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1. Integrated Genomic and Social Network Analyses of SARS-CoV-2 Transmission in the Healthcare Setting

Author

Keehner, Jocelyn, Abeles, Shira R, Longhurst, Christopher A, Horton, Lucy E, Myers, Frank E, Riggs-Rodriguez, Lindsay, Ahmad, Mohammed, Baxter, Sally, Boussina, Aaron, Cantrell, Kalen, Cardenas, Priscilla, De Hoff, Peter, El-Kareh, Robert, Holland, Jennifer, Ikeda, Daryn, Kurashige, Kirk, Laurent, Louise C, Aigner, Stefan, Andersen, Kristian G, Anderson, Catelyn, Baer, Nathan A, Barber, Tom, Bauk, Marco, Beck, Jennifer N, Belda-Ferre, Pedro, Betty, Maryann, Birmingham, Amanda, Castro-Martinez, Anelizze, Cheung, Willi, Fisch, Kathleen M, Gangavarapu, Karthik, Gargano, Isabella, Hakim, Abbas, Harsono, Shania, Henson, Benjamin, Hobbs, Charlotte, Holmes, Jacqueline, Jepsen, Kristen, Knight, Rob, Kurzban, Ezra, Marotz, Clarisse A, Matteson, Nathaniel L, Moshiri, Niema, Ngo, Toan T, Ostrander, Tyler R, Perkins, Sarah, Plascencia, Ashley, Rivera, Andrea, Rivera, Ariana, Salido, Rodolfo A, Sathe, Shashank, Seaver, Phoebe, Schwab, Madison, Veder, Anthony, Yeo, Gene W, Zeller, Mark, Lucas, Andrew, Pride, David, Tran, Allen R, Vasylyeva, Tetyana I, Yeo, Gene, Wertheim, Joel O, and Torriani, Francesca J

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Pneumonia & Influenza, Clinical Research, Emerging Infectious Diseases, Infectious Diseases, Biodefense, Lung, Genetics, Vaccine Related, Prevention, Aetiology, 2.2 Factors relating to the physical environment, Infection, Good Health and Well Being, Humans, COVID-19, SARS-CoV-2, Retrospective Studies, Cross-Sectional Studies, Health Personnel, Male, Genome, Viral, Female, Adult, Middle Aged, Aged, Social Network Analysis, Contact Tracing, Genomics, Young Adult, Adolescent, Child, Aged, 80 and over, Cross Infection, Child, Preschool, SARS-CoV-2 pandemic, infection prevention precautions, healthcare transmission of SARS-CoV-2, whole-genome sequencing, social network analyses and contact tracing, SEARCH Alliance, Biological Sciences, Medical and Health Sciences, Microbiology, Clinical sciences
Abstract

BackgroundInfection prevention (IP) measures are designed to mitigate the transmission of pathogens in healthcare. Using large-scale viral genomic and social network analyses, we determined if IP measures used during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic were adequate in protecting healthcare workers (HCWs) and patients from acquiring SARS-CoV-2.MethodsWe performed retrospective cross-sectional analyses of viral genomics from all available SARS-CoV-2 viral samples collected at UC San Diego Health and social network analysis using the electronic medical record to derive temporospatial overlap of infections among related viromes and supplemented with contact tracing data. The outcome measure was any instance of healthcare transmission, defined as cases with closely related viral genomes and epidemiological connection within the healthcare setting during the infection window. Between November 2020 through January 2022, 12 933 viral genomes were obtained from 35 666 patients and HCWs.ResultsAmong 5112 SARS-CoV-2 viral samples sequenced from the second and third waves of SARS-CoV-2 (pre-Omicron), 291 pairs were derived from persons with a plausible healthcare overlap. Of these, 34 pairs (12%) were phylogenetically linked: 19 attributable to household and 14 to healthcare transmission. During the Omicron wave, 2106 contact pairs among 7821 sequences resulted in 120 (6%) related pairs among 32 clusters, of which 10 were consistent with healthcare transmission. Transmission was more likely to occur in shared spaces in the older hospital compared with the newer hospital (2.54 vs 0.63 transmission events per 1000 admissions, P < .001).ConclusionsIP strategies were effective at identifying and preventing healthcare SARS-CoV-2 transmission.

Published
2024

2. Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever

Author

Kotliar, Dylan, Raju, Siddharth, Tabrizi, Shervin, Odia, Ikponmwosa, Goba, Augustine, Momoh, Mambu, Sandi, John Demby, Nair, Parvathy, Phelan, Eric, Tariyal, Ridhi, Eromon, Philomena E., Mehta, Samar, Robles-Sikisaka, Refugio, Siddle, Katherine J., Stremlau, Matt, Jalloh, Simbirie, Gire, Stephen K., Winnicki, Sarah, Chak, Bridget, Schaffner, Stephen F., Pauthner, Matthias, Karlsson, Elinor K., Chapin, Sarah R., Kennedy, Sharon G., Branco, Luis M., Kanneh, Lansana, Vitti, Joseph J., Broodie, Nisha, Gladden-Young, Adrianne, Omoniwa, Omowunmi, Jiang, Pan-Pan, Yozwiak, Nathan, Heuklom, Shannon, Moses, Lina M., Akpede, George O., Asogun, Danny A., Rubins, Kathleen, Kales, Susan, Happi, Anise N., Iruolagbe, Christopher O., Dic-Ijiewere, Mercy, Iraoyah, Kelly, Osazuwa, Omoregie O., Okonkwo, Alexander K., Kunz, Stefan, McCormick, Joseph B., Khan, S. Humarr, Honko, Anna N., Lander, Eric S., Oldstone, Michael B. A., Hensley, Lisa, Folarin, Onikepe A., Okogbenin, Sylvanus A., Günther, Stephan, Ollila, Hanna M., Tewhey, Ryan, Okokhere, Peter O., Schieffelin, John S., Andersen, Kristian G., Reilly, Steven K., Grant, Donald S., Garry, Robert F., Barnes, Kayla G., Happi, Christian T., and Sabeti, Pardis C.

Published
2024
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3. Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schools

Author

Fielding-Miller, Rebecca, Karthikeyan, Smruthi, Gaines, Tommi, Garfein, Richard S, Salido, Rodolfo A, Cantu, Victor J, Kohn, Laura, Martin, Natasha K, Wynn, Adriane, Wijaya, Carrissa, Flores, Marlene, Omaleki, Vinton, Majnoonian, Araz, Gonzalez-Zuniga, Patricia, Nguyen, Megan, Vo, Anh V, Le, Tina, Duong, Dawn, Hassani, Ashkan, Tweeten, Samantha, Jepsen, Kristen, Henson, Benjamin, Hakim, Abbas, Birmingham, Amanda, De Hoff, Peter, Mark, Adam M, Nasamran, Chanond A, Rosenthal, Sara Brin, Moshiri, Niema, Fisch, Kathleen M, Humphrey, Greg, Farmer, Sawyer, Tubb, Helena M, Valles, Tommy, Morris, Justin, Kang, Jaeyoung, Khaleghi, Behnam, Young, Colin, Akel, Ameen D, Eilert, Sean, Eno, Justin, Curewitz, Ken, Laurent, Louise C, Rosing, Tajana, Knight, Rob, SEARCH, Baer, Nathan A, Barber, Tom, Castro-Martinez, Anelizze, Chacón, Marisol, Cheung, Willi, Crescini, Evelyn S, Eisner, Emily R, Vargas, Lizbeth Franco, Hobbs, Charlotte, Lastrella, Alma L, Lawrence, Elijah S, Matteson, Nathaniel L, Gangavarapu, Karthik, Ngo, Toan T, Seaver, Phoebe, Smoot, Elizabeth W, Tsai, Rebecca, Xia, Bing, Aigner, Stefan, Anderson, Catelyn, Belda-Ferre, Pedro, Sathe, Shashank, Zeller, Mark, Andersen, Kristian G, Yeo, Gene W, and Kurzban, Ezra

Subjects
Public Health, Health Sciences, Coronaviruses, Emerging Infectious Diseases, Infectious Diseases, Infection, Good Health and Well Being, Wastewater surveillance, SARS-CoV-2, COVID-19 in schools, SEARCH
Abstract

BackgroundSchools are high-risk settings for SARS-CoV-2 transmission, but necessary for children's educational and social-emotional wellbeing. Previous research suggests that wastewater monitoring can detect SARS-CoV-2 infections in controlled residential settings with high levels of accuracy. However, its effective accuracy, cost, and feasibility in non-residential community settings is unknown.MethodsThe objective of this study was to determine the effectiveness and accuracy of community-based passive wastewater and surface (environmental) surveillance to detect SARS-CoV-2 infection in neighborhood schools compared to weekly diagnostic (PCR) testing. We implemented an environmental surveillance system in nine elementary schools with 1700 regularly present staff and students in southern California. The system was validated from November 2020 to March 2021.FindingsIn 447 data collection days across the nine sites 89 individuals tested positive for COVID-19, and SARS-CoV-2 was detected in 374 surface samples and 133 wastewater samples. Ninety-three percent of identified cases were associated with an environmental sample (95% CI: 88%-98%); 67% were associated with a positive wastewater sample (95% CI: 57%-77%), and 40% were associated with a positive surface sample (95% CI: 29%-52%). The techniques we utilized allowed for near-complete genomic sequencing of wastewater and surface samples.InterpretationPassive environmental surveillance can detect the presence of COVID-19 cases in non-residential community school settings with a high degree of accuracy.FundingCounty of San Diego, Health and Human Services Agency, National Institutes of Health, National Science Foundation, Centers for Disease Control.

Published
2023

4. Wastewater surveillance for public health

Author

Levy, Joshua I, Andersen, Kristian G, Knight, Rob, and Karthikeyan, Smruthi

Subjects
Engineering, Public Health, Health Sciences, Chemical Engineering, Environmental Engineering, Good Health and Well Being, Disease Outbreaks, Wastewater, Wastewater-Based Epidemiological Monitoring, Humans, General Science & Technology
Abstract

Wastewater contains information on pathogen spread, evolution, and outbreak risk.

