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1. 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

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, Influenza, Biodefense, Emerging Infectious Diseases, Pneumonia & Influenza, 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. 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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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. Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder

Author

Gandal, Michael J, Zhang, Pan, Hadjimichael, Evi, Walker, Rebecca L, Chen, Chao, Liu, Shuang, Won, Hyejung, van Bakel, Harm, Varghese, Merina, Wang, Yongjun, Shieh, Annie W, Haney, Jillian, Parhami, Sepideh, Belmont, Judson, Kim, Minsoo, Moran Losada, Patricia, Khan, Zenab, Mleczko, Justyna, Xia, Yan, Dai, Rujia, Wang, Daifeng, Yang, Yucheng T, Xu, Min, Fish, Kenneth, Hof, Patrick R, Warrell, Jonathan, Fitzgerald, Dominic, White, Kevin, Jaffe, Andrew E, Peters, Mette A, Gerstein, Mark, Liu, Chunyu, Iakoucheva, Lilia M, Pinto, Dalila, Geschwind, Daniel H, Ashley-Koch, Allison E, Crawford, Gregory E, Garrett, Melanie E, Song, Lingyun, Safi, Alexias, Johnson, Graham D, Wray, Gregory A, Reddy, Timothy E, Goes, Fernando S, Zandi, Peter, Bryois, Julien, Price, Amanda J, Ivanov, Nikolay A, Collado-Torres, Leonardo, Hyde, Thomas M, Burke, Emily E, Kleiman, Joel E, Tao, Ran, Shin, Joo Heon, Akbarian, Schahram, Girdhar, Kiran, Jiang, Yan, Kundakovic, Marija, Brown, Leanne, Kassim, Bibi S, Park, Royce B, Wiseman, Jennifer R, Zharovsky, Elizabeth, Jacobov, Rivka, Devillers, Olivia, Flatow, Elie, Hoffman, Gabriel E, Lipska, Barbara K, Lewis, David A, Haroutunian, Vahram, Hahn, Chang-Gyu, Charney, Alexander W, Dracheva, Stella, Kozlenkov, Alexey, DelValle, Diane, Francoeur, Nancy, Roussos, Panos, Fullard, John F, Bendl, Jaroslav, Hauberg, Mads E, Mangravite, Lara M, Chae, Yooree, Peng, Junmin, Niu, Mingming, Wang, Xusheng, Webster, Maree J, Beach, Thomas G, Jiang, Yi, and Grennan, Kay S

Subjects
Pharmacology and Pharmaceutical Sciences, Biological Sciences, Biomedical and Clinical Sciences, Genetics, Neurosciences, Intellectual and Developmental Disabilities (IDD), Brain Disorders, Mental Illness, Bipolar Disorder, Mental Health, Schizophrenia, Biotechnology, Serious Mental Illness, Autism, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Mental health, Good Health and Well Being, Autism Spectrum Disorder, Brain, Genetic Predisposition to Disease, Humans, Protein Isoforms, RNA Splicing, Sequence Analysis, RNA, Transcriptome, PsychENCODE Consortium, General Science & Technology
Abstract

Most genetic risk for psychiatric disease lies in regulatory regions, implicating pathogenic dysregulation of gene expression and splicing. However, comprehensive assessments of transcriptomic organization in diseased brains are limited. In this work, we integrated genotypes and RNA sequencing in brain samples from 1695 individuals with autism spectrum disorder (ASD), schizophrenia, and bipolar disorder, as well as controls. More than 25% of the transcriptome exhibits differential splicing or expression, with isoform-level changes capturing the largest disease effects and genetic enrichments. Coexpression networks isolate disease-specific neuronal alterations, as well as microglial, astrocyte, and interferon-response modules defining previously unidentified neural-immune mechanisms. We integrated genetic and genomic data to perform a transcriptome-wide association study, prioritizing disease loci likely mediated by cis effects on brain expression. This transcriptome-wide characterization of the molecular pathology across three major psychiatric disorders provides a comprehensive resource for mechanistic insight and therapeutic development.

