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2. Fitting stochastic epidemic models to gene genealogies using linear noise approximation

Author

Tang, Mingwei, Dudas, Gytis, Bedford, Trevor, and Minin, Vladimir N

Subjects
Mathematical Sciences, Statistics, Bioengineering, Infectious Diseases, Emerging Infectious Diseases, Aetiology, 2.5 Research design and methodologies (aetiology), Infection, Good Health and Well Being, Coalescent, susceptible -infectious -recovered model, state -space model, phylodynamics, Ebola virus, Susceptible-Infectious-Recovered model, state-space model, Econometrics, Statistics & Probability
Abstract

Phylodynamics is a set of population genetics tools that aim at reconstructing demographic history of a population based on molecular sequences of individuals sampled from the population of interest. One important task in phylodynamics is to estimate changes in (effective) population size. When applied to infectious disease sequences such estimation of population size trajectories can provide information about changes in the number of infections. To model changes in the number of infected individuals, current phylodynamic methods use non-parametric approaches (e.g., Bayesian curve-fitting based on change-point models or Gaussian process priors), parametric approaches (e.g., based on differential equations), and stochastic modeling in conjunction with likelihood-free Bayesian methods. The first class of methods yields results that are hard to interpret epidemiologically. The second class of methods provides estimates of important epidemiological parameters, such as infection and removal/recovery rates, but ignores variation in the dynamics of infectious disease spread. The third class of methods is the most advantageous statistically, but relies on computationally intensive particle filtering techniques that limits its applications. We propose a Bayesian model that combines phylodynamic inference and stochastic epidemic models, and achieves computational tractability by using a linear noise approximation (LNA) - a technique that allows us to approximate probability densities of stochastic epidemic model trajectories. LNA opens the door for using modern Markov chain Monte Carlo tools to approximate the joint posterior distribution of the disease transmission parameters and of high dimensional vectors describing unobserved changes in the stochastic epidemic model compartment sizes (e.g., numbers of infectious and susceptible individuals). In a simulation study, we show that our method can successfully recover parameters of stochastic epidemic models. We apply our estimation technique to Ebola genealogies estimated using viral genetic data from the 2014 epidemic in Sierra Leone and Liberia.

Published
2023

3. Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin

Author

Welsh, Frances C., Eguia, Rachel T., Lee, Juhye M., Haddox, Hugh K., Galloway, Jared, Van Vinh Chau, Nguyen, Loes, Andrea N., Huddleston, John, Yu, Timothy C., Quynh Le, Mai, Nhat, Nguyen T.D., Thi Le Thanh, Nguyen, Greninger, Alexander L., Chu, Helen Y., Englund, Janet A., Bedford, Trevor, Matsen, Frederick A., IV, Boni, Maciej F., and Bloom, Jesse D.

Published
2024
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7. Fine-scale spatial and social patterns of SARS-CoV-2 transmission from identical pathogen sequences

Author

Tran-Kiem, Cécile, primary, Paredes, Miguel I., additional, Perofsky, Amanda C., additional, Frisbie, Lauren A., additional, Xie, Hong, additional, Kong, Kevin, additional, Weixler, Amelia, additional, Greninger, Alexander L., additional, Roychoudhury, Pavitra, additional, Peterson, JohnAric M., additional, Delgado, Andrew, additional, Holstead, Holly, additional, MacKellar, Drew, additional, Dykema, Philip, additional, Gamboa, Luis, additional, Frazar, Chris D., additional, Ryke, Erica, additional, Stone, Jeremy, additional, Reinhart, David, additional, Starita, Lea, additional, Thibodeau, Allison, additional, Yun, Cory, additional, Aragona, Frank, additional, Black, Allison, additional, Viboud, Cécile, additional, and Bedford, Trevor, additional

Published
2024
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9. Genomic surveillance of SARS-CoV-2 Omicron variants on a university campus

Author

Weil, Ana A., Luiten, Kyle G., Casto, Amanda M., Bennett, Julia C., O’Hanlon, Jessica, Han, Peter D., Gamboa, Luis S., McDermot, Evan, Truong, Melissa, Gottlieb, Geoffrey S., Acker, Zack, Wolf, Caitlin R., Magedson, Ariana, Chow, Eric J., Lo, Natalie K., Pothan, Lincoln C., McDonald, Devon, Wright, Tessa C., McCaffrey, Kathryn M., Figgins, Marlin D., Englund, Janet A., Boeckh, Michael, Lockwood, Christina M., Nickerson, Deborah A., Shendure, Jay, Bedford, Trevor, Hughes, James P., Starita, Lea M., and Chu, Helen Y.