Published
2023

5. Introduction and Establishment of SARS-CoV-2 Gamma Variant in New York City in Early 2021

Author

Vasylyeva, Tetyana I, Fang, Courtney E, Su, Michelle, Havens, Jennifer L, Parker, Edyth, Wang, Jade C, Zeller, Mark, Yakovleva, Anna, Hassler, Gabriel W, Chowdhury, Moinuddin A, Andersen, Kristian G, Hughes, Scott, and Wertheim, Joel O

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Prevention, Genetics, Good Health and Well Being, Humans, SARS-CoV-2, New York City, COVID-19, Phylogeny, Gamma variant, travel restrictions, public health, Biological Sciences, Medical and Health Sciences, Microbiology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

BackgroundMonitoring the emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is an important public health objective. We investigated how the Gamma variant was established in New York City (NYC) in early 2021 in the presence of travel restrictions that aimed to prevent viral spread from Brazil, the country where the variant was first identified.MethodsWe performed phylogeographic analysis on 15 967 Gamma sequences sampled between 10 March and 1 May 2021, to identify geographic sources of Gamma lineages introduced into NYC. We identified locally circulating Gamma transmission clusters and inferred the timing of their establishment in NYC.ResultsWe identified 16 phylogenetically distinct Gamma clusters established in NYC (cluster sizes ranged 2-108 genomes); most of them were introduced from Florida and Illinois and only 1 directly from Brazil. By the time the first Gamma case was reported by genomic surveillance in NYC on 10 March, the majority (57%) of circulating Gamma lineages had already been established in the city for at least 2 weeks.ConclusionsAlthough travel from Brazil to the United States was restricted from May 2020 through the end of the study period, this restriction did not prevent Gamma from becoming established in NYC as most introductions occurred from domestic locations.

Published
2022

6. The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic

Author

Worobey, Michael, Levy, Joshua I, Serrano, Lorena Malpica, Crits-Christoph, Alexander, Pekar, Jonathan E, Goldstein, Stephen A, Rasmussen, Angela L, Kraemer, Moritz UG, Newman, Chris, Koopmans, Marion PG, Suchard, Marc A, Wertheim, Joel O, Lemey, Philippe, Robertson, David L, Garry, Robert F, Holmes, Edward C, Rambaut, Andrew, and Andersen, Kristian G

Subjects
Prevention, Emerging Infectious Diseases, Biodefense, Vaccine Related, Lung, Good Health and Well Being, Animals, COVID-19, China, Humans, Pandemics, SARS-CoV-2, Seafood, Viral Zoonoses, General Science & Technology
Abstract

Understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 is critical to preventing future zoonotic outbreaks before they become the next pandemic. The Huanan Seafood Wholesale Market in Wuhan, China, was identified as a likely source of cases in early reports, but later this conclusion became controversial. We show here that the earliest known COVID-19 cases from December 2019, including those without reported direct links, were geographically centered on this market. We report that live SARS-CoV-2-susceptible mammals were sold at the market in late 2019 and that within the market, SARS-CoV-2-positive environmental samples were spatially associated with vendors selling live mammals. Although there is insufficient evidence to define upstream events, and exact circumstances remain obscure, our analyses indicate that the emergence of SARS-CoV-2 occurred through the live wildlife trade in China and show that the Huanan market was the epicenter of the COVID-19 pandemic.

Published
2022

7. The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2

Author

Pekar, Jonathan E, Magee, Andrew, Parker, Edyth, Moshiri, Niema, Izhikevich, Katherine, Havens, Jennifer L, Gangavarapu, Karthik, Malpica Serrano, Lorena Mariana, Crits-Christoph, Alexander, Matteson, Nathaniel L, Zeller, Mark, Levy, Joshua I, Wang, Jade C, Hughes, Scott, Lee, Jungmin, Park, Heedo, Park, Man-Seong, Ching Zi Yan, Katherine, Lin, Raymond Tzer Pin, Mat Isa, Mohd Noor, Noor, Yusuf Muhammad, Vasylyeva, Tetyana I, Garry, Robert F, Holmes, Edward C, Rambaut, Andrew, Suchard, Marc A, Andersen, Kristian G, Worobey, Michael, and Wertheim, Joel O

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Clinical Sciences, Pneumonia, Biodefense, Lung, Vaccine Related, Emerging Infectious Diseases, Infectious Diseases, Prevention, Pneumonia & Influenza, Infection, Good Health and Well Being, Animals, COVID-19, Computer Simulation, Genetic Variation, Genomics, Humans, Molecular Epidemiology, Pandemics, Phylogeny, SARS-CoV-2, Viral Zoonoses, General Science & Technology
Abstract

Understanding the circumstances that lead to pandemics is important for their prevention. We analyzed the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted "A" and "B." Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October to 8 December), and the separate introduction of lineage A likely occurred within weeks of this event. These findings indicate that it is unlikely that SARS-CoV-2 circulated widely in humans before November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. As with other coronaviruses, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.

Published
2022

8. Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems

Author

Barnes, Kayla G., Levy, Joshua I., Gauld, Jillian, Rigby, Jonathan, Kanjerwa, Oscar, Uzzell, Christopher B., Chilupsya, Chisomo, Anscombe, Catherine, Tomkins-Tinch, Christopher, Mbeti, Omar, Cairns, Edward, Thole, Herbert, McSweeney, Shannon, Chibwana, Marah G., Ashton, Philip M., Jere, Khuzwayo C., Meschke, John Scott, Diggle, Peter, Cornick, Jennifer, Chilima, Benjamin, Jambo, Kondwani, Andersen, Kristian G., Kawalazira, Gift, Paterson, Steve, Nyirenda, Tonney S., and Feasey, Nicholas

Published
2023
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9. SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses

Author

Yousif, Mukhlid, Rachida, Said, Taukobong, Setshaba, Ndlovu, Nkosenhle, Iwu-Jaja, Chinwe, Howard, Wayne, Moonsamy, Shelina, Mhlambi, Nompilo, Gwala, Sipho, Levy, Joshua I., Andersen, Kristian G., Scheepers, Cathrine, von Gottberg, Anne, Wolter, Nicole, Bhiman, Jinal N., Amoako, Daniel Gyamfi, Ismail, Arshad, Suchard, Melinda, and McCarthy, Kerrigan

Published
2023
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10. Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria

Author

Olawoye, Idowu B., Oluniyi, Paul E., Oguzie, Judith U., Uwanibe, Jessica N., Kayode, Tolulope A., Olumade, Testimony J., Ajogbasile, Fehintola V., Parker, Edyth, Eromon, Philomena E., Abechi, Priscilla, Sobajo, Tope A., Ugwu, Chinedu A., George, Uwem E., Ayoade, Femi, Akano, Kazeem, Oyejide, Nicholas E., Nosamiefan, Iguosadolo, Fred-Akintunwa, Iyanuoluwa, Adedotun-Sulaiman, Kemi, Brimmo, Farida B., Adegboyega, Babatunde B., Philip, Courage, Adeleke, Richard A., Chukwu, Grace C., Ahmed, Muhammad I., Ope-Ewe, Oludayo O., Otitoola, Shobi G., Ogunsanya, Olusola A., Saibu, Mudasiru F., Sijuwola, Ayotunde E., Ezekiel, Grace O., John, Oluwagboadurami G., Akin-John, Julie O., Akinlo, Oluwasemilogo O., Fayemi, Olanrewaju O., Ipaye, Testimony O., Nwodo, Deborah C., Omoniyi, Abolade E., Omwanghe, Iyobosa B., Terkuma, Christabel A., Okolie, Johnson, Ayo-Ale, Olubukola, Ikponmwosa, Odia, Benevolence, Ebo, Naregose, Grace O., Patience, Akhilomen E., Blessing, Osiemi, Micheal, Airende, Jacqueline, Agbukor, Aiyepada, John O., Ebhodaghe, Paulson, Racheal, Omiunu, Rita, Esumeh, Rosemary, Giwa E., Solomon, Ehikhametalor, Anieno, Ekanem, Edna, Yerumoh, Chris, Aire O., Donatus, Adomeh I., Ogbaini-Emovon, Ephraim, Tatfeng, Mirabeau Y., Omunakwe, Hannah E., Bob-Manuel, Mienye, Ahmed, Rahaman A., Onwuamah, Chika K., Shaibu, Joseph O., Okwuraiwe, Azuka, Ataga, Anthony E., Bock-Oruma, Andrew, Daramola, Funmi, Yusuf, Ibrahim F., Fajola, Akinwumi, Ntia, Nsikak-Abasi, Ekpo, Julie J., Moses, Anietie E., Moore-Igwe, Beatrice W., Fakayode, Oluwatosin E., Akinola, Monilade, Kida, Ibrahim M., Oderinde, Bamidele S., Wudiri, Zara W., Adeyemi, Oluwapelumi O., Akanbi, Olusola A., Ahumibe, Anthony, Akinpelu, Afolabi, Ayansola, Oyeronke, Babatunde, Olajumoke, Omoare, Adesuyi A., Chukwu, Chimaobi, Mba, Nwando G., Omoruyi, Ewean C., Olisa, Olasunkanmi, Akande, Olatunji K., Nwafor, Ifeanyi E., Ekeh, Matthew A., Ndoma, Erim, Ewah, Richard L., Duruihuoma, Rosemary O., Abu, Augustine, Odeh, Elizabeth, Onyia, Venatius, Ojide, Chiedozie K., Okoro, Sylvanus, Igwe, Daniel, Ogah, Emeka O., Khan, Kamran, Ajayi, Nnennaya A., Ugwu, Collins N., Ukwaja, Kingsley N., Ugwu, Ngozi I., Abejegah, Chukwuyem, Adedosu, Nelson, Ayodeji, Olufemi, Liasu, Ahmed A., Isamotu, Rafiu O., Gadzama, Galadima, Petros, Brittany A., Siddle, Katherine J., Schaffner, Stephen F., Akpede, George, Erameh, Cyril Oshomah, Baba, Marycelin M., Oladiji, Femi, Audu, Rosemary, Ndodo, Nnaemeka, Fowotade, Adeola, Okogbenin, Sylvanus, Okokhere, Peter O., Park, Danny J., Mcannis, Bronwyn L., Adetifa, Ifedayo M., Ihekweazu, Chikwe, Salako, Babatunde L., Tomori, Oyewale, Happi, Anise N., Folarin, Onikepe A., Andersen, Kristian G., Sabeti, Pardis C., and Happi, Christian T.

