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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

3. Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients

Author

Diray-Arce, Joann, Fourati, Slim, Jayavelu, Naresh Doni, Patel, Ravi, Maguire, Cole, Chang, Ana C, Dandekar, Ravi, Qi, Jingjing, Lee, Brian H, van Zalm, Patrick, Schroeder, Andrew, Chen, Ernie, Konstorum, Anna, Brito, Anderson, Gygi, Jeremy P, Kho, Alvin, Chen, Jing, Pawar, Shrikant, Gonzalez-Reiche, Ana Silvia, Hoch, Annmarie, Milliren, Carly E, Overton, James A, Westendorf, Kerstin, Network, IMPACC, Abraham, James, Adkisson, Michael, Albert, Marisa, Torres, Luz Altamirano, Alvarenga, Bonny, Anderson, Matthew L, Anderson, Evan J, Arnett, Azlann, Asashima, Hiromitsu, Atkinson, Mark A, Baden, Lindsey R, Barton, Brenda, Beach, Katherine, Beagle, Elizabeth, Becker, Patrice M, Bell, Matthew R, Bernui, Mariana, Bime, Chris, Kumar, Arun Boddapati, Booth, Leland J, Borresen, Brittney, Brakenridge, Scott C, Bristow, Laurel, Bryant, Robert, Calfee, Carolyn S, Manuel, Juan Carreño, Carrillo, Sidney, Chak, Suzanna, Chang, Iris, Connors, Jennifer, Conway, Michelle, Corry, David B, Cowan, David, Croen, Brett, Dela Cruz, Charles S, Cusimano, Gina, Eaker, Lily, Edwards, Carolyn, Ehrlich, Lauren IR, Elashoff, David, Erickson, Heidi, Erle, David J, Farhadian, Shelli, Farrugia, Keith, Fatou, Benoit, Fernandes, Andrea, Fernandez-Sesma, Ana, Fragiadakis, Gabriela K, Furukawa, Sara, Geltman, Janelle N, Ghale, Rajani, Bermúdez, Maria González Carolina, Goonewardene, Michael I, Sanchez, Estella Guerrero, Guirgis, Faheem W, Hafler, David A, Hamilton, Sydney, Harris, Paul, Nemati, Arash Hayati, Hendrickson, Carolyn M, Agudelo, Nelson I Higuita, Hodder, Thomas, Holland, Steven M, Hough, Catherine L, Huerta, Christopher, Hurley, Kerin C, Hutton, Scott R, Iwasaki, Akiko, Jauregui, Alejandra, Jha, Meenakshi, Johnson, Brandi, Joyner, David, Kangelaris, Kirsten N, Kelly, Geoffrey, Khalil, Zain, and Khan, Zenab

Subjects
Biomedical and Clinical Sciences, Immunology, Prevention, Rare Diseases, Clinical Research, 2.1 Biological and endogenous factors, Detection, screening and diagnosis, Aetiology, 4.1 Discovery and preclinical testing of markers and technologies, Good Health and Well Being, Humans, COVID-19, SARS-CoV-2, Longitudinal Studies, Multiomics, Disease Progression, IMPACC Network, immunophenotyping, longitudinal modeling, multi-omics, systems immunology, Biomedical and clinical sciences
Abstract

The IMPACC cohort, composed of >1,000 hospitalized COVID-19 participants, contains five illness trajectory groups (TGs) during acute infection (first 28 days), ranging from milder (TG1-3) to more severe disease course (TG4) and death (TG5). Here, we report deep immunophenotyping, profiling of >15,000 longitudinal blood and nasal samples from 540 participants of the IMPACC cohort, using 14 distinct assays. These unbiased analyses identify cellular and molecular signatures present within 72 h of hospital admission that distinguish moderate from severe and fatal COVID-19 disease. Importantly, cellular and molecular states also distinguish participants with more severe disease that recover or stabilize within 28 days from those that progress to fatal outcomes (TG4 vs. TG5). Furthermore, our longitudinal design reveals that these biologic states display distinct temporal patterns associated with clinical outcomes. Characterizing host immune responses in relation to heterogeneity in disease course may inform clinical prognosis and opportunities for intervention.

Published
2023

4. Nirmatrelvir and molnupiravir maintain potent in vitro and in vivo antiviral activity against circulating SARS-CoV-2 omicron subvariants

Author

Alshammary, Hala, Banu, R., Farrugia, K., Gonzalez-Reiche, Ana Silvia, Paniz-Mondolfi, A., Polanco, J., Rosales, Romel, McGovern, Briana L., Rodriguez, M. Luis, Leiva-Rebollo, Rocio, Diaz-Tapia, Randy, Benjamin, Jared, Rai, Devendra K., Cardin, Rhonda D., Anderson, Annaliesa S., Sordillo, Emilia Mia, van Bakel, Harm, Simon, Viviana, García-Sastre, Adolfo, and White, Kris M.

Published
2024
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5. Defining the risk of SARS-CoV-2 variants on immune protection

Author

DeGrace, Marciela M, Ghedin, Elodie, Frieman, Matthew B, Krammer, Florian, Grifoni, Alba, Alisoltani, Arghavan, Alter, Galit, Amara, Rama R, Baric, Ralph S, Barouch, Dan H, Bloom, Jesse D, Bloyet, Louis-Marie, Bonenfant, Gaston, Boon, Adrianus CM, Boritz, Eli A, Bratt, Debbie L, Bricker, Traci L, Brown, Liliana, Buchser, William J, Carreño, Juan Manuel, Cohen-Lavi, Liel, Darling, Tamarand L, Davis-Gardner, Meredith E, Dearlove, Bethany L, Di, Han, Dittmann, Meike, Doria-Rose, Nicole A, Douek, Daniel C, Drosten, Christian, Edara, Venkata-Viswanadh, Ellebedy, Ali, Fabrizio, Thomas P, Ferrari, Guido, Fischer, Will M, Florence, William C, Fouchier, Ron AM, Franks, John, García-Sastre, Adolfo, Godzik, Adam, Gonzalez-Reiche, Ana Silvia, Gordon, Aubree, Haagmans, Bart L, Halfmann, Peter J, Ho, David D, Holbrook, Michael R, Huang, Yaoxing, James, Sarah L, Jaroszewski, Lukasz, Jeevan, Trushar, Johnson, Robert M, Jones, Terry C, Joshi, Astha, Kawaoka, Yoshihiro, Kercher, Lisa, Koopmans, Marion PG, Korber, Bette, Koren, Eilay, Koup, Richard A, LeGresley, Eric B, Lemieux, Jacob E, Liebeskind, Mariel J, Liu, Zhuoming, Livingston, Brandi, Logue, James P, Luo, Yang, McDermott, Adrian B, McElrath, Margaret J, Meliopoulos, Victoria A, Menachery, Vineet D, Montefiori, David C, Mühlemann, Barbara, Munster, Vincent J, Munt, Jenny E, Nair, Manoj S, Netzl, Antonia, Niewiadomska, Anna M, O’Dell, Sijy, Pekosz, Andrew, Perlman, Stanley, Pontelli, Marjorie C, Rockx, Barry, Rolland, Morgane, Rothlauf, Paul W, Sacharen, Sinai, Scheuermann, Richard H, Schmidt, Stephen D, Schotsaert, Michael, Schultz-Cherry, Stacey, Seder, Robert A, Sedova, Mayya, Sette, Alessandro, Shabman, Reed S, Shen, Xiaoying, Shi, Pei-Yong, Shukla, Maulik, Simon, Viviana, Stumpf, Spencer, Sullivan, Nancy J, Thackray, Larissa B, and Theiler, James

