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1. Power and sample size calculations for testing the ratio of reproductive values in phylogenetic samples

Author

McGowan, Lucy D'Agostino, Wohl, Shirlee, and Lessler, Justin

Subjects
Quantitative Biology - Populations and Evolution, Statistics - Applications, Statistics - Methodology
Abstract

The quality of the inferences we make from pathogen sequence data is determined by the number and composition of pathogen sequences that make up the sample used to drive that inference. However, there remains limited guidance on how to best structure and power studies when the end goal is phylogenetic inference. One question that we can attempt to answer with molecular data is whether some people are more likely to transmit a pathogen than others. Here we present an estimator to quantify differential transmission, as measured by the ratio of reproductive numbers between people with different characteristics, using transmission pairs linked by molecular data, along with a sample size calculation for this estimator. We also provide extensions to our method to correct for imperfect identification of transmission linked pairs, overdispersion in the transmission process, and group imbalance. We validate this method via simulation and provide tools to implement it in an R package, phylosamp.

Published
2023

2. 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, and Martin, Natasha K

Subjects
Biodefense, Human Genome, Lung, Emerging Infectious Diseases, Vaccine Related, Biotechnology, Genetics, Prevention, Infection, Good Health and Well Being, COVID-19, Humans, RNA, Viral, SARS-CoV-2, Sequence Analysis, RNA, Wastewater, Wastewater-Based Epidemiological Monitoring, General Science & Technology
Abstract

As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases1-3. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,5. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We developed and deployed improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detected emerging variants of concern up to 14 days earlier in wastewater samples, and identified multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.

Published
2022

4. 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

5. 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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6. Wastewater sequencing uncovers 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, Barrett, Kelly M Schiabor, Washington, Nicole L, Malone, John D, Schafer, Ashleigh Murphy, Gurfield, Nikos, Stous, Sarah, Fielding-Miller, Rebecca, Garfein, Richard S, Gaines, Tommi, Anderson, Cheryl, and Martin, Natasha K

Subjects
Vaccine Related, Infectious Diseases, Biodefense, Emerging Infectious Diseases, Lung, Genetics, Human Genome, Clinical Research, Prevention, Biotechnology, Infection, Good Health and Well Being
Abstract

Summary As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.

Published
2021

8. Combining genomics and epidemiology to track mumps virus transmission in the United States.

Author

Wohl, Shirlee, Metsky, Hayden C, Schaffner, Stephen F, Piantadosi, Anne, Burns, Meagan, Lewnard, Joseph A, Chak, Bridget, Krasilnikova, Lydia A, Siddle, Katherine J, Matranga, Christian B, Bankamp, Bettina, Hennigan, Scott, Sabina, Brandon, Byrne, Elizabeth H, McNall, Rebecca J, Shah, Rickey R, Qu, James, Park, Daniel J, Gharib, Soheyla, Fitzgerald, Susan, Barreira, Paul, Fleming, Stephen, Lett, Susan, Rota, Paul A, Madoff, Lawrence C, Yozwiak, Nathan L, MacInnis, Bronwyn L, Smole, Sandra, Grad, Yonatan H, and Sabeti, Pardis C

Subjects
Humans, Mumps virus, Mumps, Viral Proteins, Vaccination, Sequence Analysis, DNA, Disease Outbreaks, Phylogeny, Genotype, Mutation, Genome, Viral, United States, Molecular Epidemiology, Sequence Analysis, DNA, Genome, Viral, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Unusually large outbreaks of mumps across the United States in 2016 and 2017 raised questions about the extent of mumps circulation and the relationship between these and prior outbreaks. We paired epidemiological data from public health investigations with analysis of mumps virus whole genome sequences from 201 infected individuals, focusing on Massachusetts university communities. Our analysis suggests continuous, undetected circulation of mumps locally and nationally, including multiple independent introductions into Massachusetts and into individual communities. Despite the presence of these multiple mumps virus lineages, the genomic data show that one lineage has dominated in the US since at least 2006. Widespread transmission was surprising given high vaccination rates, but we found no genetic evidence that variants arising during this outbreak contributed to vaccine escape. Viral genomic data allowed us to reconstruct mumps transmission links not evident from epidemiological data or standard single-gene surveillance efforts and also revealed connections between apparently unrelated mumps outbreaks.

Published
2020

9. NewVibrio choleraesequences from Eastern and Southern Africa alter our understanding of regional cholera transmission

Author

Xiao, Shaoming, primary, Abade, Ahmed, additional, Boru, Waqo, additional, Kasambara, Watipaso, additional, Mwaba, John, additional, Ongole, Francis, additional, Mmanywa, Mariam, additional, Trovão, Nídia Sequeira, additional, Chilengi, Roma, additional, Kwenda, Geoffrey, additional, Orach, Christopher Garimoi, additional, Chibwe, Innocent, additional, Bwire, Godfrey, additional, Stine, O. Colin, additional, Milstone, Aaron M., additional, Lessler, Justin, additional, Azman, Andrew S., additional, Luo, Wensheng, additional, Murt, Kelsey, additional, Sack, David A., additional, Debes, Amanda K., additional, and Wohl, Shirlee, additional