Published
2018

6. 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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7. 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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8. 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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11. 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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12. Molecular evidence of SARS-CoV-2 in New York before the first pandemic wave

Author

Hernandez, Matthew M., Gonzalez-Reiche, Ana S., Alshammary, Hala, Fabre, Shelcie, Khan, Zenab, van De Guchte, Adriana, Obla, Ajay, Ellis, Ethan, Sullivan, Mitchell J., Tan, Jessica, Alburquerque, Bremy, Soto, Juan, Wang, Ching-Yi, Sridhar, Shwetha Hara, Wang, Ying-Chih, Smith, Melissa, Sebra, Robert, Paniz-Mondolfi, Alberto E., Gitman, Melissa R., Nowak, Michael D., Cordon-Cardo, Carlos, Luksza, Marta, Krammer, Florian, van Bakel, Harm, Simon, Viviana, and Sordillo, Emilia Mia

Published
2021
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13. Limited intestinal inflammation despite diarrhea, fecal viral RNA and SARS-CoV-2-specific IgA in patients with acute COVID-19

Author

Britton, Graham J., Chen-Liaw, Alice, Cossarini, Francesca, Livanos, Alexandra E., Spindler, Matthew P., Plitt, Tamar, Eggers, Joseph, Mogno, Ilaria, Gonzalez-Reiche, Ana S., Siu, Sophia, Tankelevich, Michael, Grinspan, Lauren Tal, Dixon, Rebekah E., Jha, Divya, van de Guchte, Adriana, Khan, Zenab, Martinez-Delgado, Gustavo, Amanat, Fatima, Hoagland, Daisy A., tenOever, Benjamin R., Dubinsky, Marla C., Merad, Miriam, van Bakel, Harm, Krammer, Florian, Bongers, Gerold, Mehandru, Saurabh, and Faith, Jeremiah J.

Published
2021
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17. 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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18. 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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19. Robust clinical detection of SARS‐CoV‐2 variants by RT‐PCR/MALDI‐TOF multitarget approach

Author

Hernandez, Matthew M., primary, Banu, Radhika, additional, Gonzalez‐Reiche, Ana S., additional, Guchte, Adriana, additional, Khan, Zenab, additional, Shrestha, Paras, additional, Cao, Liyong, additional, Chen, Feng, additional, Shi, Huanzhi, additional, Hanna, Ayman, additional, Alshammary, Hala, additional, Fabre, Shelcie, additional, Amoako, Angela, additional, Obla, Ajay, additional, Alburquerque, Bremy, additional, Patiño, Luz Helena, additional, Ramírez, Juan David, additional, Sebra, Robert, additional, Gitman, Melissa R., additional, Nowak, Michael D., additional, Cordon‐Cardo, Carlos, additional, Schutzbank, Ted E., additional, Simon, Viviana, additional, Bakel, Harm, additional, Sordillo, Emilia Mia, additional, and Paniz‐Mondolfi, Alberto E., additional

Published
2021
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21. Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multi-target approach

Author

Hernandez, Matthew M., primary, Banu, Radhika, additional, Gonzalez-Reiche, Ana S., additional, van de Guchte, Adriana, additional, Khan, Zenab, additional, Shrestha, Paras, additional, Cao, Liyong, additional, Chen, Feng, additional, Shi, Huanzhi, additional, Hanna, Ayman, additional, Alshammary, Hala, additional, Fabre, Shelcie, additional, Amoako, Angela, additional, Obla, Ajay, additional, Alburquerque, Bremy, additional, Helena Patiño, Luz, additional, Ramírez, Juan David, additional, Sebra, Robert, additional, Gitman, Melissa R., additional, Nowak, Michael D., additional, Cordon-Cardo, Carlos, additional, Schutzbank, Ted E., additional, Simon, Viviana, additional, van Bakel, Harm, additional, Sordillo, Emilia M., additional, and Paniz Mondolfi, Alberto E., additional

Published
2021
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22. Evolution of influenza A virus in intensive and free-range swine farms in Spain

Author

National Institute of Allergy and Infectious Diseases (US), Center for Research for Influenza Pathogenesis (US), Centers of Excellence for Influenza Research and Surveillance (US), Center of Excellence for Influenza Research and Response (US), Encinas, Paloma [0000-0001-9596-8070], Del Real Soldevilla, Gustavo [0000-0002-8171-2274], García-Sastre, Adolfo [0000-0002-6551-1827], Encinas, Paloma, Del Real Soldevilla, Gustavo, Dutta, Jayeeta, Khan, Zenab, van Bakel, Harm, Martín del Burgo, M. Ángeles, García-Sastre, Adolfo, Nelson, Martha, National Institute of Allergy and Infectious Diseases (US), Center for Research for Influenza Pathogenesis (US), Centers of Excellence for Influenza Research and Surveillance (US), Center of Excellence for Influenza Research and Response (US), Encinas, Paloma [0000-0001-9596-8070], Del Real Soldevilla, Gustavo [0000-0002-8171-2274], García-Sastre, Adolfo [0000-0002-6551-1827], Encinas, Paloma, Del Real Soldevilla, Gustavo, Dutta, Jayeeta, Khan, Zenab, van Bakel, Harm, Martín del Burgo, M. Ángeles, García-Sastre, Adolfo, and Nelson, Martha

