadler, Jonathan A, Sapp, Martin J, Scott, Rona S, Smith, Gregory A, Sorrell, Erin M, Speranza, Emily, Streblow, Daniel, Tibbetts, Scott A, Toth, Zsolt, Van Doorslaer, Koenraad, Weiss, Susan R, White, Elizabeth A, White, Timothy M, Wobus, Christiane E, Worobey, Michael, Yamaoka, Satoko, and Yurochko, Andrew

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Biomedical and Clinical Sciences, Emerging Infectious Diseases, Infectious Diseases, Prevention, Coronaviruses, Good Health and Well Being, Humans, Containment of Biohazards, COVID-19, United States, Viruses, Virology, Biomedical Research, virology, SARS-CoV-2, oversight, biosafety, emergence, Agricultural and Veterinary Sciences, Medical and Health Sciences, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract

In the United States (US), biosafety and biosecurity oversight of research on viruses is being reappraised. Safety in virology research is paramount and oversight frameworks should be reviewed periodically. Changes should be made with care, however, to avoid impeding science that is essential for rapidly reducing and responding to pandemic threats as well as addressing more common challenges caused by infectious diseases. Decades of research uniquely positioned the US to be able to respond to the COVID-19 crisis with astounding speed, delivering life-saving vaccines within a year of identifying the virus. We should embolden and empower this strength, which is a vital part of protecting the health, economy, and security of US citizens. Herein, we offer our perspectives on priorities for revised rules governing virology research in the US.

Published
2024

5. One Week of Oral Camostat Versus Placebo in Nonhospitalized Adults With Mild-to-Moderate Coronavirus Disease 2019: A Randomized Controlled Phase 2 Trial

Author

Jilg, Nikolaus, Chew, Kara W, Giganti, Mark J, Daar, Eric S, Wohl, David A, Javan, Arzhang Cyrus, Kantor, Amy, Moser, Carlee, Coombs, Robert W, Neytman, Gene, Hoover, Keila, Jana, Atasi, Hart, Phil A, Greninger, Alexander L, Szurgot, Bob, Eron, Joseph J, Currier, Judith S, Hughes, Michael D, Smith, Davey M, Li, Jonathan Z, Chew, Kara, Smith, David, Daar, Eric, Wohl, David, Currier, Judith, Eron, Joseph, Hughes, Michael, Giganti, Mark, Ritz, Justin, Hosey, Lara, Roa, Jhoanna, Patel, Nilam, Colsh, Kelly, Rwakazina, Irene, Beck, Justine, Sieg, Scott, Li, Jonathan, Fletcher, Courtney, Fischer, William, Evering, Teresa, Coombs, Robert, Ignacio, Rachel Bender, Cardoso, Sandra, Corado, Katya, Jagannathan, Prasanna, Perelson, Alan, Pillay, Sandy, Riviere, Cynthia, Singh, Upinder, Taiwo, Babafemi, Gottesman, Joan, Newell, Matthew, Pedersen, Susan, Dragavon, Joan, Jennings, Cheryl, Greenfelder, Brian, Murtaugh, William, Kosmyna, Jan, Gapara, Morgan, and Shahkolahi, Akbar

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Clinical Trials and Supportive Activities, Emerging Infectious Diseases, Infectious Diseases, Coronaviruses Therapeutics and Interventions, Coronaviruses, Clinical Research, Evaluation of treatments and therapeutic interventions, 6.1 Pharmaceuticals, Good Health and Well Being, Humans, Adult, COVID-19, SARS-CoV-2, RNA, Viral, Time Factors, Treatment Outcome, camostat, outpatient, phase 2, ACTIV-2/A5401 Study Team, Biological Sciences, Medical and Health Sciences, Microbiology, Clinical sciences
Abstract

BackgroundCamostat inhibits severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in vitro. We studied the safety and efficacy of camostat in ACTIV-2/A5401, a phase 2/3 platform trial of therapeutics for COVID-19 in nonhospitalized adults.MethodsWe conducted a phase 2 study in adults with mild-to-moderate COVID-19 randomized to oral camostat for 7 days or a pooled placebo arm. Primary outcomes were time to improvement in COVID-19 symptoms through day 28, proportion of participants with SARS-CoV-2 RNA below the lower limit of quantification (LLoQ) from nasopharyngeal swabs through day 14, and grade ≥3 treatment-emergent adverse events (TEAEs) through day 28.ResultsOf 216 participants (109 randomized to camostat, 107 to placebo) who initiated study intervention, 45% reported ≤5 days of symptoms at study entry and 26% met the protocol definition of higher risk of progression to severe COVID-19. Median age was 37 years. Median time to symptom improvement was 9 days in both arms (P = .99). There were no significant differences in the proportion of participants with SARS-CoV-2 RNA ConclusionsIn a phase 2 study of nonhospitalized adults with mild-to-moderate COVID-19, oral camostat did not accelerate viral clearance or time to symptom improvement, or reduce hospitalizations or deaths. Clinical Trials Registration. ClinicalTrials.gov identifier: NCT04518410.

Published
2023

6. Antiretroviral Therapy Intensification for Neurocognitive Impairment in Human Immunodeficiency Virus

Author

Letendre, Scott L, Chen, Huichao, McKhann, Ashley, Roa, Jhoanna, Vecchio, Alyssa, Daar, Eric S, Berzins, Baiba, Hunt, Peter W, Marra, Christina M, Campbell, Thomas B, Coombs, Robert W, Ma, Qing, Swaminathan, Shobha, Macatangay, Bernard JC, Morse, Gene D, Miller, Thomas, Rusin, David, Greninger, Alexander L, Ha, Belinda, Alston-Smith, Beverly, Robertson, Kevin, Paul, Robert, Spudich, Serena, and Team, the A5324 Study

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Infectious Diseases, Sexually Transmitted Infections, Neurosciences, Clinical Trials and Supportive Activities, Clinical Research, Brain Disorders, HIV/AIDS, Behavioral and Social Science, Depression, Mental Illness, Mental Health, 6.1 Pharmaceuticals, Infection, Good Health and Well Being, Humans, Male, Middle Aged, Female, Antiretroviral Therapy, Highly Active, HIV-1, HIV Infections, Anti-HIV Agents, CD4-Positive T-Lymphocytes, Viral Load, HIV, cognition, brain, antiretroviral therapy, A5324 Study Team, Biological Sciences, Medical and Health Sciences, Microbiology, Clinical sciences
Abstract

BackgroundNeurocognitive impairment (NCI) in people with HIV (PWH) on antiretroviral therapy (ART) is common and may result from persistent HIV replication in the central nervous system.MethodsA5324 was a randomized, double-blind, placebo-controlled, 96-week trial of ART intensification with dolutegravir (DTG) + MVC, DTG + Placebo, or Dual - Placebo in PWH with plasma HIV RNA .10).ConclusionsThis is the largest, randomized, placebo-controlled trial of ART intensification for NCI in PWH. The findings do not support empiric ART intensification as a treatment for NCI in PWH on suppressive ART. They also do not support that DTG adversely affects cognition, mood, or weight.

Published
2023

10. Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features

Author

Magaret, Craig A., Li, Li, deCamp, Allan C., Rolland, Morgane, Juraska, Michal, Williamson, Brian D., Ludwig, James, Molitor, Cindy, Benkeser, David, Luedtke, Alex, Simpkins, Brian, Heng, Fei, Sun, Yanqing, Carpp, Lindsay N., Bai, Hongjun, Dearlove, Bethany L., Giorgi, Elena E., Jongeneelen, Mandy, Brandenburg, Boerries, McCallum, Matthew, Bowen, John E., Veesler, David, Sadoff, Jerald, Gray, Glenda E., Roels, Sanne, Vandebosch, An, Stieh, Daniel J., Le Gars, Mathieu, Vingerhoets, Johan, Grinsztejn, Beatriz, Goepfert, Paul A., de Sousa, Leonardo Paiva, Silva, Mayara Secco Torres, Casapia, Martin, Losso, Marcelo H., Little, Susan J., Gaur, Aditya, Bekker, Linda-Gail, Garrett, Nigel, Truyers, Carla, Van Dromme, Ilse, Swann, Edith, Marovich, Mary A., Follmann, Dean, Neuzil, Kathleen M., Corey, Lawrence, Greninger, Alexander L., Roychoudhury, Pavitra, Hyrien, Ollivier, and Gilbert, Peter B.