Published
2022
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10. Fitness models provide accurate short-term forecasts of SARS-CoV-2 variant frequency.

Author

Abousamra, Eslam, Figgins, Marlin, and Bedford, Trevor

Subjects
SARS-CoV-2 Omicron variant, SARS-CoV-2 Delta variant, COVID-19 pandemic, SARS-CoV-2, RANDOM walks
Abstract

Genomic surveillance of pathogen evolution is essential for public health response, treatment strategies, and vaccine development. In the context of SARS-COV-2, multiple models have been developed including Multinomial Logistic Regression (MLR) describing variant frequency growth as well as Fixed Growth Advantage (FGA), Growth Advantage Random Walk (GARW) and Piantham parameterizations describing variant Rt. These models provide estimates of variant fitness and can be used to forecast changes in variant frequency. We introduce a framework for evaluating real-time forecasts of variant frequencies, and apply this framework to the evolution of SARS-CoV-2 during 2022 in which multiple new viral variants emerged and rapidly spread through the population. We compare models across representative countries with different intensities of genomic surveillance. Retrospective assessment of model accuracy highlights that most models of variant frequency perform well and are able to produce reasonable forecasts. We find that the simple MLR model provides ∼0.6% median absolute error and ∼6% mean absolute error when forecasting 30 days out for countries with robust genomic surveillance. We investigate impacts of sequence quantity and quality across countries on forecast accuracy and conduct systematic downsampling to identify that 1000 sequences per week is fully sufficient for accurate short-term forecasts. We conclude that fitness models represent a useful prognostic tool for short-term evolutionary forecasting. Author summary: Over the course of the COVID-19 pandemic, SARS-CoV-2 evolved into many different genetic variants such as the well known Alpha, Beta, Gamma and Delta variants in early 2021 and the Omicron variant in late 2021. These genetic variants could more easily spread from person to person and so outcompeted previous versions of the virus. Even if they aren't being given Greek letter names, new variants are still arising with recent waves of COVID-19 caused by variants such as XBB and JN.1. Predicting which variants will increase in frequency and which variants will decrease in frequency is important for public health, particularly in terms of updating the formulation of the annual COVID-19 vaccine. In this paper, we investigate statistical models that use observed frequencies of different variants in the past weeks to estimate the frequency of different variants today and to forecast the frequency of different variants in 30 days time. We find that in countries with sufficient amounts and timeliness of genetic sequence data, that models forecast well and can be a useful tool for public health. [ABSTRACT FROM AUTHOR]

Published
2024
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11. Comparative Diagnostic Utility of SARS-CoV-2 Rapid Antigen and Molecular Testing in a Community Setting.

Author

Kim, Ashley E, Bennett, Julia C, Luiten, Kyle, O'Hanlon, Jessica A, Wolf, Caitlin R, Magedson, Ariana, Han, Peter D, Acker, Zack, Regelbrugge, Lani, McCaffrey, Kathryn M, Stone, Jeremey, Reinhart, David, Capodanno, Benjamin J, Morse, Stephen S, Bedford, Trevor, Englund, Janet A, Boeckh, Michael, Starita, Lea M, Uyeki, Timothy M, and Carone, Marco

Subjects
REVERSE transcriptase polymerase chain reaction, RAPID diagnostic tests, SARS-CoV-2 Omicron variant, ANTIGEN analysis, SARS-CoV-2
Abstract