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Biological Sciences, Emerging Infectious Diseases, Pneumonia, Vaccine Related, Pneumonia & Influenza, Infectious Diseases, Biodefense, Immunization, Biotechnology, Prevention, Lung, Prevention of disease and conditions, and promotion of well-being, 2.1 Biological and endogenous factors, 3.4 Vaccines, Aetiology, Infection, Good Health and Well Being, Animals, Biological Evolution, COVID-19, COVID-19 Vaccines, Humans, National Institute of Allergy and Infectious Diseases (U.S.), Pandemics, Pharmacogenomic Variants, SARS-CoV-2, United States, Virulence, General Science & Technology
Abstract

The global emergence of many severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants jeopardizes the protective antiviral immunity induced after infection or vaccination. To address the public health threat caused by the increasing SARS-CoV-2 genomic diversity, the National Institute of Allergy and Infectious Diseases within the National Institutes of Health established the SARS-CoV-2 Assessment of Viral Evolution (SAVE) programme. This effort was designed to provide a real-time risk assessment of SARS-CoV-2 variants that could potentially affect the transmission, virulence, and resistance to infection- and vaccine-induced immunity. The SAVE programme is a critical data-generating component of the US Government SARS-CoV-2 Interagency Group to assess implications of SARS-CoV-2 variants on diagnostics, vaccines and therapeutics, and for communicating public health risk. Here we describe the coordinated approach used to identify and curate data about emerging variants, their impact on immunity and effects on vaccine protection using animal models. We report the development of reagents, methodologies, models and notable findings facilitated by this collaborative approach and identify future challenges. This programme is a template for the response to rapidly evolving pathogens with pandemic potential by monitoring viral evolution in the human population to identify variants that could reduce the effectiveness of countermeasures.

Published
2022

6. US National Institutes of Health Prioritization of SARS-CoV-2 Variants

Author

Turner, Sam, Alisoltani, Arghavan, Bratt, Debbie, Cohen-Lavi, Liel, Dearlove, Bethany L., Drosten, Christian, Fischer, Will M., Fouchier, Ron A.M., Gonzalez-Reiche, Ana Silvia, Jaroszewski, Lukasz, Khalil, Zain, LeGresley, Eric, Johnson, Marc, Jones, Terry C., Muhlemann, Barbara, O'Connor, David, Sedova, Mayya, Shukla, Maulik, Theiler, James, Wallace, Zachary S., Yoon, Hyejin, Zhang, Yun, van Bakel, Harm, Degrace, Marciela M., Ghedin, Elodie, Godzik, Adam, Hertz, Tomer, Korber, Bette, Lemieux, Jacob, Niewiadomska, Anna M., Post, Diane J., Rolland, Morgane, Scheuermann, Richard, and Smith, Derek J.

Subjects
Values -- Analysis, Microbial mutation -- Health aspects, Epidemiology -- Methods, Health
Abstract

As part of the US National Institutes of Health (NIH) National Institute of Allergy and Infectious Diseases (NIAID) SARS-CoV-2 Assessment of Viral Evolution (SAVE) effort to combat the SARS-CoV-2 pandemic, [...]

Published
2023
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7. Highly Pathogenic Avian Influenza A(H5N1) Virus Outbreak in New England Seals, United States

Author

Puryear, Wendy, Sawatzki, Kaitlin, Hill, Nichola, Foss, Alexa, Stone, Jonathon J., Doughty, Lynda, Walk, Dominique, Gilbert, Katie, Murray, Maureen, Cox, Elena, Patel, Priya, Mertz, Zak, Ellis, Stephanie, Taylor, Jennifer, Fauquier, Deborah, Smith, Ainsley, DiGiovanni, Robert A., Jr., van de Guchte, Adriana, Gonzalez- Reiche, Ana Silvia, Khalil, Zain, van Bakel, Harm, Torchetti, Mia K., Lantz, Kristina, Lenoch, Julianna B., and Runstadler, Jonathan

Subjects
New England -- Health aspects, Avian influenza -- Risk factors, Epidemics -- Risk factors -- United States, Harbor seal -- Diseases, Disease transmission -- Risk factors, Health
Abstract

Highly pathogenic avian influenza (HPAI) viruses are of concern because of their pandemic potential, socioeconomic impact during agricultural outbreaks, and risks to wildlife conservation. Since October 2020, HPAI A(H5N1) virus, [...]

Published
2023
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8. Cellular mechanisms associated with sub-optimal immune responses to SARS-CoV-2 bivalent booster vaccination in patients with Multiple Myeloma

Author

Alshammary, Hala, Andre, Dalles, Banu, Radhika, Beach, Katherine, Bermúdez-González, María Carolina, Chari, Ajai, Chen, Yuexing, Cho, Hearn, Firpo, Adolfo, Gonzalez-Reiche, Ana Silvia, Kim, Eun Hye, Kleiner, Giulio, Krammer, Florian, Mauldin, Jacob, Mendu, Rao, Monahan, Brian, Richard, Shambavi, Richter, Joshua, Rodriguez, Cesar, Rossi, Adrianna, Salimbangon, Ashley, Sanchez, Laryssa, Verina, Daniel, Aleman, Adolfo, van Kesteren, Morgan, Zajdman, Ariel Kogan, Srivastava, Komal, Cognigni, Christian, Mischka, Jacob, Chen, Lucia Y., Upadhyaya, Bhaskar, Serebryakova, Kseniya, Nardulli, Jessica R., Lyttle, Neko, Kappes, Katerina, Jackson, Hayley, Gleason, Charles R., Oostenink, Annika, Cai, Gianna Y., Van Oekelen, Oliver, van Bakel, Harm, Sordillo, Emilia Mia, Cordon-Cardo, Carlos, Merad, Miriam, Jagannath, Sundar, Wajnberg, Ania, Simon, Viviana, and Parekh, Samir

