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1. Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study

Author

McEnaney, Kerry, Barton, Brenda, Lentucci, Claudia, Saluvan, Mehmet, Chang, Ana C, Hoch, Annmarie, Albert, Marisa, Shaheen, Tanzia, Kho, Alvin T, Thomas, Sanya, Chen, Jing, Murphy, Maimouna D, Cooney, Mitchell, Hayati, Arash Nemati, Bryant, Robert, Abraham, James, Presnell, Scott, Jancsyk, Tomasz, Maguire, Cole, Lee, Brian, Fourati, Slim, Esserman, Denise A, Guan, Leying, Gygi, Jeremy, Pawar, Shrikant, Brito, Anderson, Fragiadakis, Gabriela K, Patel, Ravi, Tebbutt, Scott J, Overton, James A, Vita, Randi, Westendorf, Kerstin, Thyagarajan, Rama V, Rousseau, Justin F, Wylie, Dennis, Triplett, Todd A, Kojic, Erna, Chinthrajah, Sharon, Ahuja, Neera, Rogers, Angela J, Artandi, Maja, Yendewa, George, Powell, Debra L, Kim, James N, Simmons, Brent, Goonewardene, I Michael, Smith, Cecilia M, Martens, Mark, Sherman, Amy C, Walsh, Stephen R, Issa, Nicolas C, Salehi-Rad, Ramin, Dela Cruz, Charles, Farhadian, Shelli, Iwasaki, Akiko, Ko, Albert I, Anderson, Evan J, Mehta, Aneesh K, Sevransky, Jonathan E, Leligdowicz, Aleksandra, Matthay, Michael A, Singer, Jonathan P, Kangelaris, Kirsten N, Hendrickson, Carolyn M, Krummel, Matthew F, Woodruff, Prescott G, Anderson, Matthew L, Guirgis, Faheem W, Drevets, Douglas A, Brown, Brent R, Siegel, Sarah AR, Lu, Zhengchun, Mosier, Jarrod, Kimura, Hiroki, Khor, Bernard, Rahman, Adeeb, Stadlbauer, Daniel, Dutta, Jayeeta, Gonzalez-Reiche, Ana Silvia, van de Guchte, Adriana, Carreño, Juan Manuel, Singh, Gagandeep, Raskin, Ariel, Tcheou, Johnstone, Bielak, Dominika, Kawabata, Hisaaki, Xie, Hui, Kelly, Geoffrey, Patel, Manishkumar, Nie, Kai, Yellin, Temima, Fried, Miriam, Sullivan, Leeba, Morris, Sara, Sieg, Scott, van Zalm, Patrick, Fatou, Benoit, Mendez, Kevin, Lasky-Su, Jessica, and Hutton, Scott R

Subjects
Health Services and Systems, Biomedical and Clinical Sciences, Health Sciences, Prevention, Vaccine Related, Emerging Infectious Diseases, Biodefense, Brain Disorders, Infectious Diseases, Lung, Good Health and Well Being, Female, Humans, SARS-CoV-2, COVID-19, B-Lymphocytes, Body Fluids, Disease Progression, Phenotype, IMPACC Network
Abstract

Post-acute sequelae of SARS-CoV-2 (PASC) is a significant public health concern. We describe Patient Reported Outcomes (PROs) on 590 participants prospectively assessed from hospital admission for COVID-19 through one year after discharge. Modeling identified 4 PRO clusters based on reported deficits (minimal, physical, mental/cognitive, and multidomain), supporting heterogenous clinical presentations in PASC, with sub-phenotypes associated with female sex and distinctive comorbidities. During the acute phase of disease, a higher respiratory SARS-CoV-2 viral burden and lower Receptor Binding Domain and Spike antibody titers were associated with both the physical predominant and the multidomain deficit clusters. A lower frequency of circulating B lymphocytes by mass cytometry (CyTOF) was observed in the multidomain deficit cluster. Circulating fibroblast growth factor 21 (FGF21) was significantly elevated in the mental/cognitive predominant and the multidomain clusters. Future efforts to link PASC to acute anti-viral host responses may help to better target treatment and prevention of PASC.

Published
2024

2. Respiratory Tract Explant Infection Dynamics of Influenza A Virus in California Sea Lions, Northern Elephant Seals, and Rhesus Macaques

Author

Liu, Hongwei, Plancarte, Magdalena, Ball, Erin E, Weiss, Christopher M, Gonzales-Viera, Omar, Holcomb, Karen, Ma, Zhong-Min, Allen, A Mark, Reader, J Rachel, Duignan, Pádraig J, Halaska, Barbie, Khan, Zenab, Kriti, Divya, Dutta, Jayeeta, van Bakel, Harm, Jackson, Kenneth, Pesavento, Patricia A, Boyce, Walter M, and Coffey, Lark L

Subjects
Microbiology, Medical Microbiology, Biomedical and Clinical Sciences, Biological Sciences, Lung, Biodefense, Influenza, Pneumonia & Influenza, Emerging Infectious Diseases, Infectious Diseases, 2.2 Factors relating to the physical environment, Infection, Animals, Dogs, Host Specificity, Influenza A virus, Kinetics, Macaca mulatta, Madin Darby Canine Kidney Cells, Models, Biological, Orthomyxoviridae Infections, Respiratory System, Respiratory Tract Infections, Sea Lions, Seals, Earless, Species Specificity, Viral Load, Viral Tropism, explant, infection dynamics, influenza A virus, kinetics, marine mammal, respiratory viruses, rhesus macaque, tropism, Agricultural and Veterinary Sciences, Medical and Health Sciences, Virology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract

