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1. Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years

Author

Perofsky, Amanda C., Hansen, Chelsea L., Burstein, Roy, Boyle, Shanda, Prentice, Robin, Marshall, Cooper, Reinhart, David, Capodanno, Ben, Truong, Melissa, Schwabe-Fry, Kristen, Kuchta, Kayla, Pfau, Brian, Acker, Zack, Lee, Jover, Sibley, Thomas R., McDermot, Evan, Rodriguez-Salas, Leslie, Stone, Jeremy, Gamboa, Luis, Han, Peter D., Adler, Amanda, Waghmare, Alpana, Jackson, Michael L., Famulare, Michael, Shendure, Jay, Bedford, Trevor, Chu, Helen Y., Englund, Janet A., Starita, Lea M., and Viboud, Cécile

Published
2024
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2. Cryptic transmission of SARS-CoV-2 in Washington state

Author

Bedford, Trevor, Greninger, Alexander L, Roychoudhury, Pavitra, Starita, Lea M, Famulare, Michael, Huang, Meei-Li, Nalla, Arun, Pepper, Gregory, Reinhardt, Adam, Xie, Hong, Shrestha, Lasata, Nguyen, Truong N, Adler, Amanda, Brandstetter, Elisabeth, Cho, Shari, Giroux, Danielle, Han, Peter D, Fay, Kairsten, Frazar, Chris D, Ilcisin, Misja, Lacombe, Kirsten, Lee, Jover, Kiavand, Anahita, Richardson, Matthew, Sibley, Thomas R, Truong, Melissa, Wolf, Caitlin R, Nickerson, Deborah A, Rieder, Mark J, Englund, Janet A, Hadfield, James, Hodcroft, Emma B, Huddleston, John, Moncla, Louise H, Müller, Nicola F, Neher, Richard A, Deng, Xianding, Gu, Wei, Federman, Scot, Chiu, Charles, Duchin, Jeffrey S, Gautom, Romesh, Melly, Geoff, Hiatt, Brian, Dykema, Philip, Lindquist, Scott, Queen, Krista, Tao, Ying, Uehara, Anna, Tong, Suxiang, MacCannell, Duncan, Armstrong, Gregory L, Baird, Geoffrey S, Chu, Helen Y, Shendure, Jay, Jerome, Keith R, Boeckh, Michael, Lutz, Barry R, Thompson, Matthew, Huang, Shichu, Jackson, Michael L, Kimball, Louise E, Logue, Jennifer, Lyon, Victoria, Newman, Kira L, and Suchsland, Monica L Zigman

Subjects
Infectious Diseases, Pneumonia & Influenza, Lung, Prevention, Emerging Infectious Diseases, Biodefense, Vaccine Related, Pneumonia, Infection, Good Health and Well Being, Bayes Theorem, Betacoronavirus, COVID-19, Coronavirus Infections, Genome, Viral, Humans, Likelihood Functions, Pandemics, Phylogeny, Pneumonia, Viral, SARS-CoV-2, Washington, Seattle Flu Study Investigators, General Science & Technology
Abstract

After its emergence in Wuhan, China, in late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows the reconstruction of its transmission history, although this is contingent on sampling. We analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020 from infected patients in Washington state in the United States. We find that most SARS-CoV-2 infections sampled during this time derive from a single introduction in late January or early February 2020, which subsequently spread locally before active community surveillance was implemented.

Published
2020

3. "I probably shouldn't go in today": Inequitable access to paid sick leave and its impacts on health behaviors during the emergence of COVID-19 in the Seattle area.

Author

Iwu, Chidozie D., Cox, Sarah N., Sohlberg, Sarah L., Kim, Ashley E., Logue, Jennifer, Han, Peter D., Sibley, Thomas R., Ilcisin, Misja, Fay, Kairsten A., Lee, Jover, McCulloch, Denise J., Wang, Yongzhe, Boeckh, Michael, Englund, Janet A., Starita, Lea M., Hajat, Anjum, and Chu, Helen Y.

Subjects
COVID-19 pandemic, SICK leave, RACE, INCOME, ECONOMIC policy, ETHNICITY
Abstract