Background SARS-CoV-2 antigen-detection rapid diagnostic tests (Ag-RDTs) have become widely utilized but longitudinal characterization of their community-based performance remains incompletely understood. Methods This prospective longitudinal study at a large public university in Seattle, WA utilized remote enrollment, online surveys, and self-collected nasal swab specimens to evaluate Ag-RDT performance against real-time reverse transcription polymerase chain reaction (rRT-PCR) in the context of SARS-CoV-2 Omicron. Ag-RDT sensitivity and specificity within 1 day of rRT-PCR were evaluated by symptom status throughout the illness episode and Orf1b cycle threshold (Ct). Results From February to December 2022, 5757 participants reported 17 572 Ag-RDT results and completed 12 674 rRT-PCR tests, of which 995 (7.9%) were rRT-PCR positive. Overall sensitivity and specificity were 53.0% (95% confidence interval [CI], 49.6%–56.4%) and 98.8% (95% CI, 98.5%–99.0%), respectively. Sensitivity was comparatively higher for Ag-RDTs used 1 day after rRT-PCR (69.0%), 4–7 days after symptom onset (70.1%), and Orf1b Ct ≤20 (82.7%). Serial Ag-RDT sensitivity increased with repeat testing ≥ 2 (68.5%) and ≥ 4 (75.8%) days after an initial Ag-RDT-negative result. Conclusions Ag-RDT performance varied by clinical characteristics and temporal testing patterns. Our findings support recommendations for serial testing following an initial Ag-RDT-negative result, especially among recently symptomatic persons or those at high risk for SARS-CoV-2 infection. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution

Author

Wagner, Cassia, primary, Kistler, Kathryn E., additional, Perchetti, Garrett A., additional, Baker, Noah, additional, Frisbie, Lauren A., additional, Torres, Laura Marcela, additional, Aragona, Frank, additional, Yun, Cory, additional, Figgins, Marlin, additional, Greninger, Alexander L., additional, Cox, Alex, additional, Oltean, Hanna N., additional, Roychoudhury, Pavitra, additional, and Bedford, Trevor, additional

Published
2024
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14. Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county

Author

Paredes, Miguel I., primary, Perofsky, Amanda C., additional, Frisbie, Lauren, additional, Moncla, Louise H., additional, Roychoudhury, Pavitra, additional, Xie, Hong, additional, Bakhash, Shah A. Mohamed, additional, Kong, Kevin, additional, Arnould, Isabel, additional, Nguyen, Tien V., additional, Wendm, Seffir T., additional, Hajian, Pooneh, additional, Ellis, Sean, additional, Mathias, Patrick C., additional, Greninger, Alexander L., additional, Starita, Lea M., additional, Frazar, Chris D., additional, Ryke, Erica, additional, Zhong, Weizhi, additional, Gamboa, Luis, additional, Threlkeld, Machiko, additional, Lee, Jover, additional, Stone, Jeremy, additional, McDermot, Evan, additional, Truong, Melissa, additional, Shendure, Jay, additional, Oltean, Hanna N., additional, Viboud, Cécile, additional, Chu, Helen, additional, Müller, Nicola F., additional, and Bedford, Trevor, additional

Published
2024
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16. SARS-CoV-2 diversity and transmission on a university campus across two academic years during the pandemic

Author

Casto, Amanda M, primary, Paredes, Miguel I, additional, Bennett, Julia Catherine, additional, Luiten, Kyle G, additional, O'Hanlon, Jessica A., additional, Han, Peter D., additional, Gamboa, Luis, additional, McDermot, Evan, additional, Truong, Melissa, additional, Gottlieb, Geoffrey S, additional, Acker, Zack, additional, Wolf, Caitlin R, additional, Magedson, Ariana, additional, Lo, Natalie K., additional, McDonald, Devon, additional, Wright, Tessa C, additional, McCaffrey, Kathryn, additional, Figgins, Marlin D, additional, Englund, Janet A, additional, Boeckh, Michael, additional, Lockwood, Christina M, additional, Nickerson, Deborah A., additional, Shendure, Jay, additional, Uyeki, Timothy M, additional, Starita, Lea M, additional, Bedford, Trevor, additional, Chu, Helen Y, additional, and Weil, Ana A, additional

Published
2024
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17. Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States

Author

Perofsky, Amanda C, primary, Huddleston, John, additional, Hansen, Chelsea, additional, Barnes, John R, additional, Rowe, Thomas, additional, Xu, Xiyan, additional, Kondor, Rebecca, additional, Wentworth, David E, additional, Lewis, Nicola, additional, Whittaker, Lynne, additional, Ermetal, Burcu, additional, Harvey, Ruth, additional, Galiano, Monica, additional, Daniels, Rodney Stuart, additional, McCauley, John W, additional, Fujisaki, Seiichiro, additional, Nakamura, Kazuya, additional, Kishida, Noriko, additional, Watanabe, Shinji, additional, Hasegawa, Hideki, additional, Sullivan, Sheena G, additional, Barr, Ian G, additional, Subbarao, Kanta, additional, Krammer, Florian, additional, Bedford, Trevor, additional, and Viboud, Cécile, additional