Published
2024
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10. 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

13. 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

14. 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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15. 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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16. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

Author

Gire, Stephen K., Goba, Augustine, Andersen, Kristian G., Sealfon, Rachel S. G., Park, Daniel J., Kanneh, Lansana, Jalloh, Simbirie, Momoh, Mambu, Fullah, Mohamed, Dudas, Gytis, Wohl, Shirlee, Moses, Lina M., Yozwiak, Nathan L., Winnicki, Sarah, Matranga, Christian B., Malboeuf, Christine M., Qu, James, Gladden, Adrianne D., Schaffner, Stephen F., Yang, Xiao, Jiang, Pan-Pan, Nekoui, Mahan, Colubri, Andres, Coomber, Moinya Ruth, Fonnie, Mbalu, Moigboi, Alex, Gbakie, Michael, Kamara, Fatima K., Tucker, Veronica, Konuwa, Edwin, Saffa, Sidiki, Sellu, Josephine, Jalloh, Abdul Azziz, Kovoma, Alice, Koninga, James, Mustapha, Ibrahim, Kargbo, Kandeh, Foday, Momoh, Yillah, Mohamed, Kanneh, Franklyn, Robert, Willie, Massally, James L. B., Chapman, Sinéad B., Bochicchio, James, Murphy, Cheryl, Nusbaum, Chad, Young, Sarah, Birren, Bruce W., Grant, Donald S., Scheiffelin, John S., Lander, Eric S., Happi, Christian, Gevao, Sahr M., Gnirke, Andreas, Rambaut, Andrew, Garry, Robert F., Khan, S. Humarr, and Sabeti, Pardis C.

Published
2014

17. Prediction of Antibiotic Susceptibility Profiles of Vibrio cholerae Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon

Author

Fuesslin, Valeria, primary, Krautwurst, Sebastian, additional, Srivastava, Akash, additional, Winter, Doris, additional, Liedigk, Britta, additional, Thye, Thorsten, additional, Herrera-León, Silvia, additional, Wohl, Shirlee, additional, May, Jürgen, additional, Fobil, Julius N., additional, Eibach, Daniel, additional, Marz, Manja, additional, and Schuldt, Kathrin, additional

Published
2022
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18. 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, Ontiveros, Carlos O., additional, Agarwal, Rimjhim, additional, Leon, Karla P., 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
2022
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19. Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions

Author

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

Published
2022
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20. In vivo single-cell profiling of lncRNAs during Ebola virus infection

Author

Santus, Luisa, primary, García-Pérez, Raquel, additional, Sopena-Rios, Maria, additional, Lin, Aaron E, additional, Adams, Gordon C, additional, Barnes, Kayla G, additional, Siddle, Katherine J, additional, Wohl, Shirlee, additional, Reverter, Ferran, additional, Rinn, John L, additional, Bennett, Richard S, additional, Hensley, Lisa E, additional, Sabeti, Pardis C, additional, and Melé, Marta, additional

Published
2022
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22. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission

Author

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

Published
2021
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25. Regional sequencing collaboration reveals persistence of the T12 Vibrio cholerae O1 lineage in West Africa

Author

Ekeng, Eme, primary, Tchatchouang, Serges, additional, Akenji, Blaise, additional, Issaka, Bassira Boubacar, additional, Akintayo, Ifeoluwa, additional, Chukwu, Christopher, additional, Dano, Ibrahim Dan, additional, Melingui, Sylvie, additional, Ousmane, Sani, additional, Popoola, Michael Oladotun, additional, Nzouankeu, Ariane, additional, Boum, Yap, additional, Luquero, Francisco, additional, Ahumibe, Anthony, additional, Naidoo, Dhamari, additional, Azman, Andrew, additional, Lessler, Justin, additional, and Wohl, Shirlee, additional

Published
2021
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26. Author response: Regional sequencing collaboration reveals persistence of the T12 Vibrio cholerae O1 lineage in West Africa

Author

Ekeng, Eme, primary, Tchatchouang, Serges, additional, Akenji, Blaise, additional, Issaka, Bassira Boubacar, additional, Akintayo, Ifeoluwa, additional, Chukwu, Christopher, additional, Dano, Ibrahim Dan, additional, Melingui, Sylvie, additional, Ousmane, Sani, additional, Popoola, Michael Oladotun, additional, Nzouankeu, Ariane, additional, Boum, Yap, additional, Luquero, Francisco, additional, Ahumibe, Anthony, additional, Naidoo, Dhamari, additional, Azman, Andrew, additional, Lessler, Justin, additional, and Wohl, Shirlee, additional

Published
2021
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27. Sample size calculation for phylogenetic case linkage