This study examines inequities in access to paid sick leave (PSL) by race/ethnicity, income, and sex and the role of PSL access on leave-taking and care-seeking behaviors among Seattle-area workers in the months leading up to and during the emergence of COVID-19 in the region. Survey responses were collected online and in-person from individuals experiencing acute respiratory illness symptoms between November 2019 and March 2020 as part of a community-based respiratory viral surveillance study. Chi-square tests and log-binomial models were used to assess the association between PSL access and various socioeconomic indicators. A total of 66.6% (n = 2,276) respondents reported access to PSL. Proportionally, access to PSL was highest in respondents identifying as Asian (70.5%), followed by White (68.7%), Latine (58.4%), Multiracial (57.1%), Black (47.1%), and Other (43.1%). Access to PSL increased with household income. Eighty three percent of high-income respondents reported access compared to 52.9% of low-income households. Only 23.3% of the lowest-income households reported access to PSL. Fewer females (65.2%) than males (70.7%) reported access to PSL. Access to PSL is inequitably distributed across income, race/ethnicity, and sex. This study reinforces the vast body of knowledge on how socioeconomic inequalities increase individual and community-level vulnerability to the impacts of infectious disease outbreaks. It also supports the role of labor and economic policy in mitigating (or exacerbating) these impacts. Exemplified by the COVID-19 pandemic, universal access to PSL, especially for marginalized populations, benefits all. [ABSTRACT FROM AUTHOR]

Published
2024
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4. Ten recommendations for supporting open pathogen genomic analysis in public health

Author

Black, Allison, MacCannell, Duncan R., Sibley, Thomas R., and Bedford, Trevor

Subjects
Genomics -- Analysis -- Health aspects, Public health -- Genetic aspects, Biological sciences, Health
Abstract

Increasingly, public-health agencies are using pathogen genomic sequence data to support surveillance and epidemiological investigations. As access to whole-genome sequencing has grown, greater amounts of molecular data have helped improve the ability to detect and track outbreaks of diseases such as COVID-19, investigate transmission chains and explore large-scale population dynamics, such as the spread of antibiotic resistance. However, the wide adoption of whole-genome sequencing also poses new challenges for public-health agencies that must adapt to support a new set of expertise, which means that the capacity to perform genomic data assembly and analysis has not expanded as widely as the adoption of sequencing itself. In this Perspective, we make recommendations for developing an accessible, unified informatic ecosystem to support pathogen genomic analysis in public-health agencies across income settings. We hope that the creation of this ecosystem will allow agencies to effectively and efficiently share data, workflows and analyses and thereby increase the reproducibility, accessibility and auditability of pathogen genomic analysis while also supporting agency autonomy. To support progress in genomic epidemiology, a transparent, user-friendly approach is required., Author(s): Allison Black [sup.1] [sup.2] , Duncan R. MacCannell [sup.3] , Thomas R. Sibley [sup.2] , Trevor Bedford [sup.1] [sup.2] Author Affiliations: (1) Department of Epidemiology, University of Washington, Seattle, [...]

Published
2020
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5. Human mobility impacts the transmission of common respiratory viruses: A modeling study of the Seattle metropolitan area

Author

Perofsky, Amanda C., primary, Hansen, Chelsea, additional, Burstein, Roy, additional, Boyle, Shanda, additional, Prentice, Robin, additional, Marshall, Cooper, additional, Reinhart, David, additional, Capodanno, Ben, additional, Truong, Melissa, additional, Schwabe-Fry, Kristen, additional, Kuchta, Kayla, additional, Pfau, Brian, additional, Acker, Zack, additional, Lee, Jover, additional, Sibley, Thomas R., additional, McDermot, Evan, additional, Rodriguez-Salas, Leslie, additional, Stone, Jeremy, additional, Gamboa, Luis, additional, Han, Peter D., additional, Adler, Amanda, additional, Waghmare, Alpana, additional, Jackson, Michael L., additional, Famulare, Mike, additional, Shendure, Jay, additional, Bedford, Trevor, additional, Chu, Helen Y., additional, Englund, Janet A., additional, Starita, Lea M., additional, and Viboud, Cecile, additional

Published
2023
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6. Streptococcus pneumoniae nasal carriage patterns with and without common respiratory virus detections in households in Seattle, WA, USA before and during the COVID-19 pandemic

Author

Bennett, Julia C., primary, Emanuels, Anne, additional, Heimonen, Jessica, additional, O'Hanlon, Jessica, additional, Hughes, James P., additional, Han, Peter D., additional, Chow, Eric J., additional, Ogokeh, Constance E., additional, Rolfes, Melissa A., additional, Lockwood, Christine M., additional, Pfau, Brian, additional, Uyeki, Timothy M., additional, Shendure, Jay, additional, Hoag, Samara, additional, Fay, Kairsten, additional, Lee, Jover, additional, Sibley, Thomas R., additional, Rogers, Julia H., additional, Starita, Lea M., additional, Englund, Janet A., additional, and Chu, Helen Y., additional

Published
2023
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9. Trends in Risk Factors and Symptoms Associated With SARS-CoV-2 and Rhinovirus Test Positivity in King County, Washington, June 2020 to July 2022