Published
2024
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11. Therapeutic mitigation of measles-like immune amnesia and exacerbated disease after prior respiratory virus infections in ferrets

Author

Cox, Robert M., Wolf, Josef D., Lieberman, Nicole A., Lieber, Carolin M., Kang, Hae-Ji, Sticher, Zachary M., Yoon, Jeong-Joong, Andrews, Meghan K., Govindarajan, Mugunthan, Krueger, Rebecca E., Sobolik, Elizabeth B., Natchus, Michael G., Gewirtz, Andrew T., deSwart, Rik L., Kolykhalov, Alexander A., Hekmatyar, Khan, Sakamoto, Kaori, Greninger, Alexander L., and Plemper, Richard K.

Published
2024
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12. Immune Status and SARS-CoV-2 Viral Dynamics

Author

Li, Yijia, Moser, Carlee, Aga, Evgenia, Currier, Judith S, Wohl, David A, Daar, Eric S, Ritz, Justin, Greninger, Alexander L, Sieg, Scott, Parikh, Urvi M, Coombs, Robert W, Hughes, Michael D, Eron, Joseph J, Smith, Davey M, Chew, Kara W, Li, Jonathan Z, Hosey, Lara, Roa, Jhoanna, Patel, Nilam, Degli-Angeli, Emily, Goecker, Erin, Daza, Glenda, Harb, Socorro, Dragavon, Joan, Aldrovandi, Grace, Murtaugh, William, Cooper, Marlene, Gutzman, Howard, Knowles, Kevin, Bowman, Rachel, Erhardt, Bill, Warring, Lorraine, Hessinger, Diane, and Adams, Stacey

Subjects
Biomedical and Clinical Sciences, Immunology, Coronaviruses, Infectious Diseases, Emerging Infectious Diseases, Clinical Research, Clinical Trials and Supportive Activities, Infection, Good Health and Well Being, Humans, COVID-19, Immunocompromised Host, Immunosuppression Therapy, Kinetics, SARS-CoV-2, RNA, immunocompromise, ACTIV-2/A5401 Study Team, Biological Sciences, Medical and Health Sciences, Microbiology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Immunocompromised individuals are disproportionately affected by severe coronavirus disease 2019, but immune compromise is heterogenous, and viral dynamics may vary by the degree of immunosuppression. In this study, we categorized ACTIV-2/A5401 participants based on the extent of immunocompromise into none, mild, moderate, and severe immunocompromise. Moderate/severe immunocompromise was associated with higher nasal viral load at enrollment (adjusted difference in means: 0.47 95% confidence interval, .12-.83 log10 copies/mL) and showed a trend toward higher cumulative nasal RNA levels and plasma viremia compared to nonimmunocompromised individuals. Immunosuppression leads to greater viral shedding and altered severe acute respiratory syndrome coronavirus 2 viral decay kinetics. Clinical Trials Registration. NCT04518410.

Published
2023

13. Variant-Specific Viral Kinetics in Acute COVID-19

Author

Ribeiro, Ruy M, Choudhary, Manish C, Deo, Rinki, Giganti, Mark J, Moser, Carlee, Ritz, Justin, Greninger, Alexander L, Regan, James, Flynn, James P, Wohl, David A, Currier, Judith S, Eron, Joseph J, Hughes, Michael D, Smith, Davey M, Chew, Kara W, Daar, Eric S, Perelson, Alan S, Li, Jonathan Z, Hosey, Lara, Roa, Jhoanna, Patel, Nilam, Aldrovandi, Grace, Murtaugh, William, Science, Frontier, Cooper, Marlene, Gutzman, Howard, Knowles, Kevin, Bowman, Rachel, Erhardt, Bill, and Adams, Stacey

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Clinical Trials and Supportive Activities, Emerging Infectious Diseases, Infectious Diseases, Clinical Research, Coronaviruses, Infection, Humans, COVID-19, Half-Life, Kinetics, SARS-CoV-2, variant, viral kinetics, ACTIV-2/A5401 Study Team, Biological Sciences, Medical and Health Sciences, Microbiology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Understanding variant-specific differences in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral kinetics may explain differences in transmission efficiency and provide insights on pathogenesis and prevention. We evaluated SARS-CoV-2 kinetics from nasal swabs across multiple variants (Alpha, Delta, Epsilon, Gamma) in placebo recipients of the ACTIV-2/A5401 trial. Delta variant infection led to the highest maximum viral load and shortest time from symptom onset to viral load peak. There were no significant differences in time to viral clearance across the variants. Viral decline was biphasic with first- and second-phase decays having half-lives of 11 hours and 2.5 days, respectively, with differences among variants, especially in the second phase. These results suggest that while variant-specific differences in viral kinetics exist, post-peak viral load all variants appeared to be efficiently cleared by the host. Clinical Trials Registration. NCT04518410.

Published
2023

14. Statistical Challenges When Analyzing SARS-CoV-2 RNA Measurements Below the Assay Limit of Quantification in COVID-19 Clinical Trials

Author

Moser, Carlee B, Chew, Kara W, Giganti, Mark J, Li, Jonathan Z, Aga, Evgenia, Ritz, Justin, Greninger, Alexander L, Javan, Arzhang Cyrus, Ignacio, Rachel Bender, Daar, Eric S, Wohl, David A, Currier, Judith S, Eron, Joseph J, Smith, Davey M, Hughes, Michael D, Hosey, Lara, Roa, Jhoanna, Patel, Nilam, Aldrovandi, Grace, Murtaugh, William, Science, Frontier, Cooper, Marlene, Gutzman, Howard, Knowles, Kevin, Bosch, Ronald, Harrison, Linda, Erhardt, Bill, and Adams, Stacey

Subjects
Biological Sciences, Clinical Trials and Supportive Activities, Coronaviruses Therapeutics and Interventions, Emerging Infectious Diseases, Infectious Diseases, Genetics, Clinical Research, Coronaviruses, Generic health relevance, Good Health and Well Being, Humans, Antiviral Agents, Biological Assay, COVID-19, RNA, Viral, SARS-CoV-2, SARS-CoV-2 RNA, linear regression for censored data, randomized trial, ACTIV-2/A5401 Study Team, Medical and Health Sciences, Microbiology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Most clinical trials evaluating coronavirus disease 2019 (COVID-19) therapeutics include assessments of antiviral activity. In recently completed outpatient trials, changes in nasal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA levels from baseline were commonly assessed using analysis of covariance (ANCOVA) or mixed models for repeated measures (MMRM) with single imputation for results below assay lower limits of quantification (LLoQ). Analyzing changes in viral RNA levels with singly imputed values can lead to biased estimates of treatment effects. In this article, using an illustrative example from the ACTIV-2 trial, we highlight potential pitfalls of imputation when using ANCOVA or MMRM methods, and illustrate how these methods can be used when considering values

Published
2023

15. Phase 2 Safety and Antiviral Activity of SAB-185, a Novel Polyclonal Antibody Therapy for Nonhospitalized Adults With COVID-19

Author

Taiwo, Babafemi O, Chew, Kara W, Moser, Carlee, Wohl, David Alain, Daar, Eric S, Li, Jonathan Z, Greninger, Alexander L, Bausch, Christoph, Luke, Thomas, Hoover, Keila, Neytman, Gene, Giganti, Mark J, Olefsky, Maxine, Javan, Arzhang Cyrus, Fletcher, Courtney V, Eron, Joseph J, Currier, Judith S, Hughes, Michael D, Smith, Davey M, Hosey, Lara, Roa, Jhoanna, Patel, Nilam, Coombs, Robert, Degli-Angeli, Emily, Goecker, Erin, Daza, Glenda, Harb, Socorro, Dragavon, Joan, Aldrovandi, Grace, Murtaugh, William, Cooper, Marlene, Gutzman, Howard, Knowles, Kevin, Erhardt, Bill, Waring, Lorraine, Hessinger, Diane, Meintjes, Graeme A, Murray, Barbara E, Ray, Stuart Campbell, Rolla, Valeria Cavalcanti, Saloojee, Haroon, Tsiatis, Anastasios A, Volberding, Paul A, Kimmelman, Jonathan, Glidden, David, and Hunsberger, Sally

