Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host
Choi, Bina, Choudhary, Manish C, Regan, James, Sparks, Jeffrey A, Padera, Robert F, Qiu, Xueting, Solomon, Isaac H, Kuo, Hsiao-Hsuan, Boucau, Julie, Bowman, Kathryn, Adhikari, U. Das, Winkler, Marisa L, Mueller, Alisa A, Hsu, Tiffany Y.-T, Desjardins, Michaël, Baden, Lindsey R, Chan, Brian T, Walker, Bruce D, Lichterfeld, Mathias, Brigl, Manfred, Kwon, Douglas S, Kanjilal, Sanjat, Richardson, Eugene T, Jonsson, A. Helena, Alter, Galit, Barczak, Amy K, Hanage, William P, Yu, Xu G, Gaiha, Gaurav D, Seaman, Michael S, Cernadas, Manuela, Li, Jonathan Z
Published in New England Journal of Medicine (03.12.2020)
Published in New England Journal of Medicine (03.12.2020)
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Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Sequence Characteristics of Coronavirus Disease 2019 (COVID-19) Persistence and Reinfection
Choudhary, Manish C, Crain, Charles R, Qiu, Xueting, Hanage, William, Li, Jonathan Z
Published in Clinical Infectious Diseases (29.01.2022)
Published in Clinical Infectious Diseases (29.01.2022)
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SARS-CoV-2 evolution in an immunocompromised host reveals shared neutralization escape mechanisms
Clark, Sarah A., Clark, Lars E., Pan, Junhua, Coscia, Adrian, McKay, Lindsay G.A., Shankar, Sundaresh, Johnson, Rebecca I., Brusic, Vesna, Choudhary, Manish C., Regan, James, Li, Jonathan Z., Griffiths, Anthony, Abraham, Jonathan
Published in Cell (13.05.2021)
Published in Cell (13.05.2021)
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An enhanced isothermal amplification assay for viral detection
Qian, Jason, Boswell, Sarah A, Chidley, Christopher, Lu, Zhi-Xiang, Pettit, Mary E, Gaudio, Benjamin L, Fajnzylber, Jesse M, Ingram, Ryan T, Ward, Rebecca H, Li, Jonathan Z, Springer, Michael
Published in Nature communications (20.11.2020)
Published in Nature communications (20.11.2020)
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Duration of Shedding of Culturable Virus in SARS-CoV-2 Omicron (BA.1) Infection
Boucau, Julie, Marino, Caitlin, Regan, James, Uddin, Rockib, Choudhary, Manish C., Flynn, James P., Chen, Geoffrey, Stuckwisch, Ashley M., Mathews, Josh, Liew, May Y., Singh, Arshdeep, Lipiner, Taryn, Kittilson, Autumn, Melberg, Meghan, Li, Yijia, Gilbert, Rebecca F., Reynolds, Zahra, Iyer, Surabhi L., Chamberlin, Grace C., Vyas, Tammy D., Goldberg, Marcia B., Vyas, Jatin M., Li, Jonathan Z., Lemieux, Jacob E., Siedner, Mark J., Barczak, Amy K.