Published
2023
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11. Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions

Author

Parker, Edyth, Anderson, Catelyn, Zeller, Mark, Tibi, Ahmad, Havens, Jennifer L, Laroche, Geneviève, Benlarbi, Mehdi, Ariana, Ardeshir, Robles-Sikisaka, Refugio, Latif, Alaa Abdel, Watts, Alexander, Awidi, Abdalla, Jaradat, Saied A, Gangavarapu, Karthik, Ramesh, Karthik, Kurzban, Ezra, Matteson, Nathaniel L, Han, Alvin X, Hughes, Laura D, McGraw, Michelle, Spencer, Emily, Nicholson, Laura, Khan, Kamran, Suchard, Marc A, Wertheim, Joel O, Wohl, Shirlee, Côté, Marceline, Abdelnour, Amid, Andersen, Kristian G, and Abu-Dayyeh, Issa

Subjects
Life on Land, COVID-19, Humans, Middle East, Pandemics, SARS-CoV-2, Travel
Abstract

Regional connectivity and land travel have been identified as important drivers of SARS-CoV-2 transmission. However, the generalizability of this finding is understudied outside of well-sampled, highly connected regions. In this study, we investigated the relative contributions of regional and intercontinental connectivity to the source-sink dynamics of SARS-CoV-2 for Jordan and the Middle East. By integrating genomic, epidemiological and travel data we show that the source of introductions into Jordan was dynamic across 2020, shifting from intercontinental seeding in the early pandemic to more regional seeding for the travel restrictions period. We show that land travel, particularly freight transport, drove introduction risk during the travel restrictions period. High regional connectivity and land travel also drove Jordan's export risk. Our findings emphasize regional connectedness and land travel as drivers of transmission in the Middle East.

Published
2022

12. Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades

Author

Klitting, Raphaëlle, Kafetzopoulou, Liana E, Thiery, Wim, Dudas, Gytis, Gryseels, Sophie, Kotamarthi, Anjali, Vrancken, Bram, Gangavarapu, Karthik, Momoh, Mambu, Sandi, John Demby, Goba, Augustine, Alhasan, Foday, Grant, Donald S, Okogbenin, Sylvanus, Ogbaini-Emovo, Ephraim, Garry, Robert F, Smither, Allison R, Zeller, Mark, Pauthner, Matthias G, McGraw, Michelle, Hughes, Laura D, Duraffour, Sophie, Günther, Stephan, Suchard, Marc A, Lemey, Philippe, Andersen, Kristian G, and Dellicour, Simon

Subjects
Infectious Diseases, Emerging Infectious Diseases, Rare Diseases, Aetiology, 2.2 Factors relating to the physical environment, Infection, Life on Land, Animals, Humans, Lassa Fever, Lassa virus, Phylogeography, Risk Factors, Rodentia
Abstract

Lassa fever is a severe viral hemorrhagic fever caused by a zoonotic virus that repeatedly spills over to humans from its rodent reservoirs. It is currently not known how climate and land use changes could affect the endemic area of this virus, currently limited to parts of West Africa. By exploring the environmental data associated with virus occurrence using ecological niche modelling, we show how temperature, precipitation and the presence of pastures determine ecological suitability for virus circulation. Based on projections of climate, land use, and population changes, we find that regions in Central and East Africa will likely become suitable for Lassa virus over the next decades and estimate that the total population living in ecological conditions that are suitable for Lassa virus circulation may drastically increase by 2070. By analysing geotagged viral genomes using spatially-explicit phylogeography and simulating virus dispersal, we find that in the event of Lassa virus being introduced into a new suitable region, its spread might remain spatially limited over the first decades.

Published
2022

13. Lassa Virus Genetics

Author

Klitting, Raphaëlle, Mehta, Samar B., Oguzie, Judith U., Oluniyi, Paul E., Pauthner, Matthias G., Siddle, Katherine J., Andersen, Kristian G., Happi, Christian T., Sabeti, Pardis C., and Garry, Robert, editor

Published
2023
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15. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations

Author

Gangavarapu, Karthik, Latif, Alaa Abdel, Mullen, Julia L., Alkuzweny, Manar, Hufbauer, Emory, Tsueng, Ginger, Haag, Emily, Zeller, Mark, Aceves, Christine M., Zaiets, Karina, Cano, Marco, Zhou, Xinghua, Qian, Zhongchao, Sattler, Rachel, Matteson, Nathaniel L., Levy, Joshua I., Lee, Raphael T. C., Freitas, Lucas, Maurer-Stroh, Sebastian, Suchard, Marc A., Wu, Chunlei, Su, Andrew I., Andersen, Kristian G., and Hughes, Laura D.

Published
2023
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16. The origins of SARS-CoV-2: A critical review

Author

Holmes, Edward C, Goldstein, Stephen A, Rasmussen, Angela L, Robertson, David L, Crits-Christoph, Alexander, Wertheim, Joel O, Anthony, Simon J, Barclay, Wendy S, Boni, Maciej F, Doherty, Peter C, Farrar, Jeremy, Geoghegan, Jemma L, Jiang, Xiaowei, Leibowitz, Julian L, Neil, Stuart JD, Skern, Tim, Weiss, Susan R, Worobey, Michael, Andersen, Kristian G, Garry, Robert F, and Rambaut, Andrew

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Pneumonia, Emerging Infectious Diseases, Biodefense, Vaccine Related, Infectious Diseases, Prevention, Pneumonia & Influenza, Lung, Good Health and Well Being, Animals, Biological Evolution, COVID-19, Humans, Laboratories, SARS-CoV-2, Zoonoses, evolution, origins, zoonosis, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

Since the first reports of a novel severe acute respiratory syndrome (SARS)-like coronavirus in December 2019 in Wuhan, China, there has been intense interest in understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the human population. Recent debate has coalesced around two competing ideas: a "laboratory escape" scenario and zoonotic emergence. Here, we critically review the current scientific evidence that may help clarify the origin of SARS-CoV-2.

Published
2021

17. Emergence of an early SARS-CoV-2 epidemic in the United States.

Author

Zeller, Mark, Gangavarapu, Karthik, Anderson, Catelyn, Smither, Allison R, Vanchiere, John A, Rose, Rebecca, Snyder, Daniel J, Dudas, Gytis, Watts, Alexander, Matteson, Nathaniel L, Robles-Sikisaka, Refugio, Marshall, Maximilian, Feehan, Amy K, Sabino-Santos, Gilberto, Bell-Kareem, Antoinette R, Hughes, Laura D, Alkuzweny, Manar, Snarski, Patricia, Garcia-Diaz, Julia, Scott, Rona S, Melnik, Lilia I, Klitting, Raphaëlle, McGraw, Michelle, Belda-Ferre, Pedro, DeHoff, Peter, Sathe, Shashank, Marotz, Clarisse, Grubaugh, Nathan D, Nolan, David J, Drouin, Arnaud C, Genemaras, Kaylynn J, Chao, Karissa, Topol, Sarah, Spencer, Emily, Nicholson, Laura, Aigner, Stefan, Yeo, Gene W, Farnaes, Lauge, Hobbs, Charlotte A, Laurent, Louise C, Knight, Rob, Hodcroft, Emma B, Khan, Kamran, Fusco, Dahlene N, Cooper, Vaughn S, Lemey, Phillipe, Gardner, Lauren, Lamers, Susanna L, Kamil, Jeremy P, Garry, Robert F, Suchard, Marc A, and Andersen, Kristian G

Subjects
Humans, Risk Factors, Disease Outbreaks, Phylogeny, Travel, United States, Louisiana, Texas, Databases as Topic, Epidemics, COVID-19, SARS-CoV-2, genomic epidemiology, mobility, phylogenetics, viral emergence, viral sequencing, Emerging Infectious Diseases, Biodefense, Prevention, Vaccine Related, Lung, Developmental Biology, Biological Sciences, Medical and Health Sciences
Abstract

The emergence of the COVID-19 epidemic in the United States (U.S.) went largely undetected due to inadequate testing. New Orleans experienced one of the earliest and fastest accelerating outbreaks, coinciding with Mardi Gras. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large-scale events accelerate transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana had limited diversity compared to other U.S. states and that one introduction of SARS-CoV-2 led to almost all of the early transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras, and the festival dramatically accelerated transmission. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate epidemics.