Published
2024
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20. Changing genomic epidemiology of COVID-19 in long-term care facilities during the 2020–2022 pandemic, Washington State

Author

Oltean, Hanna N., primary, Black, Allison, additional, Lunn, Stephanie M., additional, Smith, Nailah, additional, Templeton, Allison, additional, Bevers, Elyse, additional, Kibiger, Lynae, additional, Sixberry, Melissa, additional, Bickel, Josina B., additional, Hughes, James P., additional, Lindquist, Scott, additional, Baseman, Janet G., additional, and Bedford, Trevor, additional

Published
2024
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21. Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin

Author

Welsh, Frances C., primary, Eguia, Rachel T., additional, Lee, Juhye M., additional, Haddox, Hugh K., additional, Galloway, Jared, additional, Chau, Nguyen Van Vinh, additional, Loes, Andrea N., additional, Huddleston, John, additional, Yu, Timothy C., additional, Le, Mai Quynh, additional, Nhat, Nguyen T.D., additional, Thanh, Nguyen Thi Le, additional, Greninger, Alexander L., additional, Chu, Helen Y., additional, Englund, Janet A., additional, Bedford, Trevor, additional, Matsen, Frederick A., additional, Boni, Maciej F., additional, and Bloom, Jesse D., additional

Published
2023
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22. 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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23. Tracing the Origin, Spread, and Molecular Evolution of Zika Virus in Puerto Rico, 2016-2017

Author

Santiago, Gilberto A., Kalinich, Chaney C., Cruz-Lopez, Fabiola, Gonzalez, Glenda L., Flores, Betzabel, Hentoff, Aaron, Charriez, Keyla N., Fauver, Joseph R., Adams, Laura E., Sharp, Tyler M., Black, Allison, Bedford, Trevor, Ellis, Esther, Ellis, Brett, Waterman, Steve H., Paz-Bailey, Gabriela, Grubaugh, Nathan D., and Munoz-Jordan, Jorge L.

Subjects
Epidemics -- Causes of -- Distribution -- Puerto Rico, Genomics -- Research, Molecular evolution -- Research, Virus research, Company distribution practices, Health
Abstract

Puerto Rico reported the first confirmed case of Zika virus (ZIKV) disease in November 2015 and subsequently experienced epidemic transmission that peaked by mid-August 2016 (1). Despite the large number [...]

Published
2021
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24. Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States

Author

Perofsky, Amanda C, primary, Huddleston, John, additional, Hansen, Chelsea, additional, Barnes, John R, additional, Rowe, Thomas, additional, Xu, Xiyan, additional, Kondor, Rebecca, additional, Wentworth, David E, additional, Lewis, Nicola, additional, Whittaker, Lynne, additional, Ermetal, Burcu, additional, Harvey, Ruth, additional, Galiano, Monica, additional, Daniels, Rodney Stuart, additional, McCauley, John W, additional, Fujisaki, Seiichiro, additional, Nakamura, Kazuya, additional, Kishida, Noriko, additional, Watanabe, Shinji, additional, Hasegawa, Hideki, additional, Sullivan, Sheena G, additional, Barr, Ian G, additional, Subbarao, Kanta, additional, Krammer, Florian, additional, Bedford, Trevor, additional, and Viboud, Cécile, additional

Published
2023
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29. Sentinel Surveillance System Implementation and Evaluation for SARS-CoV-2 Genomic Data, Washington, USA, 2020–2021

Author

Oltean, Hanna N., primary, Allen, Krisandra J., additional, Frisbie, Lauren, additional, Lunn, Stephanie M., additional, Torres, Laura Marcela, additional, Manahan, Lillian, additional, Painter, Ian, additional, Russell, Denny, additional, Singh, Avi, additional, Peterson, JohnAric MoonDance, additional, Grant, Kristin, additional, Peter, Cara, additional, Cao, Rebecca, additional, Garcia, Katelynn, additional, Mackellar, Drew, additional, Jones, Lisa, additional, Halstead, Holly, additional, Gray, Hannah, additional, Melly, Geoff, additional, Nickerson, Deborah, additional, Starita, Lea, additional, Frazar, Chris, additional, Greninger, Alexander L., additional, Roychoudhury, Pavitra, additional, Mathias, Patrick C., additional, Kalnoski, Michael H., additional, Ting, Chao-Nan, additional, Lykken, Marisa, additional, Rice, Tana, additional, Gonzalez-Robles, Daniel, additional, Bina, David, additional, Johnson, Kelly, additional, Wiley, Carmen L., additional, Magnuson, Shaun C., additional, Parsons, Christopher M., additional, Chapman, Eugene D., additional, Valencia, C. Alexander, additional, Fortna, Ryan R., additional, Wolgamot, Gregory, additional, Hughes, James P., additional, Baseman, Janet G., additional, Bedford, Trevor, additional, and Lindquist, Scott, additional