Author

Wohl, Shirlee, Giles, John R., and Lessler, Justin

Subjects
0301 basic medicine, Heredity, Computer science, Genetic Linkage, Epidemiology, computer.software_genre, Pathology and Laboratory Medicine, law.invention, 0302 clinical medicine, law, Medicine and Health Sciences, Biology (General), Phylogeny, Data Management, education.field_of_study, Ecology, Phylogenetic tree, Genomics, Phylogenetics, Computational Theory and Mathematics, Research Design, Modeling and Simulation, Genetic Epidemiology, Viruses, Data mining, Pathogens, Research Article, Computer and Information Sciences, Substitution Mutation, QH301-705.5, Population, Linkage (mechanical), Infections, Sensitivity and Specificity, 03 medical and health sciences, Cellular and Molecular Neuroscience, Component (UML), Genetics, Humans, Evolutionary Systematics, Sensitivity (control systems), education, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Taxonomy, Evolutionary Biology, Bacteria, Counterintuitive, Computational Biology, Biology and Life Sciences, 030104 developmental biology, Transmission (telecommunications), Sample size determination, Sample Size, Mutation, computer, 030217 neurology & neurosurgery
Abstract

Sample size calculations are an essential component of the design and evaluation of scientific studies. However, there is a lack of clear guidance for determining the sample size needed for phylogenetic studies, which are becoming an essential part of studying pathogen transmission. We introduce a statistical framework for determining the number of true infector-infectee transmission pairs identified by a phylogenetic study, given the size and population coverage of that study. We then show how characteristics of the criteria used to determine linkage and aspects of the study design can influence our ability to correctly identify transmission links, in sometimes counterintuitive ways. We test the overall approach using outbreak simulations and provide guidance for calculating the sensitivity and specificity of the linkage criteria, the key inputs to our approach. The framework is freely available as the R package phylosamp, and is broadly applicable to designing and evaluating a wide array of pathogen phylogenetic studies., Author summary Sequencing the genetic material of viral and bacterial pathogens has become an important part of tracking and combating human infectious diseases. Specifically, comparing the pathogen DNA or RNA sequences collected from infected individuals can allow researchers and public health experts to determine who infected whom, or detect when a pathogen entered a specific country or geographic area. However, it is often impossible to collect samples from every single infected person, and these missing sequences can pose problems for this type of analysis, especially if there is some bias behind which samples were selected for sequencing. We have developed a mathematical framework that allows users to determine the probability their conclusions about pathogen transmission are correct given the number and proportion of samples from a pathogen outbreak they have sequenced. This framework is freely available, easy to use, and broadly generalizable to any pathogen, and we hope that it can be used to inform the design and sampling strategies behind future sequencing-based studies.

Published
2020

28. VIRAL EVOLUTION: Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

Author

Gire, Stephen K., Goba, Augustine, Andersen, Kristian G., Sealfon, Rachel S. G., Park, Daniel J., Kanneh, Lansana, Jalloh, Simbirie, Momoh, Mambu, Fullah, Mohamed, Dudas, Gytis, Wohl, Shirlee, Moses, Lina M., Yozwiak, Nathan L., Winnicki, Sarah, Matranga, Christian B., Malboeuf, Christine M., Qu, James, Gladden, Adrianne D., Schaffner, Stephen F., Yang, Xiao, Jiang, Pan-Pan, Nekoui, Mahan, Colubri, Andres, Coomber, Moinya Ruth, Fonnie, Mbalu, Moigboi, Alex, Gbakie, Michael, Kamara, Fatima K., Tucker, Veronica, Konuwa, Edwin, Saffa, Sidiki, Sellu, Josephine, Jalloh, Abdul Azziz, Kovoma, Alice, Koninga, James, Mustapha, Ibrahim, Kargbo, Kandeh, Foday, Momoh, Yillah, Mohamed, Kanneh, Franklyn, Robert, Willie, Massally, James L. B., Chapman, Sinéad B., Bochicchio, James, Murphy, Cheryl, Nusbaum, Chad, Young, Sarah, Birren, Bruce W., Grant, Donald S., Scheiffelin, John S., Lander, Eric S., Happi, Christian, Gevao, Sahr M., Gnirke, Andreas, Rambaut, Andrew, Garry, Robert F., Khan, S. Humarr, and Sabeti, Pardis C.

Published
2014
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29. Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore–Washington metropolitan area

Author

Thielen, Peter M., primary, Wohl, Shirlee, additional, Mehoke, Thomas, additional, Ramakrishnan, Srividya, additional, Kirsche, Melanie, additional, Falade-Nwulia, Oluwaseun, additional, Trovão, Nídia S., additional, Ernlund, Amanda, additional, Howser, Craig, additional, Sadowski, Norah, additional, Morris, C. Paul, additional, Hopkins, Mark, additional, Schwartz, Matthew, additional, Fan, Yunfan, additional, Gniazdowski, Victoria, additional, Lessler, Justin, additional, Sauer, Lauren, additional, Schatz, Michael C., additional, Evans, Jared D., additional, Ray, Stuart C., additional, Timp, Winston, additional, and Mostafa, Heba H., additional

Published
2021
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31. Zika virus evolution and spread in the Americas