Published
2021

18. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics

Author

Matteson, Nathaniel L., Hassler, Gabriel W., Kurzban, Ezra, Schwab, Madison A., Perkins, Sarah A., Gangavarapu, Karthik, Levy, Joshua I., Parker, Edyth, Pride, David, Hakim, Abbas, De Hoff, Peter, Cheung, Willi, Castro-Martinez, Anelizze, Rivera, Andrea, Veder, Anthony, Rivera, Ariana, Wauer, Cassandra, Holmes, Jacqueline, Wilson, Jedediah, Ngo, Shayla N., Plascencia, Ashley, Lawrence, Elijah S., Smoot, Elizabeth W., Eisner, Emily R., Tsai, Rebecca, Chacón, Marisol, Baer, Nathan A., Seaver, Phoebe, Salido, Rodolfo A., Aigner, Stefan, Ngo, Toan T., Barber, Tom, Ostrander, Tyler, Fielding-Miller, Rebecca, Simmons, Elizabeth H., Zazueta, Oscar E., Serafin-Higuera, Idanya, Sanchez-Alavez, Manuel, Moreno-Camacho, Jose L., García-Gil, Abraham, Murphy Schafer, Ashleigh R., McDonald, Eric, Corrigan, Jeremy, Malone, John D., Stous, Sarah, Shah, Seema, Moshiri, Niema, Weiss, Alana, Anderson, Catelyn, Aceves, Christine M., Spencer, Emily G., Hufbauer, Emory C., Lee, Justin J., King, Alison J., Ramesh, Karthik S., Nguyen, Kelly N., Saucedo, Kieran, Robles-Sikisaka, Refugio, Fisch, Kathleen M., Gonias, Steven L., Birmingham, Amanda, McDonald, Daniel, Karthikeyan, Smruthi, Martin, Natasha K., Schooley, Robert T., Negrete, Agustin J., Reyna, Horacio J., Chavez, Jose R., Garcia, Maria L., Cornejo-Bravo, Jose M., Becker, David, Isaksson, Magnus, Washington, Nicole L., Lee, William, Garfein, Richard S., Luna-Ruiz Esparza, Marco A., Alcántar-Fernández, Jonathan, Henson, Benjamin, Jepsen, Kristen, Olivares-Flores, Beatriz, Barrera-Badillo, Gisela, Lopez-Martínez, Irma, Ramírez-González, José E., Flores-León, Rita, Kingsmore, Stephen F., Sanders, Alison, Pradenas, Allorah, White, Benjamin, Matthews, Gary, Hale, Matt, McLawhon, Ronald W., Reed, Sharon L., Winbush, Terri, McHardy, Ian H., Fielding, Russel A., Nicholson, Laura, Quigley, Michael M., Harding, Aaron, Mendoza, Art, Bakhtar, Omid, Browne, Sara H., Olivas Flores, Jocelyn, Rincon Rodríguez, Diana G., Gonzalez Ibarra, Martin, Robles Ibarra, Luis C., Arellano Vera, Betsy J., Gonzalez Garcia, Jonathan, Harvey-Vera, Alicia, Knight, Rob, Laurent, Louise C., Yeo, Gene W., Wertheim, Joel O., Ji, Xiang, Worobey, Michael, Suchard, Marc A., Andersen, Kristian G., Campos-Romero, Abraham, Wohl, Shirlee, and Zeller, Mark

Published
2023
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19. Ebola vaccine–induced protection in nonhuman primates correlates with antibody specificity and Fc-mediated effects

Author

Meyer, Michelle, Gunn, Bronwyn M, Malherbe, Delphine C, Gangavarapu, Karthik, Yoshida, Asuka, Pietzsch, Colette, Kuzmina, Natalia A, Saphire, Erica Ollmann, Collins, Peter L, Crowe, James E, Zhu, James J, Suchard, Marc A, Brining, Douglas L, Mire, Chad E, Cross, Robert W, Geisbert, Joan B, Samal, Siba K, Andersen, Kristian G, Alter, Galit, Geisbert, Thomas W, and Bukreyev, Alexander

Subjects
Emerging Infectious Diseases, Vaccine Related, Biodefense, Vaccine Related (AIDS), Biotechnology, Prevention, Immunization, 3.4 Vaccines, Prevention of disease and conditions, and promotion of well-being, Good Health and Well Being, Animals, Antibodies, Neutralizing, Antibodies, Viral, Antibody Specificity, Ebola Vaccines, Ebolavirus, Hemorrhagic Fever, Ebola, Humans, Primates, Biological Sciences, Medical and Health Sciences
Abstract

Although substantial progress has been made with Ebola virus (EBOV) vaccine measures, the immune correlates of vaccine-mediated protection remain uncertain. Here, five mucosal vaccine vectors based on human and avian paramyxoviruses provided nonhuman primates with varying degrees of protection, despite expressing the same EBOV glycoprotein (GP) immunogen. Each vaccine produced antibody responses that differed in Fc-mediated functions and isotype composition, as well as in magnitude and coverage toward GP and its conformational and linear epitopes. Differences in the degree of protection and comprehensive characterization of the response afforded the opportunity to identify which features and functions were elevated in survivors and could therefore serve as vaccine correlates of protection. Pairwise network correlation analysis of 139 immune- and vaccine-related parameters was performed to demonstrate relationships with survival. Total GP-specific antibodies, as measured by biolayer interferometry, but not neutralizing IgG or IgA titers, correlated with survival. Fc-mediated functions and the amount of receptor binding domain antibodies were associated with improved survival outcomes, alluding to the protective mechanisms of these vaccines. Therefore, functional qualities of the antibody response, particularly Fc-mediated effects and GP specificity, rather than simply magnitude of the response, appear central to vaccine-induced protection against EBOV. The heterogeneity of the response profile between the vaccines indicates that each vaccine likely exhibits its own protective signature and the requirements for an efficacious EBOV vaccine are complex.

Published
2021

20. Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States.

Author

Washington, Nicole L, Gangavarapu, Karthik, Zeller, Mark, Bolze, Alexandre, Cirulli, Elizabeth T, Schiabor Barrett, Kelly M, Larsen, Brendan B, Anderson, Catelyn, White, Simon, Cassens, Tyler, Jacobs, Sharoni, Levan, Geraint, Nguyen, Jason, Ramirez, Jimmy M, Rivera-Garcia, Charlotte, Sandoval, Efren, Wang, Xueqing, Wong, David, Spencer, Emily, Robles-Sikisaka, Refugio, Kurzban, Ezra, Hughes, Laura D, Deng, Xianding, Wang, Candace, Servellita, Venice, Valentine, Holly, De Hoff, Peter, Seaver, Phoebe, Sathe, Shashank, Gietzen, Kimberly, Sickler, Brad, Antico, Jay, Hoon, Kelly, Liu, Jingtao, Harding, Aaron, Bakhtar, Omid, Basler, Tracy, Austin, Brett, MacCannell, Duncan, Isaksson, Magnus, Febbo, Phillip G, Becker, David, Laurent, Marc, McDonald, Eric, Yeo, Gene W, Knight, Rob, Laurent, Louise C, de Feo, Eileen, Worobey, Michael, Chiu, Charles Y, Suchard, Marc A, Lu, James T, Lee, William, and Andersen, Kristian G

Subjects
Humans, Models, Biological, United States, Female, Male, COVID-19, SARS-CoV-2, 501Y.V1, B.1.1.7, VOC-202012/01, genomic epidemiology, variant of concern, Vaccine Related, Genetics, Human Genome, Biodefense, Prevention, Lung, Pneumonia, Good Health and Well Being, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

The highly transmissible B.1.1.7 variant of SARS-CoV-2, first identified in the United Kingdom, has gained a foothold across the world. Using S gene target failure (SGTF) and SARS-CoV-2 genomic sequencing, we investigated the prevalence and dynamics of this variant in the United States (US), tracking it back to its early emergence. We found that, while the fraction of B.1.1.7 varied by state, the variant increased at a logistic rate with a roughly weekly doubling rate and an increased transmission of 40%-50%. We revealed several independent introductions of B.1.1.7 into the US as early as late November 2020, with community transmission spreading it to most states within months. We show that the US is on a similar trajectory as other countries where B.1.1.7 became dominant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.

Published
2021

21. EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

Author

Cantrell, Kalen, Fedarko, Marcus W, Rahman, Gibraan, McDonald, Daniel, Yang, Yimeng, Zaw, Thant, Gonzalez, Antonio, Janssen, Stefan, Estaki, Mehrbod, Haiminen, Niina, Beck, Kristen L, Zhu, Qiyun, Sayyari, Erfan, Morton, James T, Armstrong, George, Tripathi, Anupriya, Gauglitz, Julia M, Marotz, Clarisse, Matteson, Nathaniel L, Martino, Cameron, Sanders, Jon G, Carrieri, Anna Paola, Song, Jin, Swafford, Austin D, Dorrestein, Pieter C, Andersen, Kristian G, Parida, Laxmi, Kim, Ho-Cheol, Vázquez-Baeza, Yoshiki, and Knight, Rob

Subjects
Information and Computing Sciences, Graphics, Augmented Reality and Games, Biological Sciences, Human Genome, Genetics, bioinformatics, microbial ecology
Abstract

Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool for visualizing trees in the context of microbiome, metabolome, and other community data scalable to trees with well over 500,000 nodes. EMPress provides novel functionality-including ordination integration and animations-alongside many standard tree visualization features and thus simplifies exploratory analyses of many forms of 'omic data.IMPORTANCE Phylogenetic trees are integral data structures for the analysis of microbial communities. Recent work has also shown the utility of trees constructed from certain metabolomic data sets, further highlighting their importance in microbiome research. The ever-growing scale of modern microbiome surveys has led to numerous challenges in visualizing these data. In this paper we used five diverse data sets to showcase the versatility and scalability of EMPress, an interactive web visualization tool. EMPress addresses the growing need for exploratory analysis tools that can accommodate large, complex multi-omic data sets.

Published
2021

22. Ebola Virus Transmission Initiated by Relapse of Systemic Ebola Virus Disease

Author

Mbala-Kingebeni, Placide, Pratt, Catherine, Ruffin, Mbusa Mutafali, Pauthner, Matthias G, Bile, Faustin, Ndaye, Antoine Nkuba, Black, Allison, Lusamaki, Eddy Kinganda, Faye, Martin, Aziza, Amuri, Diagne, Moussa M, Mukadi, Daniel, White, Bailey, Hadfield, James, Gangavarapu, Karthik, Bisento, Nella, Kazadi, Donatien, Nsunda, Bibiche, Akonga, Marceline, Tshiani, Olivier, Misasi, John, Ploquin, Aurelie, Epaso, Victor, Paka, Emilia Sana, N’kasar, Yannick Tutu Tshia, Mambu, Fabrice, Edidi, Francois, Matondo, Meris, Bula, Bula, Diallo, Boubacar, Keita, Mory, Belizaire, Marie Roseline Darnycka, Fall, Ibrahima Soce, Yam, Abdoulaye, Sabue, Mulangu, Rimion, Anne W, Salfati, Elias, Torkamani, Ali, Suchard, Marc A, Crozier, Ian, Hensley, Lisa, Rambaut, Andrew, Faye, Ousmane, Sall, Amadou, Sullivan, Nancy J, Bedford, Trevor, Andersen, Kristian G, Wiley, Michael R, Ahuka-Mundeke, Steve, and Tamfum, Jean-Jacques Muyembe

Subjects
Biodefense, Vaccine Related, Prevention, Infectious Diseases, Biotechnology, Rare Diseases, Emerging Infectious Diseases, Immunization, Infection, Good Health and Well Being, Adult, Bayes Theorem, Democratic Republic of the Congo, Ebola Vaccines, Ebolavirus, Fatal Outcome, Genome, Viral, Hemorrhagic Fever, Ebola, Humans, Male, Mutation, Phylogeny, RNA, Viral, Recurrence, Medical and Health Sciences, General & Internal Medicine
Abstract

During the 2018-2020 Ebola virus disease (EVD) outbreak in North Kivu province in the Democratic Republic of Congo, EVD was diagnosed in a patient who had received the recombinant vesicular stomatitis virus-based vaccine expressing a ZEBOV glycoprotein (rVSV-ZEBOV) (Merck). His treatment included an Ebola virus (EBOV)-specific monoclonal antibody (mAb114), and he recovered within 14 days. However, 6 months later, he presented again with severe EVD-like illness and EBOV viremia, and he died. We initiated epidemiologic and genomic investigations that showed that the patient had had a relapse of acute EVD that led to a transmission chain resulting in 91 cases across six health zones over 4 months. (Funded by the Bill and Melinda Gates Foundation and others.).