Published
2023
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31. Local-Scale phylodynamics reveal differential community impact of SARS-CoV-2 in metropolitan US county

Author

Paredes, Miguel I., primary, Perofsky, Amanda C., additional, Frisbie, Lauren, additional, Moncla, Louise H., additional, Roychoudhury, Pavitra, additional, Xie, Hong, additional, Mohamed Bakhash, Shah A., additional, Kong, Kevin, additional, Arnould, Isabel, additional, Nguyen, Tien V., additional, Wendm, Seffir T., additional, Hajian, Pooneh, additional, Ellis, Sean, additional, Mathias, Patrick C., additional, Greninger, Alexander L., additional, Starita, Lea M., additional, Frazar, Chris D., additional, Ryke, Erica, additional, Zhong, Weizhi, additional, Gamboa, Luis, additional, Threlkeld, Machiko, additional, Lee, Jover, additional, Stone, Jeremy, additional, McDermot, Evan, additional, Truong, Melissa, additional, Shendure, Jay, additional, Oltean, Hanna N., additional, Viboud, Cécile, additional, Chu, Helen, additional, Müller, Nicola F., additional, and Bedford, Trevor, additional

Published
2022
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32. 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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33. Author Correction: Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution.

Author

Wagner, Cassia, Kistler, Kathryn E., Perchetti, Garrett A., Baker, Noah, Frisbie, Lauren A., Torres, Laura Marcela, Aragona, Frank, Yun, Cory, Figgins, Marlin, Greninger, Alexander L., Cox, Alex, Oltean, Hanna N., Roychoudhury, Pavitra, and Bedford, Trevor

Subjects
INTERNET publishing, SARS-CoV-2
Abstract

This document is a correction notice for an article titled "Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution" published in Nature Communications. The correction addresses an error in Figure 5 of the original article, which contained an incorrect version of panel B. The correction has been made in both the PDF and HTML versions of the article. The authors of the article are listed as Cassia Wagner, Kathryn E. Kistler, Garrett A. Perchetti, Noah Baker, Lauren A. Frisbie, Laura Marcela Torres, Frank Aragona, Cory Yun, Marlin Figgins, Alexander L. Greninger, Alex Cox, Hanna N. Oltean, Pavitra Roychoudhury, and Trevor Bedford. [Extracted from the article]

Published
2024
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34. Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus [perspective]

Author

Happi, Christian, Adetifa, Ifedayo, Mbala, Placide, Njouom, Richard, Nakoune, Emmanuel, Happi, Anise, Ndodo, Nnaemeka, Ayansola, Oyeronke, Mboowa, Gerald, Bedford, Trevor, Neher, Richard A, Roemer, Cornelius, Hodcroft, Emma, Tegally, Houriiyah, O'Toole, Áine, Rambaut, Andrew, Pybus, Oliver, Kraemer, Moritz U G, Wilkinson, Eduan, Isidro, Joana, Borges, Vítor, Pinto, Miguel, Gomes, João Paulo, Freitas, Lucas, Resende, Paola C, Lee, Raphael T C, Maurer-Stroh, Sebastian, Baxter, Cheryl, Lessells, Richard, Ogwell, Ahmed E, Kebede, Yenew, Tessema, Sofonias K, and de Oliveira, Tulio

Subjects
360 Social problems & social services, 610 Medicine & health
Abstract

We propose a novel, non-discriminatory classification of monkeypox virus. Together with the World Health Organization, we named three clades (I, IIa and IIb) in order of detection. Within IIb, the cause the current global outbreak, we identified multiple lineages (A.1, A.2, A.1.1 and B.1) to support real-time genomics surveillance.

