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1. Viral and host factors associated with SARS-CoV-2 disease severity in Georgia, USA

Author

Carmola, Ludy R., primary, Roebling, Allison Dorothy, additional, Khosravi, Dara, additional, Langsjoen, Rose M., additional, Bombin, Andrei, additional, Bixler, Bri, additional, Reid, Alex, additional, Chen, Cara, additional, Wang, Ethan, additional, Lu, Yang, additional, Zheng, Ziduo, additional, Zhang, Rebecca, additional, Nguyen, Phuong-Vi, additional, Arthur, Robert A., additional, Fitts, Eric, additional, Gulick, Dalia Arafat, additional, Higginbotham, Dustin, additional, Taz, Azmain, additional, Ahmed, Alaa, additional, Crumpler, John Hunter, additional, Kraft, Colleen, additional, Lam, Wilbur A., additional, Babiker, Ahmed, additional, Waggoner, Jesse J., additional, Openo, Kyle P., additional, Johnson, Laura M., additional, Westbrook, Adrianna, additional, and Piantadosi, Anne, additional

Published
2023
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4. Severe Acute Respiratory Syndrome Coronavirus 2 Evolution and Escape From Combination Monoclonal Antibody Treatment in a Person With HIV

Author

Khosravi, Dara, primary, Soloff, Hannah, additional, Langsjoen, Rose M, additional, Bombin, Andrei, additional, Kelley, Colleen F, additional, Ray, Susan M, additional, Gunthel, Clifford J, additional, Zanoni, Brian C, additional, Nguyen, Phuong-Vi, additional, Waggoner, Jesse J, additional, Wang, Yun F, additional, Cantos, Valeria D, additional, and Piantadosi, Anne, additional

Published
2023
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6. Phylodynamics of deer tick virus in North America

Author

McMinn, Rebekah J, primary, Langsjoen, Rose M, additional, Bombin, Andrei, additional, Robich, Rebecca M, additional, Ojeda, Erick, additional, Normandin, Erica, additional, Goethert, Heidi K, additional, Lubelczyk, Charles B, additional, Schneider, Elizabeth, additional, Cosenza, Danielle, additional, Meagher, Molly, additional, Prusinski, Melissa A, additional, Sabeti, Pardis C, additional, Smith, Robert P, additional, Telford, Sam, additional, Piantadosi, Anne, additional, and Ebel, Gregory D, additional

Published
2023
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7. SARS-CoV-2 Evolution and Immune Escape in Immunocompromised Patients

Author

Scherer, Erin M., primary, Babiker, Ahmed, additional, Adelman, Max W., additional, Allman, Brent, additional, Key, Autum, additional, Kleinhenz, Jennifer M., additional, Langsjoen, Rose M., additional, Nguyen, Phuong-Vi, additional, Onyechi, Ivy, additional, Sherman, Jacob D., additional, Simon, Trevor W., additional, Soloff, Hannah, additional, Tarabay, Jessica, additional, Varkey, Jay, additional, Webster, Andrew S., additional, Weiskopf, Daniela, additional, Weissman, Daniel B., additional, Xu, Yongxian, additional, Waggoner, Jesse J., additional, Koelle, Katia, additional, Rouphael, Nadine, additional, Pouch, Stephanie M., additional, and Piantadosi, Anne, additional

Published
2022
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8. Chikungunya virus as cause of febrile illness outbreak, Chiapas, Mexico, 2014

Author

Kautz, Tiffany F., Diaz-Gonzalez, Esteban E., Erasmus, Jesse H., Malo-Garcia, Iliana R., Langsjoen, Rose M., Patterson, Edward I., Auguste, Dawn I., Forrester, Naomi L., Sanchez-Casas, Rosa Maria, Hernandez-Avila, Mauricio, Alpuche-Aranda, Celia M., Weaver, Scott C., and Fernandez-Salas, Ildefonso

Subjects
Chikungunya fever -- Research -- Risk factors -- Development and progression -- Care and treatment, RNA viruses -- Research -- Genetic aspects, Health
Abstract

Chikungunya virus (CHIKV), an arbovirus in genus Alphavirus, family Togaviridae, has undergone a rapid geographic expansion during the past decade (1). CHIKV is the causative agent of chikungunya fever, which [...]