Published
2021

23. Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States.

Author

Washington, Nicole L, Gangavarapu, Karthik, Zeller, Mark, Bolze, Alexandre, Cirulli, Elizabeth T, Barrett, Kelly M Schiabor, Larsen, Brendan B, Anderson, Catelyn, White, Simon, Cassens, Tyler, Jacobs, Sharoni, Levan, Geraint, Nguyen, Jason, Ramirez, Jimmy M, Rivera-Garcia, Charlotte, Sandoval, Efren, Wang, Xueqing, Wong, David, Spencer, Emily, Robles-Sikisaka, Refugio, Kurzban, Ezra, Hughes, Laura D, Deng, Xianding, Wang, Candace, Servellita, Venice, Valentine, Holly, De Hoff, Peter, Seaver, Phoebe, Sathe, Shashank, Gietzen, Kimberly, Sickler, Brad, Antico, Jay, Hoon, Kelly, Liu, Jingtao, Harding, Aaron, Bakhtar, Omid, Basler, Tracy, Austin, Brett, Isaksson, Magnus, Febbo, Phillip G, Becker, David, Laurent, Marc, McDonald, Eric, Yeo, Gene W, Knight, Rob, Laurent, Louise C, de Feo, Eileen, Worobey, Michael, Chiu, Charles, Suchard, Marc A, Lu, James T, Lee, William, and Andersen, Kristian G

Subjects
Vaccine Related, Prevention, Biodefense, Lung, Good Health and Well Being
Abstract

As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first identified in the United Kingdom (U.K.), has gained a strong foothold across the world. Because of the sudden and rapid rise of B.1.1.7, we investigated the prevalence and growth dynamics of this variant in the United States (U.S.), tracking it back to its early emergence and onward local transmission. We found that the RT-qPCR testing anomaly of S gene target failure (SGTF), first observed in the U.K., was a reliable proxy for B.1.1.7 detection. We sequenced 212 B.1.1.7 SARS-CoV-2 genomes collected from testing facilities in the U.S. from December 2020 to January 2021. We found that while the fraction of B.1.1.7 among SGTF samples varied by state, detection of the variant increased at a logistic rate similar to those observed elsewhere, with a doubling rate of a little over a week and an increased transmission rate of 35-45%. By performing time-aware Bayesian phylodynamic analyses, we revealed several independent introductions of B.1.1.7 into the U.S. as early as late November 2020, with onward community transmission enabling the variant to spread to at least 30 states as of January 2021. Our study shows that the U.S. is on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.

Published
2021

24. Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework.

Author

Dellicour, Simon, Lequime, Sebastian, Vrancken, Bram, Gill, Mandev S, Bastide, Paul, Gangavarapu, Karthik, Matteson, Nathaniel L, Tan, Yi, du Plessis, Louis, Fisher, Alexander A, Nelson, Martha I, Gilbert, Marius, Suchard, Marc A, Andersen, Kristian G, Grubaugh, Nathan D, Pybus, Oliver G, and Lemey, Philippe

Subjects
Animals, Bird Diseases, Ecosystem, Environment, Genetic Variation, Genome, Viral, Humans, North America, Phylogeny, Phylogeography, West Nile Fever, West Nile virus, Genome, Viral
Abstract

Computational analyses of pathogen genomes are increasingly used to unravel the dispersal history and transmission dynamics of epidemics. Here, we show how to go beyond historical reconstructions and use spatially-explicit phylogeographic and phylodynamic approaches to formally test epidemiological hypotheses. We illustrate our approach by focusing on the West Nile virus (WNV) spread in North America that has substantially impacted public, veterinary, and wildlife health. We apply an analytical workflow to a comprehensive WNV genome collection to test the impact of environmental factors on the dispersal of viral lineages and on viral population genetic diversity through time. We find that WNV lineages tend to disperse faster in areas with higher temperatures and we identify temporal variation in temperature as a main predictor of viral genetic diversity through time. By contrasting inference with simulation, we find no evidence for viral lineages to preferentially circulate within the same migratory bird flyway, suggesting a substantial role for non-migratory birds or mosquito dispersal along the longitudinal gradient.

Published
2020

25. Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2.

Author

Lemey, Philippe, Hong, Samuel L, Hill, Verity, Baele, Guy, Poletto, Chiara, Colizza, Vittoria, O'Toole, Áine, McCrone, John T, Andersen, Kristian G, Worobey, Michael, Nelson, Martha I, Rambaut, Andrew, and Suchard, Marc A

Subjects
Humans, Pneumonia, Viral, Coronavirus Infections, Bayes Theorem, Phylogeny, Genome, Viral, Travel, Pandemics, Phylogeography, Betacoronavirus, COVID-19, SARS-CoV-2, Genome, Viral, Pneumonia
Abstract

Spatiotemporal bias in genome sampling can severely confound discrete trait phylogeographic inference. This has impeded our ability to accurately track the spread of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, despite the availability of unprecedented numbers of SARS-CoV-2 genomes. Here, we present an approach to integrate individual travel history data in Bayesian phylogeographic inference and apply it to the early spread of SARS-CoV-2. We demonstrate that including travel history data yields i) more realistic hypotheses of virus spread and ii) higher posterior predictive accuracy compared to including only sampling location. We further explore methods to ameliorate the impact of sampling bias by augmenting the phylogeographic analysis with lineages from undersampled locations. Our reconstructions reinforce specific transmission hypotheses suggested by the inclusion of travel history data, but also suggest alternative routes of virus migration that are plausible within the epidemiological context but are not apparent with current sampling efforts.

Published
2020

26. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission

Author

Karthikeyan, Smruthi, Levy, Joshua I., De Hoff, Peter, Humphrey, Greg, Birmingham, Amanda, Jepsen, Kristen, Farmer, Sawyer, Tubb, Helena M., Valles, Tommy, Tribelhorn, Caitlin E., Tsai, Rebecca, Aigner, Stefan, Sathe, Shashank, Moshiri, Niema, Henson, Benjamin, Mark, Adam M., Hakim, Abbas, Baer, Nathan A., Barber, Tom, Belda-Ferre, Pedro, Chacón, Marisol, Cheung, Willi, Cresini, Evelyn S., Eisner, Emily R., Lastrella, Alma L., Lawrence, Elijah S., Marotz, Clarisse A., Ngo, Toan T., Ostrander, Tyler, Plascencia, Ashley, Salido, Rodolfo A., Seaver, Phoebe, Smoot, Elizabeth W., McDonald, Daniel, Neuhard, Robert M., Scioscia, Angela L., Satterlund, Alysson M., Simmons, Elizabeth H., Abelman, Dismas B., Brenner, David, Bruner, Judith C., Buckley, Anne, Ellison, Michael, Gattas, Jeffrey, Gonias, Steven L., Hale, Matt, Hawkins, Faith, Ikeda, Lydia, Jhaveri, Hemlata, Johnson, Ted, Kellen, Vince, Kremer, Brendan, Matthews, Gary, McLawhon, Ronald W., Ouillet, Pierre, Park, Daniel, Pradenas, Allorah, Reed, Sharon, Riggs, Lindsay, Sanders, Alison, Sollenberger, Bradley, Song, Angela, White, Benjamin, Winbush, Terri, Aceves, Christine M., Anderson, Catelyn, Gangavarapu, Karthik, Hufbauer, Emory, Kurzban, Ezra, Lee, Justin, Matteson, Nathaniel L., Parker, Edyth, Perkins, Sarah A., Ramesh, Karthik S., Robles-Sikisaka, Refugio, Schwab, Madison A., Spencer, Emily, Wohl, Shirlee, Nicholson, Laura, McHardy, Ian H., Dimmock, David P., Hobbs, Charlotte A., Bakhtar, Omid, Harding, Aaron, Mendoza, Art, Bolze, Alexandre, Becker, David, Cirulli, Elizabeth T., Isaksson, Magnus, Schiabor Barrett, Kelly M., Washington, Nicole L., Malone, John D., Schafer, Ashleigh Murphy, Gurfield, Nikos, Stous, Sarah, Fielding-Miller, Rebecca, Garfein, Richard S., Gaines, Tommi, Anderson, Cheryl, Martin, Natasha K., Schooley, Robert, Austin, Brett, MacCannell, Duncan R., Kingsmore, Stephen F., Lee, William, Shah, Seema, McDonald, Eric, Yu, Alexander T., Zeller, Mark, Fisch, Kathleen M., Longhurst, Christopher, Maysent, Patty, Pride, David, Khosla, Pradeep K., Laurent, Louise C., Yeo, Gene W., Andersen, Kristian G., and Knight, Rob

Published
2022
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27. Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