Published
2023
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9. Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients

Author

Abraham, James, Adkisson, Michael, Albert, Marisa, Altamirano, Luz Torres, Alvarenga, Bonny, Anderson, Matthew L., Anderson, Evan J., Arnett, Azlann, Asashima, Hiromitsu, Atkinson, Mark A., Baden, Lindsey R., Barton, Brenda, Beach, Katherine, Beagle, Elizabeth, Becker, Patrice M., Bell, Matthew R., Bernui, Mariana, Bime, Christian, Boddapati, Arun Kumar, Booth, J. Leland, Borresen, Brittney, Brakenridge, Scott C., Bristow, Laurel, Bryant, Robert, Calfee, Carolyn S., Carreño, Juan Manuel, Carrillo, Sidney, Chak, Suzanna, Chang, Iris, Connors, Jennifer, Conway, Michelle, Corry, David B., Cowan, David, Croen, Brett, Dela Cruz, Charles S., Cusimano, Gina, Eaker, Lily, Edwards, Carolyn, Ehrlich, Lauren I.R., Elashoff, David, Erickson, Heidi, Erle, David J., Farhadian, Shelli, Farrugia, Keith, Fatou, Benoit, Fernandes, Andrea, Fernandez-Sesma, Ana, Fragiadakis, Gabriela K., Furukawa, Sara, Geltman, Janelle N., Ghale, Rajani, Bermúdez González, Maria Carolina, Goonewardene, I. Michael, Guerrero, Estella Sanchez, Guirgis, Faheem W., Hafler, David A., Hamilton, Sydney, Harris, Paul, Hayati, Arash Nemati, Hendrickson, Carolyn M., Agudelo Higuita, Nelson I., Hodder, Thomas, Holland, Steven M., Hough, Catherine L., Huerta, Christopher, Hurley, Kerin C., Hutton, Scott R., Iwasaki, Akiko, Jauregui, Alejandra, Jha, Meenakshi, Johnson, Brandi, Joyner, David, Kangelaris, Kirsten N., Kelly, Geoffrey, Khalil, Zain, Khan, Zenab, Kheradmand, Farrah, Kim, James N., Kimura, Hiroki, Ko, Albert I., Kohr, Bernard, Kraft, Monica, Krummel, Matthew, Kutzler, Michele A., Lasky-Su, Jessica, Lee, Serena, Lee, Deanna, Leipold, Michael, Lentucci, Claudia, Leroux, Carolyn, Lin, Edward, Liu, Shanshan, Love, Christina, Lu, Zhengchun, Maliskova, Lenka, Manning, Brittany Roth, Manohar, Monali, Martens, Mark, McComsey, Grace A., McEnaney, Kerry, McLin, Renee, Melamed, Esther, Melnyk, Nataliya, Mendez, Kevin, Messer, William B., Metcalf, Jordan P., Michelotti, Gregory, Mick, Eran, Mohanty, Subhasis, Mosier, Jarrod, Mulder, Lubbertus C.F., Murphy, Maimouna, Nadeau, Kari R.C., Nelson, Ebony, Nelson, Allison, Nguyen, Viet, Oberhaus, Jordan, Panganiban, Bernadine, Pellegrini, Kathryn L., Pickering, Harry C., Powell, Debra L., Presnell, Scott, Pulendran, Bali, Rahman, Adeeb H., Rashid, Ahmad Sadeed, Raskin, Ariel, Reed, Elaine F., Ribeiro, Susan Pereira, Rivera, Adreanne M., Rogers, Jacob E., Rogers, Angela, Rogowski, Brandon, Rooks, Rebecca, Rosenberg-Hasson, Yael, Rothman, Jessica, Rousseau, Justin F., Salehi-Rad, Ramin, Saluvan, Mehmet, Samaha, Hady, Schaenman, Joanna, Schunk, Ron, Semenza, Nicholas C., Sen, Subha, Sevransky, Jonathan, Seyfert-Margolis, Vicki, Shaheen, Tanzia, Shaw, Albert C., Sieg, Scott, Siegel, Sarah A.R., Sigal, Natalia, Siles, Nadia, Simmons, Brent, Simon, Viviana, Singh, Gagandeep, Sinko, Lauren, Smith, Cecilia M., Smolen, Kinga K., Song, Li-Zhen, Srivastava, Komal, Sullivan, Peter, Syphurs, Caitlin, Tcheou, Johnstone, Tegos, George P., Tharp, Greg K., Tong, Alexandra, Tsitsiklis, Alexandra, Ungaro, Ricardo F., Vaysman, Tatyana, Viode, Arthur, Vita, Randi, Wang, Xiaomei, Ward, Alyssa, Ward, Dawn C., Willmore, Andrew, Woloszczuk, Kyra, Wong, Kari, Woodruff, Prescott G., Xu, Leqi, van Haren, Simon, van de Guchte, Adriana, Zhao, Yujiao, Diray-Arce, Joann, Fourati, Slim, Doni Jayavelu, Naresh, Patel, Ravi, Maguire, Cole, Chang, Ana C., Dandekar, Ravi, Qi, Jingjing, Lee, Brian H., van Zalm, Patrick, Schroeder, Andrew, Chen, Ernie, Konstorum, Anna, Brito, Anderson, Gygi, Jeremy P., Kho, Alvin, Chen, Jing, Pawar, Shrikant, Gonzalez-Reiche, Ana Silvia, Hoch, Annmarie, Milliren, Carly E., Overton, James A., Westendorf, Kerstin, Cairns, Charles B., Rouphael, Nadine, Bosinger, Steven E., Kim-Schulze, Seunghee, Krammer, Florian, Rosen, Lindsey, Grubaugh, Nathan D., van Bakel, Harm, Wilson, Michael, Rajan, Jayant, Steen, Hanno, Eckalbar, Walter, Cotsapas, Chris, Langelier, Charles R., Levy, Ofer, Altman, Matthew C., Maecker, Holden, Montgomery, Ruth R., Haddad, Elias K., Sekaly, Rafick P., Esserman, Denise, Ozonoff, Al, Augustine, Alison D., Guan, Leying, Peters, Bjoern, and Kleinstein, Steven H.