To understand susceptibility of wild California sea lions and Northern elephant seals to influenza A virus (IAV), we developed an ex vivo respiratory explant model and used it to compare infection kinetics for multiple IAV subtypes. We first established the approach using explants from colonized rhesus macaques, a model for human IAV. Trachea, bronchi, and lungs from 11 California sea lions, 2 Northern elephant seals, and 10 rhesus macaques were inoculated within 24 h postmortem with 6 strains representing 4 IAV subtypes. Explants from the 3 species showed similar IAV infection kinetics, with peak viral titers 48 to 72 h post-inoculation that increased by 2 to 4 log10 PFU/explant relative to the inoculum. Immunohistochemistry localized IAV infection to apical epithelial cells. These results demonstrate that respiratory tissue explants from wild marine mammals support IAV infection. In the absence of the ability to perform experimental infections of marine mammals, this ex vivo culture of respiratory tissues mirrors the in vivo environment and serves as a tool to study IAV susceptibility, host range, and tissue tropism. IMPORTANCE Although influenza A virus can infect marine mammals, a dearth of marine mammal cell lines and ethical and logistical challenges prohibiting experimental infections of living marine mammals mean that little is known about IAV infection kinetics in these species. We circumvented these limitations by adapting a respiratory tract explant model first to establish the approach with rhesus macaques and then for use with explants from wild marine mammals euthanized for nonrespiratory medical conditions. We observed that multiple strains representing 4 IAV subtypes infected trachea, bronchi, and lungs of macaques and marine mammals with variable peak titers and kinetics. This ex vivo model can define infection dynamics for IAV in marine mammals. Further, use of explants from animals euthanized for other reasons reduces use of animals in research.

Published
2021

3. Phylogenetic analysis and comparative genomics of SARS-CoV-2 from survivor and non-survivor COVID-19 patients in Cordoba, Argentina

Author

Olivero, Nadia B., Gonzalez-Reiche, Ana S., Re, Viviana E., Castro, Gonzalo M., Pisano, María B., Sicilia, Paola, Barbas, María G., Khan, Zenab, van de Guchte, Adriana, Dutta, Jayeeta, Cortes, Paulo R., Hernandez-Morfa, Mirelys, Zappia, Victoria E., Ortiz, Lucia, Geiger, Ginger, Rajao, Daniela, Perez, Daniel R., van Bakel, Harm, and Echenique, Jose

Published
2022
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4. Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study