Author

Metsky, Hayden C., Matranga, Christian B., Wohl, Shirlee, Schaffner, Stephen F., Freije, Catherine A., Winnicki, Sarah M., West, Kendra, Qu, James, Baniecki, Mary Lynn, Gladden-Young, Adrianne, Lin, Aaron E., Tomkins-Tinch, Christopher H., Ye, Simon H., Park, Daniel J., Luo, Cynthia Y., Barnes, Kayla G., Shah, Rickey R., Chak, Bridget, Barbosa-Lima, Giselle, Delatorre, Edson, Vieira, Yasmine R., Paul, Lauren M., Tan, Amanda L., Barcellona, Carolyn M., Porcelli, Mario C., Vasquez, Chalmers, Cannons, Andrew C., Cone, Marshall R., Hogan, Kelly N., Kopp, Edgar W., Anzinger, Joshua J., Garcia, Kimberly F., Parham, Leda A., Ramrez, Rosa M. Glvez, Montoya, Maria C. Miranda, Rojas, Diana P., Brown, Catherine M., Hennigan, Scott, Sabina, Brandon, Scotland, Sarah, Gangavarapu, Karthik, Grubaugh, Nathan D., Oliveira, Glenn, Robles-Sikisaka, Refugio, Rambaut, Andrew, Gehrke, Lee, Smole, Sandra, Halloran, M. Elizabeth, Villar, Luis, Mattar, Salim, Lorenzana, Ivette, Cerbino-Neto, Jose, Valim, Clarissa, Degrave, Wim, Bozza, Patricia T., Gnirke, Andreas, Andersen, Kristian G., Isern, Sharon, Michael, Scott F., Bozza, Fernando A., Souza, Thiago M. L., Bosch, Irene, Yozwiak, Nathan L., MacInnis, Bronwyn L., and Sabeti, Pardis C.

Subjects
America -- Health aspects, Zika virus -- Natural history, Zika virus infection -- Distribution, Company distribution practices, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Hayden C. Metsky [1, 2]; Christian B. Matranga [1]; Shirlee Wohl [1, 3]; Stephen F. Schaffner [1, 3, 4]; Catherine A. Freije [1, 3]; Sarah M. Winnicki [1]; Kendra [...]

Published
2017
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32. Genomic epidemiology reveals multiple introductions of Zika virus into the United States

Author

Grubaugh, Nathan D., Ladner, Jason T., Kraemer, Moritz U. G., Dudas, Gytis, Tan, Amanda L., Gangavarapu, Karthik, Wiley, Michael R., White, Stephen, Thz, Julien, Magnani, Diogo M., Prieto, Karla, Reyes, Daniel, Bingham, Andrea M., Paul, Lauren M., Robles-Sikisaka, Refugio, Oliveira, Glenn, Pronty, Darryl, Barcellona, Carolyn M., Metsky, Hayden C., Baniecki, Mary Lynn, Barnes, Kayla G., Chak, Bridget, Freije, Catherine A., Gladden-Young, Adrianne, Gnirke, Andreas, Luo, Cynthia, MacInnis, Bronwyn, Matranga, Christian B., Park, Daniel J., Qu, James, Schaffner, Stephen F., Tomkins-Tinch, Christopher, West, Kendra L., Winnicki, Sarah M., Wohl, Shirlee, Yozwiak, Nathan L., Quick, Joshua, Fauver, Joseph R., Khan, Kamran, Brent, Shannon E., Reiner, Robert C., Jr, Lichtenberger, Paola N., Ricciardi, Michael J., Bailey, Varian K., Watkins, David I., Cone, Marshall R., Kopp, Edgar W., IV, Hogan, Kelly N., Cannons, Andrew C., Jean, Reynald, Monaghan, Andrew J., Garry, Robert F., Loman, Nicholas J., Faria, Nuno R., Porcelli, Mario C., Vasquez, Chalmers, Nagle, Elyse R., Cummings, Derek A. T., Stanek, Danielle, Rambaut, Andrew, Sanchez-Lockhart, Mariano, Sabeti, Pardis C., Gillis, Leah D., Michael, Scott F., Bedford, Trevor, Pybus, Oliver G., Isern, Sharon, Palacios, Gustavo, and Andersen, Kristian G.

Subjects
Zika virus -- Health aspects -- Genetic aspects, Gene expression -- Health aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Nathan D. Grubaugh [1]; Jason T. Ladner [2]; Moritz U. G. Kraemer [3, 4, 5]; Gytis Dudas [6]; Amanda L. Tan [7]; Karthik Gangavarapu [1]; Michael R. Wiley [2, [...]