Author

Hansen, Chelsea, primary, Perofsky, Amanda C., additional, Burstein, Roy, additional, Famulare, Michael, additional, Boyle, Shanda, additional, Prentice, Robin, additional, Marshall, Cooper, additional, McCormick, Benjamin J. J., additional, Reinhart, David, additional, Capodanno, Ben, additional, Truong, Melissa, additional, Schwabe-Fry, Kristen, additional, Kuchta, Kayla, additional, Pfau, Brian, additional, Acker, Zack, additional, Lee, Jover, additional, Sibley, Thomas R., additional, McDermot, Evan, additional, Rodriguez-Salas, Leslie, additional, Stone, Jeremy, additional, Gamboa, Luis, additional, Han, Peter D., additional, Duchin, Jeffery S., additional, Waghmare, Alpana, additional, Englund, Janet A., additional, Shendure, Jay, additional, Bedford, Trevor, additional, Chu, Helen Y., additional, Starita, Lea M., additional, and Viboud, Cécile, additional

Published
2022
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10. Trends in risk factors and symptoms associated with SARS-CoV-2 and Rhinovirus test positivity in King County, Washington: A Test-Negative Design Study of the Greater Seattle Coronavirus Assessment Network

Author

Hansen, Chelsea L., primary, Perofsky, Amanda, additional, Burstein, Roy, additional, Famulare, Michael, additional, Boyle, Shanda, additional, Prentice, Robin, additional, Marshall, Cooper, additional, McCormick, Benjamin JJ, additional, Reinhart, David, additional, Capodanno, Ben, additional, Truong, Melissa, additional, Schwabe-Fry, Kristen, additional, Kuchta, Kayla, additional, Pfau, Brian, additional, Acker, Zack, additional, Lee, Jover, additional, Sibley, Thomas R., additional, McDermot, Evan, additional, Rodriguez-Salas, Leslie, additional, Stone, Jeremy, additional, Gamboa, Luis, additional, Han, Peter D., additional, Duchin, Jeffery S., additional, Waghmare, Alpana, additional, Englund, Janet A., additional, Shendure, Jay, additional, Bedford, Trevor, additional, Chu, Helen Y., additional, Starita, Lea M., additional, and Viboud, Cécile, additional

Published
2022
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11. Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data

Author

Burstein, Roy, primary, Althouse, Benjamin M., additional, Adler, Amanda, additional, Akullian, Adam, additional, Brandstetter, Elizabeth, additional, Cho, Shari, additional, Emanuels, Anne, additional, Fay, Kairsten, additional, Gamboa, Luis, additional, Han, Peter, additional, Huden, Kristen, additional, Ilcisin, Misja, additional, Izzo, Mandy, additional, Jackson, Michael L., additional, Kim, Ashley E., additional, Kimball, Louise, additional, Lacombe, Kirsten, additional, Lee, Jover, additional, Logue, Jennifer K., additional, Rogers, Julia, additional, Chung, Erin, additional, Sibley, Thomas R., additional, Van Raay, Katrina, additional, Wenger, Edward, additional, Wolf, Caitlin R., additional, Boeckh, Michael, additional, Chu, Helen, additional, Duchin, Jeff, additional, Rieder, Mark, additional, Shendure, Jay, additional, Starita, Lea M., additional, Viboud, Cecile, additional, Bedford, Trevor, additional, Englund, Janet A., additional, and Famulare, Michael, additional

Published
2022
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13. SARS-CoV-2 Epidemiology on a Public University Campus in Washington State

Author

Weil, Ana A, primary, Sohlberg, Sarah L, additional, O’Hanlon, Jessica A, additional, Casto, Amanda M, additional, Emanuels, Anne W, additional, Lo, Natalie K, additional, Greismer, Emily P, additional, Magedson, Ariana M, additional, Wilcox, Naomi C, additional, Kim, Ashley E, additional, Back, Lewis, additional, Frazar, Christian D, additional, Pelle, Ben, additional, Sibley, Thomas R, additional, Ilcisin, Misja, additional, Lee, Jover, additional, Ryke, Erica L, additional, Craft, J Chris, additional, Schwabe-Fry, Kristen M, additional, Fay, Kairsten A, additional, Cho, Shari, additional, Han, Peter D, additional, Heidl, Sarah J, additional, Pfau, Brian A, additional, Truong, Melissa, additional, Zhong, Weizhi, additional, Srivatsan, Sanjay R, additional, Harb, Katia F, additional, Gottlieb, Geoffrey S, additional, Hughes, James P, additional, Nickerson, Deborah A, additional, Lockwood, Christina M, additional, Starita, Lea M, additional, Bedford, Trevor, additional, Shendure, Jay A, additional, and Chu, Helen Y, additional

Published
2021
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14. Additional file 1 of Effects of weather-related social distancing on city-scale transmission of respiratory viruses: a retrospective cohort study

Author

Jackson, Michael L., Hart, Gregory R., McCulloch, Denise J., Adler, Amanda, Brandstetter, Elisabeth, Kairsten Fay, Han, Peter, Lacombe, Kirsten, Jover Lee, Sibley, Thomas R., Nickerson, Deborah A., Rieder, Mark J., Starita, Lea, Englund, Janet A., Bedford, Trevor, Chu, Helen, and Famulare, Michael

Subjects
Data_FILES
Abstract

Additional file 1.