Author

Ozonoff, Al, Schaenman, Joanna, Jayavelu, Naresh Doni, Milliren, Carly E., Calfee, Carolyn S., Cairns, Charles B., Kraft, Monica, Baden, Lindsey R., Shaw, Albert C., Krammer, Florian, van Bakel, Harm, Esserman, Denise A., Liu, Shanshan, Sesma, Ana Fernandez, Simon, Viviana, Hafler, David A., Montgomery, Ruth R., Kleinstein, Steven H., Levy, Ofer, Bime, Chris, Haddad, Elias K., Erle, David J., Pulendran, Bali, Nadeau, Kari C., Davis, Mark M, Hough, Catherine L., Messer, William B., Higuita, Nelson I. Agudelo, Metcalf, Jordan P., Atkinson, Mark A., Brakenridge, Scott C., Corry, David, Kheradmand, Farrah, Ehrlich, Lauren I.R., Melamed, Esther, McComsey, Grace A., Sekaly, Rafick, Diray-Arce, Joann, Peters, Bjoern, Augustine, Alison D., Reed, Elaine F., McEnaney, Kerry, Barton, Brenda, Lentucci, Claudia, Saluvan, Mehmet, Chang, Ana C., Hoch, Annmarie, Albert, Marisa, Shaheen, Tanzia, Kho, Alvin T., Thomas, Sanya, Chen, Jing, Murphy, Maimouna D., Cooney, Mitchell, Presnell, Scott, Fragiadakis, Gabriela K., Patel, Ravi, Guan, Leying, Gygi, Jeremy, Pawar, Shrikant, Brito, Anderson, Khalil, Zain, Maguire, Cole, Fourati, Slim, Overton, James A., Vita, Randi, Westendorf, Kerstin, Salehi-Rad, Ramin, Leligdowicz, Aleksandra, Matthay, Michael A., Singer, Jonathan P., Kangelaris, Kirsten N., Hendrickson, Carolyn M., Krummel, Matthew F., Langelier, Charles R., Woodruff, Prescott G., Powell, Debra L., Kim, James N., Simmons, Brent, Goonewardene, I. Michael, Smith, Cecilia M., Martens, Mark, Mosier, Jarrod, Kimura, Hiroki, Sherman, Amy C., Walsh, Stephen R., Issa, Nicolas C., Dela Cruz, Charles, Farhadian, Shelli, Iwasaki, Akiko, Ko, Albert I., Chinthrajah, Sharon, Ahuja, Neera, Rogers, Angela J., Artandi, Maja, Siegel, Sarah A.R., Lu, Zhengchun, Drevets, Douglas A., Brown, Brent R., Anderson, Matthew L., Guirgis, Faheem W., Thyagarajan, Rama V., Rousseau, Justin F., Wylie, Dennis, Busch, Johanna, Gandhi, Saurin, Triplett, Todd A., Yendewa, George, Giddings, Olivia, Anderson, Evan J., Mehta, Aneesh K., Sevransky, Jonathan E., Khor, Bernard, Rahman, Adeeb, Stadlbauer, Daniel, Dutta, Jayeeta, Xie, Hui, Kim-Schulze, Seunghee, Gonzalez-Reiche, Ana Silvia, van de Guchte, Adriana, Farrugia, Keith, Khan, Zenab, Maecker, Holden T., Elashoff, David, Brook, Jenny, Ramires-Sanchez, Estefania, Llamas, Megan, Rivera, Adreanne, Perdomo, Claudia, Ward, Dawn C., Magyar, Clara E., Fulcher, Jennifer A., Abe-Jones, Yumiko, Asthana, Saurabh, Beagle, Alexander, Bhide, Sharvari, Carrillo, Sidney A., Chak, Suzanna, Ghale, Rajani, Gonzalez, Ana, Jauregui, Alejandra, Jones, Norman, Lea, Tasha, Lee, Deanna, Lota, Raphael, Milush, Jeff, Nguyen, Viet, Pierce, Logan, Prasad, Priya A., Rao, Arjun, Samad, Bushra, Shaw, Cole, Sigman, Austin, Sinha, Pratik, Ward, Alyssa, Willmore, Andrew, Zhan, Jenny, Rashid, Sadeed, Rodriguez, Nicklaus, Tang, Kevin, Altamirano, Luz Torres, Betancourt, Legna, Curiel, Cindy, Sutter, Nicole, Paz, Maria Tercero, Tietje-Ulrich, Gayelan, Leroux, Carolyn, Connors, Jennifer, Bernui, Mariana, Kutzler, Michel A., Edwards, Carolyn, Lee, Edward, Lin, Edward, Croen, Brett, Semenza, Nicholas C., Rogowski, Brandon, Melnyk, Nataliya, Woloszczuk, Kyra, Cusimano, Gina, Bell, Mathew R., Furukawa, Sara, McLin, Renee, Marrero, Pamela, Sheidy, Julie, Tegos, George P., Nagle, Crystal, Mege, Nathan, Ulring, Kristen, Seyfert-Margolis, Vicki, Conway, Michelle, Francisco, Dave, Molzahn, Allyson, Erickson, Heidi, Wilson, Connie Cathleen, Schunk, Ron, Sierra, Bianca, Hughes, Trina, Smolen, Kinga, Desjardins, Michael, van Haren, Simon, Mitre, Xhoi, Cauley, Jessica, Li, Xiaofang, Tong, Alexandra, Evans, Bethany, Montesano, Christina, Licona, Jose Humberto, Krauss, Jonathan, Chang, Jun Bai Park, Izaguirre, Natalie, Chaudhary, Omkar, Coppi, Andreas, Fournier, John, Mohanty, Subhasis, Muenker, M. Catherine, Nelson, Allison, Raddassi, Khadir, Rainone, Michael, Ruff, William E., Salahuddin, Syim, Schulz, Wade L., Vijayakumar, Pavithra, Wang, Haowei, Wunder Jr., Elsio, Young, H. Patrick, Zhao, Yujiao, Saksena, Miti, Altman, Deena, Kojic, Erna, Srivastava, Komal, Eaker, Lily Q., Bermúdez-González, Maria C., Beach, Katherine F., Sominsky, Levy A., Azad, Arman R., Carreño, Juan Manuel, Singh, Gagandeep, Raskin, Ariel, Tcheou, Johnstone, Bielak, Dominika, Kawabata, Hisaaki, Mulder, Lubbertus CF, Kleiner, Giulio, Lee, Alexandra S., Do, Evan Do, Fernandes, Andrea, Manohar, Monali, Hagan, Thomas, Blish, Catherine A., Din, Hena Naz, Roque, Jonasel, Yang, Samuel, Brunton, Amanda, Sullivan, Peter E., Strnad, Matthew, Lyski, Zoe L., Coulter, Felicity J., Booth, J. Leland, Sinko, Lauren A., Moldawer, Lyle L., Borresen, Brittany, Roth-Manning, Brittney, Song, Li-Zhen, Nelson, Ebony, Lewis-Smith, Megan, Smith, Jacob, Tipan, Pablo Guaman, Siles, Nadia, Bazzi, Sam, Geltman, Janelle, Hurley, Kerin, Gabriele, Gio, Sieg, Scott, Vaysman, Tatyana, Bristow, Laurel, Hussaini, Laila, Hellmeister, Kieffer, Samaha, Hady, Cheng, Andrew, Spainhour, Christine, Scherer, Erin M., Johnson, Brandi, Bechnak, Amer, Ciric, Caroline R., Hewitt, Lauren, Carter, Erin, Mcnair, Nina, Panganiban, Bernadine, Huerta, Christopher, Usher, Jacob, Ribeiro, Susan Pereira, Altman, Matthew C., Becker, Patrice M., Rouphael, Nadine, Bime, Christian, and Davis, Mark M.