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Clinical Research, Clinical Trials and Supportive Activities, Infectious Diseases, Coronaviruses, Emerging Infectious Diseases, 6.1 Pharmaceuticals, Good Health and Well Being, Adult, Humans, COVID-19, SARS-CoV-2, Antiviral Agents, RNA, Viral, Immunoglobulin G, Double-Blind Method, SAB-185, antibody, polyclonal, transchromosomic, treatment, ACTIV-2/A5401 Study Team, Biological Sciences, Medical and Health Sciences, Microbiology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

BackgroundSAB-185, a novel fully human IgG polyclonal immunoglobulin product, underwent phase 2 evaluation for nonhospitalized adults with mild-moderate coronavirus disease 2019 (COVID-19).MethodsParticipants received intravenous SAB-185 3840 units/kg (low-dose) or placebo, or 10 240 units/kg (high-dose) or placebo. Primary outcome measures were nasopharyngeal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA < lower limit of quantification (LLOQ) at study days 3, 7, and 14, time to symptomatic improvement, and safety through day 28.ResultsTwo-hundred thirteen participants received low-dose SAB-185/placebo (n = 107/106) and 215 high-dose SAB-185/placebo (n = 110/105). The proportions with SARS-CoV-2 RNA < LLOQ were higher for SAB-185 versus placebo at days 3 and 7 and similar at day 14, and significantly higher at day 7 for high-dose SAB-185 versus placebo only, relative risk 1.23 (95% confidence interval, 1.01-1.49). At day 3, SARS-CoV-2 RNA levels were lower with low-dose and high-dose SAB-185 versus placebo: differences in medians of -0.78 log10 copies/mL (P = .08) and -0.71 log10 copies/mL (P = .10), respectively. No difference was observed in time to symptom improvement: median 11/10 days (P = .24) for low-dose SAB-185/placebo and 8/10 days (P = .50) for high-dose SAB-185/placebo. Grade ≥3 adverse events occurred in 5%/13% of low-dose SAB-185/placebo and 9%/12% of high-dose SAB-185/placebo.ConclusionsSAB-185 was safe and generally well tolerated and demonstrated modest antiviral activity in predominantly low-risk nonhospitalized adults with COVID-19. Clinical Trials Registration. NCT04518410.

Published
2023

16. Symptom and Viral Rebound in Untreated SARS-CoV-2 Infection

Author

Deo, Rinki, Choudhary, Manish C, Moser, Carlee, Ritz, Justin, Daar, Eric S, Wohl, David A, Greninger, Alexander L, Eron, Joseph J, Currier, Judith S, Hughes, Michael D, Smith, Davey M, Chew, Kara W, Li, Jonathan Z, Javan, Arzhang Cyrus, Giganti, Mark, Hosey, Lara, Roa, Jhoanna, Patel, Nilam, Colsh, Kelly, Rwakazina, Irene, Beck, Justine, Sieg, Scott, Fletcher, Courtney, Fischer, William, Evering, Teresa, Ignacio, Rachel Bender, Cardoso, Sandra, Corado, Katya, Jagannathan, Prasanna, Jilg, Nikolaus, Perelson, Alan, Pillay, Sandy, Riviere, Cynthia, Singh, Upinder, Taiwo, Babafemi, Gottesman, Joan, Newell, Matthew, Pedersen, Susan, Dragavon, Joan, Jennings, Cheryl, Greenfelder, Brian, Murtaugh, William, Kosmyna, Jan, Gapara, Morgan, and Shahkolahi, Akbar

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Emerging Infectious Diseases, Clinical Trials and Supportive Activities, Clinical Research, Brain Disorders, Infectious Diseases, 6.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Infection, Good Health and Well Being, Humans, COVID-19, SARS-CoV-2, Retrospective Studies, RNA, Viral, ACTIV-2/A5401 Study Team, Medical and Health Sciences, General & Internal Medicine, Clinical sciences
Abstract

BackgroundAlthough symptom and viral rebound have been reported after nirmatrelvir-ritonavir treatment, the trajectories of symptoms and viral load during the natural course of COVID-19 have not been well described.ObjectiveTo characterize symptom and viral rebound in untreated outpatients with mild to moderate COVID-19.DesignRetrospective analysis of participants in a randomized, placebo-controlled trial. (ClinicalTrials.gov: NCT04518410).SettingMulticenter trial.Patients563 participants receiving placebo in the ACTIV-2/A5401 (Adaptive Platform Treatment Trial for Outpatients With COVID-19) platform trial.MeasurementsParticipants recorded the severity of 13 symptoms daily between days 0 and 28. Nasal swabs were collected for SARS-CoV-2 RNA testing on days 0 to 14, 21, and 28. Symptom rebound was defined as a 4-point increase in total symptom score after improvement any time after study entry. Viral rebound was defined as an increase of at least 0.5 log10 RNA copies/mL from the immediately preceding time point to a viral load of 3.0 log10 copies/mL or higher. High-level viral rebound was defined as an increase of at least 0.5 log10 RNA copies/mL to a viral load of 5.0 log10 copies/mL or higher.ResultsSymptom rebound was identified in 26% of participants at a median of 11 days after initial symptom onset. Viral rebound was detected in 31% and high-level viral rebound in 13% of participants. Most symptom and viral rebound events were transient, because 89% of symptom rebound and 95% of viral rebound events occurred at only a single time point before improving. The combination of symptom and high-level viral rebound was observed in 3% of participants.LimitationA largely unvaccinated population infected with pre-Omicron variants was evaluated.ConclusionSymptom or viral relapse in the absence of antiviral treatment is common, but the combination of symptom and viral rebound is rare.Primary funding sourceNational Institute of Allergy and Infectious Diseases.

Published
2023

17. Repeated mRNA vaccination sequentially boosts SARS-CoV-2-specific CD8+ T cells in persons with previous COVID-19

Author

Ford, Emily S., Mayer-Blackwell, Koshlan, Jing, Lichen, Laing, Kerry J., Sholukh, Anton M., St. Germain, Russell, Bossard, Emily L., Xie, Hong, Pulliam, Thomas H., Jani, Saumya, Selke, Stacy, Burrow, Carlissa J., McClurkan, Christopher L., Wald, Anna, Greninger, Alexander L., Holbrook, Michael R., Eaton, Brett, Eudy, Elizabeth, Murphy, Michael, Postnikova, Elena, Robins, Harlan S., Elyanow, Rebecca, Gittelman, Rachel M., Ecsedi, Matyas, Wilcox, Elise, Chapuis, Aude G., Fiore-Gartland, Andrew, and Koelle, David M.

Published
2024
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18. Using time‐weighted average change from baseline of SARS‐CoV‐2 viral load to assess impact of hydroxychloroquine as postexposure prophylaxis and early treatment for COVID‐19

Author

Kumbhakar, Raaka, Neradilek, Moni, Barnabas, Ruanne V, Stewart, Jenell, Karita, Helen C Stankiewicz, Landovitz, Raphael J, Kissinger, Patricia J, Jerome, Keith R, Paasche‐Orlow, Michael K, Bershteyn, Anna, Chu, Helen Y, Neuzil, Kathleen M, Greninger, Alexander L, Luk, Alfred, Wald, Anna, Brown, Elizabeth R, and Johnston, Christine

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Pneumonia, Prevention, Infectious Diseases, Emerging Infectious Diseases, Clinical Research, Clinical Trials and Supportive Activities, Lung, Infection, Good Health and Well Being, COVID-19, Humans, Hydroxychloroquine, SARS-CoV-2, Viral Load, COVID-19 Drug Treatment, early treatment, hydroxychloroquine, PEP, Microbiology, Virology, Clinical sciences, Medical microbiology
Abstract

Two randomized controlled trials demonstrated no clinical benefit of hydroxychloroquine (HCQ) for either postexposure prophylaxis or early treatment of SARS-CoV-2 infection. Using data from these studies, we calculated the time-weighted average change from baseline SARS-CoV-2 viral load and demonstrated that HCQ did not affect viral clearance.