Published
2023
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10. 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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11. SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters

Author

Halfmann, Peter J., Iida, Shun, Iwatsuki-Horimoto, Kiyoko, Maemura, Tadashi, Kiso, Maki, Scheaffer, Suzanne M., Darling, Tamarand L., Joshi, Astha, Loeber, Samantha, Singh, Gagandeep, Foster, Stephanie L., Ying, Baoling, Case, James Brett, Chong, Zhenlu, Whitener, Bradley, Moliva, Juan, Floyd, Katharine, Ujie, Michiko, Nakajima, Noriko, Ito, Mutsumi, Wright, Ryan, Uraki, Ryuta, Warang, Prajakta, Gagne, Matthew, Li, Rong, Sakai-Tagawa, Yuko, Liu, Yanan, Larson, Deanna, Osorio, Jorge E., Hernandez-Ortiz, Juan P., Henry, Amy R., Ciuoderis, Karl, Florek, Kelsey R., Patel, Mit, Odle, Abby, Wong, Lok-Yin Roy, Bateman, Allen C., Wang, Zhongde, Edara, Venkata-Viswanadh, Chong, Zhenlu, Franks, John, Jeevan, Trushar, Fabrizio, Thomas, DeBeauchamp, Jennifer, Kercher, Lisa, Seiler, Patrick, Gonzalez-Reiche, Ana Silvia, Sordillo, Emilia Mia, Chang, Lauren A., van Bakel, Harm, Simon, Viviana, Douek, Daniel C., Sullivan, Nancy J., Thackray, Larissa B., Ueki, Hiroshi, Yamayoshi, Seiya, Imai, Masaki, Perlman, Stanley, Webby, Richard J., Seder, Robert A., Suthar, Mehul S., García-Sastre, Adolfo, Schotsaert, Michael, Suzuki, Tadaki, Boon, Adrianus C. M., Diamond, Michael S., and Kawaoka, Yoshihiro

Published
2022
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12. Activity of convalescent and vaccine serum against SARS-CoV-2 Omicron

Author

Carreño, Juan Manuel, Alshammary, Hala, Tcheou, Johnstone, Singh, Gagandeep, Raskin, Ariel J., Kawabata, Hisaaki, Sominsky, Levy A., Clark, Jordan J., Adelsberg, Daniel C., Bielak, Dominika A., Gonzalez-Reiche, Ana Silvia, Dambrauskas, Nicholas, Vigdorovich, Vladimir, Srivastava, Komal, Sather, D. Noah, Sordillo, Emilia Mia, Bajic, Goran, van Bakel, Harm, Simon, Viviana, and Krammer, Florian

Published
2022
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13. Cellular mechanisms associated with sub-optimal immune responses to SARS-CoV-2 bivalent booster vaccination in patients with Multiple Myeloma

Author

Aleman, Adolfo, primary, van Kesteren, Morgan, additional, Zajdman, Ariel Kogan, additional, Srivastava, Komal, additional, Cognigni, Christian, additional, Mischka, Jacob, additional, Chen, Lucia Y., additional, Upadhyaya, Bhaskar, additional, Serebryakova, Kseniya, additional, Nardulli, Jessica R., additional, Lyttle, Neko, additional, Kappes, Katerina, additional, Jackson, Hayley, additional, Gleason, Charles R., additional, Oostenink, Annika, additional, Cai, Gianna Y., additional, Van Oekelen, Oliver, additional, van Bakel, Harm, additional, Sordillo, Emilia Mia, additional, Cordon-Cardo, Carlos, additional, Merad, Miriam, additional, Jagannath, Sundar, additional, Wajnberg, Ania, additional, Simon, Viviana, additional, Parekh, Samir, additional, Alshammary, Hala, additional, Andre, Dalles, additional, Banu, Radhika, additional, Beach, Katherine, additional, Bermúdez-González, María Carolina, additional, Chari, Ajai, additional, Chen, Yuexing, additional, Cho, Hearn, additional, Firpo, Adolfo, additional, Gonzalez-Reiche, Ana Silvia, additional, Kim, Eun Hye, additional, Kleiner, Giulio, additional, Krammer, Florian, additional, Mauldin, Jacob, additional, Mendu, Rao, additional, Monahan, Brian, additional, Richard, Shambavi, additional, Richter, Joshua, additional, Rodriguez, Cesar, additional, Rossi, Adrianna, additional, Salimbangon, Ashley, additional, Sanchez, Laryssa, additional, and Verina, Daniel, additional

Published
2023
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14. Phylogenetic landscape of Monkeypox Virus (MPV) during the early outbreak in New York City, 2022.

Author

Patiño, Luz H., Guerra, Susana, Muñoz, Marina, Luna, Nicolas, Farrugia, Keith, van de Guchte, Adriana, Khalil, Zain, Gonzalez-Reiche, Ana Silvia, Hernandez, Matthew M., Banu, Radhika, Shrestha, Paras, Liggayu, Bernadette, Firpo Betancourt, Adolfo, Reich, David, Cordon-Cardo, Carlos, Albrecht, Randy, Pearl, Rebecca, Simon, Viviana, Rooker, Aria, and Sordillo, Emilia Mia

Published
2023
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16. Blue-Winged Teals in Guatemala and Their Potential Role in the Ecology of H14 Subtype Influenza a Viruses

Author

Ortiz, Lucia, primary, Geiger, Ginger, additional, Ferreri, Lucas, additional, Moran, David, additional, Mendez, Dione, additional, Gonzalez-Reiche, Ana Silvia, additional, Alvarez, Danilo, additional, Motta, Mayra, additional, Escobar, Francisco, additional, Rajao, Daniela, additional, Cordon-Rosales, Celia, additional, Nelson, Martha I., additional, and Perez, Daniel R., additional

Published
2023
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18. Genomic and ultrastructural analysis of monkeypox virus in skin lesions and in human/animal infected cells reveals further morphofunctional insights into viral pathogenicity.