Abstract

Swine harbor genetically diverse influenza A viruses (IAVs) with the capacity to host-switch to humans, causing global pandemics. Spain is the largest swine producer in Europe and has a mixed production system that includes 'white coat' pigs raised intensively in modern buildings and free-range Iberian pigs that interface differently with humans, wildlife, and other swine. Through active longitudinal IAV surveillance in nine Spanish provinces during 2015-9, we generated forty-seven complete or near-complete genome sequences from IAVs collected from swine in both systems. Genetically diverse IAVs were identified in intensively raised white pigs and free-range Iberian pigs, including new H3N1 reassortants. Both systems are dynamic environments for IAV evolution, but driven by different processes. IAVs in white pigs were genetically related to viruses found in swine raised intensively in other European countries, reflecting high rates of viral introduction following European trade routes. In contrast, IAVs in Iberian pigs have a genetic makeup shaped by frequent introductions of human IAVs, reflecting rearing practices with high rates of human contact. Transmission between white and Iberian pigs also occurred. In conclusion, Iberian swine with high rates of human contact harbor genetically diverse IAVs and potentially serve as intermediary hosts between white pigs and humans, presenting an understudied zoonotic risk that requires further investigation.

Published
2021

23. 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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24. Before the Surge: Molecular Evidence of SARS-CoV-2 in New York City Prior to the First Report

Author

Hernandez, Matthew M., primary, Gonzalez-Reiche, Ana S., additional, Alshammary, Hala, additional, Fabre, Shelcie, additional, Khan, Zenab, additional, van De Guchte, Adriana, additional, Obla, Ajay, additional, Ellis, Ethan, additional, Sullivan, Mitchell J., additional, Tan, Jessica, additional, Alburquerque, Bremy, additional, Soto, Juan, additional, Wang, Ching-Yi, additional, Sridhar, Shwetha Hara, additional, Wang, Ying-Chih, additional, Smith, Melissa, additional, Sebra, Robert, additional, Paniz-Mondolfi, Alberto E., additional, Gitman, Melissa R., additional, Nowak, Michael D., additional, Cordon-Cardo, Carlos, additional, Luksza, Marta, additional, Krammer, Florian, additional, van Bakel, Harm, additional, Simon, Viviana, additional, and Sordillo, Emilia Mia, additional

Published
2021
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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
2021
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26. Robust clinical detection of SARS‐CoV‐2 variants by RT‐PCR/MALDI‐TOF multitarget approach.

Author

Hernandez, Matthew M., Banu, Radhika, Gonzalez‐Reiche, Ana S., van de Guchte, Adriana, Khan, Zenab, Shrestha, Paras, Cao, Liyong, Chen, Feng, Shi, Huanzhi, Hanna, Ayman, Alshammary, Hala, Fabre, Shelcie, Amoako, Angela, Obla, Ajay, Alburquerque, Bremy, Patiño, Luz Helena, Ramírez, Juan David, Sebra, Robert, Gitman, Melissa R., and Nowak, Michael D.

Subjects
SARS-CoV-2, COVID-19
Abstract

The coronavirus disease 2019 (COVID‐19) pandemic has sparked the rapid development of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) diagnostics. However, emerging variants pose the risk for target dropout and false‐negative results secondary to primer/probe binding site (PBS) mismatches. The Agena MassARRAY® SARS‐CoV‐2 Panel combines reverse‐transcription polymerase chain reaction and matrix‐assisted laser desorption/ionization time‐of‐flight mass‐spectrometry to probe for five targets across N and ORF1ab genes, which provides a robust platform to accommodate PBS mismatches in divergent viruses. Herein, we utilize a deidentified data set of 1262 SARS‐CoV‐2‐positive specimens from Mount Sinai Health System (New York City) from December 2020 to April 2021 to evaluate target results and corresponding sequencing data. Overall, the level of PBS mismatches was greater in specimens with target dropout. Of specimens with N3 target dropout, 57% harbored an A28095T substitution that is highly specific for the Alpha (B.1.1.7) variant of concern. These data highlight the benefit of redundancy in target design and the potential for target performance to illuminate the dynamics of circulating SARS‐CoV‐2 variants. Highlights: SARS‐CoV‐2 variation introduces mismatches at diagnostic primer/probe sites.A multi‐target RT‐PCR/MALDI‐TOF assay captures emergent variants in NYC patients.Paired sequencing data reveals the Alpha‐specific A28095T causes target dropout.Diagnostic target performance illuminates dynamics of circulating SARS‐CoV‐2. [ABSTRACT FROM AUTHOR]