Published
2017
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33. Repeated Coronavirus Disease 2019 Molecular Testing: Correlation of Severe Acute Respiratory Syndrome Coronavirus 2 Culture With Molecular Assays and Cycle Thresholds

Author

Gniazdowski, Victoria, primary, Paul Morris, C, additional, Wohl, Shirlee, additional, Mehoke, Thomas, additional, Ramakrishnan, Srividya, additional, Thielen, Peter, additional, Powell, Harrison, additional, Smith, Brendan, additional, Armstrong, Derek T, additional, Herrera, Monica, additional, Reifsnyder, Carolyn, additional, Sevdali, Maria, additional, Carroll, Karen C, additional, Pekosz, Andrew, additional, and Mostafa, Heba H, additional

Published
2020
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34. Successive epidemic waves of cholera in South Sudan, 2014 - 2017

Author

Jones, Forrest K, primary, Wamala, Joseph F, additional, Rumunu, John, additional, Mawien, Pinyi Nyimol, additional, Tut, Kol Mathew, additional, Wohl, Shirlee, additional, Deng, Lul, additional, Pezzoli, Lorenzo, additional, Omar, Linda Haj, additional, Lessler, Justin, additional, Quilici, Marie-Laure, additional, Luquero, Francisco J, additional, and Azman, Andrew S, additional

Published
2020
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35. Persistence of the T12 Vibrio cholerae O1 lineage in West Africa: Insights from a Regional Sequencing Workshop

Author

Ekeng, Eme, primary, Tchatchouang, Serges, additional, Akenji, Blaise, additional, Issaka, Bassira Boubacar, additional, Akintayo, Ifeoluwa, additional, Chukwu, Christopher, additional, Dan Dano, Ibrahim, additional, Melingui, Sylvie, additional, Sani, Ousmane, additional, Popoola, Michael Oladotun, additional, Nzouankeu, Ariane, additional, Boum, Yap, additional, Luquero, Francisco J, additional, Ahumibe, Anthony, additional, Naidoo, Dhamari, additional, Azman, Andrew S, additional, Lessler, Justin, additional, and Wohl, Shirlee, additional

Published
2020
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36. Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region

Author

Thielen, Peter M., primary, Wohl, Shirlee, additional, Mehoke, Thomas, additional, Ramakrishnan, Srividya, additional, Kirsche, Melanie, additional, Falade-Nwulia, Oluwaseun, additional, Trovão, Nídia S., additional, Ernlund, Amanda, additional, Howser, Craig, additional, Sadowski, Norah, additional, Morris, Paul, additional, Hopkins, Mark, additional, Schwartz, Matthew, additional, Fan, Yunfan, additional, Gniazdowski, Victoria, additional, Lessler, Justin, additional, Sauer, Lauren, additional, Schatz, Michael C., additional, Evans, Jared D., additional, Ray, Stuart C., additional, Timp, Winston, additional, and Mostafa, Heba H., additional

Published
2020
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38. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design

Author

Metsky, Hayden C, Siddle, Katherine J, Gladden-Young, Adrianne, Qu, James, Yang, David K, Brehio, Patrick, Goldfarb, Andrew, Piantadosi, Anne, Wohl, Shirlee, Carter, Amber, Lin, Aaron E, Barnes, Kayla G, Tully, Damien C, Corleis, Bjӧrn, Hennigan, Scott, Barbosa-Lima, Giselle, Vieira, Yasmine R, Paul, Lauren M, Tan, Amanda L, Garcia, Kimberly F, Parham, Leda A, Odia, Ikponmwosa, Eromon, Philomena, Folarin, Onikepe A, Goba, Augustine, Viral Hemorrhagic Fever Consortium, Simon-Lorière, Etienne, Hensley, Lisa, Balmaseda, Angel, Harris, Eva, Kwon, Douglas S, Allen, Todd M, Runstadler, Jonathan A, Smole, Sandra, Bozza, Fernando A, Souza, Thiago ML, Isern, Sharon, Michael, Scott F, Lorenzana, Ivette, Gehrke, Lee, Bosch, Irene, Ebel, Gregory, Grant, Donald S, Happi, Christian T, Park, Daniel J, Gnirke, Andreas, Sabeti, Pardis C, and Matranga, Christian B

Abstract

Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. Here we present CATCH, a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs optimal probe sets, with a specified number of oligonucleotides, that achieve full coverage of, and scale well with, known sequence diversity. We focus on applying CATCH to capture viral genomes in complex metagenomic samples. We design, synthesize, and validate multiple probe sets, including one that targets the whole genomes of the 356 viral species known to infect humans. Capture with these probe sets enriches unique viral content on average 18-fold, allowing us to assemble genomes that could not be recovered without enrichment, and accurately preserves within-sample diversity. We also use these probe sets to recover genomes from the 2018 Lassa fever outbreak in Nigeria and to improve detection of uncharacterized viral infections in human and mosquito samples. The results demonstrate that CATCH enables more sensitive and cost-effective metagenomic sequencing.

Published
2019

39. Repeated Coronavirus Disease 2019 Molecular Testing: Correlation of Severe Acute Respiratory Syndrome Coronavirus 2 Culture With Molecular Assays and Cycle Thresholds.