Published
2022
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5. SARS-CoV-2 in Transit: Characterization of SARS-CoV-2 Genomes From Venezuelan Migrants in Colombia

Author

Patiño, Luz H., Ballesteros, Nathalia, Muñoz, Marina, Castañeda, Sergio, Hernández, Carolina, Gomez, Sergio, Florez, Carolina, Rico, Angelica, Pardo, Liseth, Hernandez-Pereira, Carlos E., Delgado-Noguera, Lourdes, Grillet, Maria E., Hernandez, Matthew M., Khan, Zenab, van de Guchte, Adriana, Dutta, Jayeeta, Gonzalez-Reiche, Ana S, Simon, Viviana, van Bakel, Harm, Sordillo, Emilia Mia, Ramírez, Juan David, and Paniz-Mondolfi, Alberto E.

Published
2021
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6. SARS-CoV-2 Outbreak Dynamics in an Isolated US Military Recruit Training Center With Rigorous Prevention Measures

Author

Lizewski, Rhonda A., Sealfon, Rachel S. G., Park, Sang Woo, Smith, Gregory R., Porter, Chad K., Gonzalez-Reiche, Ana S., Ge, Yongchao, Miller, Clare M., Goforth, Carl W., Pincas, Hanna, Termini, Michael S., Ramos, Irene, Nair, Venugopalan D., Lizewski, Stephen E., Alshammary, Hala, Cer, Regina Z., Chen, Hua Wei, George, Mary-Catherine, Arnold, Catherine E., Glang, Lindsay A., Long, Kyle A., Malagon, Francisco, Marayag, Jan J., Nunez, Edgar, Rice, Gregory K., Santa Ana, Ernesto, Schilling, Megan A., Smith, Darci R., Sugiharto, Victor A., Sun, Peifang, van de Guchte, Adriana, Khan, Zenab, Dutta, Jayeeta, Vangeti, Sindhu, Voegtly, Logan J., Weir, Dawn L., Metcalf, C. Jessica E., Troyanskaya, Olga G., Bishop-Lilly, Kimberly A., Grenfell, Bryan T., van Bakel, Harm, Letizia, Andrew G., and Sealfon, Stuart C.

Published
2022
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7. Influenza A variants with reduced susceptibility to baloxavir isolated from Japanese patients are fit and transmit through respiratory droplets

Author

Imai, Masaki, Yamashita, Makoto, Sakai-Tagawa, Yuko, Iwatsuki-Horimoto, Kiyoko, Kiso, Maki, Murakami, Jurika, Yasuhara, Atsuhiro, Takada, Kosuke, Ito, Mutsumi, Nakajima, Noriko, Takahashi, Kenta, Lopes, Tiago J. S., Dutta, Jayeeta, Khan, Zenab, Kriti, Divya, van Bakel, Harm, Tokita, Akifumi, Hagiwara, Haruhisa, Izumida, Naomi, Kuroki, Haruo, Nishino, Tamon, Wada, Noriyuki, Koga, Michiko, Adachi, Eisuke, Jubishi, Daisuke, Hasegawa, Hideki, and Kawaoka, Yoshihiro

Published
2020
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10. Human influenza A virus H1N1 in marine mammals in California, 2019

Author

Plancarte, Magdalena, primary, Kovalenko, Ganna, additional, Baldassano, Julie, additional, Ramírez, Ana L., additional, Carrillo, Selina, additional, Duignan, Pádraig J., additional, Goodfellow, Ian, additional, Bortz, Eric, additional, Dutta, Jayeeta, additional, van Bakel, Harm, additional, and Coffey, Lark L., additional

Published
2023
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12. Human influenza A virus H1N1 in marine mammals in California, 2019

Author

Plancarte, Magdalena, Kovalenko, Ganna, Baldassano, Julie, Ramírez, Ana L, Carrillo, Selina, Duignan, Pádraig J, Goodfellow, Ian, Bortz, Eric, Dutta, Jayeeta, Van Bakel, Harm, Coffey, Lark L, Coffey, Lark L [0000-0002-0718-5146], and Apollo - University of Cambridge Repository

Subjects
Influenza A Virus, H1N1 Subtype, Influenza A virus, Seals, Earless, Influenza, Human, Animals, Humans, California, Caniformia
Abstract