Published
2022
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27. 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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28. 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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29. Real-Time Investigation of a Large Nosocomial Influenza A Outbreak Informed by Genomic Epidemiology

Author

Javaid, Waleed, primary, Ehni, Jordan, additional, Gonzalez-Reiche, Ana S, additional, Carreño, Juan Manuel, additional, Hirsch, Elena, additional, Tan, Jessica, additional, Khan, Zenab, additional, Kriti, Divya, additional, Ly, Thanh, additional, Kranitzky, Bethany, additional, Barnett, Barbara, additional, Cera, Freddy, additional, Prespa, Lenny, additional, Moss, Marie, additional, Albrecht, Randy A, additional, Mustafa, Ala, additional, Herbison, Ilka, additional, Hernandez, Matthew M, additional, Pak, Theodore R, additional, Alshammary, Hala A, additional, Sebra, Robert, additional, Smith, Melissa L, additional, Krammer, Florian, additional, Gitman, Melissa R, additional, Sordillo, Emilia Mia, additional, Simon, Viviana, additional, and van Bakel, Harm, additional

Published
2020
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30. 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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31. 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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32. 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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33. 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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36. Real-Time Investigation of a Large Nosocomial Influenza A Outbreak Informed by Genomic Epidemiology.

Author

Javaid, Waleed, Ehni, Jordan, Gonzalez-Reiche, Ana S, Carreño, Juan Manuel, Hirsch, Elena, Tan, Jessica, Khan, Zenab, Kriti, Divya, Ly, Thanh, Kranitzky, Bethany, Barnett, Barbara, Cera, Freddy, Prespa, Lenny, Moss, Marie, Albrecht, Randy A, Mustafa, Ala, Herbison, Ilka, Hernandez, Matthew M, Pak, Theodore R, and Alshammary, Hala A

Subjects
PREVENTION of infectious disease transmission, INFLUENZA prevention, INFLUENZA diagnosis, CROSS infection prevention, PREVENTION of epidemics, INFLUENZA epidemiology, PUBLIC health surveillance, INFLUENZA vaccines, INFLUENZA A virus, SEQUENCE analysis, IMMUNIZATION, PREVENTION of communicable diseases, CROSS infection, COMMUNITY health services, EPIDEMICS, GENOMICS, URBAN health, ELECTRONIC health records, ALLIED health personnel, DATA mining
Abstract

Background Nosocomial respiratory virus outbreaks represent serious public health challenges. Rapid and precise identification of cases and tracing of transmission chains is critical to end outbreaks and to inform prevention measures. Methods We combined conventional surveillance with influenza A virus (IAV) genome sequencing to identify and contain a large IAV outbreak in a metropolitan healthcare system. A total of 381 individuals, including 91 inpatients and 290 healthcare workers (HCWs), were included in the investigation. Results During a 12-day period in early 2019, infection preventionists identified 89 HCWs and 18 inpatients as cases of influenza-like illness (ILI), using an amended definition without the requirement for fever. Sequencing of IAV genomes from available nasopharyngeal specimens identified 66 individuals infected with a nearly identical strain of influenza A H1N1pdm09 (43 HCWs, 17 inpatients, and 6 with unspecified affiliation). All HCWs infected with the outbreak strain had received the seasonal influenza virus vaccination. Characterization of 5 representative outbreak viral isolates did not show antigenic drift. In conjunction with IAV genome sequencing, mining of electronic records pinpointed the origin of the outbreak as a single patient and a few interactions in the emergency department that occurred 1 day prior to the index ILI cluster. Conclusions We used precision surveillance to delineate a large nosocomial IAV outbreak, mapping the source of the outbreak to a single patient rather than HCWs as initially assumed based on conventional epidemiology. These findings have important ramifications for more-effective prevention strategies to curb nosocomial respiratory virus outbreaks. [ABSTRACT FROM AUTHOR]