Published
2021
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15. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

Author

Müller, Nicola F., primary, Wagner, Cassia, additional, Frazar, Chris D., additional, Roychoudhury, Pavitra, additional, Lee, Jover, additional, Moncla, Louise H., additional, Pelle, Benjamin, additional, Richardson, Matthew, additional, Ryke, Erica, additional, Xie, Hong, additional, Shrestha, Lasata, additional, Addetia, Amin, additional, Rachleff, Victoria M., additional, Lieberman, Nicole A. P., additional, Huang, Meei-Li, additional, Gautom, Romesh, additional, Melly, Geoff, additional, Hiatt, Brian, additional, Dykema, Philip, additional, Adler, Amanda, additional, Brandstetter, Elisabeth, additional, Han, Peter D., additional, Fay, Kairsten, additional, Ilcisin, Misja, additional, Lacombe, Kirsten, additional, Sibley, Thomas R., additional, Truong, Melissa, additional, Wolf, Caitlin R., additional, Boeckh, Michael, additional, Englund, Janet A., additional, Famulare, Michael, additional, Lutz, Barry R., additional, Rieder, Mark J., additional, Thompson, Matthew, additional, Duchin, Jeffrey S., additional, Starita, Lea M., additional, Chu, Helen Y., additional, Shendure, Jay, additional, Jerome, Keith R., additional, Lindquist, Scott, additional, Greninger, Alexander L., additional, Nickerson, Deborah A., additional, and Bedford, Trevor, additional

Published
2021
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16. Evaluating Specimen Quality and Results from a Community-Wide, Home-Based Respiratory Surveillance Study

Author

Kim, Ashley E., primary, Brandstetter, Elisabeth, additional, Wilcox, Naomi, additional, Heimonen, Jessica, additional, Graham, Chelsey, additional, Han, Peter D., additional, Starita, Lea M., additional, McCulloch, Denise J., additional, Casto, Amanda M., additional, Nickerson, Deborah A., additional, Van de Loo, Margaret M., additional, Mooney, Jennifer, additional, Ilcisin, Misja, additional, Fay, Kairsten A., additional, Lee, Jover, additional, Sibley, Thomas R., additional, Lyon, Victoria, additional, Geyer, Rachel E., additional, Thompson, Matthew, additional, Lutz, Barry R., additional, Rieder, Mark J., additional, Bedford, Trevor, additional, Boeckh, Michael, additional, Englund, Janet A., additional, and Chu, Helen Y., additional

Published
2021
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17. SARS-CoV-2 Epidemiology on a Public University Campus in Washington State

Author

Weil, Ana A., primary, Sohlberg, Sarah L., additional, O’Hanlon, Jessica A., additional, Casto, Amanda M., additional, Emanuels, Anne W, additional, Lo, Natalie K., additional, Greismer, Emily P., additional, Magedson, Ariana M., additional, Wilcox, Naomi C., additional, Kim, Ashley E., additional, Back, Lewis, additional, Frazar, Christian D., additional, Pelle, Ben, additional, Sibley, Thomas R., additional, Ilcisin, Misja, additional, Lee, Jover, additional, Ryke, Erica L., additional, Chris Craft, J., additional, Schwabe-Fry, Kristen M., additional, Fay, Kairsten A., additional, Cho, Shari, additional, Han, Peter D., additional, Heidl, Sarah J., additional, Pfau, Brian A., additional, Truong, Melissa, additional, Zhong, Weizhi, additional, Srivatsan, Sanjay R., additional, Harb, Katia F., additional, Gottlieb, Geoffrey S., additional, Hughes, James P., additional, Nickerson, Deborah A., additional, Lockwood, Christina M., additional, Starita, Lea M., additional, Bedford, Trevor, additional, Shendure, Jay A., additional, and Chu, Helen Y., additional

Published
2021
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18. Characteristics of COVID-19 in Homeless Shelters

Author

Rogers, Julia H., primary, Link, Amy C., additional, McCulloch, Denise, additional, Brandstetter, Elisabeth, additional, Newman, Kira L., additional, Jackson, Michael L., additional, Hughes, James P., additional, Englund, Janet A., additional, Boeckh, Michael, additional, Sugg, Nancy, additional, Ilcisin, Misja, additional, Sibley, Thomas R., additional, Fay, Kairsten, additional, Lee, Jover, additional, Han, Peter, additional, Truong, Melissa, additional, Richardson, Matthew, additional, Nickerson, Deborah A., additional, Starita, Lea M., additional, Bedford, Trevor, additional, and Chu, Helen Y., additional