Published
2022

19. Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial

Author

Choudhary, Manish C, Chew, Kara W, Deo, Rinki, Flynn, James P, Regan, James, Crain, Charles R, Moser, Carlee, Hughes, Michael D, Ritz, Justin, Ribeiro, Ruy M, Ke, Ruian, Dragavon, Joan A, Javan, Arzhang Cyrus, Nirula, Ajay, Klekotka, Paul, Greninger, Alexander L, Fletcher, Courtney V, Daar, Eric S, Wohl, David A, Eron, Joseph J, Currier, Judith S, Parikh, Urvi M, Sieg, Scott F, Perelson, Alan S, Coombs, Robert W, Smith, Davey M, and Li, Jonathan Z

Subjects
Microbiology, Biological Sciences, Clinical Trials and Supportive Activities, Biotechnology, Vaccine Related, Infectious Diseases, Antimicrobial Resistance, Emerging Infectious Diseases, Biodefense, Prevention, Clinical Research, Lung, Pneumonia, Cancer, Pneumonia & Influenza, Evaluation of treatments and therapeutic interventions, 6.1 Pharmaceuticals, Infection, Good Health and Well Being, Humans, SARS-CoV-2, Antibodies, Monoclonal, Humanized, Mutation, Antibodies, Monoclonal, COVID-19 Drug Treatment, ACTIV-2/A5401 Study Team, Medical Microbiology
Abstract

SARS-CoV-2 mutations that cause resistance to monoclonal antibody (mAb) therapy have been reported. However, it remains unclear whether in vivo emergence of SARS-CoV-2 resistance mutations alters viral replication dynamics or therapeutic efficacy in the immune-competent population. As part of the ACTIV-2/A5401 randomized clinical trial (NCT04518410), non-hospitalized participants with symptomatic SARS-CoV-2 infection were given bamlanivimab (700 mg or 7,000 mg) or placebo treatment. Here¸ we report that treatment-emergent resistance mutations [detected through targeted Spike (S) gene next-generation sequencing] were significantly more likely to be detected after bamlanivimab 700 mg treatment compared with the placebo group (7% of 111 vs 0% of 112 participants, P = 0.003). No treatment-emergent resistance mutations among the 48 participants who received 7,000 mg bamlanivimab were recorded. Participants in which emerging mAb resistant virus mutations were identified showed significantly higher pretreatment nasopharyngeal and anterior nasal viral loads. Daily respiratory tract viral sampling through study day 14 showed the dynamic nature of in vivo SARS-CoV-2 infection and indicated a rapid and sustained viral rebound after the emergence of resistance mutations. Participants with emerging bamlanivimab resistance often accumulated additional polymorphisms found in current variants of concern/interest that are associated with immune escape. These results highlight the potential for rapid emergence of resistance during mAb monotherapy treatment that results in prolonged high-level respiratory tract viral loads. Assessment of viral resistance should be prioritized during the development and clinical implementation of antiviral treatments for COVID-19.

Published
2022

20. Thermodynamically coupled biosensors for detecting neutralizing antibodies against SARS-CoV-2 variants

Author

Zhang, Jason Z, Yeh, Hsien-Wei, Walls, Alexandra C, Wicky, Basile IM, Sprouse, Kaitlin R, VanBlargan, Laura A, Treger, Rebecca, Quijano-Rubio, Alfredo, Pham, Minh N, Kraft, John C, Haydon, Ian C, Yang, Wei, DeWitt, Michelle, Bowen, John E, Chow, Cameron M, Carter, Lauren, Ravichandran, Rashmi, Wener, Mark H, Stewart, Lance, Veesler, David, Diamond, Michael S, Greninger, Alexander L, Koelle, David M, and Baker, David

Subjects
Analytical Chemistry, Information and Computing Sciences, Chemical Sciences, Bioengineering, Pneumonia, Lung, Emerging Infectious Diseases, Vaccine Related, Infectious Diseases, Prevention, Pneumonia & Influenza, Biodefense, Biotechnology, Good Health and Well Being, Antibodies, Neutralizing, Antibodies, Viral, Biosensing Techniques, COVID-19, Humans, Neutralization Tests, SARS-CoV-2, Spike Glycoprotein, Coronavirus, Callicarpa nudiflora Hook, luteolin 3 '-O-beta-D-6 ''-acetyl glucopyranoside, pachypodol, hepatocellular carcinoma, cytotoxicity
Abstract

We designed a protein biosensor that uses thermodynamic coupling for sensitive and rapid detection of neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in serum. The biosensor is a switchable, caged luciferase-receptor-binding domain (RBD) construct that detects serum-antibody interference with the binding of virus RBD to angiotensin-converting enzyme 2 (ACE-2) as a proxy for neutralization. Our coupling approach does not require target modification and can better distinguish sample-to-sample differences in analyte binding affinity and abundance than traditional competition-based assays.

Published
2022

21. CMV reactivation during pretransplantation evaluation: a novel risk factor for posttransplantation CMV reactivation

Author

Zamora, Danniel, Xie, Hu, Sadowska-Klasa, Alicja, Kampouri, Eleftheria, Biernacki, Melinda A., Ueda Oshima, Masumi, Duke, Elizabeth, Green, Margaret L., Kimball, Louise E., Holmberg, Leona, Waghmare, Alpana, Greninger, Alexander L., Jerome, Keith R., Hill, Geoffrey R., Hill, Joshua A., Leisenring, Wendy M., and Boeckh, Michael J.

Published
2024
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22. Self-Assessed Severity as a Determinant of Coronavirus Disease 2019 Symptom Specificity: A Longitudinal Cohort Study

Author

Bershteyn, Anna, Dahl, Angela M, Dong, Tracy Q, Deming, Meagan E, Celum, Connie L, Chu, Helen Y, Kottkamp, Angelica C, Greninger, Alexander L, Hoffman, Risa M, Jerome, Keith R, Johnston, Christine M, Kissinger, Patricia J, Landovitz, Raphael J, Laufer, Miriam K, Luk, Alfred, Neuzil, Kathleen M, Paasche-Orlow, Michael K, Pitts, Robert A, Schwartz, Mark D, Stankiewicz Karita, Helen C, Thorpe, Lorna E, Wald, Anna, Zheng, Crystal Y, Wener, Mark H, Barnabas, Ruanne V, and Brown, Elizabeth R

Subjects
Prevention, Biodefense, Clinical Research, Emerging Infectious Diseases, Infectious Diseases, Vaccine Related, Pneumonia & Influenza, Pneumonia, Lung, Good Health and Well Being, COVID-19, COVID-19 Testing, Humans, Longitudinal Studies, SARS-CoV-2, symptoms, screening, severity, Biological Sciences, Medical and Health Sciences, Microbiology
Abstract

Coronavirus disease 2019 symptom definitions rarely include symptom severity. We collected daily nasal swab samples and symptom diaries from contacts of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) case patients. Requiring ≥1 moderate or severe symptom reduced sensitivity to predict SARS-CoV-2 shedding from 60.0% (95% confidence interval [CI], 52.9%-66.7%) to 31.5% (95% CI, 25.7%- 38.0%) but increased specificity from 77.5% (95% CI, 75.3%-79.5%) to 93.8% (95% CI, 92.7%-94.8%).