Acknowledgements: We acknowledge Jesierose Poblacion, Carlos Rios, Christine Fontaine, Barbie Halaska, and the veterinary staff at TMMC, who conducted marine mammal sampling and provided swabs and serum under NOAA permit 18786–04. We thank Wendy Puryear, Nichola Hill, and Jonathan Runstadler at Tufts University, who provided HI protocols, and Randy Albrecht at the Icahn School of Medicine at Mount Sinai, who provided control sera for HI assays. Hon Ip at the National Wildlife Health Center provided the IAV H3N8 isolate. We are grateful to all authors from the originating laboratories responsible for obtaining the human specimens, as well as the submitting laboratories where the genome data were generated and shared via GISAID., Funder: UC Davis School of Veterinary Medicine Endowment Fund, From 2011-2018, we conducted surveillance in marine mammals along the California coast for influenza A virus (IAV), frequently detecting anti-influenza antibodies and intermittently detecting IAV. In spring 2019, this pattern changed. Despite no change in surveillance intensity, we detected IAV RNA in 10 samples in March and April, mostly in nasal and rectal swabs from northern elephant seals (Mirounga angustirostris). Although virus isolation was unsuccessful, IAV sequenced from one northern elephant seal nasal swab showed close genetic identity with pandemic H1N1 IAV subclade 6B.1A.1 that was concurrently circulating in humans in the 2018/19 influenza season. This represents the first report of human A(H1N1)pdm09 IAV in northern elephant seals since 2010, suggesting IAV continues to spill over from humans to pinnipeds.

Published
2023

13. Human influenza A virus H1N1 in marine mammals in California, 2019

Author

Plancarte, Magdalena, primary, Kovalenko, Ganna, additional, Baldassano, Julie, additional, Ramírez, Ana L., additional, Carrillo, Selina, additional, Duignan, Pádraig J., additional, Goodfellow, Ian, additional, Bortz, Eric, additional, Dutta, Jayeeta, additional, van Bakel, Harm, additional, and Coffey, Lark L., additional

Published
2022
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14. Additional file 4 of Phylogenetic analysis and comparative genomics of SARS-CoV-2 from survivor and non-survivor COVID-19 patients in Cordoba, Argentina

Author

Olivero, Nadia B., Gonzalez-Reiche, Ana S., Re, Viviana E., Castro, Gonzalo M., Pisano, María B., Sicilia, Paola, Barbas, María G., Khan, Zenab, van de Guchte, Adriana, Dutta, Jayeeta, Cortes, Paulo R., Hernandez-Morfa, Mirelys, Zappia, Victoria E., Ortiz, Lucia, Geiger, Ginger, Rajao, Daniela, Perez, Daniel R., van Bakel, Harm, and Echenique, Jose

Subjects
Data_FILES
Abstract

Additional file 4: Table S3.

Published
2022
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15. Additional file 2 of Phylogenetic analysis and comparative genomics of SARS-CoV-2 from survivor and non-survivor COVID-19 patients in Cordoba, Argentina

Author

Olivero, Nadia B., Gonzalez-Reiche, Ana S., Re, Viviana E., Castro, Gonzalo M., Pisano, María B., Sicilia, Paola, Barbas, María G., Khan, Zenab, van de Guchte, Adriana, Dutta, Jayeeta, Cortes, Paulo R., Hernandez-Morfa, Mirelys, Zappia, Victoria E., Ortiz, Lucia, Geiger, Ginger, Rajao, Daniela, Perez, Daniel R., van Bakel, Harm, and Echenique, Jose

Subjects
Data_FILES
Abstract

Additional file 2: Table S1.

Published
2022
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18. Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin

Author

Ballesteros, Nathalia, primary, Muñoz, Marina, additional, Patiño, Luz Helena, additional, Hernández, Carolina, additional, González-Casabianca, Felipe, additional, Carroll, Iván, additional, Santos-Vega, Mauricio, additional, Cascante, Jaime, additional, Angel, Andrés, additional, Feged-Rivadeneira, Alejandro, additional, Palma-Cuero, Mónica, additional, Flórez, Carolina, additional, Gomez, Sergio, additional, van de Guchte, Adriana, additional, Khan, Zenab, additional, Dutta, Jayeeta, additional, Obla, Ajay, additional, Alshammary, Hala Alejel, additional, Gonzalez-Reiche, Ana S., additional, Hernandez, Matthew M., additional, Sordillo, Emilia Mia, additional, Simon, Viviana, additional, van Bakel, Harm, additional, Paniz-Mondolfi, Alberto E., additional, and Ramírez, Juan David, additional

Published
2021
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19. A household case evidences shorter shedding of SARS-CoV-2 in naturally infected cats compared to their human owners

Author

Neira, Víctor, primary, Brito, Bárbara, additional, Agüero, Belén, additional, Berrios, Felipe, additional, Valdés, Valentina, additional, Gutierrez, Alberto, additional, Ariyama, Naomi, additional, Espinoza, Patricio, additional, Retamal, Patricio, additional, Holmes, Edward C., additional, Gonzalez-Reiche, Ana S., additional, Khan, Zenab, additional, van de Guchte, Adriana, additional, Dutta, Jayeeta, additional, Miorin, Lisa, additional, Kehrer, Thomas, additional, Galarce, Nicolás, additional, Almonacid, Leonardo I., additional, Levican, Jorge, additional, van Bakel, Harm, additional, García-Sastre, Adolfo, additional, and Medina, Rafael A., additional

Published
2021
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20. Shedding of Viable SARS-CoV-2 after Immunosuppressive Therapy for Cancer