Published in New England Journal of Medicine (21.07.2022)
Published in New England Journal of Medicine (21.07.2022)
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Characterization of Virologic Rebound Following Nirmatrelvir-Ritonavir Treatment for Coronavirus Disease 2019 (COVID-19)
Boucau, Julie, Uddin, Rockib, Marino, Caitlin, Regan, James, Flynn, James P, Choudhary, Manish C, Chen, Geoffrey, Stuckwisch, Ashley M, Mathews, Josh, Liew, May Y, Singh, Arshdeep, Reynolds, Zahra, Iyer, Surabhi L, Chamberlin, Grace C, Vyas, Tammy D, Vyas, Jatin M, Turbett, Sarah E, Li, Jonathan Z, Lemieux, Jacob E, Barczak, Amy K, Siedner, Mark J
Published in Clinical infectious diseases (08.02.2023)
Published in Clinical infectious diseases (08.02.2023)
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Learning From the Exceptions: HIV Remission in Post-treatment Controllers
Etemad, Behzad, Esmaeilzadeh, Elmira, Li, Jonathan Z
Published in Frontiers in immunology (24.07.2019)
Published in Frontiers in immunology (24.07.2019)
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Assessment of Maternal and Neonatal SARS-CoV-2 Viral Load, Transplacental Antibody Transfer, and Placental Pathology in Pregnancies During the COVID-19 Pandemic
Edlow, Andrea G, Li, Jonathan Z, Collier, Ai-Ris Y, Atyeo, Caroline, James, Kaitlyn E, Boatin, Adeline A, Gray, Kathryn J, Bordt, Evan A, Shook, Lydia L, Yonker, Lael M, Fasano, Alessio, Diouf, Khady, Croul, Natalie, Devane, Samantha, Yockey, Laura J, Lima, Rosiane, Shui, Jessica, Matute, Juan D, Lerou, Paul H, Akinwunmi, Babatunde O, Schmidt, Aaron, Feldman, Jared, Hauser, Blake M, Caradonna, Timothy M, De la Flor, Denis, D'Avino, Paolo, Regan, James, Corry, Heather, Coxen, Kendyll, Fajnzylber, Jesse, Pepin, David, Seaman, Michael S, Barouch, Dan H, Walker, Bruce D, Yu, Xu G, Kaimal, Anjali J, Roberts, Drucilla J, Alter, Galit
Published in JAMA network open (22.12.2020)
Published in JAMA network open (22.12.2020)
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Time to Viral Rebound After Interruption of Modern Antiretroviral Therapies
Li, Jonathan Z, Aga, Evgenia, Bosch, Ronald J, Pilkinton, Mark, Kroon, Eugène, MacLaren, Lynsay, Keefer, Michael, Fox, Lawrence, Barr, Liz, Acosta, Edward, Ananworanich, Jintanat, Coombs, Robert, Mellors, John W, Landay, Alan L, Macatangay, Bernard, Deeks, Steven, Gandhi, Rajesh T, Smith, Davey M
Published in Clinical infectious diseases (09.03.2022)
Published in Clinical infectious diseases (09.03.2022)
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A minor population of macrophage-tropic HIV-1 variants is identified in recrudescing viremia following analytic treatment interruption
Andrade, Viviane M., Mavian, Carla, Babic, Dunja, Cordeiro, Thaissa, Sharkey, Mark, Barrios, Labelle, Brander, Christian, Martinez-Picado, Javier, Dalmau, Judith, Llano, Anuska, Li, Jonathan Z., Jacobson, Jeffrey, Lavine, Christy L., Seaman, Michael S., Salemi, Marco, Stevenson, Mario
Published in Proceedings of the National Academy of Sciences - PNAS (05.05.2020)
Published in Proceedings of the National Academy of Sciences - PNAS (05.05.2020)
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Predictions of time to HIV viral rebound following ART suspension that incorporate personal biomarkers
Conway, Jessica M, Perelson, Alan S, Li, Jonathan Z
Published in PLoS computational biology (01.07.2019)
Published in PLoS computational biology (01.07.2019)
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Understanding early HIV-1 rebound dynamics following antiretroviral therapy interruption: The importance of effector cell expansion
Phan, Tin, Conway, Jessica M, Pagane, Nicole, Kreig, Jasmine, Sambaturu, Narmada, Iyaniwura, Sarafa, Li, Jonathan Z, Ribeiro, Ruy M, Ke, Ruian, Perelson, Alan S