Published
2015
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9. SARS-CoV-2 evolution and immune escape in immunocompromised patients treated with exogenous antibodies

Author

Scherer, Erin M., primary, Babiker, Ahmed, additional, Adelman, Max W., additional, Allman, Brent, additional, Key, Autum, additional, Kleinhenz, Jennifer M., additional, Langsjoen, Rose M., additional, Nguyen, Phuong-Vi, additional, Onyechi, Ivy, additional, Sherman, Jacob D., additional, Simon, Trevor W., additional, Soloff, Hannah, additional, Tarabay, Jessica, additional, Varkey, Jay, additional, Webster, Andrew S., additional, Weiskopf, Daniela, additional, Weissman, Daniel B., additional, Xu, Yongxian, additional, Waggoner, Jesse J., additional, Koelle, Katia, additional, Rouphael, Nadine, additional, Pouch, Stephanie M., additional, and Piantadosi, Anne, additional

Published
2022
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11. Mouse-adapted SARS-CoV-2 protects animals from lethal SARS-CoV challenge

Author

Muruato, Antonio, primary, Vu, Michelle N., additional, Johnson, Bryan A., additional, Davis-Gardner, Meredith E., additional, Vanderheiden, Abigail, additional, Lokugamage, Kumari, additional, Schindewolf, Craig, additional, Crocquet-Valdes, Patricia A., additional, Langsjoen, Rose M., additional, Plante, Jessica A., additional, Plante, Kenneth S., additional, Weaver, Scott C., additional, Debbink, Kari, additional, Routh, Andrew L., additional, Walker, David, additional, Suthar, Mehul S., additional, Shi, Pei-Yong, additional, Xie, Xuping, additional, and Menachery, Vineet D., additional

Published
2021
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12. Isolation of a novel insect-specific flavivirus with immunomodulatory effects in vertebrate systems

Author

Auguste, Albert J., primary, Langsjoen, Rose M., additional, Porier, Danielle L., additional, Erasmus, Jesse H., additional, Bergren, Nicholas A., additional, Bolling, Bethany G., additional, Luo, Huanle, additional, Singh, Ankita, additional, Guzman, Hilda, additional, Popov, Vsevolod L., additional, Travassos da Rosa, Amelia P.A., additional, Wang, Tian, additional, Kang, Lin, additional, Allen, Irving C., additional, Carrington, Christine V.F., additional, Tesh, Robert B., additional, and Weaver, Scott C., additional

Published
2021
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13. Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variants

Author

Jaworski, Elizabeth, primary, Langsjoen, Rose M, additional, Mitchell, Brooke, additional, Judy, Barbara, additional, Newman, Patrick, additional, Plante, Jessica A, additional, Plante, Kenneth S, additional, Miller, Aaron L, additional, Zhou, Yiyang, additional, Swetnam, Daniele, additional, Sotcheff, Stephanea, additional, Morris, Victoria, additional, Saada, Nehad, additional, Machado, Rafael RG, additional, McConnell, Allan, additional, Widen, Steven G, additional, Thompson, Jill, additional, Dong, Jianli, additional, Ren, Ping, additional, Pyles, Rick B, additional, Ksiazek, Thomas G, additional, Menachery, Vineet D, additional, Weaver, Scott C, additional, and Routh, Andrew L, additional

Published
2021
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14. Author response: Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variants

Author

Jaworski, Elizabeth, primary, Langsjoen, Rose M, additional, Mitchell, Brooke, additional, Judy, Barbara, additional, Newman, Patrick, additional, Plante, Jessica A, additional, Plante, Kenneth S, additional, Miller, Aaron L, additional, Zhou, Yiyang, additional, Swetnam, Daniele, additional, Sotcheff, Stephanea, additional, Morris, Victoria, additional, Saada, Nehad, additional, Machado, Rafael RG, additional, McConnell, Allan, additional, Widen, Steven G, additional, Thompson, Jill, additional, Dong, Jianli, additional, Ren, Ping, additional, Pyles, Rick B, additional, Ksiazek, Thomas G, additional, Menachery, Vineet D, additional, Weaver, Scott C, additional, and Routh, Andrew L, additional

Published
2021
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15. Chikungunya Virus Strains Show Lineage-Specific Variations in Virulence and Cross-Protective Ability in Murine and Nonhuman Primate Models

Author

Langsjoen, Rose M., primary, Haller, Sherry L., additional, Roy, Chad J., additional, Vinet-Oliphant, Heather, additional, Bergren, Nicholas A., additional, Erasmus, Jesse H., additional, Livengood, Jill A., additional, Powell, Tim D., additional, Weaver, Scott C., additional, and Rossi, Shannan L., additional

Published
2018
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17. Host oxidative folding pathways offer novel anti-chikungunya virus drug targets with broad spectrum potential

Author

Langsjoen, Rose M., primary, Auguste, Albert J., additional, Rossi, Shannan L., additional, Roundy, Christopher M., additional, Penate, Heidy N., additional, Kastis, Maria, additional, Schnizlein, Matthew K., additional, Le, Kevin C., additional, Haller, Sherry L., additional, Chen, Rubing, additional, Watowich, Stanley J., additional, and Weaver, Scott C., additional