Author

Deng, Xianding, Gu, Wei, Federman, Scot, du Plessis, Louis, Pybus, Oliver G, Faria, Nuno, Wang, Candace, Yu, Guixia, Bushnell, Brian, Pan, Chao-Yang, Guevara, Hugo, Sotomayor-Gonzalez, Alicia, Zorn, Kelsey, Gopez, Allan, Servellita, Venice, Hsu, Elaine, Miller, Steve, Bedford, Trevor, Greninger, Alexander L, Roychoudhury, Pavitra, Starita, Lea M, Famulare, Michael, Chu, Helen Y, Shendure, Jay, Jerome, Keith R, Anderson, Catie, Gangavarapu, Karthik, Zeller, Mark, Spencer, Emily, Andersen, Kristian G, MacCannell, Duncan, Paden, Clinton R, Li, Yan, Zhang, Jing, Tong, Suxiang, Armstrong, Gregory, Morrow, Scott, Willis, Matthew, Matyas, Bela T, Mase, Sundari, Kasirye, Olivia, Park, Maggie, Masinde, Godfred, Chan, Curtis, Yu, Alexander T, Chai, Shua J, Villarino, Elsa, Bonin, Brandon, Wadford, Debra A, and Chiu, Charles Y

Subjects
Pneumonia, Lung, Infectious Diseases, Emerging Infectious Diseases, Vaccine Related, Pneumonia & Influenza, Prevention, Biodefense, Infection, Good Health and Well Being, Betacoronavirus, COVID-19, California, Coronavirus Infections, Epidemiological Monitoring, Genome, Viral, Humans, Pandemics, Phylogeny, Pneumonia, Viral, SARS-CoV-2, Sequence Alignment, Ships, Travel, Washington, General Science & Technology
Abstract

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally, with >365,000 cases in California as of 17 July 2020. We investigated the genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-March 2020, using samples from 36 patients spanning nine counties and the Grand Princess cruise ship. Phylogenetic analyses revealed the cryptic introduction of at least seven different SARS-CoV-2 lineages into California, including epidemic WA1 strains associated with Washington state, with lack of a predominant lineage and limited transmission among communities. Lineages associated with outbreak clusters in two counties were defined by a single base substitution in the viral genome. These findings support contact tracing, social distancing, and travel restrictions to contain the spread of SARS-CoV-2 in California and other states.

Published
2020

28. A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

Author

Deng, Xianding, Gu, Wei, Federman, Scot, du Plessis, Louis, Pybus, Oliver G, Faria, Nuno, Wang, Candace, Yu, Guixia, Pan, Chao-Yang, Guevara, Hugo, Sotomayor-Gonzalez, Alicia, Zorn, Kelsey, Gopez, Allan, Servellita, Venice, Hsu, Elaine, Miller, Steve, Bedford, Trevor, Greninger, Alexander L, Roychoudhury, Pavitra, Starita, Lea M, Famulare, Michael, Chu, Helen Y, Shendure, Jay, Jerome, Keith R, Anderson, Catie, Gangavarapu, Karthik, Zeller, Mark, Spencer, Emily, Andersen, Kristian G, MacCannell, Duncan, Paden, Clinton R, Li, Yan, Zhang, Jing, Tong, Suxiang, Armstrong, Gregory, Morrow, Scott, Willis, Matthew, Matyas, Bela T, Mase, Sundari, Kasirye, Olivia, Park, Maggie, Chan, Curtis, Yu, Alexander T, Chai, Shua J, Villarino, Elsa, Bonin, Brandon, Wadford, Debra A, and Chiu, Charles Y

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Biological Sciences, Lung, Infectious Diseases, Biotechnology, Prevention, Biodefense, Emerging Infectious Diseases, Vaccine Related, Aetiology, 2.2 Factors relating to the physical environment, Infection, Good Health and Well Being
Abstract

The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has spread globally, resulting in >300,000 reported cases worldwide as of March 21st, 2020. Here we investigate the genetic diversity and genomic epidemiology of SARS-CoV-2 in Northern California using samples from returning travelers, cruise ship passengers, and cases of community transmission with unclear infection sources. Virus genomes were sampled from 29 patients diagnosed with COVID-19 infection from Feb 3rd through Mar 15th. Phylogenetic analyses revealed at least 8 different SARS-CoV-2 lineages, suggesting multiple independent introductions of the virus into the state. Virus genomes from passengers on two consecutive excursions of the Grand Princess cruise ship clustered with those from an established epidemic in Washington State, including the WA1 genome representing the first reported case in the United States on January 19th. We also detected evidence for presumptive transmission of SARS-CoV-2 lineages from one community to another. These findings suggest that cryptic transmission of SARS-CoV-2 in Northern California to date is characterized by multiple transmission chains that originate via distinct introductions from international and interstate travel, rather than widespread community transmission of a single predominant lineage. Rapid testing and contact tracing, social distancing, and travel restrictions are measures that will help to slow SARS-CoV-2 spread in California and other regions of the USA.

Published
2020

29. Correction for Rasmussen et al., “Virology—the path forward”

Author

Rasmussen, Angela L., primary, Gronvall, Gigi K., additional, Lowen, Anice C., additional, Goodrum, Felicia, additional, Alwine, James, additional, Andersen, Kristian G., additional, Anthony, Simon J., additional, Baines, Joel, additional, Banerjee, Arinjay, additional, Broadbent, Andrew J., additional, Brooke, Christopher B., additional, Campos, Samuel K., additional, Caposio, Patrizia, additional, Casadevall, Arturo, additional, Chan, Gary C., additional, Cliffe, Anna R., additional, Collins-McMillen, Donna, additional, Connell, Nancy, additional, Damania, Blossom, additional, Daugherty, Matthew D., additional, Debbink, Kari, additional, Dermody, Terence S., additional, DiMaio, Daniel, additional, Duprex, W. Paul, additional, Emerman, Michael, additional, Galloway, Denise A., additional, Garry, Robert F., additional, Goldstein, Stephen A., additional, Greninger, Alexander L., additional, Hartman, Amy L., additional, Hogue, Brenda G., additional, Horner, Stacy M., additional, Hotez, Peter J., additional, Jung, Jae U., additional, Kamil, Jeremy P., additional, Karst, Stephanie M., additional, Laimins, Lou, additional, Lakdawala, Seema S., additional, Landais, Igor, additional, Letko, Michael, additional, Lindenbach, Brett, additional, Liu, Shan-Lu, additional, Luftig, Micah, additional, McFadden, Grant, additional, Mehle, Andrew, additional, Morrison, Juliet, additional, Moscona, Anne, additional, Mühlberger, Elke, additional, Munger, Joshua, additional, Münger, Karl, additional, Murphy, Eain, additional, Neufeldt, Christopher J., additional, Nikolich, Janko Z., additional, O'Connor, Christine M., additional, Pekosz, Andrew, additional, Permar, Sallie R., additional, Pfeiffer, Julie K., additional, Popescu, Saskia V., additional, Purdy, John G., additional, Racaniello, Vincent R., additional, Rice, Charles M., additional, Runstadler, Jonathan A., additional, Sapp, Martin J., additional, Scott, Rona S., additional, Smith, Gregory A., additional, Sorrell, Erin M., additional, Speranza, Emily, additional, Streblow, Daniel, additional, Tibbetts, Scott A., additional, Toth, Zsolt, additional, Van Doorslaer, Koenraad, additional, Weiss, Susan R., additional, White, Elizabeth A., additional, White, Timothy M., additional, Wobus, Christiane E., additional, Worobey, Michael, additional, Yamaoka, Satoko, additional, and Yurochko, Andrew, additional

Published
2024
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32. Virology—the path forward

Author

Rasmussen, Angela L., primary, Gronvall, Gigi K., additional, Lowen, Anice C., additional, Goodrum, Felicia, additional, Alwine, James, additional, Andersen, Kristian G., additional, Anthony, Simon J., additional, Baines, Joel, additional, Banerjee, Arinjay, additional, Broadbent, Andrew J., additional, Brooke, Christopher B., additional, Campos, Samuel K., additional, Caposio, Patrizia, additional, Casadevall, Arturo, additional, Chan, Gary C., additional, Cliffe, Anna R., additional, Collins-McMillen, Donna, additional, Connell, Nancy, additional, Damania, Blossom, additional, Daugherty, Matthew D., additional, Debbink, Kari, additional, Dermody, Terence S., additional, DiMaio, Daniel, additional, Duprex, W. Paul, additional, Emerman, Michael, additional, Galloway, Denise A., additional, Garry, Robert F., additional, Goldstein, Stephen A., additional, Greninger, Alexander L., additional, Hartman, Amy L., additional, Hogue, Brenda G., additional, Horner, Stacy M., additional, Hotez, Peter J., additional, Jung, Jae U., additional, Kamil, Jeremy P., additional, Karst, Stephanie M., additional, Laimins, Lou, additional, Lakdawala, Seema S., additional, Landais, Igor, additional, Letko, Michael, additional, Lindenbach, Brett, additional, Liu, Shan-Lu, additional, Luftig, Micah, additional, McFadden, Grant, additional, Mehle, Andrew, additional, Morrison, Juliet, additional, Moscona, Anne, additional, Mühlberger, Elke, additional, Munger, Joshua, additional, Münger, Karl, additional, Murphy, Eain, additional, Neufeldt, Christopher J., additional, Nikolich, Janko Z., additional, O'Connor, Christine M., additional, Pekosz, Andrew, additional, Permar, Sallie R., additional, Pfeiffer, Julie K., additional, Popescu, Saskia V., additional, Purdy, John G., additional, Racaniello, Vincent R., additional, Rice, Charles M., additional, Runstadler, Jonathan A., additional, Sapp, Martin J., additional, Scott, Rona S., additional, Smith, Gregory A., additional, Sorrell, Erin M., additional, Speranza, Emily, additional, Streblow, Daniel, additional, Tibbetts, Scott A., additional, Toth, Zsolt, additional, Van Doorslaer, Koenraad, additional, Weiss, Susan R., additional, White, Elizabeth A., additional, White, Timothy M., additional, Wobus, Christiane E., additional, Worobey, Michael, additional, Yamaoka, Satoko, additional, and Yurochko, Andrew, additional

Published
2024
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33. Virus genomes reveal factors that spread and sustained the Ebola epidemic