Published in PLoS pathogens (29.07.2024)
Published in PLoS pathogens (29.07.2024)
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Non-invasive plasma glycomic and metabolic biomarkers of post-treatment control of HIV
Giron, Leila B., Palmer, Clovis S., Liu, Qin, Yin, Xiangfan, Papasavvas, Emmanouil, Sharaf, Radwa, Etemad, Behzad, Damra, Mohammad, Goldman, Aaron R., Tang, Hsin-Yao, Johnston, Rowena, Mounzer, Karam, Kostman, Jay R., Tebas, Pablo, Landay, Alan, Montaner, Luis J., Jacobson, Jeffrey M., Li, Jonathan Z., Abdel-Mohsen, Mohamed
Published in Nature communications (29.06.2021)
Published in Nature communications (29.06.2021)
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Antiviral and clinical activity of bamlanivimab in a randomized trial of non-hospitalized adults with COVID-19
Chew, Kara W, Moser, Carlee, Daar, Eric S, Wohl, David A, Li, Jonathan Z, Coombs, Robert W, Ritz, Justin, Giganti, Mark, Javan, Arzhang Cyrus, Li, Yijia, Choudhary, Manish C, Deo, Rinki, Malvestutto, Carlos, Klekotka, Paul, Price, Karen, Nirula, Ajay, Fischer, William, Bala, Veenu, Ribeiro, Ruy M, Perelson, Alan S, Fletcher, Courtney V, Eron, Joseph J, Currier, Judith S, Hughes, Michael D, Smith, Davey M
Published in Nature communications (22.08.2022)
Published in Nature communications (22.08.2022)
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Transcriptomic Signatures of Human Immunodeficiency Virus Post-Treatment Control
Wedrychowski, Adam, Martin, Holly Anne, Li, Yijia, Telwatte, Sushama, Kadiyala, Gayatri Nikhila, Melberg, Meghan, Etemad, Behzad, Connick, Elizabeth, Jacobson, Jeffrey M, Margolis, David M, Skiest, Daniel, Volberding, Paul, Hecht, Frederick, Deeks, Steven, Wong, Joseph K, Li, Jonathan Z, Yukl, Steven A
Published in Journal of virology (31.01.2023)
Published in Journal of virology (31.01.2023)
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Immune-profiling of SARS-CoV-2 viremic patients reveals dysregulated innate immune responses
Sun, Xiaoming, Gao, Ce, Zhao, Ke, Yang, Yanhui, Rassadkina, Yelizaveta, Fajnzylber, Jesse, Regan, James, Li, Jonathan Z., Lichterfeld, Mathias, Yu, Xu G.
Published in Frontiers in immunology (09.11.2022)
Published in Frontiers in immunology (09.11.2022)
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Viral and immunologic evaluation of smokers with severe COVID-19
Vecchio, Joseph, Regan, James, Jiang, Yuting, Li, Roy, Romain, Hannah, Yousuf, Fizah, Adel, Thomas, Hall, Kevin, DaCosta, Jeffrey M, Yu, Xu, Li, Jonathan Z, Fofana, Ismael Ben
Published in Scientific reports (19.10.2023)
Published in Scientific reports (19.10.2023)
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Innate lymphoid cells and COVID-19 severity in SARS-CoV-2 infection
Silverstein, Noah J, Wang, Yetao, Manickas-Hill, Zachary, Carbone, Claudia, Dauphin, Ann, Boribong, Brittany P, Loiselle, Maggie, Davis, Jameson, Leonard, Maureen M, Kuri-Cervantes, Leticia, Meyer, Nuala J, Betts, Michael R, Li, Jonathan Z, Walker, Bruce D, Yu, Xu G, Yonker, Lael M, Luban, Jeremy
Published in eLife (11.03.2022)
Published in eLife (11.03.2022)
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Modeling the emergence of viral resistance for SARS-CoV-2 during treatment with an anti-spike monoclonal antibody
Phan, Tin, Zitzmann, Carolin, Chew, Kara W, Smith, Davey M, Daar, Eric S, Wohl, David A, Eron, Joseph J, Currier, Judith S, Hughes, Michael D, Choudhary, Manish C, Deo, Rinki, Li, Jonathan Z, Ribeiro, Ruy M, Ke, Ruian, Perelson, Alan S
Published in PLoS pathogens (18.04.2024)
Published in PLoS pathogens (18.04.2024)
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