Published
2021
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37. A Complete Genome Screening Program of Clinical Methicillin-Resistant Staphylococcus aureus Isolates Identifies the Origin and Progression of a Neonatal Intensive Care Unit Outbreak

Author

Sullivan, Mitchell J., primary, Altman, Deena R., additional, Chacko, Kieran I., additional, Ciferri, Brianne, additional, Webster, Elizabeth, additional, Pak, Theodore R., additional, Deikus, Gintaras, additional, Lewis-Sandari, Martha, additional, Khan, Zenab, additional, Beckford, Colleen, additional, Rendo, Angela, additional, Samaroo, Flora, additional, Sebra, Robert, additional, Karam-Howlin, Ramona, additional, Dingle, Tanis, additional, Hamula, Camille, additional, Bashir, Ali, additional, Schadt, Eric, additional, Patel, Gopi, additional, Wallach, Frances, additional, Kasarskis, Andrew, additional, Gibbs, Kathleen, additional, and van Bakel, Harm, additional

Published
2019
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38. 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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40. Complete genome screening of clinical MRSA isolates identifies lineage diversity and provides full resolution of transmission and outbreak events

Author

Sullivan, Mitchell J, primary, Altman, Deena R, additional, Chacko, Kieran I, additional, Ciferri, Brianne, additional, Webster, Elizabeth, additional, Pak, Theodore R., additional, Deikus, Gintaras, additional, Lewis-Sandari, Martha, additional, Khan, Zenab, additional, Beckford, Colleen, additional, Rendo, Angela, additional, Samaroo, Flora, additional, Sebra, Robert, additional, Karam-Howlin, Ramona, additional, Dingle, Tanis, additional, Hamula, Camille, additional, Bashir, Ali, additional, Schadt, Eric, additional, Patel, Gopi, additional, Wallach, Frances, additional, Kasarskis, Andrew, additional, Gibbs, Kathleen, additional, and van Bakel, Harm, additional

Published
2019
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41. Remote ischemic post-conditioning promotes hematoma resolution via AMPK-dependent immune regulation

Author

Vaibhav, Kumar, primary, Braun, Molly, additional, Khan, Mohammad Badruzzaman, additional, Fatima, Sumbul, additional, Saad, Nancy, additional, Shankar, Adarsh, additional, Khan, Zenab T., additional, Harris, Ruth B.S., additional, Yang, Qiuhua, additional, Huo, Yuqing, additional, Arbab, Ali S., additional, Giri, Shailendra, additional, Alleyne, Cargill H., additional, Vender, John R., additional, Hess, David C., additional, Baban, Babak, additional, Hoda, Md Nasrul, additional, and Dhandapani, Krishnan M., additional

Published
2018
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42. Closed Loop Supply Chain Under Consignment Stock Partnership

Author

Hariga, Moncer, As'ad, Rami, Khan, Zenab, Hariga, Moncer, As'ad, Rami, and Khan, Zenab

Abstract

A Master of Science thesis in Engineering Systems Management by Zenab Khan entitled, "Closed Loop Supply Chain Under Consignment Stock Partnership," submitted in May 2015. Thesis advisor is Dr. Moncer Hariga and thesis co-advisor is Dr. Rami As'ad. Soft and hard copy available., The emerging field of reverse logistics or closed loop supply chain management seeks to efficiently handle all the activities pertaining to the retrieval of products from end customers along with the proper reuse or disposal of those products. This thesis addresses a closed loop supply chain comprised of a single vendor and a single buyer operating under a consignment stock (CS) strategy. Following this sort of partnership, the buyer agrees to store the products at its premises where, in return, the payment for those products is made only after being sold to the end customer. We develop a mixed integer non-linear program that seeks to minimize the closed loop chain-wide total cost by jointly optimizing the length of the production cycle, the number and the sequence of the newly manufactured and the remanufactured batches, as well as the inventory levels of the finished and recovered products at the beginning of the cycle. Extensive numerical experiments are also conducted in order to assess the impact of key problem parameters on the behavior of the model. The results indicate that, for low values of the setup cost associated with newly manufactured batches, the vendor might be better off adopting intermittent schedules in which he would alternate between the production of new and remanufactured batches more than once. The economic merits of the generalized model are also assessed through calculating the cost percentage increase when adopting special production sequences such as consecutive remanufacturing batches followed by consecutive newly manufacturing batches, and other sequences with single manufactured or remanufactured batch., College of Engineering, Department of Industrial Engineering