Author

Paniz‐Mondolfi, Alberto, Reidy, Jason, Pagani, Nina, Lednicky, John A., McGrail, Joseph Patrick, Kasminskaya, Yana, Patino, Luz H., Garcia‐Sastre, Adolfo, Palacios, Gustavo, Gonzalez‐Reiche, Ana Silvia, van Bakel, Harm, Firpo Betancourt, Adolfo, Hernandez, Matthew M., Cordon‐Cardo, Carlos, Simon, Viviana, Sordillo, Emilia M., Ramírez, Juan David, and Guerra, Susana

Subjects
MONKEYPOX, GENOMICS, ZOONOSES, VIRAL tropism, RESPIRATORY mucosa, ELECTRON microscopy, FOOT & mouth disease
Abstract

Monkeypox (MPOX) is a zoonotic disease that affects humans and other primates, resulting in a smallpox‐like illness. It is caused by monkeypox virus (MPXV), which belongs to the Poxviridae family. Clinically manifested by a range of cutaneous and systemic findings, as well as variable disease severity phenotypes based on the genetic makeup of the virus, the cutaneous niche and respiratory mucosa are the epicenters of MPXV pathogenicity. Herein, we describe the ultrastructural features of MPXV infection in both human cultured cells and cutaneous clinical specimens collected during the 2022–2023 MPOX outbreak in New York City that were revealed through electron microscopy. We observed typical enveloped virions with brick‐shaped morphologies that contained surface protrusions, consistent with the classic ultrastructural features of MPXV. In addition, we describe morpho‐functional evidence that point to roles of distinct cellular organelles in viral assembly during clinical MPXV infection. Interestingly, in skin lesions, we found abundant melanosomes near viral assembly sites, particularly in the vicinity of mature virions, which provides further insight into virus‐host interactions at the subcellular level that contribute to MPXV pathogenesis. These findings not only highlight the importance of electron microscopic studies for further investigation of this emerging pathogen but also in characterizing MPXV pathogenesis during human infection. [ABSTRACT FROM AUTHOR]

Published
2023
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19. Outbreak of Highly Pathogenic Avian Influenza H5N1 in New England Seals

Author

Puryear, Wendy, primary, Sawatzki, Kaitlin, additional, Hill, Nichola, additional, Foss, Alexa, additional, Stone, Jonathon J., additional, Doughty, Lynda, additional, Walk, Dominique, additional, Gilbert, Katie, additional, Murray, Maureen, additional, Cox, Elena, additional, Patel, Priya, additional, Mertz, Zak, additional, Ellis, Stephanie, additional, Taylor, Jennifer, additional, Fauquier, Deborah, additional, Smith, Ainsley, additional, DiGiovanni, Robert A., additional, van de Guchte, Adriana, additional, Gonzalez-Reiche, Ana Silvia, additional, Khalil, Zain, additional, van Bakel, Harm, additional, Torchetti, Mia K., additional, Lenoch, Julianna B., additional, Lantz, Kristina, additional, and Runstadler, Jonathan, additional

Published
2022
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21. Defining the risk of SARS-CoV-2 variants on immune protection

Author

DeGrace, Marciela M., Ghedin, Elodie, Frieman, Matthew B., Krammer, Florian, Grifoni, Alba, Alisoltani, Arghavan, Alter, Galit, Amara, Rama R., Baric, Ralph S., Barouch, Dan H., Bloom, Jesse D., Bloyet, Louis Marie, Bonenfant, Gaston, Boon, Adrianus C.M., Boritz, Eli A., Bratt, Debbie L., Bricker, Traci L., Brown, Liliana, Buchser, William J., Carreño, Juan Manuel, Cohen-Lavi, Liel, Darling, Tamarand L., Davis-Gardner, Meredith E., Dearlove, Bethany L., Di, Han, Dittmann, Meike, Doria-Rose, Nicole A., Douek, Daniel C., Drosten, Christian, Edara, Venkata Viswanadh, Ellebedy, Ali, Fabrizio, Thomas P., Ferrari, Guido, Fischer, Will M., Florence, William C., Fouchier, Ron A.M., Franks, John, García-Sastre, Adolfo, Godzik, Adam, Gonzalez-Reiche, Ana Silvia, Gordon, Aubree, Haagmans, Bart L., Halfmann, Peter J., Ho, David D., Holbrook, Michael R., Huang, Yaoxing, James, Sarah L., Jaroszewski, Lukasz, Jeevan, Trushar, Johnson, Robert M., Jones, Terry C., Joshi, Astha, Kawaoka, Yoshihiro, Kercher, Lisa, Koopmans, Marion P.G., Korber, Bette, Koren, Eilay, Koup, Richard A., LeGresley, Eric B., Lemieux, Jacob E., Liebeskind, Mariel J., Liu, Zhuoming, Livingston, Brandi, Logue, James P., Luo, Yang, McDermott, Adrian B., McElrath, Margaret J., Meliopoulos, Victoria A., Menachery, Vineet D., Montefiori, David C., Mühlemann, Barbara, Munster, Vincent J., Munt, Jenny E., Nair, Manoj S., Netzl, Antonia, Niewiadomska, Anna M., O’Dell, Sijy, Pekosz, Andrew, Perlman, Stanley, Pontelli, Marjorie C., Rockx, Barry, Rolland, Morgane, Rothlauf, Paul W., Sacharen, Sinai, Scheuermann, Richard H., Schmidt, Stephen D., Schotsaert, Michael, Schultz-Cherry, Stacey, Seder, Robert A., Sedova, Mayya, Sette, Alessandro, Shabman, Reed S., Shen, Xiaoying, Shi, Pei Yong, Shukla, Maulik, Simon, Viviana, Stumpf, Spencer, Sullivan, Nancy J., Thackray, Larissa B., Theiler, James, Thomas, Paul G., Trifkovic, Sanja, Türeli, Sina, Turner, Samuel A., Vakaki, Maria A., van Bakel, Harm, VanBlargan, Laura A., Vincent, Leah R., Wallace, Zachary S., Wang, Li, Wang, Maple, Wang, Pengfei, Wang, Wei, Weaver, Scott C., Webby, Richard J., Weiss, Carol D., Wentworth, David E., Weston, Stuart M., Whelan, Sean P.J., Whitener, Bradley M., Wilks, Samuel H., Xie, Xuping, Ying, Baoling, Yoon, Hyejin, Zhou, Bin, Hertz, Tomer, Smith, Derek J., Diamond, Michael S., Post, Diane J., Suthar, Mehul S., DeGrace, Marciela M., Ghedin, Elodie, Frieman, Matthew B., Krammer, Florian, Grifoni, Alba, Alisoltani, Arghavan, Alter, Galit, Amara, Rama R., Baric, Ralph S., Barouch, Dan H., Bloom, Jesse D., Bloyet, Louis Marie, Bonenfant, Gaston, Boon, Adrianus C.M., Boritz, Eli A., Bratt, Debbie L., Bricker, Traci L., Brown, Liliana, Buchser, William J., Carreño, Juan Manuel, Cohen-Lavi, Liel, Darling, Tamarand L., Davis-Gardner, Meredith E., Dearlove, Bethany L., Di, Han, Dittmann, Meike, Doria-Rose, Nicole A., Douek, Daniel C., Drosten, Christian, Edara, Venkata Viswanadh, Ellebedy, Ali, Fabrizio, Thomas P., Ferrari, Guido, Fischer, Will M., Florence, William C., Fouchier, Ron A.M., Franks, John, García-Sastre, Adolfo, Godzik, Adam, Gonzalez-Reiche, Ana Silvia, Gordon, Aubree, Haagmans, Bart L., Halfmann, Peter J., Ho, David D., Holbrook, Michael R., Huang, Yaoxing, James, Sarah L., Jaroszewski, Lukasz, Jeevan, Trushar, Johnson, Robert M., Jones, Terry C., Joshi, Astha, Kawaoka, Yoshihiro, Kercher, Lisa, Koopmans, Marion P.G., Korber, Bette, Koren, Eilay, Koup, Richard A., LeGresley, Eric B., Lemieux, Jacob E., Liebeskind, Mariel J., Liu, Zhuoming, Livingston, Brandi, Logue, James P., Luo, Yang, McDermott, Adrian B., McElrath, Margaret J., Meliopoulos, Victoria A., Menachery, Vineet D., Montefiori, David C., Mühlemann, Barbara, Munster, Vincent J., Munt, Jenny E., Nair, Manoj S., Netzl, Antonia, Niewiadomska, Anna M., O’Dell, Sijy, Pekosz, Andrew, Perlman, Stanley, Pontelli, Marjorie C., Rockx, Barry, Rolland, Morgane, Rothlauf, Paul W., Sacharen, Sinai, Scheuermann, Richard H., Schmidt, Stephen D., Schotsaert, Michael, Schultz-Cherry, Stacey, Seder, Robert A., Sedova, Mayya, Sette, Alessandro, Shabman, Reed S., Shen, Xiaoying, Shi, Pei Yong, Shukla, Maulik, Simon, Viviana, Stumpf, Spencer, Sullivan, Nancy J., Thackray, Larissa B., Theiler, James, Thomas, Paul G., Trifkovic, Sanja, Türeli, Sina, Turner, Samuel A., Vakaki, Maria A., van Bakel, Harm, VanBlargan, Laura A., Vincent, Leah R., Wallace, Zachary S., Wang, Li, Wang, Maple, Wang, Pengfei, Wang, Wei, Weaver, Scott C., Webby, Richard J., Weiss, Carol D., Wentworth, David E., Weston, Stuart M., Whelan, Sean P.J., Whitener, Bradley M., Wilks, Samuel H., Xie, Xuping, Ying, Baoling, Yoon, Hyejin, Zhou, Bin, Hertz, Tomer, Smith, Derek J., Diamond, Michael S., Post, Diane J., and Suthar, Mehul S.