Author

Dudas, Gytis, Carvalho, Luiz Max, Bedford, Trevor, Tatem, Andrew J, Baele, Guy, Faria, Nuno R, Park, Daniel J, Ladner, Jason T, Arias, Armando, Asogun, Danny, Bielejec, Filip, Caddy, Sarah L, Cotten, Matthew, D’Ambrozio, Jonathan, Dellicour, Simon, Di Caro, Antonino, Diclaro, Joseph W, Duraffour, Sophie, Elmore, Michael J, Fakoli, Lawrence S, Faye, Ousmane, Gilbert, Merle L, Gevao, Sahr M, Gire, Stephen, Gladden-Young, Adrianne, Gnirke, Andreas, Goba, Augustine, Grant, Donald S, Haagmans, Bart L, Hiscox, Julian A, Jah, Umaru, Kugelman, Jeffrey R, Liu, Di, Lu, Jia, Malboeuf, Christine M, Mate, Suzanne, Matthews, David A, Matranga, Christian B, Meredith, Luke W, Qu, James, Quick, Joshua, Pas, Suzan D, Phan, My VT, Pollakis, Georgios, Reusken, Chantal B, Sanchez-Lockhart, Mariano, Schaffner, Stephen F, Schieffelin, John S, Sealfon, Rachel S, Simon-Loriere, Etienne, Smits, Saskia L, Stoecker, Kilian, Thorne, Lucy, Tobin, Ekaete Alice, Vandi, Mohamed A, Watson, Simon J, West, Kendra, Whitmer, Shannon, Wiley, Michael R, Winnicki, Sarah M, Wohl, Shirlee, Wölfel, Roman, Yozwiak, Nathan L, Andersen, Kristian G, Blyden, Sylvia O, Bolay, Fatorma, Carroll, Miles W, Dahn, Bernice, Diallo, Boubacar, Formenty, Pierre, Fraser, Christophe, Gao, George F, Garry, Robert F, Goodfellow, Ian, Günther, Stephan, Happi, Christian T, Holmes, Edward C, Kargbo, Brima, Keïta, Sakoba, Kellam, Paul, Koopmans, Marion PG, Kuhn, Jens H, Loman, Nicholas J, Magassouba, N’Faly, Naidoo, Dhamari, Nichol, Stuart T, Nyenswah, Tolbert, Palacios, Gustavo, Pybus, Oliver G, Sabeti, Pardis C, Sall, Amadou, Ströher, Ute, Wurie, Isatta, Suchard, Marc A, Lemey, Philippe, and Rambaut, Andrew

Subjects
Infectious Diseases, Emerging Infectious Diseases, Biodefense, Vaccine Related, Prevention, Infection, Good Health and Well Being, Climate, Disease Outbreaks, Ebolavirus, Genome, Viral, Geography, Hemorrhagic Fever, Ebola, Humans, Internationality, Linear Models, Molecular Epidemiology, Phylogeny, Travel, General Science & Technology
Abstract

The 2013-2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic 'gravity' model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, we reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics.

Published
2017

34. Integration of genomic sequencing into the response to the Ebola virus outbreak in Nord Kivu, Democratic Republic of the Congo

Author

Kinganda-Lusamaki, Eddy, Black, Allison, Mukadi, Daniel B., Hadfield, James, Mbala-Kingebeni, Placide, Pratt, Catherine B., Aziza, Amuri, Diagne, Moussa M., White, Bailey, Bisento, Nella, Nsunda, Bibiche, Akonga, Marceline, Faye, Martin, Faye, Ousmane, Edidi-Atani, Francois, Matondo-Kuamfumu, Meris, Mambu-Mbika, Fabrice, Bulabula, Junior, Di Paola, Nicholas, Pauthner, Matthias G., Andersen, Kristian G., Palacios, Gustavo, Delaporte, Eric, Sall, Amadou Alpha, Peeters, Martine, Wiley, Michael R., Ahuka-Mundeke, Steve, Bedford, Trevor, and Tamfum, Jean-Jacques Muyembe

Published
2021
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35. Upper Airway Epithelial Tissue Transcriptome Analysis Reveals Immune Signatures Associated with COVID-19 Severity in Ghanaians.

Author

Sandi, John Demby, Levy, Joshua I., Tapela, Kesego, Zeller, Mark, Yeboah, Joshua Afari, Saka, Daniel Frimpong, Grant, Donald S., Awandare, Gordon A., Quashie, Peter K., Andersen, Kristian G., and Paemka, Lily

Subjects
SARS-CoV-2, COVID-19, EPITHELIUM, TISSUE analysis, GHANAIANS
Abstract

The immunological signatures driving the severity of coronavirus disease 19 (COVID-19) in Ghanaians remain poorly understood. We performed bulk transcriptome sequencing of nasopharyngeal samples from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-infected Ghanaians with mild and severe COVID-19, as well as healthy controls to characterize immune signatures at the primary SARS-CoV-2 infection site and identify drivers of disease severity. Generally, a heightened antiviral response was observed in SARS-CoV-2-infected Ghanaians compared with uninfected controls. COVID-19 severity was associated with immune suppression, overexpression of proinflammatory cytokines, including CRNN, IL1A, S100A7, and IL23A, and activation of pathways involved in keratinocyte proliferation. SAMD9L was among the differentially regulated interferon-stimulated genes in our mild and severe disease cohorts, suggesting that it may play a critical role in SARS-CoV-2 pathogenesis. By comparing our data with a publicly available dataset from a non-African (Indians) (GSE166530), an elevated expression of antiviral response-related genes was noted in COVID-19-infected Ghanaians. Overall, the study describes immune signatures driving COVID-19 severity in Ghanaians and identifies immune drivers that could serve as potential prognostic markers for future outbreaks or pandemics. It further provides important preliminary evidence suggesting differences in antiviral response at the upper respiratory interface in sub-Saharan Africans (Ghanaians) and non-Africans, which could be contributing to the differences in disease outcomes. Further studies using larger datasets from different populations will expand on these findings. [ABSTRACT FROM AUTHOR]

Published
2024
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37. Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic

Author

Crits-Christoph, Alexander, primary, Levy, Joshua I., additional, Pekar, Jonathan, additional, Goldstein, Stephen A., additional, Singh, Reema, additional, Hensel, Zach, additional, Gangavarapu, Karthik, additional, Rogers, Matthew B., additional, Moshiri, Niema, additional, Garry, Robert f, additional, Holmes, Edward C, additional, Koopmans, Marion P. G., additional, Lemey, Philippe, additional, Popescu, Saskia, additional, Rambaut, Andrew, additional, Robertson, David L, additional, Suchard, Marc A., additional, Wertheim, Joel, additional, Rasmussen, Angela L., additional, Andersen, Kristian G, additional, Worobey, Michael, additional, and Débarre, Florence, additional

Published
2023
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38. Analysis of CD8⁺ T cell response during the 2013–2016 Ebola epidemic in West Africa

Author

Sakabe, Saori, Sullivan, Brian M., Hartnett, Jessica N., Robles-Sikisaka, Refugio, Gangavarapu, Karthik, Cubitt, Beatrice, Ware, Brian C., Kotliar, Dylan, Branco, Luis M., Goba, Augustine, Momoh, Mambu, Sandi, John Demby, Kanneh, Lansana, Grant, Donald S., Garry, Robert F., Andersen, Kristian G., de la Torre, Juan Carlos, Sabeti, Pardis C., Schieffelin, John S., and Oldstone, Michael B. A.

Published
2018

39. Lassa Virus Genetics

Author

Klitting, Raphaëlle, primary, Mehta, Samar B., additional, Oguzie, Judith U., additional, Oluniyi, Paul E., additional, Pauthner, Matthias G., additional, Siddle, Katherine J., additional, Andersen, Kristian G., additional, Happi, Christian T., additional, and Sabeti, Pardis C., additional

Published
2020
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43. Novel Tools for Lassa Virus Surveillance in Peri-domestic Rodents

Author

Smither, Allison R., primary, Koninga, James, additional, Kanneh, Franklyn B., additional, Foday, Momoh, additional, Boisen, Matthew L., additional, Bond, Nell G., additional, Momoh, Mambu, additional, Demby Sandi, John, additional, Kanneh, Lansana, additional, Alhasan, Foday, additional, Mustapha Kanneh, Ibrahim, additional, Yillah, Mohamed S., additional, Grant, Donald S., additional, Bush, Duane J., additional, Nelson, Diana K.S., additional, Cruz, Kaitlin M., additional, Klitting, Raphaelle, additional, Pauthner, Matthias, additional, Andersen, Kristian G., additional, Shaffer, Jeffrey G., additional, Cross, Robert W., additional, Schieffelin, John S., additional, and Garry, Robert F., additional

Published
2023
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44. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics

Author

Matteson, Nathaniel L., primary, Hassler, Gabriel W., additional, Kurzban, Ezra, additional, Schwab, Madison A., additional, Perkins, Sarah A., additional, Gangavarapu, Karthik, additional, Levy, Joshua I., additional, Parker, Edyth, additional, Pride, David, additional, Hakim, Abbas, additional, Hoff, Peter De, additional, Cheung, Willi, additional, Castro-Martinez, Anelizze, additional, Rivera, Andrea, additional, Veder, Anthony, additional, Rivera, Ariana, additional, Wauer, Cassandra, additional, Holmes, Jacqueline, additional, Wilson, Jedediah, additional, Ngo, Shayla N., additional, Plascencia, Ashley, additional, Lawrence, Elijah S., additional, Smoot, Elizabeth W., additional, Eisner, Emily R., additional, Tsai, Rebecca, additional, Chacón, Marisol, additional, Baer, Nathan A., additional, Seaver, Phoebe, additional, Salido, Rodolfo A., additional, Aigner, Stefan, additional, Ngo, Toan T., additional, Barber, Tom, additional, Ostrander, Tyler, additional, Fielding-Miller, Rebecca, additional, Simmons, Elizabeth H., additional, Zazueta, Oscar E., additional, Serafin-Higuera, Idanya, additional, Sanchez-Alavez, Manuel, additional, Moreno-Camacho, Jose L., additional, García-Gil, Abraham, additional, Murphy Schafer, Ashleigh R., additional, McDonald, Eric, additional, Corrigan, Jeremy, additional, Malone, John D., additional, Stous, Sarah, additional, Shah, Seema, additional, Moshiri, Niema, additional, Weiss, Alana, additional, Anderson, Catelyn, additional, Aceves, Christine M., additional, Spencer, Emily G., additional, Hufbauer, Emory C., additional, Lee, Justin J., additional, Ramesh, Karthik S., additional, Nguyen, Kelly N., additional, Saucedo, Kieran, additional, Robles-Sikisaka, Refugio, additional, Fisch, Kathleen M., additional, Gonias, Steven L., additional, Birmingham, Amanda, additional, McDonald, Daniel, additional, Karthikeyan, Smruthi, additional, Martin, Natasha K., additional, Schooley, Robert T., additional, Negrete, Agustin J., additional, Reyna, Horacio J., additional, Chavez, Jose R., additional, Garcia, Maria L., additional, Cornejo-Bravo, Jose M., additional, Becker, David, additional, Isaksson, Magnus, additional, Washington, Nicole L., additional, Lee, William, additional, Garfein, Richard S., additional, Luna-Ruiz Esparza, Marco A., additional, Alcántar-Fernández, Jonathan, additional, Henson, Benjamin, additional, Jepsen, Kristen, additional, Olivares-Flores, Beatriz, additional, Barrera-Badillo, Gisela, additional, Lopez-Martínez, Irma, additional, Ramírez-González, José E., additional, Flores-León, Rita, additional, Kingsmore, Stephen F., additional, Sanders, Alison, additional, Pradenas, Allorah, additional, White, Benjamin, additional, Matthews, Gary, additional, Hale, Matt, additional, McLawhon, Ronald W., additional, Reed, Sharon L., additional, Winbush, Terri, additional, McHardy, Ian H., additional, Fielding, Russel A., additional, Nicholson, Laura, additional, Quigley, Michael M., additional, Harding, Aaron, additional, Mendoza, Art, additional, Bakhtar, Omid, additional, Browne, Sara H., additional, Flores, Jocelyn Olivas, additional, Rincon Rodríguez, Diana G., additional, Ibarra, Martin Gonzalez, additional, Robles Ibarra, Luis C., additional, Arellano Vera, Betsy J., additional, Garcia, Jonathan Gonzalez, additional, Harvey-Vera, Alicia, additional, Knight, Rob, additional, Laurent, Louise C., additional, Yeo, Gene W., additional, Wertheim, Joel O., additional, Ji, Xiang, additional, Worobey, Michael, additional, Suchard, Marc A., additional, Andersen, Kristian G., additional, Campos-Romero, Abraham, additional, Wohl, Shirlee, additional, and Zeller, Mark, additional

Published
2023
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45. Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schools

Author

Fielding-Miller, Rebecca, primary, Karthikeyan, Smruthi, additional, Gaines, Tommi, additional, Garfein, Richard S., additional, Salido, Rodolfo A., additional, Cantu, Victor J., additional, Kohn, Laura, additional, Martin, Natasha K., additional, Wynn, Adriane, additional, Wijaya, Carrissa, additional, Flores, Marlene, additional, Omaleki, Vinton, additional, Majnoonian, Araz, additional, Gonzalez-Zuniga, Patricia, additional, Nguyen, Megan, additional, Vo, Anh V., additional, Le, Tina, additional, Duong, Dawn, additional, Hassani, Ashkan, additional, Tweeten, Samantha, additional, Jepsen, Kristen, additional, Henson, Benjamin, additional, Hakim, Abbas, additional, Birmingham, Amanda, additional, De Hoff, Peter, additional, Mark, Adam M., additional, Nasamran, Chanond A., additional, Rosenthal, Sara Brin, additional, Moshiri, Niema, additional, Fisch, Kathleen M., additional, Humphrey, Greg, additional, Farmer, Sawyer, additional, Tubb, Helena M., additional, Valles, Tommy, additional, Morris, Justin, additional, Kang, Jaeyoung, additional, Khaleghi, Behnam, additional, Young, Colin, additional, Akel, Ameen D., additional, Eilert, Sean, additional, Eno, Justin, additional, Curewitz, Ken, additional, Laurent, Louise C., additional, Rosing, Tajana, additional, Knight, Rob, additional, Baer, Nathan A., additional, Barber, Tom, additional, Castro-Martinez, Anelizze, additional, Chacón, Marisol, additional, Cheung, Willi, additional, Crescini, Evelyn S., additional, Eisner, Emily R., additional, Franco Vargas, Lizbeth, additional, Hobbs, Charlotte, additional, Lastrella, Alma L., additional, Lawrence, Elijah S., additional, Matteson, Nathaniel L., additional, Gangavarapu, Karthik, additional, Ngo, Toan T., additional, Seaver, Phoebe, additional, Smoot, Elizabeth W., additional, Tsai, Rebecca, additional, Xia, Bing, additional, Aigner, Stefan, additional, Anderson, Catelyn, additional, Belda-Ferre, Pedro, additional, Sathe, Shashank, additional, Zeller, Mark, additional, Andersen, Kristian G., additional, Yeo, Gene W., additional, and Kurzban, Ezra, additional

Published
2023
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46. Genomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineages

Author

Oliveira, Glenn, primary, Vogels, Chantal B. F., additional, Zolfaghari, Ashley, additional, Saraf, Sharada, additional, Klitting, Raphaelle, additional, Weger-Lucarelli, James, additional, P. Leon, Karla, additional, Ontiveros, Carlos O., additional, Agarwal, Rimjhim, additional, Tsetsarkin, Konstantin A., additional, Harris, Eva, additional, Ebel, Gregory D., additional, Wohl, Shirlee, additional, Grubaugh, Nathan D., additional, and Andersen, Kristian G., additional

Published
2023
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47. An Outbreak of Ebola Virus Disease in the Lassa Fever Zone

Author

Goba, Augustine, Khan, S. Humarr, Fonnie, Mbalu, Fullah, Mohamed, Moigboi, Alex, Kovoma, Alice, Sinnah, Vandi, Yoko, Nancy, Rogers, Hawa, Safai, Siddiki, Momoh, Mambu, Koroma, Veronica, Kamara, Fatima K., Konowu, Edwin, Yillah, Mohamed, French, Issa, Mustapha, Ibraham, Kanneh, Franklyn, Foday, Momoh, McCarthy, Helena, Kallon, Tiangay, Kallon, Mustupha, Naiebu, Jenneh, Sellu, Josephine, Jalloh, Abdul A., Gbakie, Michael, Kanneh, Lansana, Massaly, James L. B., Kargbo, David, Kargbo, Brima, Vandi, Mohamed, Gbetuwa, Momoh, Gevao, Sahr M., Sandi, John D., Jalloh, Simbirie C., Grant, Donald S., Blyden, Sylvia O., Crozier, Ian, Schieffelin, John S., McLellan, Susan L., Jacob, Shevin T., Boisen, Matt L., Hartnett, Jessica N., Cross, Robert W., Branco, Luis M., Andersen, Kristian G., Yozwiak, Nathan L., Gire, Stephen K., Tariyal, Ridhi, Park, Daniel J., Haislip, Allyson M., Bishop, Christopher M., Melnik, Lilia I., Gallaher, William R., Wimley, William C., He, Jing, Shaffer, Jeffrey G., Sullivan, Brian M., Grillo, Sonia, Oman, Scott, Garry, Courtney E., Edwards, Donna R., McCormick, Stephanie J., Elliott, Deborah H., Rouelle, Julie A., Kannadka, Chandrika B., Reyna, Ashley A., Bradley, Benjamin T., Yu, Haini, Yenni, Rachael E., Hastie, Kathryn M., Geisbert, Joan B., Kulakosky, Peter C., Wilson, Russell B., Oldstone, Michael B. A., Pitts, Kelly R., Henderson, Lee A., Robinson, James E., Geisbert, Thomas W., Saphire, Erica Ollmann, Happi, Christian T., Asogun, Danny A., Sabeti, Pardis C., and Garry, Robert F.

Published
2016

48. Ebola Virus Epidemiology and Evolution in Nigeria

Author

Folarin, Onikepe A., Ehichioya, Deborah, Schaffner, Stephen F., Winnicki, Sarah M., Wohl, Shirlee, Eromon, Philomena, West, Kendra L., Gladden-Young, Adrianne, Oyejide, Nicholas E., Matranga, Christian B., Deme, Awa Bineta, James, Ayorinde, Tomkins-Tinch, Christopher, Onyewurunwa, Kenneth, Ladner, Jason T., Palacios, Gustavo, Nosamiefan, Iguosadolo, Andersen, Kristian G., Omilabu, Sunday, Park, Daniel J., Yozwiak, Nathan L., Nasidi, Abdusallam, Garry, Robert F., Tomori, Oyewale, Sabeti, Pardis C., and Happi, Christian T.

Published
2016

49. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

Author

Grubaugh, Nathan D., Gangavarapu, Karthik, Quick, Joshua, Matteson, Nathaniel L., De Jesus, Jaqueline Goes, Main, Bradley J., Tan, Amanda L., Paul, Lauren M., Brackney, Doug E., Grewal, Saran, Gurfield, Nikos, Van Rompay, Koen K. A., Isern, Sharon, Michael, Scott F., Coffey, Lark L., Loman, Nicholas J., and Andersen, Kristian G.

Published
2019
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50. Genetic evidence of susceptible wildlife in SARS-CoV-2 positive samples at the Huanan Wholesale Seafood Market, Wuhan: Analysis and interpretation of data released by the Chinese Center for Disease Control

Author

Crits-Christoph, Alex, Gangavarapu, Karthik, Pekar, Jonathan E., Moshiri, Niema, Singh, Reema, Levy, Joshua I., Goldstein, Stephen A., Suchard, Marc A., Popescu, Saskia, Robertson, David L., Lemey, Philippe, Wertheim, Joel O., Garry, Robert F., Rasmussen, Angela L., Andersen, Kristian G., Holmes, Edward C., Rambaut, Andrew, Worobey, Michael, and Débarre, Florence

Abstract

Report: Genetic evidence of susceptible wildlife in SARS-CoV-2 positive samples at the Huanan Wholesale Seafood Market, Wuhan: Analysis and interpretation of data released by the Chinese Center for Disease Control &nbsp

Published
2023
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