Published
2022

23. Monoclonal antibody treatment drives rapid culture conversion in SARS-CoV-2 infection

Author

Boucau, Julie, Chew, Kara W, Choudhary, Manish C, Deo, Rinki, Regan, James, Flynn, James P, Crain, Charles R, Hughes, Michael D, Ritz, Justin, Moser, Carlee, Dragavon, Joan A, Javan, Arzhang C, Nirula, Ajay, Klekotka, Paul, Greninger, Alexander L, Coombs, Robert W, Fischer, William A, Daar, Eric S, Wohl, David A, Eron, Joseph J, Currier, Judith S, Smith, Davey M, team, the POSITIVES study, Li, Jonathan Z, Barczak, Amy K, and Team, the ACTIV-2 A5401 Study

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Clinical Research, Infectious Diseases, Vaccine Related, Biodefense, Biotechnology, Lung, Immunization, Prevention, Emerging Infectious Diseases, Pneumonia, Pneumonia & Influenza, Clinical Trials and Supportive Activities, Infection, Good Health and Well Being, Antibodies, Monoclonal, Antibodies, Monoclonal, Humanized, Antibodies, Neutralizing, Humans, SARS-CoV-2, COVID-19 Drug Treatment, POSITIVES study team, ACTIV-2/A5401 Study Team, COVID, COVID therapies, COVID-19, mAbs, monoclonal antibodies, resistance, viral culture, Biomedical and clinical sciences
Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) monoclonal antibodies (mAbs) are among the treatments recommended for high-risk ambulatory persons with coronavirus 2019 (COVID-19). Here, we study viral culture dynamics post-treatment in a subset of participants receiving the mAb bamlanivimab in the ACTIV-2 trial (ClinicalTrials.gov: NCT04518410). Viral load by qPCR and viral culture are performed from anterior nasal swabs collected on study days 0 (day of treatment), 1, 2, 3, and 7. Treatment with mAbs results in rapid clearance of culturable virus. One day after treatment, 0 of 28 (0%) participants receiving mAbs and 16 of 39 (41%) receiving placebo still have culturable virus (p

Published
2022

24. Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin

Author

Welsh, Frances C., Eguia, Rachel T., Lee, Juhye M., Haddox, Hugh K., Galloway, Jared, Van Vinh Chau, Nguyen, Loes, Andrea N., Huddleston, John, Yu, Timothy C., Quynh Le, Mai, Nhat, Nguyen T.D., Thi Le Thanh, Nguyen, Greninger, Alexander L., Chu, Helen Y., Englund, Janet A., Bedford, Trevor, Matsen, Frederick A., IV, Boni, Maciej F., and Bloom, Jesse D.

Published
2024
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25. Surveillance of Vermont wildlife in 2021–2022 reveals no detected SARS-CoV-2 viral RNA

Author

Despres, Hannah W., Mills, Margaret G., Schmidt, Madaline M., Gov, Jolene, Perez, Yael, Jindrich, Mars, Crawford, Allison M. L., Kohl, Warren T., Rosenblatt, Elias, Kubinski, Hannah C., Simmons, Benjamin C., Nippes, Miles C., Goldenberg, Anne J., Murtha, Kristina E., Nicoloro, Samantha, Harris, Mia J., Feeley, Avery C., Gelinas, Taylor K., Cronin, Maeve K., Frederick, Robert S., Thomas, Matthew, Johnson, Meaghan E., Murphy, James, Lenzini, Elle B., Carr, Jr., Peter A., Berger, Danielle H., Mehta, Soham P., Floreani, Christopher J., Koval, Amelia C., Young, Aleah L., Fish, Jess H., Wallace, Jack, Chaney, Ella, Ushay, Grace, Ross, Rebecca S., Vostal, Erin M., Thisner, Maya C., Gonet, Kyliegh E., Deane, Owen C., Pelletiere, Kari R., Rockafeller, Vegas C., Waterman, Madeline, Barry, Tyler W., Goering, Catriona C., Shipman, Sarah D., Shiers, Allie C., Reilly, Claire E., Duff, Alanna M., Madruga, Sarah L., Shirley, David J., Jerome, Keith R., Pérez-Osorio, Ailyn C., Greninger, Alexander L., Fortin, Nick, Mosher, Brittany A., and Bruce, Emily A.

Published
2023
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28. Oral linezolid compared with benzathine penicillin G for treatment of early syphilis in adults (Trep-AB Study) in Spain: a prospective, open-label, non-inferiority, randomised controlled trial

Author

Ubals, Maria, Nadal-Baron, Patricia, Arando, Maider, Rivero, Ángel, Mendoza, Adrià, Descalzo Jorro, Vicent, Ouchi, Dan, Pérez-Mañá, Clara, Álvarez, Marlene, Alemany, Andrea, Hoyos-Mallecot, Yannick, Nunley, Ethan, Lieberman, Nicole A P, Greninger, Alexander L, Galván-Casas, Cristina, Suñer, Clara, G-Beiras, Camila, Paredes, Roger, Rodríguez-Gascón, Alicia, Canut, Andrés, García-Patos, Vicente, Farré, Magí, Marks, Michael, Giacani, Lorenzo, Vall-Mayans, Martí, and Mitjà, Oriol

Published
2024
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31. Genomic Characterization of Respiratory Syncytial Virus during 2022-23 Outbreak, Washington, USA

Author

Goya, Stephanie, Sereewit, Jaydee, Pfalmer, Daniel, Nguyen, Tien V., Bakhash, Shah A.K. Mohamed, Sobolik, Elizabeth B., and Greninger, Alexander L.

Subjects
Washington -- Health aspects, Epidemics -- Causes of -- Distribution, Respiratory syncytial virus infection -- Causes of -- Distribution, Respiratory syncytial virus -- Identification and classification -- Genetic aspects -- Distribution, Company distribution practices, Health
Abstract

Annual seasonality of respiratory syncytial virus (RSV) in Washington, USA, has been limited primarily to late autumn and winter (1). However, an RSV outbreak was not detected during the 2020-21 [...]

Published
2023

34. Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites: A Joint Report of the Association for Molecular Pathology, American Society for Microbiology, Infectious Diseases Society of America, and Pan American Society for Clinical Virology

Author

Lewinski, Michael A., Alby, Kevin, Babady, N. Esther, Butler-Wu, Susan M., Bard, Jennifer Dien, Greninger, Alexander L., Hanson, Kimberly, Naccache, Samia N., Newton, Duane, Temple-Smolkin, Robyn L., and Nolte, Frederick

Published
2023
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35. Hydroxychloroquine as Postexposure Prophylaxis to Prevent Severe Acute Respiratory Syndrome Coronavirus 2 Infection

Author

Barnabas, Ruanne V, Brown, Elizabeth R, Bershteyn, Anna, Stankiewicz Karita, Helen C, Johnston, Christine, Thorpe, Lorna E, Kottkamp, Angelica, Neuzil, Kathleen M, Laufer, Miriam K, Deming, Meagan, Paasche-Orlow, Michael K, Kissinger, Patricia J, Luk, Alfred, Paolino, Kristopher, Landovitz, Raphael J, Hoffman, Risa, Schaafsma, Torin T, Krows, Meighan L, Thomas, Katherine K, Morrison, Susan, Haugen, Harald S, Kidoguchi, Lara, Wener, Mark, Greninger, Alexander L, Huang, Meei-Li, Jerome, Keith R, Wald, Anna, Celum, Connie, Chu, Helen Y, and Baeten, Jared M

Subjects
Clinical Trials and Supportive Activities, Clinical Research, Vaccine Related, Pneumonia, Emerging Infectious Diseases, Prevention, Lung, Infectious Diseases, Infection, Good Health and Well Being, Adolescent, Adult, Aged, Aged, 80 and over, Antiviral Agents, COVID-19, COVID-19 Nucleic Acid Testing, Double-Blind Method, Female, Humans, Hydroxychloroquine, Male, Middle Aged, Post-Exposure Prophylaxis, SARS-CoV-2, Time Factors, Treatment Outcome, United States, Young Adult, COVID-19 Drug Treatment, Hydroxychloroquine COVID-19 PEP Study Team, Clinical Sciences, Public Health and Health Services
Abstract

BackgroundEffective prevention against coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is currently limited to nonpharmaceutical strategies. Laboratory and observational data suggested that hydroxychloroquine had biological activity against SARS-CoV-2, potentially permitting its use for prevention.ObjectiveTo test hydroxychloroquine as postexposure prophylaxis for SARS-CoV-2 infection.DesignHousehold-randomized, double-blind, controlled trial of hydroxychloroquine postexposure prophylaxis. (ClinicalTrials.gov: NCT04328961).SettingNational U.S. multicenter study.ParticipantsClose contacts recently exposed ( 0.20). The frequency of participants experiencing adverse events was higher in the hydroxychloroquine group than the control group (66 [16.2%] versus 46 [10.9%], respectively; P = 0.026).LimitationThe delay between exposure, and then baseline testing and the first dose of hydroxychloroquine or ascorbic acid, was a median of 2 days.ConclusionThis rigorous randomized controlled trial among persons with recent exposure excluded a clinically meaningful effect of hydroxychloroquine as postexposure prophylaxis to prevent SARS-CoV-2 infection.Primary funding sourceBill & Melinda Gates Foundation.