Published
2021
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19. Evaluating Specimen Quality and Results from a Community-Wide, Home-Based Respiratory Surveillance Study

Author

Kim, Ashley E., primary, Brandstetter, Elisabeth, additional, Wilcox, Naomi, additional, Heimonen, Jessica, additional, Graham, Chelsey, additional, Han, Peter D., additional, Starita, Lea M., additional, McCulloch, Denise J., additional, Casto, Amanda M., additional, Nickerson, Deborah A., additional, Van de Loo, Margaret M., additional, Mooney, Jennifer, additional, Ilcisin, Misja, additional, Fay, Kairsten A., additional, Lee, Jover, additional, Sibley, Thomas R., additional, Lyon, Victoria, additional, Geyer, Rachel E., additional, Thompson, Matthew, additional, Lutz, Barry R., additional, Rieder, Mark J., additional, Bedford, Trevor, additional, Boeckh, Michael, additional, Englund, Janet A., additional, and Chu, Helen Y., additional

Published
2020
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20. The Seattle Flu Study: a multiarm community-based prospective study protocol for assessing influenza prevalence, transmission and genomic epidemiology

Author

Chu, Helen Y, primary, Boeckh, Michael, additional, Englund, Janet A, additional, Famulare, Michael, additional, Lutz, Barry, additional, Nickerson, Deborah A, additional, Rieder, Mark, additional, Starita, Lea M, additional, Adler, Amanda, additional, Brandstetter, Elisabeth, additional, Frazer, Chris D, additional, Han, Peter D, additional, Gulati, Reena K, additional, Hadfield, James, additional, Jackson, Michael, additional, Kiavand, Anahita, additional, Kimball, Louise E, additional, Lacombe, Kirsten, additional, Newman, Kira, additional, Sibley, Thomas R, additional, Logue, Jennifer K, additional, Lyon, Victoria Rachel, additional, Wolf, Caitlin R, additional, Zigman Suchsland, Monica, additional, Shendure, Jay, additional, and Bedford, Trevor, additional

Published
2020
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21. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

Author

Müller, Nicola F., primary, Wagner, Cassia, additional, Frazar, Chris D., additional, Roychoudhury, Pavitra, additional, Lee, Jover, additional, Moncla, Louise H., additional, Pelle, Benjamin, additional, Richardson, Matthew, additional, Ryke, Erica, additional, Xie, Hong, additional, Shrestha, Lasata, additional, Addetia, Amin, additional, Rachleff, Victoria M., additional, Lieberman, Nicole A. P., additional, Huang, Meei-Li, additional, Gautom, Romesh, additional, Melly, Geoff, additional, Hiatt, Brian, additional, Dykema, Philip, additional, Adler, Amanda, additional, Brandstetter, Elisabeth, additional, Han, Peter D., additional, Fay, Kairsten, additional, Ilcisin, Misja, additional, Lacombe, Kirsten, additional, Sibley, Thomas R., additional, Truong, Melissa, additional, Wolf, Caitlin R., additional, Boeckh, Michael, additional, Englund, Janet A., additional, Famulare, Michael, additional, Lutz, Barry R., additional, Rieder, Mark J., additional, Thompson, Matthew, additional, Duchin, Jeffrey S., additional, Starita, Lea M., additional, Chu, Helen Y., additional, Shendure, Jay, additional, Jerome, Keith R., additional, Lindquist, Scott, additional, Greninger, Alexander L., additional, Nickerson, Deborah A., additional, and Bedford, Trevor, additional

Published
2020
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22. Early Detection of Covid-19 through a Citywide Pandemic Surveillance Platform

Author

Chu, Helen Y., primary, Englund, Janet A., additional, Starita, Lea M., additional, Famulare, Michael, additional, Brandstetter, Elisabeth, additional, Nickerson, Deborah A., additional, Rieder, Mark J., additional, Adler, Amanda, additional, Lacombe, Kirsten, additional, Kim, Ashley E., additional, Graham, Chelsey, additional, Logue, Jennifer, additional, Wolf, Caitlin R., additional, Heimonen, Jessica, additional, McCulloch, Denise J., additional, Han, Peter D., additional, Sibley, Thomas R., additional, Lee, Jover, additional, Ilcisin, Misja, additional, Fay, Kairsten, additional, Burstein, Roy, additional, Martin, Beth, additional, Lockwood, Christina M., additional, Thompson, Matthew, additional, Lutz, Barry, additional, Jackson, Michael, additional, Hughes, James P., additional, Boeckh, Michael, additional, Shendure, Jay, additional, and Bedford, Trevor, additional