Abstract

The global emergence of many severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants jeopardizes the protective antiviral immunity induced after infection or vaccination. To address the public health threat caused by the increasing SARS-CoV-2 genomic diversity, the National Institute of Allergy and Infectious Diseases within the National Institutes of Health established the SARS-CoV-2 Assessment of Viral Evolution (SAVE) programme. This effort was designed to provide a real-time risk assessment of SARS-CoV-2 variants that could potentially affect the transmission, virulence, and resistance to infection- and vaccine-induced immunity. The SAVE programme is a critical data-generating component of the US Government SARS-CoV-2 Interagency Group to assess implications of SARS-CoV-2 variants on diagnostics, vaccines and therapeutics, and for communicating public health risk. Here we describe the coordinated approach used to identify and curate data about emerging variants, their impact on immunity and effects on vaccine protection using animal models. We report the development of reagents, methodologies, models and notable findings facilitated by this collaborative approach and identify future challenges. This programme is a template for the response to rapidly evolving pathogens with pandemic potential by monitoring viral evolution in the human population to identify variants that could reduce the effectiveness of countermeasures.

Published
2022

22. Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients

Author

Carreño, Juan Manuel, primary, Alshammary, Hala, additional, Singh, Gagandeep, additional, Raskin, Ariel, additional, Amanat, Fatima, additional, Amoako, Angela, additional, Gonzalez-Reiche, Ana Silvia, additional, van de Guchte, Adriana, additional, study group, PARIS, additional, Srivastava, Komal, additional, Sordillo, Emilia Mia, additional, Sather, D. Noah, additional, van Bakel, Harm, additional, Krammer, Florian, additional, and Simon, Viviana, additional

Published
2021
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24. Improved detection of influenza A virus from blue‐winged teals by sequencing directly from swab material

Author

Ferreri, Lucas M., primary, Ortiz, Lucia, additional, Geiger, Ginger, additional, Barriga, Gonzalo P., additional, Poulson, Rebecca, additional, Gonzalez‐Reiche, Ana Silvia, additional, Crum, Jo Anne, additional, Stallknecht, David, additional, Moran, David, additional, Cordon‐Rosales, Celia, additional, Rajao, Daniela, additional, and Perez, Daniel R., additional

Published
2019
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25. Homologous and heterologous protection against influenza B virus following live attenuated influenza virus (LAIV) immunization

Author

Santos, Jefferson, primary, Finch, Courtney, additional, Sutton, Troy, additional, Obadan, Adebimpe, additional, Aguirre, Isabel, additional, Wan, Zhimin, additional, Lopez, Diego, additional, Geiger, Ginger, additional, Gonzalez-Reiche, Ana Silvia, additional, Ferreri, Lucas, additional, and Perez, Daniel R., additional

Published
2018
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26. Development of an Alternative Modified Live Influenza B Virus Vaccine

Author

Santos, Jefferson J. S., primary, Finch, Courtney, additional, Sutton, Troy, additional, Obadan, Adebimpe, additional, Aguirre, Isabel, additional, Wan, Zhimin, additional, Lopez, Diego, additional, Geiger, Ginger, additional, Gonzalez-Reiche, Ana Silvia, additional, Ferreri, Lucas, additional, and Perez, Daniel R., additional

Published
2017
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27. Ecology and Molecular Epidemiology of Avian and Swine Influenza A viruses in Guatemala