Author

Gniazdowski, Victoria, Morris, C Paul, Wohl, Shirlee, Mehoke, Thomas, Ramakrishnan, Srividya, Thielen, Peter, Powell, Harrison, Smith, Brendan, Armstrong, Derek T, Herrera, Monica, Reifsnyder, Carolyn, Sevdali, Maria, Carroll, Karen C, Pekosz, Andrew, and Mostafa, Heba H

Subjects
RNA analysis, CELL culture, MOLECULAR diagnosis, COVID-19, SEQUENCE analysis, MEDICAL screening, RETROSPECTIVE studies, GENOTYPES, DESCRIPTIVE statistics, COVID-19 testing, SARS virus, POLYMERASE chain reaction, DIAGNOSTIC errors, LONGITUDINAL method
Abstract

Background Repeated coronavirus disease 2019 (COVID-19) molecular testing can lead to positive test results after negative results and to multiple positive results over time. The association between positive test results and infectious virus is important to quantify. Methods A 2-month cohort of retrospective data and consecutively collected specimens from patients with COVID-19 or patients under investigation were used to understand the correlation between prolonged viral RNA positive test results, cycle threshold (Ct) values and growth of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in cell culture. Whole-genome sequencing was used to confirm virus genotype in patients with prolonged viral RNA detection. Droplet digital polymerase chain reaction was used to assess the rate of false-negative COVID-19 diagnostic test results. Results In 2 months, 29 686 specimens were tested and 2194 patients underwent repeated testing. Virus recovery in cell culture was noted in specimens with a mean Ct value of 18.8 (3.4) for SARS-CoV-2 target genes. Prolonged viral RNA shedding was associated with positive virus growth in culture in specimens collected up to 21 days after the first positive result but mostly in individuals symptomatic at the time of sample collection. Whole-genome sequencing provided evidence the same virus was carried over time. Positive test results following negative results had Ct values >29.5 and were not associated with virus culture. Droplet digital polymerase chain reaction results were positive in 5.6% of negative specimens collected from patients with confirmed or clinically suspected COVID-19. Conclusions Low Ct values in SARS-CoV-2 diagnostic tests were associated with virus growth in cell culture. Symptomatic patients with prolonged viral RNA shedding can also be infectious. [ABSTRACT FROM AUTHOR]

Published
2021
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41. Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018

Author

Siddle, Katherine J., primary, Eromon, Philomena, additional, Barnes, Kayla G., additional, Mehta, Samar, additional, Oguzie, Judith U., additional, Odia, Ikponmwosa, additional, Schaffner, Stephen F., additional, Winnicki, Sarah M., additional, Shah, Rickey R., additional, Qu, James, additional, Wohl, Shirlee, additional, Brehio, Patrick, additional, Iruolagbe, Christopher, additional, Aiyepada, John, additional, Uyigue, Eghosa, additional, Akhilomen, Patience, additional, Okonofua, Grace, additional, Ye, Simon, additional, Kayode, Tolulope, additional, Ajogbasile, Fehintola, additional, Uwanibe, Jessica, additional, Gaye, Amy, additional, Momoh, Mambu, additional, Chak, Bridget, additional, Kotliar, Dylan, additional, Carter, Amber, additional, Gladden-Young, Adrianne, additional, Freije, Catherine A., additional, Omoregie, Omigie, additional, Osiemi, Blessing, additional, Muoebonam, Ekene B., additional, Airende, Michael, additional, Enigbe, Rachael, additional, Ebo, Benevolence, additional, Nosamiefan, Iguosadolo, additional, Oluniyi, Paul, additional, Nekoui, Mahan, additional, Ogbaini-Emovon, Ephraim, additional, Garry, Robert F., additional, Andersen, Kristian G., additional, Park, Daniel J., additional, Yozwiak, Nathan L., additional, Akpede, George, additional, Ihekweazu, Chikwe, additional, Tomori, Oyewale, additional, Okogbenin, Sylvanus, additional, Folarin, Onikepe A., additional, Okokhere, Peter O., additional, MacInnis, Bronwyn L., additional, Sabeti, Pardis C., additional, and Happi, Christian T., additional

Published
2018
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42. Genome sequencing reveals Zika virus diversity and spread in the Americas

Author

Metsky, Hayden C, Matranga, Christian B, Wohl, Shirlee, Schaffner, Stephen F., Freije, Catherine A, Winnicki, Sarah, West, Kendra, Qu, J, Baniecki, Mary Lynn, Gladden-Young, Adrianne, Lin, Aaron E., Christopher, Tomkins-Tinch, Ye, S.H, Park, Daniel J, Luo, Cynthia, Barnes, Kayla G, Shah, R.R., Chak, Bridget, Barbosa-Lima, G., Delatorre, E., Vieira, Y.R., Paul, Lauren M, Tan, Amanda L, Barcellona, Carolyn M, Porcelli, Mario C, Vasquez, Chalmers, Cannons, Andrew C, Cone, Marshall R, Hogan, Kelly N, Kopp IV, Edgar W, Anzinger, J.J., Garcia, K.F., Parhap, L.A., Gelvez Ramirez, R.M., Montoya, Miranda, Rojas, D.P., Brown, C.M., Hennigan, S., Sabina, B., Scotland, S., Gangavarapu, K., Grubaugh, N.D., Oliveira, G., Robles-Sikisaka, R., Rambaut, Andrew, Gehrke, L., Smole, S., Halloran, M.E., Villar Centeno, L.A., Mattar, S., Lorenzana, I., Cerbino-Neto, J., Valim, C., Degrave, W., Bozza, P.T., Souza, T.M.L., Bosch, I., Yozwiak, N.L., MacInnis, B.L., and Sabeti, P.C.