Published
2021

36. Sentinel Surveillance System Implementation and Evaluation for SARS-CoV-2 Genomic Data, Washington, USA, 2020-2021

Author

Oltean, Hanna N., Allen, Krisandra J., Frisbie, Lauren, Lunn, Stephanie M., Torres, Laura Marcela, Manahan, Lillian, Painter, Ian, Russel, Denny, Singh, Avi, Aric, JohnAric MoonDance, Grant, Kristin, Peter, Cara, Cao, Rebecca, Garcia, Katelynn, Mackellar, Drew, Jones, Lisa, Halstead, Holly, Gray, Hannah, Melly, Geoff, Nickerson, Deborah, Starita, Lea, Frazar, Chris, Greninger, Alexander L., Roychoudhury, Pavitra, Mathias, Patrick C., Kalnoski, Michael H., Ting, Chao-Nan, Lykken, Marisa, and Rice, Tana

Subjects
Washington -- Health aspects, Epidemics -- Statistics -- Genetic aspects, Sentinel health events -- Methods, Data entry -- Methods, Health
Abstract

Virus genome data can provide useful information for public health practice, particularly when combined with epidemiologic data in real time. Goals of genomic surveillance can include monitoring circulating and emerging [...]

Published
2023
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38. Diminished humoral and cellular responses to SARS-CoV-2 vaccines in patients with chronic lymphocytic leukemia

Author

Ujjani, Chaitra, Gooley, Ted A., Spurgeon, Stephen E., Stephens, Deborah M., Lai, Catherine, Broome, Catherine M., O’Brien, Susan, Zhu, Haiying, Laing, Kerry J., Winter, Allison M., Pongas, Georgios, Greninger, Alexander L, Koelle, David M., Siddiqi, Tanya, Davids, Matthew S., Rogers, Kerry A., Danilov, Alexey V., Sperling, Amy, Tu, Brian, Sorensen, Tyler, Launchbury, Kelsey, Burrow, Carlissa J., Quezada, Genesis, Hill, Joshua A., Shadman, Mazyar, and Thompson, Philip A.

Published
2023
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39. CrAssphage and its bacterial host in cat feces

Author

Li, Yanpeng, Gordon, Emilia, Shean, Ryan C, Idle, Amanda, Deng, Xutao, Greninger, Alexander L, and Delwart, Eric

Subjects
Microbiology, Biological Sciences, Genetics, Human Genome, Aging, Animals, Bacteriophages, Bacteroides, Cats, Environmental Monitoring, Feces, Humans, Phylogeny, Sequence Analysis, DNA, Sewage, Water Pollution
Abstract

CrAssphages are a diverse group of related phages detected in human feces where they are the most prevalent and abundant prokaryotic virus. CrAssphages' cellular host has been identified as the anaerobic Bacteroides intestinalis. CrAssphage has also been reported in non-human primates and environmental samples and has been proposed as a marker of human fecal contamination. Here we describe crAssphage DNA in a feline fecal sample. 95% of the ~ 100 Kb genome could be assembled and classified in genus 1 of the recently proposed Alphacrassvirinae subfamily. The cat origin of the fecal sample was confirmed by partial mitochondrial DNA sequencing. High levels of Bacteroides intestinalis DNA could also be detected in this cat's feces. Fecal samples longitudinally collected over a 4-week period showed the continuous shedding of crAssphage DNA. We therefore report the first genome sequence-confirmed detection of crAssphage in fecal samples of a non-primate mammal.

Published
2021

40. Cryptic transmission of SARS-CoV-2 in Washington state

Author

Bedford, Trevor, Greninger, Alexander L, Roychoudhury, Pavitra, Starita, Lea M, Famulare, Michael, Huang, Meei-Li, Nalla, Arun, Pepper, Gregory, Reinhardt, Adam, Xie, Hong, Shrestha, Lasata, Nguyen, Truong N, Adler, Amanda, Brandstetter, Elisabeth, Cho, Shari, Giroux, Danielle, Han, Peter D, Fay, Kairsten, Frazar, Chris D, Ilcisin, Misja, Lacombe, Kirsten, Lee, Jover, Kiavand, Anahita, Richardson, Matthew, Sibley, Thomas R, Truong, Melissa, Wolf, Caitlin R, Nickerson, Deborah A, Rieder, Mark J, Englund, Janet A, Hadfield, James, Hodcroft, Emma B, Huddleston, John, Moncla, Louise H, Müller, Nicola F, Neher, Richard A, Deng, Xianding, Gu, Wei, Federman, Scot, Chiu, Charles, Duchin, Jeffrey S, Gautom, Romesh, Melly, Geoff, Hiatt, Brian, Dykema, Philip, Lindquist, Scott, Queen, Krista, Tao, Ying, Uehara, Anna, Tong, Suxiang, MacCannell, Duncan, Armstrong, Gregory L, Baird, Geoffrey S, Chu, Helen Y, Shendure, Jay, Jerome, Keith R, Boeckh, Michael, Lutz, Barry R, Thompson, Matthew, Huang, Shichu, Jackson, Michael L, Kimball, Louise E, Logue, Jennifer, Lyon, Victoria, Newman, Kira L, and Suchsland, Monica L Zigman

Subjects
Infectious Diseases, Pneumonia & Influenza, Lung, Prevention, Emerging Infectious Diseases, Biodefense, Vaccine Related, Pneumonia, Infection, Good Health and Well Being, Bayes Theorem, Betacoronavirus, COVID-19, Coronavirus Infections, Genome, Viral, Humans, Likelihood Functions, Pandemics, Phylogeny, Pneumonia, Viral, SARS-CoV-2, Washington, Seattle Flu Study Investigators, General Science & Technology
Abstract

After its emergence in Wuhan, China, in late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows the reconstruction of its transmission history, although this is contingent on sampling. We analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020 from infected patients in Washington state in the United States. We find that most SARS-CoV-2 infections sampled during this time derive from a single introduction in late January or early February 2020, which subsequently spread locally before active community surveillance was implemented.