Author

Gonzalez Reiche, Ana Silvia

Subjects
low pathogenicity influenza virus, Animal diseases, swine influenza, Virology, Veterinary medicine, zoonosis, molecular epidemiology, wild birds, influenza virus
Abstract

The greatest diversity of Influenza A viruses (IAV) is found in waterfowl species from numerous geographic locations. In addition, multiple IAV are, and continue to be, perpetuated in swine populations around the globe. Due to the zoonotic potential of IAV and to respond more effectively to potential agricultural and public health threats, there is a need to increase surveillance in avian and swine hosts in understudied geographical regions. In Latin America, avian influenza surveillance has been scarce, localized only to places where outbreaks in poultry have occurred. Similarly, active swine influenza surveillance was implemented only after the emergence of the 2009 pandemic strain (pH1N1). The project presented here was aimed at investigating the circulation of IAV in wild birds and pigs in Guatemala. Over 2200 birds were sampled during six consecutive migration seasons from 2007 to 2013 in different locations. Virus prevalence detected by rRT-PCR in positive species ranged from 5.2% to 38%. Preliminary data indicates temporal variation of IAV prevalence in migratory waterfowl. Eighty-three viruses were recovered with 22 different subtype combinations. Through phylogenetic inferences and the analysis of virus genotypes and gene constellations of 60 fully sequenced genomes, we provide a detailed description of the genetic structure of avian IAV circulating in Guatemala. Our results suggest that the virus diversity in this location is sourced from multiple migration flyways from North America. Overlap of these flyways, in a natural geographical bottleneck such as the Neotropics, may contribute to the patterns of extensive genetic reassortment observed at a continental scale. In addition, the results from two nationwide multistage random surveys in pigs demonstrated circulation of swine influenza in commercial and peridomestic herds in Guatemala. Herd prevalence of IAV was 36.3% in 2010 and 34.6% in 2011. Viruses of the H1N1 and H3N2 subtypes and antibodies against viruses of distinct genetic lineages of these subtypes were detected. Our results indicate that human-animal contact likely plays a role in the IAV epidemiology in local swine populations. The findings from this research constitute the most abundant data on the ecology and epidemiology of animal influenza currently available for Central America.

Published
2015
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30. Defining the risk of SARS-CoV-2 variants on immune protection

Author

Marciela M. DeGrace, Elodie Ghedin, Matthew B. Frieman, Florian Krammer, Alba Grifoni, Arghavan Alisoltani, Galit Alter, Rama R. Amara, Ralph S. Baric, Dan H. Barouch, Jesse D. Bloom, Louis-Marie Bloyet, Gaston Bonenfant, Adrianus C. M. Boon, Eli A. Boritz, Debbie L. Bratt, Traci L. Bricker, Liliana Brown, William J. Buchser, Juan Manuel Carreño, Liel Cohen-Lavi, Tamarand L. Darling, Meredith E. Davis-Gardner, Bethany L. Dearlove, Han Di, Meike Dittmann, Nicole A. Doria-Rose, Daniel C. Douek, Christian Drosten, Venkata-Viswanadh Edara, Ali Ellebedy, Thomas P. Fabrizio, Guido Ferrari, Will M. Fischer, William C. Florence, Ron A. M. Fouchier, John Franks, Adolfo García-Sastre, Adam Godzik, Ana Silvia Gonzalez-Reiche, Aubree Gordon, Bart L. Haagmans, Peter J. Halfmann, David D. Ho, Michael R. Holbrook, Yaoxing Huang, Sarah L. James, Lukasz Jaroszewski, Trushar Jeevan, Robert M. Johnson, Terry C. Jones, Astha Joshi, Yoshihiro Kawaoka, Lisa Kercher, Marion P. G. Koopmans, Bette Korber, Eilay Koren, Richard A. Koup, Eric B. LeGresley, Jacob E. Lemieux, Mariel J. Liebeskind, Zhuoming Liu, Brandi Livingston, James P. Logue, Yang Luo, Adrian B. McDermott, Margaret J. McElrath, Victoria A. Meliopoulos, Vineet D. Menachery, David C. Montefiori, Barbara Mühlemann, Vincent J. Munster, Jenny E. Munt, Manoj S. Nair, Antonia Netzl, Anna M. Niewiadomska, Sijy O’Dell, Andrew Pekosz, Stanley Perlman, Marjorie C. Pontelli, Barry Rockx, Morgane Rolland, Paul W. Rothlauf, Sinai Sacharen, Richard H. Scheuermann, Stephen D. Schmidt, Michael Schotsaert, Stacey Schultz-Cherry, Robert A. Seder, Mayya Sedova, Alessandro Sette, Reed S. Shabman, Xiaoying Shen, Pei-Yong Shi, Maulik Shukla, Viviana Simon, Spencer Stumpf, Nancy J. Sullivan, Larissa B. Thackray, James Theiler, Paul G. Thomas, Sanja Trifkovic, Sina Türeli, Samuel A. Turner, Maria A. Vakaki, Harm van Bakel, Laura A. VanBlargan, Leah R. Vincent, Zachary S. Wallace, Li Wang, Maple Wang, Pengfei Wang, Wei Wang, Scott C. Weaver, Richard J. Webby, Carol D. Weiss, David E. Wentworth, Stuart M. Weston, Sean P. J. Whelan, Bradley M. Whitener, Samuel H. Wilks, Xuping Xie, Baoling Ying, Hyejin Yoon, Bin Zhou, Tomer Hertz, Derek J. Smith, Michael S. Diamond, Diane J. Post, Mehul S. Suthar, Ghedin, Elodie [0000-0002-1515-725X], Frieman, Matthew B [0000-0003-0107-0775], Krammer, Florian [0000-0003-4121-776X], Grifoni, Alba [0000-0002-2209-5966], Alter, Galit [0000-0002-7680-9215], Amara, Rama R [0000-0002-6309-6797], Baric, Ralph S [0000-0001-6827-8701], Barouch, Dan H [0000-0001-5127-4659], Bloom, Jesse D [0000-0003-1267-3408], Bloyet, Louis-Marie [0000-0002-5648-3190], Boon, Adrianus CM [0000-0002-4700-8224], Bratt, Debbie L [0000-0002-5822-5558], Buchser, William J [0000-0002-6675-6359], Cohen-Lavi, Liel [0000-0001-6909-4779], Dearlove, Bethany L [0000-0003-3653-4592], Drosten, Christian [0000-0001-7923-0519], Edara, Venkata-Viswanadh [0000-0001-9321-7839], Ellebedy, Ali [0000-0002-6129-2532], Fabrizio, Thomas P [0000-0002-8960-0728], Fouchier, Ron AM [0000-0001-8095-2869], García-Sastre, Adolfo [0000-0002-6551-1827], Godzik, Adam [0000-0002-2425-852X], Gonzalez-Reiche, Ana Silvia [0000-0003-3583-4497], Gordon, Aubree [0000-0002-9352-7877], Haagmans, Bart L [0000-0001-6221-2015], Ho, David D [0000-0003-1627-149X], Holbrook, Michael R [0000-0002-0824-2667], Huang, Yaoxing [0000-0001-6270-1644], James, Sarah L [0000-0002-6969-1167], Johnson, Robert M [0000-0002-1976-7688], Jones, Terry C [0000-0003-1120-9531], Joshi, Astha [0000-0003-4914-8228], Kawaoka, Yoshihiro [0000-0001-5061-8296], Kercher, Lisa [0000-0001-6300-0452], Koopmans, Marion PG [0000-0002-5204-2312], Korber, Bette [0000-0002-2026-5757], LeGresley, Eric B [0000-0002-5286-5693], Liebeskind, Mariel J [0000-0003-4595-0651], Liu, Zhuoming [0000-0001-8198-0976], Logue, James P [0000-0002-7410-9741], Luo, Yang [0000-0003-3277-8792], McDermott, Adrian B [0000-0003-0616-9117], Meliopoulos, Victoria A [0000-0003-1442-9177], Menachery, Vineet D [0000-0001-8803-7606], Munster, Vincent J [0000-0002-2288-3196], Nair, Manoj S [0000-0002-5994-3957], Netzl, Antonia [0000-0001-8034-2382], Pekosz, Andrew [0000-0003-3248-1761], Perlman, Stanley [0000-0003-4213-2354], Rockx, Barry [0000-0003-2463-027X], Rolland, Morgane [0000-0003-3650-8490], Rothlauf, Paul W [0000-0002-0941-4467], Scheuermann, Richard H [0000-0003-1355-892X], Schotsaert, Michael [0000-0003-3156-3132], Schultz-Cherry, Stacey [0000-0002-2021-727X], Seder, Robert A [0000-0003-3133-0849], Shabman, Reed S [0000-0003-3272-3484], Shi, Pei-Yong [0000-0001-5553-1616], Simon, Viviana [0000-0002-6416-5096], Thackray, Larissa B [0000-0002-9380-6569], Thomas, Paul G [0000-0001-7955-0256], Trifkovic, Sanja [0000-0002-0710-9514], Türeli, Sina [0000-0001-7342-9295], van Bakel, Harm [0000-0002-1376-6916], VanBlargan, Laura A [0000-0002-8922-8946], Vincent, Leah R [0000-0001-9262-1813], Wallace, Zachary S [0000-0003-0237-501X], Wang, Pengfei [0000-0003-2454-7652], Weaver, Scott C [0000-0001-8016-8556], Webby, Richard J [0000-0002-4397-7132], Weiss, Carol D [0000-0002-9965-1289], Wentworth, David E [0000-0002-5190-980X], Weston, Stuart M [0000-0001-9840-2953], Whelan, Sean PJ [0000-0003-1564-8590], Whitener, Bradley M [0000-0001-6652-0701], Xie, Xuping [0000-0003-0918-016X], Yoon, Hyejin [0000-0002-3344-9096], Hertz, Tomer [0000-0002-0561-1578], Smith, Derek J [0000-0002-2393-1890], Diamond, Michael S [0000-0002-8791-3165], Post, Diane J [0000-0003-3890-9116], Suthar, Mehul S [0000-0002-2686-8380], and Apollo - University of Cambridge Repository