Published
2016

44. Continuous Surveillance by Whole-Genome Sequencing to Identify and Manage Methicillin-Resistant Staphylococcus aureus Outbreaks

Author

Sullivan, Mitchell, primary, Altman, Deena, additional, Webster, Elizabeth, additional, Lewis, Martha, additional, Khan, Zenab, additional, Beckford, Colleen, additional, Ciferri, Brianne, additional, Deikus, Gintaras, additional, Rendo, Angela, additional, Samaroo, Flora, additional, Sebra, Robert, additional, Wallach, Fran, additional, Patel, Gopi, additional, Hamula, Camille, additional, Bashir, Ali, additional, Schadt, Eric, additional, Kasarskis, Andrew, additional, Gibbs, Kathleen, additional, and Van Bakel, Harm, additional

Published
2016
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45. A Complete Genome Screening Program of Clinical Methicillin-Resistant Staphylococcus aureusIsolates Identifies the Origin and Progression of a Neonatal Intensive Care Unit Outbreak

Author

Sullivan, Mitchell J., Altman, Deena R., Chacko, Kieran I., Ciferri, Brianne, Webster, Elizabeth, Pak, Theodore R., Deikus, Gintaras, Lewis-Sandari, Martha, Khan, Zenab, Beckford, Colleen, Rendo, Angela, Samaroo, Flora, Sebra, Robert, Karam-Howlin, Ramona, Dingle, Tanis, Hamula, Camille, Bashir, Ali, Schadt, Eric, Patel, Gopi, Wallach, Frances, Kasarskis, Andrew, Gibbs, Kathleen, and van Bakel, Harm

Abstract

Whole-genome sequencing (WGS) of Staphylococcus aureusis increasingly used as part of infection prevention practices. In this study, we established a long-read technology-based WGS screening program of all first-episode methicillin-resistant Staphylococcus aureus(MRSA) blood infections at a major urban hospital.

Published
2019
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46. 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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47. Limited intestinal inflammation despite diarrhea, fecal viral RNA and SARS-CoV-2-specific IgA in patients with acute COVID-19.

Author

Britton GJ, Chen-Liaw A, Cossarini F, Livanos AE, Spindler MP, Plitt T, Eggers J, Mogno I, Gonzalez-Reiche AS, Siu S, Tankelevich M, Grinspan LT, Dixon RE, Jha D, van de Guchte A, Khan Z, Martinez-Delgado G, Amanat F, Hoagland DA, tenOever BR, Dubinsky MC, Merad M, van Bakel H, Krammer F, Bongers G, Mehandru S, and Faith JJ

Abstract

We sought to characterize the role of the gastrointestinal immune system in the pathogenesis of the inflammatory response associated with COVID-19. We measured cytokines, inflammatory markers, viral RNA, microbiome composition and antibody responses in stool from a cohort of 44 hospitalized COVID-19 patients. SARS-CoV-2 RNA was detected in stool of 41% of patients and more frequently in patients with diarrhea. Patients who survived had lower fecal viral RNA than those who died. Strains isolated from stool and nasopharynx of an individual were the same. Compared to uninfected controls, COVID-19 patients had higher fecal levels of IL-8 and lower levels of fecal IL-10. Stool IL-23 was higher in patients with more severe COVID-19 disease, and we found evidence of intestinal virus-specific IgA responses associated with more severe disease. We provide evidence for an ongoing humeral immune response to SARS-CoV-2 in the gastrointestinal tract, but little evidence of overt inflammation., Competing Interests: Declaration of interests: M.C.D is a consultant for Abbvie, Arena, BMS, Boehringer Ingelheim, Genentech, Janssen, Pfizer, Prometheus Biosciences, Takeda, Target RWE and UCB, has received research support from Janssen, Pfizer, Prometheus Biosciences and Abbvie and is co-founder of Cornerstones Health, Mitest Health, Trellus Health, M.M. is a consultant for Takeda, Genentech, Regeneron, Compugen, Myeloid Therapeutics. F.K. declares that The Icahn School of Medicine at Mount Sinai has filed patent applications regarding SARS-CoV-2 serology assays and has licensed reagents to several commercial entities. J.J.F. serves on the scientific advisor board of Vedanta Biosciences. The remaining authors declare no competing of interest.

Published
2020
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