Published
2020
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23. Seattle Flu Study - Swab and Send: Study Protocol for At-Home Surveillance Methods to Estimate the Burden of Respiratory Pathogens on a City-Wide Scale

Author

Kim, Ashley E., primary, Brandstetter, Elisabeth, additional, Graham, Chelsey, additional, Heimonen, Jessica, additional, Osterbind, Audrey, additional, McCulloch, Denise J., additional, Han, Peter D., additional, Starita, Lea M., additional, Nickerson, Deborah A., additional, Van de Loo, Margaret M., additional, Mooney, Jennifer, additional, Rieder, Mark J., additional, Ilcisin, Misja, additional, Fay, Kairsten A., additional, Lee, Jover, additional, Sibley, Thomas R., additional, Bedford, Trevor, additional, Englund, Janet A., additional, Boeckh, Michael, additional, and Chu, Helen Y., additional

Published
2020
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24. Minority and majority pretreatment HIV-1 drug resistance associated with failure of first-line nonnucleoside reverse-transcriptase inhibitor antiretroviral therapy in Kenyan women

Author

Milne, Ross S., Silverman, Rachel A., Beck, Ingrid A., McKernan-Mullin, Jennifer, Deng, Wenjie, Sibley, Thomas R., Dross, Sandra, Kiarie, James N., Sakr, Samah R., Coombs, Robert W., Chung, Michael H., and Frenkel, Lisa M.

Subjects
Adult, Genotype, Adolescent, Genotyping Techniques, nevirapine, Oligonucleotide Ligation Assay, Immunology, antiretroviral therapy, prevention of mother-to-child transmission, Cross-Resistance, Preexposure Prophylaxis, HIV Infections, Young Adult, Dolutegravir Monotherapy, Virology, HIV drug resistance, Drug Resistance, Viral, Humans, Women, 11 Medical and Health Sciences, Retrospective Studies, To-Child Transmission, Variants, virus diseases, quasispecies, 06 Biological Sciences, Kenya, 17 Psychology and Cognitive Sciences, Single-Dose Nevirapine, Infectious Diseases, Anti-Retroviral Agents, Mutation, HIV-1, Female, Naive Adults, Virological Failure, Mutations
Abstract

Objectives: Among women initiating first-line nonnucleoside reverse-transcriptase inhibitor (NNRTI)-based-ART with and without a history of single-dose nevirapine (sdNVP) with or without zidovudine with or without lamivudine (ZDV with and without 3TC) for prevention of mother-to-child HIV transmission (PMTCT), we hypothesized that pre-ART HIV-drug resistance would be associated with virologic failure. Design/Methods: In a prospectively enrolled study, three genotypic drug-resistance assays [oligonucleotide-ligation-assay (OLA), consensus sequencing, and next-generation sequencing by Illumina] were retrospectively performed to detect pre-ART drug resistance. Minority or majority drug-resistant variants identified in pre-ART RNA and/or DNA, a history of antiretrovirals for PMTCT, and other risk factors were assessed for association with virologic failure. Results: Failure occurred in 38/169 (22.5%) women, and was associated with pre-ART drug resistance detected by any assay (OLA of plasma or PBMC, consensus sequencing of PBMC and/or plasma, and next-generation sequencing of PBMC at frequencies of at least 10% and as minority variants; all P

Published
2019

26. LB21. The Seattle Flu Study: A Community-Based Study of Influenza

Author

Chu, Helen Y, primary, Chu, Helen Y, additional, Boeckh, Michael, additional, Englund, Janet A, additional, Famulare, Michael, additional, Lutz, Barry R, additional, Nickerson, Deborah A, additional, Rieder, Mark, additional, Starita, Lea, additional, Thompson, Matthew, additional, Shendure, Jay, additional, Bedford, Trevor, additional, Adler, Amanda, additional, Brandstetter, Elisabeth, additional, Bosua, Jeris, additional, Frazar, Christian D, additional, Han, Peter D, additional, Gulati, Reena, additional, Hadfield, James, additional, Huang, ShiChu, additional, Jackson, Michael L, additional, Kiavand, Anahita, additional, Kimball, Louise E, additional, Lacombe, Kirsten, additional, Logue, Jennifer, additional, Lyon, Victoria, additional, Sibley, Thomas R, additional, Zigman Suchsland, Monica L, additional, and Wolf, Caitlin R, additional

Published
2019
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27. Minority and majority pretreatment HIV-1 drug resistance associated with failure of first-line nonnucleoside reverse-transcriptase inhibitor antiretroviral therapy in Kenyan women

Author

Milne, Ross S., primary, Silverman, Rachel A., additional, Beck, Ingrid A., additional, Mckernan-Mullin, Jennifer, additional, Deng, Wenjie, additional, Sibley, Thomas R., additional, Dross, Sandra, additional, Kiarie, James N., additional, Sakr, Samah R., additional, Coombs, Robert W., additional, Chung, Michael H., additional, and Frenkel, Lisa M., additional

Published
2019
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28. Effects of weather-related social distancing on city-scale transmission of respiratory viruses: a retrospective cohort study.