Author

Aydillo, Teresa, primary, Gonzalez-Reiche, Ana S., additional, Aslam, Sadaf, additional, van de Guchte, Adriana, additional, Khan, Zenab, additional, Obla, Ajay, additional, Dutta, Jayeeta, additional, van Bakel, Harm, additional, Aberg, Judith, additional, García-Sastre, Adolfo, additional, Shah, Gunjan, additional, Hohl, Tobias, additional, Papanicolaou, Genovefa, additional, Perales, Miguel-Angel, additional, Sepkowitz, Kent, additional, Babady, N. Esther, additional, and Kamboj, Mini, additional

Published
2020
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21. SARS-CoV-2 Transmission among Marine Recruits during Quarantine

Author

Letizia, Andrew G., primary, Ramos, Irene, additional, Obla, Ajay, additional, Goforth, Carl, additional, Weir, Dawn L., additional, Ge, Yongchao, additional, Bamman, Marcas M., additional, Dutta, Jayeeta, additional, Ellis, Ethan, additional, Estrella, Luis, additional, George, Mary-Catherine, additional, Gonzalez-Reiche, Ana S., additional, Graham, William D., additional, van de Guchte, Adriana, additional, Gutierrez, Ramiro, additional, Jones, Franca, additional, Kalomoiri, Aspasia, additional, Lizewski, Rhonda, additional, Lizewski, Stephen, additional, Marayag, Jan, additional, Marjanovic, Nada, additional, Millar, Eugene V., additional, Nair, Venugopalan D., additional, Nudelman, German, additional, Nunez, Edgar, additional, Pike, Brian L., additional, Porter, Chad, additional, Regeimbal, James, additional, Rirak, Stas, additional, Santa Ana, Ernesto, additional, Sealfon, Rachel S.G., additional, Sebra, Robert, additional, Simons, Mark P., additional, Soares-Schanoski, Alessandra, additional, Sugiharto, Victor, additional, Termini, Michael, additional, Vangeti, Sindhu, additional, Williams, Carlos, additional, Troyanskaya, Olga G., additional, van Bakel, Harm, additional, and Sealfon, Stuart C., additional

Published
2020
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22. SARS-CoV-2 spread across the Colombian-Venezuelan border

Author

Paniz-Mondolfi, Alberto, primary, Muñoz, Marina, additional, Florez, Carolina, additional, Gomez, Sergio, additional, Rico, Angelica, additional, Pardo, Lisseth, additional, Barros, Esther C., additional, Hernández, Carolina, additional, Delgado, Lourdes, additional, Jaimes, Jesús E., additional, Pérez, Luis, additional, Teherán, Aníbal A., additional, Alshammary, Hala Alejel, additional, Obla, Ajay, additional, Khan, Zenab, additional, Dutta, Jayeeta, additional, van de Guchte, Adriana, additional, Gonzalez-Reiche, Ana S., additional, Hernandez, Matthew M., additional, Sordillo, Emilia Mia, additional, Simon, Viviana, additional, van Bakel, Harm, additional, Llewellyn, Martin S., additional, and Ramírez, Juan David, additional

Published
2020
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24. A Heterogeneous Swine Show Circuit Drives Zoonotic Transmission of Influenza A Viruses in the United States

Author

Nelson, Martha I., primary, Perofsky, Amanda, additional, McBride, Dillon S., additional, Rambo-Martin, Benjamin L., additional, Wilson, Malania M., additional, Barnes, John R., additional, van Bakel, Harm, additional, Khan, Zenab, additional, Dutta, Jayeeta, additional, Nolting, Jacqueline M., additional, and Bowman, Andrew S., additional

Published
2020
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25. A household case evidences shorter shedding of SARS-CoV-2 in naturally infected cats compared to their human owners

Author

Neira, Víctor, primary, Brito, Bárbara, additional, Agüero, Belén, additional, Berrios, Felipe, additional, Valdés, Valentina, additional, Gutierrez, Alberto, additional, Ariyama, Naomi, additional, Espinoza, Patricio, additional, Retamal, Patricio, additional, Holmes, Edward C., additional, Gonzalez-Reiche, Ana S., additional, Khan, Zenab, additional, van de Guchte, Adriana, additional, Dutta, Jayeeta, additional, Miorin, Lisa, additional, Kehrer, Thomas, additional, Galarce, Nicolás, additional, Almonacid, Leonardo I., additional, Levican, Jorge, additional, van Bakel, Harm, additional, García-Sastre, Adolfo, additional, and Medina, Rafael A., additional

Published
2020
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26. Respiratory tract explant infection dynamics of influenza A virus in California sea lions, northern elephant seals, and rhesus macaques

Author

Liu, Hongwei, primary, Plancarte, Magdalena, additional, Ball, Erin. E., additional, Weiss, Christopher M., additional, Gonzales-Viera, Omar, additional, Holcomb, Karen, additional, Ma, Zhong-Min, additional, Allen, A. Mark, additional, Reader, J. Rachel, additional, Duignan, Pádraig J., additional, Halaska, Barbie, additional, Khan, Zenab, additional, Kriti, Divya, additional, Dutta, Jayeeta, additional, van Bakel, Harm, additional, Jackson, Kenneth, additional, Pesavento, Patricia A., additional, Boyce, Walter M., additional, and Coffey, Lark L., additional

Published
2020
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27. Introductions and early spread of SARS-CoV-2 in the New York City area