Abstract

Despite great attention given to the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects1,2, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part due to a lack of genomic data. We applied multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analyzed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental US. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of viral surveillance. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those potentially relevant to the effectiveness of diagnostic tests.

Published
2017

43. Co-circulating mumps lineages at multiple geographic scales

Author

Wohl, Shirlee, primary, Metsky, Hayden C., additional, Schaffner, Stephen F., additional, Piantadosi, Anne, additional, Burns, Meagan, additional, Lewnard, Joseph A., additional, Chak, Bridget, additional, Krasilnikova, Lydia A., additional, Siddle, Katherine J., additional, Matranga, Christian B., additional, Bankamp, Bettina, additional, Hennigan, Scott, additional, Sabina, Brandon, additional, Byrne, Elizabeth H., additional, McNall, Rebecca J., additional, Park, Daniel J., additional, Gharib, Soheyla, additional, Fitzgerald, Susan, additional, Barriera, Paul, additional, Fleming, Stephen, additional, Lett, Susan, additional, Rota, Paul A., additional, Madoff, Lawrence C., additional, MacInnis, Bronwyn L., additional, Yozwiak, Nathan L., additional, Smole, Sandra, additional, Grad, Yonatan H., additional, and Sabeti, Pardis C., additional

Published
2018
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44. Multiple introductions of Zika virus into the United States revealed through genomic epidemiology

Author

Grubaugh, Nathan D, primary, Ladner, Jason T, additional, Kraemer, Moritz UG, additional, Dudas, Gytis, additional, Tan, Amanda L, additional, Gangavarapu, Karthik, additional, Wiley, Michael R, additional, White, Stephen, additional, Thézé, Julien, additional, Magnani, Diogo M, additional, Prieto, Karla, additional, Reyes, Daniel, additional, Bingham, Andrea, additional, Paul, Lauren M, additional, Robles-Sikisaka, Refugio, additional, Oliveira, Glenn, additional, Pronty, Darryl, additional, Metsky, Hayden C, additional, Baniecki, Mary Lynn, additional, Barnes, Kayla G, additional, Chak, Bridget, additional, Freije, Catherine A, additional, Gladden-Young, Adrianne, additional, Gnirke, Andreas, additional, Luo, Cynthia, additional, MacInnis, Bronwyn, additional, Matranga, Christian B, additional, Park, Daniel J, additional, Qu, James, additional, Schaffner, Stephen F, additional, Tomkins-Tinch, Christopher, additional, West, Kendra L, additional, Winnicki, Sarah M, additional, Wohl, Shirlee, additional, Yozwiak, Nathan L, additional, Quick, Joshua, additional, Fauver, Joseph R, additional, Khan, Kamran, additional, Brent, Shannon E, additional, Reiner, Robert C, additional, Lichtenberger, Paola N, additional, Ricciardi, Michael, additional, Bailey, Varian K, additional, Watkins, David I, additional, Cone, Marshall R, additional, Kopp, Edgar W, additional, Hogan, Kelly N, additional, Cannons, Andrew C, additional, Jean, Reynald, additional, Garry, Robert F, additional, Loman, Nicholas J, additional, Faria, Nuno R, additional, Porcelli, Mario C, additional, Vasquez, Chalmers, additional, Nagle, Elyse R, additional, Cummings, Derek AT, additional, Stanek, Danielle, additional, Rambaut, Andrew, additional, Sanchez-Lockhart, Mariano, additional, Sabeti, Pardis C, additional, Gillis, Leah D, additional, Michael, Scott F, additional, Bedford, Trevor, additional, Pybus, Oliver G, additional, Isern, Sharon, additional, Palacios, Gustavo, additional, and Andersen, Kristian G, additional

Published
2017
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46. Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic

Author

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

Published
2016
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47. Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone

Author

Park, Daniel J., primary, Dudas, Gytis, additional, Wohl, Shirlee, additional, Goba, Augustine, additional, Whitmer, Shannon L.M., additional, Andersen, Kristian G., additional, Sealfon, Rachel S., additional, Ladner, Jason T., additional, Kugelman, Jeffrey R., additional, Matranga, Christian B., additional, Winnicki, Sarah M., additional, Qu, James, additional, Gire, Stephen K., additional, Gladden-Young, Adrianne, additional, Jalloh, Simbirie, additional, Nosamiefan, Dolo, additional, Yozwiak, Nathan L., additional, Moses, Lina M., additional, Jiang, Pan-Pan, additional, Lin, Aaron E., additional, Schaffner, Stephen F., additional, Bird, Brian, additional, Towner, Jonathan, additional, Mamoh, Mambu, additional, Gbakie, Michael, additional, Kanneh, Lansana, additional, Kargbo, David, additional, Massally, James L.B., additional, Kamara, Fatima K., additional, Konuwa, Edwin, additional, Sellu, Josephine, additional, Jalloh, Abdul A., additional, Mustapha, Ibrahim, additional, Foday, Momoh, additional, Yillah, Mohamed, additional, Erickson, Bobbie R., additional, Sealy, Tara, additional, Blau, Dianna, additional, Paddock, Christopher, additional, Brault, Aaron, additional, Amman, Brian, additional, Basile, Jane, additional, Bearden, Scott, additional, Belser, Jessica, additional, Bergeron, Eric, additional, Campbell, Shelley, additional, Chakrabarti, Ayan, additional, Dodd, Kimberly, additional, Flint, Mike, additional, Gibbons, Aridth, additional, Goodman, Christin, additional, Klena, John, additional, McMullan, Laura, additional, Morgan, Laura, additional, Russell, Brandy, additional, Salzer, Johanna, additional, Sanchez, Angela, additional, Wang, David, additional, Jungreis, Irwin, additional, Tomkins-Tinch, Christopher, additional, Kislyuk, Andrey, additional, Lin, Michael F., additional, Chapman, Sinead, additional, MacInnis, Bronwyn, additional, Matthews, Ashley, additional, Bochicchio, James, additional, Hensley, Lisa E., additional, Kuhn, Jens H., additional, Nusbaum, Chad, additional, Schieffelin, John S., additional, Birren, Bruce W., additional, Forget, Marc, additional, Nichol, Stuart T., additional, Palacios, Gustavo F., additional, Ndiaye, Daouda, additional, Happi, Christian, additional, Gevao, Sahr M., additional, Vandi, Mohamed A., additional, Kargbo, Brima, additional, Holmes, Edward C., additional, Bedford, Trevor, additional, Gnirke, Andreas, additional, Ströher, Ute, additional, Rambaut, Andrew, additional, Garry, Robert F., additional, and Sabeti, Pardis C., additional

Published
2015
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48. Evaluation of the Potential Impact of Ebola Virus Genomic Drift on the Efficacy of Sequence-Based Candidate Therapeutics

Author

Kugelman, Jeffrey R., primary, Sanchez-Lockhart, Mariano, additional, Andersen, Kristian G., additional, Gire, Stephen, additional, Park, Daniel J., additional, Sealfon, Rachel, additional, Lin, Aaron E., additional, Wohl, Shirlee, additional, Sabeti, Pardis C., additional, Kuhn, Jens H., additional, and Palacios, Gustavo F., additional

Published
2015
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49. Genomic Analysis of Viral Outbreaks

Author

Wohl, Shirlee

Subjects
Biology, Genetics, Biology, Virology, Biology, Bioinformatics
Abstract

Due to recent advances in sequencing technologies, genomics has emerged as a powerful tool for combating viral outbreaks. In this dissertation, I show how genomic data can be used to understand the transmission, as well as the origin and evolution, of three different viruses. In Chapter 2, I describe Ebola virus (EBOV) sequences from the 2014–2016 outbreak in Sierra Leone, and what they tell us about cross-border and individual transmission, as well as evolution of the virus. In Chapter 3, we apply these findings to the 2014 EBOV outbreak in Nigeria. I present a direct comparison between genomic data and contact tracing performed during the outbreak, and show that these methods suggest similar transmission patterns, but that viral sequences provide additional information about the origins of the outbreak. In Chapter 4, I describe our efforts to characterize the movement of Zika virus (ZIKV) throughout the Americas in 2016, and I explain how we dealt with challenges related to low viral content in ZIKV samples. In Chapter 5, I explain how mumps virus (MuV) sequences from 2016–2017 informed our understanding of disease spread at multiple geographic scales. I explain the evidence for ongoing MuV transmission in the United States, and show that pairing genomic and detailed epidemiological data reveals transmission within a local community. Taken together, these chapters demonstrate the emerging capabilities of genomics, including how genomic analysis can inform our understanding of viral transmission, and show how viral sequence data can influence public health at local, national, and international scales.

Published
2018

50. New Vibrio cholerae sequences from Eastern and Southern Africa alter our understanding of regional cholera transmission.

Author

Xiao S, Abade A, Boru W, Kasambara W, Mwaba J, Ongole F, Mmanywa M, Trovão NS, Chilengi R, Kwenda G, Orach CG, Chibwe I, Bwire G, Stine OC, Milstone AM, Lessler J, Azman AS, Luo W, Murt K, Sack DA, Debes AK, and Wohl S

Abstract

Despite ongoing containment and vaccination efforts, cholera remains prevalent in many countries in sub-Saharan Africa. Part of the difficulty in containing cholera comes from our lack of understanding of how it circulates throughout the region. To better characterize regional transmission, we generated and analyzed 118 Vibrio cholerae genomes collected between 2007-2019 from five different countries in Southern and Eastern Africa. We showed that V. cholerae sequencing can be successful from a variety of sample types and filled in spatial and temporal gaps in our understanding of circulating lineages, including providing some of the first sequences from the 2018-2019 outbreaks in Uganda, Kenya, Tanzania, Zambia, and Malawi. Our results present a complex picture of cholera transmission in the region, with multiple lineages found to be co-circulating within several countries. We also find evidence that previously identified sporadic cases may be from larger, undersampled outbreaks, highlighting the need for careful examination of sampling biases and underscoring the need for continued and expanded cholera surveillance across the African continent.

Published
2024
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