Author

Jackson, Michael L., Hart, Gregory R., McCulloch, Denise J., Adler, Amanda, Brandstetter, Elisabeth, Fay, Kairsten, Han, Peter, Lacombe, Kirsten, Lee, Jover, Sibley, Thomas R., Nickerson, Deborah A., Rieder, Mark J., Starita, Lea, Englund, Janet A., Bedford, Trevor, Chu, Helen, Famulare, Michael, on behalf of the Seattle Flu Study Investigators, Chu, Helen Y., and Boeckh, Michael

Subjects
SOCIAL distancing, DISEASE incidence, VIRUSES, COHORT analysis, TRAFFIC flow
Abstract

Background: Unusually high snowfall in western Washington State in February 2019 led to widespread school and workplace closures. We assessed the impact of social distancing caused by this extreme weather event on the transmission of respiratory viruses.Methods: Residual specimens from patients evaluated for acute respiratory illness at hospitals in the Seattle metropolitan area were screened for a panel of respiratory viruses. Transmission models were fit to each virus to estimate the magnitude reduction in transmission due to weather-related disruptions. Changes in contact rates and care-seeking were informed by data on local traffic volumes and hospital visits.Results: Disruption in contact patterns reduced effective contact rates during the intervention period by 16 to 95%, and cumulative disease incidence through the remainder of the season by 3 to 9%. Incidence reductions were greatest for viruses that were peaking when the disruption occurred and least for viruses in an early epidemic phase.Conclusion: High-intensity, short-duration social distancing measures may substantially reduce total incidence in a respiratory virus epidemic if implemented near the epidemic peak. For SARS-CoV-2, this suggests that, even when SARS-CoV-2 spread is out of control, implementing short-term disruptions can prevent COVID-19 deaths. [ABSTRACT FROM AUTHOR]

Published
2021
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30. ISDB: a database toolkit for storing and analyzing viral integration site data.

Author

Sibley, Thomas R, Silberman, Evan J, and Mullins, James I

Subjects
*HIV infections, *GENE expression, *ANTIRETROVIRAL agents, *BIOINFORMATICS, *DATABASES
Abstract

Summary We introduce ISDB, a set of software tools for the creation and administration of relational databases of viral integration site (IS) data. Using ISDB, investigators can curate a private database from any heterogeneous set of data sources, including previously-published datasets and internal, work-in-progress data. To make data visible and accessible to collaborators with varying degrees of computational expertise, ISDB automatically generates web sites describing database contents and data exports in several common formats. Compared to a public depository database, the ability to build local, private databases makes ISDB suitable for use in testing hypotheses and developing analyses in the long pre-publication phase of most research. Availability and implementation Installation and usage documentation for ISDB are provided on our website https://mullinslab.microbiol.washington.edu/isdb/. Source code is available under the open source MIT license from https://github.com/MullinsLab/ISDB. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Published
2019
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31. Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data.

Author

Burstein R, Althouse BM, Adler A, Akullian A, Brandstetter E, Cho S, Emanuels A, Fay K, Gamboa L, Han P, Huden K, Ilcisin M, Izzo M, Jackson ML, Kim AE, Kimball L, Lacombe K, Lee J, Logue JK, Rogers J, Chung E, Sibley TR, Van Raay K, Wenger E, Wolf CR, Boeckh M, Chu H, Duchin J, Rieder M, Shendure J, Starita LM, Viboud C, Bedford T, Englund JA, and Famulare M

Abstract

Background: Co-circulating respiratory pathogens can interfere with or promote each other, leading to important effects on disease epidemiology. Estimating the magnitude of pathogen-pathogen interactions from clinical specimens is challenging because sampling from symptomatic individuals can create biased estimates., Methods: We conducted an observational, cross-sectional study using samples collected by the Seattle Flu Study between 11 November 2018 and 20 August 2021. Samples that tested positive via RT-qPCR for at least one of 17 potential respiratory pathogens were included in this study. Semi-quantitative cycle threshold (Ct) values were used to measure pathogen load. Differences in pathogen load between monoinfected and coinfected samples were assessed using linear regression adjusting for age, season, and recruitment channel., Results: 21,686 samples were positive for at least one potential pathogen. Most prevalent were rhinovirus (33·5%), Streptococcus pneumoniae ( SPn , 29·0%), SARS-CoV-2 (13.8%) and influenza A/H1N1 (9·6%). 140 potential pathogen pairs were included for analysis, and 56 (40%) pairs yielded significant Ct differences (p < 0.01) between monoinfected and co-infected samples. We observed no virus-virus pairs showing evidence of significant facilitating interactions, and found significant viral load decrease among 37 of 108 (34%) assessed pairs. Samples positive with SPn and a virus were consistently associated with increased SPn load., Conclusions: Viral load data can be used to overcome sampling bias in studies of pathogen-pathogen interactions. When applied to respiratory pathogens, we found evidence of viral- SPn facilitation and several examples of viral-viral interference. Multipathogen surveillance is a cost-efficient data collection approach, with added clinical and epidemiological informational value over single-pathogen testing, but requires careful analysis to mitigate selection bias.