Author

Gonzalez-Reiche, Ana S., primary, Hernandez, Matthew M., additional, Sullivan, Mitchell J., additional, Ciferri, Brianne, additional, Alshammary, Hala, additional, Obla, Ajay, additional, Fabre, Shelcie, additional, Kleiner, Giulio, additional, Polanco, Jose, additional, Khan, Zenab, additional, Alburquerque, Bremy, additional, van de Guchte, Adriana, additional, Dutta, Jayeeta, additional, Francoeur, Nancy, additional, Melo, Betsaida Salom, additional, Oussenko, Irina, additional, Deikus, Gintaras, additional, Soto, Juan, additional, Sridhar, Shwetha Hara, additional, Wang, Ying-Chih, additional, Twyman, Kathryn, additional, Kasarskis, Andrew, additional, Altman, Deena R., additional, Smith, Melissa, additional, Sebra, Robert, additional, Aberg, Judith, additional, Krammer, Florian, additional, García-Sastre, Adolfo, additional, Luksza, Marta, additional, Patel, Gopi, additional, Paniz-Mondolfi, Alberto, additional, Gitman, Melissa, additional, Sordillo, Emilia Mia, additional, Simon, Viviana, additional, and van Bakel, Harm, additional

Published
2020
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28. Influenza A variants with reduced susceptibility to baloxavir isolated from Japanese patients are fit and transmit through respiratory droplets

Author

Imai, Masaki, primary, Yamashita, Makoto, additional, Sakai-Tagawa, Yuko, additional, Iwatsuki-Horimoto, Kiyoko, additional, Kiso, Maki, additional, Murakami, Jurika, additional, Yasuhara, Atsuhiro, additional, Takada, Kosuke, additional, Ito, Mutsumi, additional, Nakajima, Noriko, additional, Takahashi, Kenta, additional, Lopes, Tiago J. S., additional, Dutta, Jayeeta, additional, Khan, Zenab, additional, Kriti, Divya, additional, van Bakel, Harm, additional, Tokita, Akifumi, additional, Hagiwara, Haruhisa, additional, Izumida, Naomi, additional, Kuroki, Haruo, additional, Nishino, Tamon, additional, Wada, Noriyuki, additional, Koga, Michiko, additional, Adachi, Eisuke, additional, Jubishi, Daisuke, additional, Hasegawa, Hideki, additional, and Kawaoka, Yoshihiro, additional

Published
2019
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30. A30 Avian influenza viruses in wild birds: Virus evolution in a multi-host ecosystem

Author

Venkatesh, Divya, primary, Poen, Marjolein J, additional, Bestebroer, Theo M, additional, Scheuer, Rachel D, additional, Vuong, Oanh, additional, Chkhaidze, Mzia, additional, Machablishvili, Anna, additional, Mamuchadze, Jimsher, additional, Ninua, Levan, additional, Fedorova, Nadia B, additional, Halpin, Rebecca A, additional, Lin, Xudong, additional, Ransier, Amy, additional, Stockwell, Timothy B, additional, Wentworth, David E, additional, Kriti, Divya, additional, Dutta, Jayeeta, additional, van Bakel, Harm, additional, Puranik, Anita, additional, Slomka, Marek J, additional, Essen, Steve, additional, Brown, Ian H, additional, Fouchier, Ron A M, additional, and Lewis, Nicola S, additional

Published
2019
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31. Isolation of Highly Pathogenic H5N1 Influenza Viruses in 2009–2013 in Vietnam

Author

Zhong, Gongxun, primary, Fan, Shufang, additional, Lopes, Tiago J. S., additional, Le, Mai Quynh, additional, van Bakel, Harm, additional, Dutta, Jayeeta, additional, Smith, Gavin J. D., additional, Jayakumar, Jayanthi, additional, Nguyen, Hang Le Khanh, additional, Hoang, Phuong Vu Mai, additional, Halfmann, Peter, additional, Hatta, Masato, additional, Su, Yvonne C. F., additional, Neumann, Gabriele, additional, and Kawaoka, Yoshihiro, additional

Published
2019
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33. Avian Influenza Viruses in Wild Birds: Virus Evolution in a Multihost Ecosystem

Author

Venkatesh, Divya, primary, Poen, Marjolein J., additional, Bestebroer, Theo M., additional, Scheuer, Rachel D., additional, Vuong, Oanh, additional, Chkhaidze, Mzia, additional, Machablishvili, Anna, additional, Mamuchadze, Jimsher, additional, Ninua, Levan, additional, Fedorova, Nadia B., additional, Halpin, Rebecca A., additional, Lin, Xudong, additional, Ransier, Amy, additional, Stockwell, Timothy B., additional, Wentworth, David E., additional, Kriti, Divya, additional, Dutta, Jayeeta, additional, van Bakel, Harm, additional, Puranik, Anita, additional, Slomka, Marek J., additional, Essen, Steve, additional, Brown, Ian H., additional, Fouchier, Ron A. M., additional, and Lewis, Nicola S., additional

Published
2018
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34. Avian influenza viruses in wild birds: virus evolution in a multi-host ecosystem