Published
2017
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18. Molecular Virologic and Clinical Characteristics of a Chikungunya Fever Outbreak in La Romana, Dominican Republic, 2014

Author

Langsjoen, Rose M., primary, Rubinstein, Rebecca J., additional, Kautz, Tiffany F., additional, Auguste, Albert J., additional, Erasmus, Jesse H., additional, Kiaty-Figueroa, Liddy, additional, Gerhardt, Renessa, additional, Lin, David, additional, Hari, Kumar L., additional, Jain, Ravi, additional, Ruiz, Nicolas, additional, Muruato, Antonio E., additional, Silfa, Jael, additional, Bido, Franklin, additional, Dacso, Matthew, additional, and Weaver, Scott C., additional

Published
2016
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19. Characterization of a Novel Murine Model to Study Zika Virus

Author

Rossi, Shannan L., primary, Tesh, Robert B., additional, Azar, Sasha R., additional, Muruato, Antonio E., additional, Hanley, Kathryn A., additional, Auguste, Albert J., additional, Langsjoen, Rose M., additional, Paessler, Slobodan, additional, Vasilakis, Nikos, additional, and Weaver, Scott C., additional

Published
2016
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20. First Report of Aedes aegypti Transmission of Chikungunya Virus in the Americas

Author

Díaz-González, Esteban E., primary, Malo-García, Iliana R., additional, Laguna-Aguilar, Maricela, additional, Weaver, Scott C., additional, Chen, Rubing, additional, Fernández-Salas, Ildefonso, additional, Dorantes-Delgado, Alicia, additional, Sánchez-Casas, Rosa M., additional, Langsjoen, Rose M., additional, Danis-Lozano, Rogelio, additional, Kautz, Tiffany F., additional, and Auguste, Dawn I., additional

Published
2015
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21. Viral and host factors associated with SARS-CoV-2 disease severity in Georgia, USA.

Author

Carmola LR, Roebling AD, Khosravi D, Langsjoen RM, Bombin A, Bixler B, Reid A, Chen C, Wang E, Lu Y, Zheng Z, Zhang R, Nguyen PV, Arthur RA, Fitts E, Gulick DA, Higginbotham D, Taz A, Ahmed A, Crumpler JH, Kraft C, Lam WA, Babiker A, Waggoner JJ, Openo KP, Johnson LM, Westbrook A, and Piantadosi A

Abstract

While SARS-CoV-2 vaccines have shown strong efficacy, their suboptimal uptake combined with the continued emergence of new viral variants raises concerns about the ongoing and future public health impact of COVID-19. We investigated viral and host factors, including vaccination status, that were associated with SARS-CoV-2 disease severity in a setting with low vaccination rates. We analyzed clinical and demographic data from 1,957 individuals in the state of Georgia, USA, coupled with viral genome sequencing from 1,185 samples. We found no difference in disease severity between individuals infected with Delta and Omicron variants among the participants in this study, after controlling for other factors, and we found no specific mutations associated with disease severity. Compared to those who were unvaccinated, vaccinated individuals experienced less severe SARS-CoV-2 disease, and the effect was similar for both variants. Vaccination within 270 days before infection was associated with decreased odds of moderate and severe outcomes, with the strongest association observed at 91-270 days post-vaccination. Older age and underlying health conditions, especially immunosuppression and renal disease, were associated with increased disease severity. Overall, this study provides insights into the impact of vaccination status, variants/mutations, and clinical factors on disease severity in SARS-CoV-2 infection when vaccination rates are low. Understanding these associations will help refine and reinforce messaging around the crucial importance of vaccination in mitigating the severity of SARS-CoV-2 disease., Competing Interests: Competing interests: The authors have declared that no competing interests exist.

Published
2023
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22. Chikungunya Virus Infects the Heart and Induces Heart-Specific Transcriptional Changes in an Immunodeficient Mouse Model of Infection.