Published
2022
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32. Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens.

Author

Huddleston J, Hadfield J, Sibley TR, Lee J, Fay K, Ilcisin M, Harkins E, Bedford T, Neher RA, and Hodcroft EB

Abstract

The analysis of human pathogens requires a diverse collection of bioinformatics tools. These tools include standard genomic and phylogenetic software and custom software developed to handle the relatively numerous and short genomes of viruses and bacteria. Researchers increasingly depend on the outputs of these tools to infer transmission dynamics of human diseases and make actionable recommendations to public health officials (Black et al., 2020; Gardy et al., 2015). In order to enable real-time analyses of pathogen evolution, bioinformatics tools must scale rapidly with the number of samples and be flexible enough to adapt to a variety of questions and organisms. To meet these needs, we developed Augur, a bioinformatics toolkit designed for phylogenetic analyses of human pathogens.

Published
2021
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33. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State.

Author

Müller NF, Wagner C, Frazar CD, Roychoudhury P, Lee J, Moncla LH, Pelle B, Richardson M, Ryke E, Xie H, Shrestha L, Addetia A, Rachleff VM, Lieberman NAP, Huang ML, Gautom R, Melly G, Hiatt B, Dykema P, Adler A, Brandstetter E, Han PD, Fay K, Llcisin M, Lacombe K, Sibley TR, Truong M, Wolf CR, Boeckh M, Englund JA, Famulare M, Lutz BR, Rieder MJ, Thompson M, Duchin JS, Starita LM, Chu HY, Shendure J, Jerome KR, Lindquist S, Greninger AL, Nickerson DA, and Bedford T

Abstract

The rapid spread of SARS-CoV-2 has gravely impacted societies around the world. Outbreaks in different parts of the globe are shaped by repeated introductions of new lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State to characterize how the spread of SARS-CoV-2 in Washington State (USA) was shaped by differences in timing of mitigation strategies across counties, as well as by repeated introductions of viral lineages into the state. Additionally, we show that the increase in frequency of a potentially more transmissible viral variant (614G) over time can potentially be explained by regional mobility differences and multiple introductions of 614G, but not the other variant (614D) into the state. At an individual level, we see evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we do not find any evidence that the 614G variant impacts clinical severity or patient outcomes. Overall, this suggests that at least to date, the behavior of individuals has been more important in shaping the course of the pandemic than changes in the virus.

Published
2020
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34. Cryptic transmission of SARS-CoV-2 in Washington State.

Author

Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang ML, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, Giroux D, Han PD, Fay K, Frazar CD, Ilcisin M, Lacombe K, Lee J, Kiavand A, Richardson M, Sibley TR, Truong M, Wolf CR, Nickerson DA, Rieder MJ, Englund JA, Hadfield J, Hodcroft EB, Huddleston J, Moncla LH, Müller NF, Neher RA, Deng X, Gu W, Federman S, Chiu C, Duchin J, Gautom R, Melly G, Hiatt B, Dykema P, Lindquist S, Queen K, Tao Y, Uehara A, Tong S, MacCannell D, Armstrong GL, Baird GS, Chu HY, Shendure J, and Jerome KR

Abstract

Following its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread throughout the world. On March 11, 2020, the World Health Organization declared Coronavirus Disease 2019 (COVID-19) a pandemic. Genome sequencing of SARS-CoV-2 strains allows for the reconstruction of transmission history connecting these infections. Here, we analyze 346 SARS-CoV-2 genomes from samples collected between 20 February and 15 March 2020 from infected patients in Washington State, USA. We found that the large majority of SARS-CoV-2 infections sampled during this time frame appeared to have derived from a single introduction event into the state in late January or early February 2020 and subsequent local spread, strongly suggesting cryptic spread of COVID-19 during the months of January and February 2020, before active community surveillance was implemented. We estimate a common ancestor of this outbreak clade as occurring between 18 January and 9 February 2020. From genomic data, we estimate an exponential doubling between 2.4 and 5.1 days. These results highlight the need for large-scale community surveillance for SARS-CoV-2 introductions and spread and the power of pathogen genomics to inform epidemiological understanding.

Published
2020
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