Subjects
Multidisciplinary, COVID-19 Vaccines, Pharmacogenomic Variants, Virulence, SARS-CoV-2, COVID-19, Biological Evolution, Article, United States, SDG 3 - Good Health and Well-being, National Institute of Allergy and Infectious Diseases (U.S.), Animals, Humans, Pandemics
Abstract

The global emergence of many severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants jeopardizes the protective antiviral immunity induced following infection or vaccination. To address the public health threat caused by the increasing SARS-CoV-2 genomic diversity, the National Institute of Allergy and Infectious Diseases (NIAID) within the National Institutes of Health (NIH) established the SARS-CoV-2 Assessment of Viral Evolution (SAVE) program. This effort was designed to provide a real-time risk assessment of SARS-CoV-2 variants potentially impacting transmission, virulence, and resistance to convalescent and vaccine-induced immunity. The SAVE program serves as a critical data-generating component of the United States Government SARS-CoV-2 Interagency Group to assess implications of SARS-CoV-2 variants on diagnostics, vaccines, and therapeutics and for communicating public health risk. Here we describe the coordinated approach used to identify and curate data about emerging variants, their impact on immunity, and effects on vaccine protection using animal models. We report the development of reagents, methodologies, models, and pivotal findings facilitated by this collaborative approach and identify future challenges. This program serves as a template for the response against rapidly evolving pandemic pathogens by monitoring viral evolution in the human population to identify variants that could erode the effectiveness of countermeasures.

Published
2022

31. Plasmid-Based Reverse Genetics of Influenza A Virus.

Author

Perez DR, Angel M, Gonzalez-Reiche AS, Santos J, Obadan A, and Martinez-Sobrido L

Subjects
Animals, Cell Line, Cloning, Molecular, DNA, Complementary, Gene Expression, Genetic Vectors genetics, Genome, Viral, Humans, RNA, Viral, Recombination, Genetic, Transfection, Virus Replication, Influenza A virus genetics, Plasmids genetics, Reverse Genetics methods
Abstract

Influenza A viruses have broad host range with a recognized natural reservoir in wild aquatic birds. From this reservoir, novel strains occasionally emerge with the potential to establish stable lineages in other avian and mammalian species, including humans. Understanding the molecular changes that allow influenza A viruses to change host range is essential to better assess their animal and public health risks. Reverse genetics systems have transformed the ability to manipulate and study negative strand RNA viruses. In the particular case of influenza A viruses, plasmid-based reverse genetics approaches have allowed for a better understanding of, among others, virulence, transmission, mechanisms of antiviral resistance, and the development of alternative vaccines and vaccination strategies. In this chapter we describe the cloning of cDNA copies of viral RNA segments derived from a type A influenza virus into reverse genetics plasmid vectors and the experimental procedures for the successful generation of recombinant influenza A viruses.

Published
2017
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