Published
2020

41. Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

Author

Deng, Xianding, Gu, Wei, Federman, Scot, du Plessis, Louis, Pybus, Oliver G, Faria, Nuno, Wang, Candace, Yu, Guixia, Bushnell, Brian, Pan, Chao-Yang, Guevara, Hugo, Sotomayor-Gonzalez, Alicia, Zorn, Kelsey, Gopez, Allan, Servellita, Venice, Hsu, Elaine, Miller, Steve, Bedford, Trevor, Greninger, Alexander L, Roychoudhury, Pavitra, Starita, Lea M, Famulare, Michael, Chu, Helen Y, Shendure, Jay, Jerome, Keith R, Anderson, Catie, Gangavarapu, Karthik, Zeller, Mark, Spencer, Emily, Andersen, Kristian G, MacCannell, Duncan, Paden, Clinton R, Li, Yan, Zhang, Jing, Tong, Suxiang, Armstrong, Gregory, Morrow, Scott, Willis, Matthew, Matyas, Bela T, Mase, Sundari, Kasirye, Olivia, Park, Maggie, Masinde, Godfred, Chan, Curtis, Yu, Alexander T, Chai, Shua J, Villarino, Elsa, Bonin, Brandon, Wadford, Debra A, and Chiu, Charles Y

Subjects
Pneumonia, Lung, Infectious Diseases, Emerging Infectious Diseases, Vaccine Related, Pneumonia & Influenza, Prevention, Biodefense, Infection, Good Health and Well Being, Betacoronavirus, COVID-19, California, Coronavirus Infections, Epidemiological Monitoring, Genome, Viral, Humans, Pandemics, Phylogeny, Pneumonia, Viral, SARS-CoV-2, Sequence Alignment, Ships, Travel, Washington, General Science & Technology
Abstract

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally, with >365,000 cases in California as of 17 July 2020. We investigated the genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-March 2020, using samples from 36 patients spanning nine counties and the Grand Princess cruise ship. Phylogenetic analyses revealed the cryptic introduction of at least seven different SARS-CoV-2 lineages into California, including epidemic WA1 strains associated with Washington state, with lack of a predominant lineage and limited transmission among communities. Lineages associated with outbreak clusters in two counties were defined by a single base substitution in the viral genome. These findings support contact tracing, social distancing, and travel restrictions to contain the spread of SARS-CoV-2 in California and other states.

Published
2020

42. A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

Author

Deng, Xianding, Gu, Wei, Federman, Scot, du Plessis, Louis, Pybus, Oliver G, Faria, Nuno, Wang, Candace, Yu, Guixia, Pan, Chao-Yang, Guevara, Hugo, Sotomayor-Gonzalez, Alicia, Zorn, Kelsey, Gopez, Allan, Servellita, Venice, Hsu, Elaine, Miller, Steve, Bedford, Trevor, Greninger, Alexander L, Roychoudhury, Pavitra, Starita, Lea M, Famulare, Michael, Chu, Helen Y, Shendure, Jay, Jerome, Keith R, Anderson, Catie, Gangavarapu, Karthik, Zeller, Mark, Spencer, Emily, Andersen, Kristian G, MacCannell, Duncan, Paden, Clinton R, Li, Yan, Zhang, Jing, Tong, Suxiang, Armstrong, Gregory, Morrow, Scott, Willis, Matthew, Matyas, Bela T, Mase, Sundari, Kasirye, Olivia, Park, Maggie, Chan, Curtis, Yu, Alexander T, Chai, Shua J, Villarino, Elsa, Bonin, Brandon, Wadford, Debra A, and Chiu, Charles Y

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Biological Sciences, Lung, Infectious Diseases, Biotechnology, Prevention, Biodefense, Emerging Infectious Diseases, Vaccine Related, Aetiology, 2.2 Factors relating to the physical environment, Infection, Good Health and Well Being
Abstract

The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has spread globally, resulting in >300,000 reported cases worldwide as of March 21st, 2020. Here we investigate the genetic diversity and genomic epidemiology of SARS-CoV-2 in Northern California using samples from returning travelers, cruise ship passengers, and cases of community transmission with unclear infection sources. Virus genomes were sampled from 29 patients diagnosed with COVID-19 infection from Feb 3rd through Mar 15th. Phylogenetic analyses revealed at least 8 different SARS-CoV-2 lineages, suggesting multiple independent introductions of the virus into the state. Virus genomes from passengers on two consecutive excursions of the Grand Princess cruise ship clustered with those from an established epidemic in Washington State, including the WA1 genome representing the first reported case in the United States on January 19th. We also detected evidence for presumptive transmission of SARS-CoV-2 lineages from one community to another. These findings suggest that cryptic transmission of SARS-CoV-2 in Northern California to date is characterized by multiple transmission chains that originate via distinct introductions from international and interstate travel, rather than widespread community transmission of a single predominant lineage. Rapid testing and contact tracing, social distancing, and travel restrictions are measures that will help to slow SARS-CoV-2 spread in California and other regions of the USA.

Published
2020

43. Human Parainfluenza Virus in Homeless Shelters before and during the COVID-19 Pandemic, Washington, USA

Author

Chow, Eric J., Casto, Amanda M., Sampoleo, Reigran, Mills, Margaret G., Han, Peter D., Xie, Hong, Pfau, Brian, Nguyen, Tien V., Sereewit, Jaydee, Rogers, Julia H., Cox, Sarah N., Rolfes, Melissa A., Ogokeh, Constance, Mosites, Emily, Uyeki, Timothy M., Greninger, Alexander L., Hughes, James P., Shim, M. Mia, Sugg, Nancy, Duchin, Jeffrey S., Starita, Lea M., Englund, Janet A., Roychoudhury, Pavitra, and Chu, Helen Y.

Subjects
Washington -- Health aspects, Parainfluenza viruses -- Distribution, Respiratory tract infections -- Causes of -- Demographic aspects, Pediatric research, Homeless shelters -- Health aspects, Company distribution practices, Health
Abstract

Human parainfluenza virus (HPIV) contributes to acute respiratory tract infection burden in young children (1) and adults (2). Persons experiencing homelessness are among those at risk for respiratory viral complications [...]

Published
2022
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44. Duration of viral infectiousness and correlation with symptoms and diagnostic testing in non-hospitalized adults during acute SARS-CoV-2 infection: A longitudinal cohort study

Author

Drain, Paul K., Dalmat, Ronit R., Hao, Linhui, Bemer, Meagan J., Budiawan, Elvira, Morton, Jennifer F., Ireton, Renee C., Hsiang, Tien-Ying, Marfatia, Zarna, Prabhu, Roshni, Woosley, Claire, Gichamo, Adanech, Rechkina, Elena, Hamilton, Daphne, Montaño, Michalina, Cantera, Jason L., Ball, Alexey S., Golez, Inah, Smith, Elise, Greninger, Alexander L., McElrath, M.Juliana, Thompson, Matthew, Grant, Benjamin D., Meisner, Allison, Gottlieb, Geoffrey S., and Gale, Michael, Jr.

Published
2023
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47. Genomic Analysis of Early Monkeypox Virus Outbreak Strains, Washington, USA

Author

Roychoudhury, Pavitra, Sereewit, Jaydee, Xie, Hong, Nunley, Ethan, Bakhash, Shah M., Lieberman, Nicole A.P., and Greninger, Alexander L.

Subjects
Washington -- Health aspects, Nucleotide sequencing -- Usage, Human monkeypox -- Statistics -- Genetic aspects -- Causes of, Epidemics -- Statistics -- Genetic aspects -- Causes of -- United States, DNA sequencing -- Usage, Health
Abstract

The World Health Organization declared the 2022 mpox (formerly monkeypox) outbreak a public health emergency of international concern on July 23, 2022, after cases were identified in nearly 80 countries [...]