Author

Venkatesh, Divya, primary, Poen, Marjolein J., additional, Bestebroer, Theo M., additional, Scheuer, Rachel D., additional, Vuong, Oanh, additional, Chkhaidze, Mzia, additional, Machablishvili, Anna, additional, Mamuchadze, Jimsher, additional, Ninua, Levan, additional, Fedorova, Nadia B., additional, Halpin, Rebecca A., additional, Lin, Xudong, additional, Ransier, Amy, additional, Stockwell, Timothy B, additional, Wentworth, David E., additional, Kriti, Divya, additional, Dutta, Jayeeta, additional, van Bakel, Harm, additional, Puranik, Anita, additional, Slomka, Marek J, additional, Essen, Steve, additional, Brown, Ian H., additional, Fouchier, Ron A.M., additional, and Lewis, Nicola S., additional

Published
2018
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36. Genomic confirmation of vancomycin-resistant Enterococcus transmission from deceased donor to liver transplant recipient

Author

Bashir, Ali, primary, Attie, Oliver, additional, Sullivan, Mitchell, additional, Sebra, Robert, additional, Singh, Kavindra V., additional, Altman, Deena, additional, Pak, Theodore, additional, Dutta, Jayeeta, additional, Chacko, Kieran, additional, Webster, Elizabeth, additional, Lewis, Martha, additional, Hamula, Camille, additional, Delli Carpini, Kristin W., additional, Murray, Barbara E., additional, Kasarskis, Andrew, additional, van Bakel, Harm, additional, and Huprikar, Shirish, additional

Published
2017
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37. Origins of the 2009 H1N1 influenza pandemic in swine in Mexico

Author

Mena, Ignacio, primary, Nelson, Martha I, additional, Quezada-Monroy, Francisco, additional, Dutta, Jayeeta, additional, Cortes-Fernández, Refugio, additional, Lara-Puente, J Horacio, additional, Castro-Peralta, Felipa, additional, Cunha, Luis F, additional, Trovão, Nídia S, additional, Lozano-Dubernard, Bernardo, additional, Rambaut, Andrew, additional, van Bakel, Harm, additional, and García-Sastre, Adolfo, additional

Published
2016
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38. Author response: Origins of the 2009 H1N1 influenza pandemic in swine in Mexico

Author

Mena, Ignacio, primary, Nelson, Martha I, additional, Quezada-Monroy, Francisco, additional, Dutta, Jayeeta, additional, Cortes-Fernández, Refugio, additional, Lara-Puente, J Horacio, additional, Castro-Peralta, Felipa, additional, Cunha, Luis F, additional, Trovão, Nídia S, additional, Lozano-Dubernard, Bernardo, additional, Rambaut, Andrew, additional, van Bakel, Harm, additional, and García-Sastre, Adolfo, additional

Published
2016
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40. Sequential topoisomerase targeting and analysis of mechanisms of resistance to topotecan in patients with acute myelogenous leukemia

Author

Saraiya, Biren, primary, Gounder, Murugesan, additional, Dutta, Jayeeta, additional, Saleem, Ahamed, additional, Collazo, Celeste, additional, Zimmerman, Luz, additional, Nazar, Ahamed, additional, Gharibo, Mecide, additional, Schaar, Dale, additional, Lin, Yong, additional, Shih, Weichung, additional, Aisner, Joseph, additional, Strair, Roger K., additional, and Rubin, Eric H., additional

Published
2008
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41. Respiratory Tract Explant Infection Dynamics of Influenza A Virus in California Sea Lions, Northern Elephant Seals, and Rhesus Macaques.

Author

Hongwei Liu, Plancarte, Magdalena, Ball, Erin E., Weiss, Christopher M., Gonzales-Viera, Omar, Holcomb, Karen, Zhong-Min Ma, Allen, A. Mark, Reader, J. Rachel, Duignan, Pádraig J., Halaska, Barbie, Khan, Zenab, Kriti, Divya, Dutta, Jayeeta, van Bakel, Harm, Jackson, Kenneth, Pesavento, Patricia A., Boyce, Walter M., and Coffey, Lark L.

Subjects
*SEA lions, *RHESUS monkeys, *INFLUENZA A virus, *INFLUENZA viruses, *MACAQUES, *MARINE mammals, *RESPIRATORY infections, *INFLUENZA
Abstract

To understand susceptibility of wild California sea lions and Northern elephant seals to influenza A virus (IAV), we developed an ex vivo respiratory explant model and used it to compare infection kinetics for multiple IAV subtypes. We first established the approach using explants from colonized rhesus macaques, a model for human IAV. Trachea, bronchi, and lungs from 11 California sea lions, 2 Northern elephant seals, and 10 rhesus macaques were inoculated within 24 h postmortem with 6 strains representing 4 IAV subtypes. Explants from the 3 species showed similar IAV infection kinetics, with peak viral titers 48 to 72 h post-inoculation that increased by 2 to 4 log10 PFU/explant relative to the inoculum. Immunohistochemistry localized IAV infection to apical epithelial cells. These results demonstrate that respiratory tissue explants from wild marine mammals support IAV infection. In the absence of the ability to perform experimental infections of marine mammals, this ex vivo culture of respiratory tissues mirrors the in vivo environment and serves as a tool to study IAV susceptibility, host range, and tissue tropism. [ABSTRACT FROM AUTHOR]

Published
2021
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