Author

Langsjoen RM, Zhou Y, Holcomb RJ, and Routh AL

Subjects
Animals, Disease Models, Animal, Mice, Mice, Nude, Viral Nonstructural Proteins genetics, Virus Replication, Chikungunya Fever physiopathology, Chikungunya virus genetics, Chikungunya virus pathogenicity, Heart microbiology, Heart physiopathology
Abstract

Chikungunya virus (CHIKV) is a mosquito-transmitted pathogen in family Togaviridae, genus Alphavirus. Although CHIKV is well known for its ability to cause debilitating rheumatoid-like arthritis, it has been also been observed to cause cardiovascular symptoms such as arrhythmias. Here, using samples from a previous study, we sequenced RNA from serum, kidney, skeletal muscle, and cardiac muscle from CHIKV- and mock-infected IFN-αR-/- mice using two sequencing techniques to investigate heart-specific changes in virus mutational profiles and host gene expression. Mutation rates were similar across muscle tissues although heart tissue carried heart-specific CHIKV minority variants, one of which had a coding change in the nsP3 gene and another in the 3'UTR. Importantly, heart-specific transcriptional changes included differential expression of genes critical for ion transport and muscle contraction. These results demonstrate that CHIKV replicates in the hearts of immunodeficient mice and induce heart-specific mutations and host responses with implications for cardiac pathologies.

Published
2021
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23. Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variants.

Author

Jaworski E, Langsjoen RM, Mitchell B, Judy B, Newman P, Plante JA, Plante KS, Miller AL, Zhou Y, Swetnam D, Sotcheff S, Morris V, Saada N, Machado R, McConnell A, Widen S, Thompson J, Dong J, Ren P, Pyles RB, Ksiazek T, Menachery VD, Weaver SC, and Routh A

Abstract

High-throughput genomics of SARS-CoV-2 is essential to characterize virus evolution and to identify adaptations that affect pathogenicity or transmission. While single-nucleotide variations (SNVs) are commonly considered as driving virus adaption, RNA recombination events that delete or insert nucleic acid sequences are also critical. Whole genome targeting sequencing of SARS-CoV-2 is typically achieved using pairs of primers to generate cDNA amplicons suitable for Next-Generation Sequencing (NGS). However, paired-primer approaches impose constraints on where primers can be designed, how many amplicons are synthesized and requires multiple PCR reactions with non-overlapping primer pools. This imparts sensitivity to underlying SNVs and fails to resolve RNA recombination junctions that are not flanked by primer pairs. To address these limitations, we have designed an approach called ' Tiled-ClickSeq ', which uses hundreds of tiled-primers spaced evenly along the virus genome in a single reverse-transcription reaction. The other end of the cDNA amplicon is generated by azido-nucleotides that stochastically terminate cDNA synthesis, removing the need for a paired-primer. A sequencing adaptor containing a Unique Molecular Identifier (UMI) is appended to the cDNA fragment using click-chemistry and a PCR reaction generates a final NGS library. Tiled-ClickSeq provides complete genome coverage, including the 5'UTR, at high depth and specificity to the virus on both Illumina and Nanopore NGS platforms. Here, we analyze multiple SARS-CoV-2 isolates and clinical samples to simultaneously characterize minority variants, sub-genomic mRNAs (sgmRNAs), structural variants (SVs) and D-RNAs. Tiled-ClickSeq therefore provides a convenient and robust platform for SARS-CoV-2 genomics that captures the full range of RNA species in a single, simple assay., Competing Interests: Conflict of Interest Statement E.J. and A.R. are co-founders and owners of ‘ClickSeq Technologies LLC’, a Texas-based Next-Generation Sequencing provider offering ClickSeq kits and services including the methods described in this manuscript. E.J. and A.R have a patent-pending on the method and use of single-primer tiled sequencing.

Published
2021
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24. Mouse Adapted SARS-CoV-2 protects animals from lethal SARS-CoV challenge.

Author

Muruato A, Vu MN, Johnson BA, Davis-Gardner ME, Vanderheiden A, Lokugmage K, Schindewolf C, Crocquet-Valdes PA, Langsjoen RM, Plante JA, Plante KS, Weaver SC, Debbink K, Routh AL, Walker D, Suthar MS, Xie X, Shi PY, Xie X, and Menachery VD

Abstract

The emergence of SARS-CoV-2 has resulted in a worldwide pandemic causing significant damage to public health and the economy. Efforts to understand the mechanisms of COVID-19 disease have been hampered by the lack of robust mouse models. To overcome this barrier, we utilized a reverse genetic system to generate a mouse-adapted strain of SARS-CoV-2. Incorporating key mutations found in SARSCoV-2 variants, this model recapitulates critical elements of human infection including viral replication in the lung, immune cell infiltration, and significant in vivo disease. Importantly, mouse-adaptation of SARS-CoV-2 does not impair replication in human airway cells and maintains antigenicity similar to human SARS-CoV-2 strains. Utilizing this model, we demonstrate that SARS-CoV-2 infected mice are protected from lethal challenge with the original SARS-CoV, suggesting immunity from heterologous CoV strains. Together, the results highlight the utility of this mouse model for further study of SARS-CoV-2 infection and disease.

Published
2021
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