Published
2023
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49. Near-Universal Resistance to Macrolides of Treponema pallidum in North America

Author

Lieberman, Nicole A.P., primary, Reid, Tara B., additional, Cannon, Chase A., additional, Nunley, B. Ethan, additional, Berzkalns, Anna, additional, Cohen, Stephanie E., additional, Newman, Lori M., additional, Aldrete, Sol, additional, Xu, Linda H., additional, Thornlund, Clinton P., additional, Pettus, Kevin, additional, Lundy, Stephanie, additional, Kron, Michael, additional, Soge, Olusegun O., additional, Workowski, Kimberly, additional, Perlowski, Charlotte, additional, Hook, Edward W., additional, Dionne, Jodie A., additional, Golden, Matthew R., additional, Lieberman, Joshua A., additional, Lee, Min-Kuang, additional, Morshed, Muhammad, additional, Naidu, Prenilla, additional, Cao, Weiping, additional, Pillay, Allan, additional, Giacani, Lorenzo, additional, and Greninger, Alexander L., additional

Published
2024
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50. Efficacy, safety, and immunogenicity of a booster regimen of Ad26.COV2.S vaccine against COVID-19 (ENSEMBLE2): results of a randomised, double-blind, placebo-controlled, phase 3 trial

Author

Garibaldi, Brian T., Albertson, Timothy E., Sandrock, Christian, Lee, Janet S., Looney, Mark R., Tapson, Victor F., Wiysonge, Charles Shey, Velarde, Luis Humberto Anaya, Backenroth, Daniel, Bhushanan, Jisha, Brandenburg, Börries, Cárdenas, Vicky, Chen, Bohang, Chen, Fei, Chetty, Polan, Chu, Pei-Ling, Cooper, Kimberly, Custers, Jerome, Delanghe, Hilde, Duca, Anna, Henrick, Tracy, Juraszek, Jarek, Nalpas, Catherine, Peeters, Monika, Pinheiro, Jose, Roels, Sanne, Ryser, Martin F., Salas, Jose, Santoro Matias, Samantha, Scheys, Ilse, Shetty, Pallavi, Shukarev, Georgi, Stoddard, Jeffrey, Talloen, Willem, Tran, NamPhuong, Vaissiere, Nathalie, van Son-Palmen, Elisabeth, Xu, Jiajun, Goecker, Erin A., Greninger, Alexander L., Jerome, Keith R., Roychoudhury, Pavitra, Takuva, Simbarashe G., Accini Mendoza, Jose Luis, Achtyes, Eric, Ahsan, Habibul, Alhatemi, Azhar, Allen, Nancy, Arribas, Jose R., Bahrami, Ghazaleh, Bailon, Lucia, Bajwa, Ali, Baker, Jonathan, Baron, Mira, Benet, Susana, Berdaï, Driss, Berger, Patrick, Bertoch, Todd, Bethune, Claire, Bevilacqua, Sybille, Biagioni Santos, Maria Silvia, Binnian, Ian, Bisnauthsing, Karen, Boivin, Jean-Marc, Bollen, Hilde, Bonnet, Sandrine, Borobia, Alberto M., Botelho-Nevers, Elisabeth, Bright, Phil, Britten, Vianne, Brown, Claire, Buadi, Amanda, Buntinx, Erik, Burgess, Lesley, Bush, Larry, Capeding, Maria Rosario, Carr, Quito Osuna, Carrasco Mas, Amparo, Catala, Hélène, Cathie, Katrina, Caudill, T. Shawn, Cereto Castro, Fernando, Chau, Kénora, Chavoustie, Steven, Chowdhury, Marie, Chronos, Nicolas, Cicconi, Paola, Cifuentes, Liliana, Cobo, Sara Maria, Collins, Helen, Colton, Hayley, Cuaño, Carlos Rolando G., D'Onofrio, Valentino, Dargan, Paul, Darton, Thomas, Deane, Peter, Del Pozo, Jose Luis, Derdelinckx, Inge, Desai, Amisha, Dever, Michael, Díaz-Pollán, Beatriz, DiBuono, Mark, Doust, Matthew, Duncan, Christopher, Echave-Sustaeta, Jose Maria, Eder, Frank, Ellis, Kimberly, Elzi, Stanton, Emmett, Stevan, Engelbrecht, Johannes, Evans, Mim, Farah, Theo, Felton, Timothy, Ferreira, João Pedro, Floutier, Catherine, Flume, Patrick, Ford, Stacy, Fragoso, Veronica, Freedman, Andrew, Frentiu, Emilia, Galloway, Christopher, Galtier, Florence, Garcia Diaz, Julia, García García, Irene, Garcia, Alcaide, Gardener, Zoe, Gauteul, Pascale, Geller, Steven, Gibson, Andrew, Gillet, Claudia, Girerd, Nicolas, Girodet, Pierre-Olivier, Gler, Maria Tarcela, Glover, Richard, Go, Herschel Don D., Gokani, Karishma, Gonthier, Damien, Green, Christopher, Greenberg, Richard, Griffin, Carl, Grobbelaar, Coert, Guancia, Adonis, Hakkarainen, Gloria, Harris, James, Hassman, Michael, Heimer, Deirdre, Hellstrom-Louw, Elizabeth, Herades, Yoan, Holroyd, Christopher, Hussen, Nazreen, Isidro, Marie Grace Dawn, Jackson, Yvonne, Jain, Manish, João Filho, Esaú Custódio, Johnson, Daniel, Jones, Ben, Joseph, Natasha, Jumeras, Analyn, Junquera, Patricia, Kellett-Wright, Johanna, Kennedy, Patrick, Kilgore, Paul E., Kim, Kenneth, Kimmel, Murray, Konis, George, Kutner, Mark, Lacombe, Karine, Launay, Odile, Lazarus, Rajeka, Lederman, Samuel, Lefebvre, Gigi, Lennon Collins, Katrina, Leroux-Roels, Isabel, Lim, Kenneth Wilson O., Lins, Muriel, Liu, Edward, Llewelyn, Martin, Mahomed, Akbar, Maia, Bernardo Porto, Marín-Candon, Alícia, Martínez-Gómez, Xavier, Martinot, Jean Benoit, Mazzella, Andrea, McCaughan, Frank, McCormack, Louise, McGettigan, John, Mehra, Purvi, Mejeur, Rhonda, Miller, Vicki, Mills, Anthony, Molto Marhuenda, Jose, Moodley, Prebashan, Mora-Rillo, Marta, Mothe, Beatriz, Mullan, Daniel, Munro, Alasdair, Myers, Paul, Nell, Jeremy, Newman Lobato Souza, Tamara, O'Halloran, Jane A., Ochoa Mazarro, Maria Dolores, Oliver, Abigail, Onate Gutierrez, Jose Millan, Ortega, Jessica, Oshita, Masaru, Otero Romero, Susana, Overcash, Jeffrey Scott, Owens, Daniel, Packham, Alice, Pacurar, Mihaela, Paiva de Sousa, Leonardo, Palfreeman, Adrian, Pallares, Christian José, Patel, Rahul, Patel, Suchet, Pelkey, Leslie, Peluso, Denise, Penciu, Florentina, Pinto, S. Jerry, Pounds, Kevin, Pouzar, Joe, Pragalos, Antoinette, Presti, Rachel, Price, David, Qureshi, Ehsaan, Ramalho Madruga, José Valdez, Ramesh, Mayur, Rankin, Bruce, Razat, Béatrice, Riegel Santos, Breno, Riesenberg, Robert, Riffer, Ernie, Roche, Siobhan, Rose, Katie, Rosellini, Pietro, Rossignol, Patrick, Safirstein, Beth, Salazar, Hernan, Sanchez Vallejo, Gregorio, Santhosh, Smrithi, Seco-Meseguer, Enrique, Seep, Michael, Sherry, Emma, Short, Philip, Soentjens, Patrick, Solis, Joel, Soriano Viladomiu, Alejandro, Sorli, Caroline, Spangenthal, Selwyn, Spence, Niamh, Stephenson, Elaine, Strout, Cynthia, Surowitz, Ronald, Taladua, Kristy Michelle, Tellalian, David, Thalamas, Claire, Thiriphoo, Nang, Thomas, Judith, Thomas, Nicholas, Trout, Guillermo, Urroz, Mikel, Veekmans, Bernard, Veekmans, Laurent, Villalobos, Ralph Elvi M., Warren, Sarah, Webster, Brian, White, Alexander, Williams, Gail, Williams, Hayes, Wilson, Barbara, Winston, Alan, Wiselka, Martin, Zervos, Marcus, Hardt, Karin, Vandebosch, An, Sadoff, Jerald, Le Gars, Mathieu, Truyers, Carla, Lowson, David, Van Dromme, Ilse, Vingerhoets, Johan, Kamphuis, Tobias, Scheper, Gert, Ruiz-Guiñazú, Javier, Faust, Saul N, Spinner, Christoph D, Schuitemaker, Hanneke, Van Hoof, Johan, Douoguih, Macaya, and Struyf, Frank

Published
2022
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