Published
2022

36. Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus

Author

Happi, Christian, primary, Adetifa, Ifedayo, additional, Mbala, Placide, additional, Njouom, Richard, additional, Nakoune, Emmanuel, additional, Happi, Anise, additional, Ndodo, Nnaemeka, additional, Ayansola, Oyeronke, additional, Mboowa, Gerald, additional, Bedford, Trevor, additional, Neher, Richard A., additional, Roemer, Cornelius, additional, Hodcroft, Emma, additional, Tegally, Houriiyah, additional, O’Toole, Áine, additional, Rambaut, Andrew, additional, Pybus, Oliver, additional, Kraemer, Moritz U. G., additional, Wilkinson, Eduan, additional, Isidro, Joana, additional, Borges, Vítor, additional, Pinto, Miguel, additional, Gomes, João Paulo, additional, Freitas, Lucas, additional, Resende, Paola C., additional, Lee, Raphael T. C., additional, Maurer-Stroh, Sebastian, additional, Baxter, Cheryl, additional, Lessells, Richard, additional, Ogwell, Ahmed E., additional, Kebede, Yenew, additional, Tessema, Sofonias K., additional, and de Oliveira, Tulio, additional

Published
2022
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37. 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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39. Mapping the emergence of SARS-CoV-2 Omicron variants on a university campus

Author

Weil, Ana A., primary, Luiten, Kyle G., additional, Casto, Amanda M., additional, Bennett, Julia C., additional, O’Hanlon, Jessica, additional, Han, Peter D., additional, Gamboa, Luis, additional, McDermot, Evan, additional, Truong, Melissa, additional, Gottlieb, Geoffrey S., additional, Acker, Zack, additional, Wolf, Caitlin R., additional, Magedson, Ariana, additional, Chow, Eric J., additional, Lo, Natalie K., additional, Pothan, Lincoln C., additional, McDonald, Devon, additional, Wright, Tessa, additional, McCaffrey, Kathryn, additional, Figgins, Marlin D., additional, Englund, Janet A., additional, Boeckh, Michael, additional, Lockwood, Christina M., additional, Nickerson, Deborah A., additional, Shendure, Jay, additional, Bedford, Trevor, additional, Hughes, James P., additional, Starita, Lea M., additional, and Chu, Helen Y., additional

Published
2022
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40. The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

Author

Tegally, Houriiyah, primary, San, James E., additional, Cotten, Matthew, additional, Tegomoh, Bryan, additional, Mboowa, Gerald, additional, Martin, Darren P., additional, Baxter, Cheryl, additional, Moir, Monika, additional, Lambisia, Arnold, additional, Diallo, Amadou, additional, Amoako, Daniel G., additional, Diagne, Moussa M., additional, Sisay, Abay, additional, Zekri, Abdel-Rahman N., additional, Barakat, Abdelhamid, additional, Gueye, Abdou Salam, additional, Sangare, Abdoul K., additional, Ouedraogo, Abdoul-Salam, additional, Sow, Abdourahmane, additional, Musa, Abdualmoniem O., additional, Sesay, Abdul K., additional, Lagare, Adamou, additional, Kemi, Adedotun-Sulaiman, additional, Abar, Aden Elmi, additional, Johnson, Adeniji A., additional, Fowotade, Adeola, additional, Olubusuyi, Adewumi M., additional, Oluwapelumi, Adeyemi O., additional, Amuri, Adrienne A., additional, Juru, Agnes, additional, Ramadan, Ahmad Mabrouk, additional, Kandeil, Ahmed, additional, Mostafa, Ahmed, additional, Rebai, Ahmed, additional, Sayed, Ahmed, additional, Kazeem, Akano, additional, Balde, Aladje, additional, Christoffels, Alan, additional, Trotter, Alexander J., additional, Campbell, Allan, additional, Keita, Alpha Kabinet, additional, Kone, Amadou, additional, Bouzid, Amal, additional, Souissi, Amal, additional, Agweyu, Ambrose, additional, Gutierrez, Ana V., additional, Page, Andrew J., additional, Yadouleton, Anges, additional, Vinze, Anika, additional, Happi, Anise N., additional, Chouikha, Anissa, additional, Iranzadeh, Arash, additional, Maharaj, Arisha, additional, Batchi-Bouyou, Armel Landry, additional, Ismail, Arshad, additional, Sylverken, Augustina, additional, Goba, Augustine, additional, Femi, Ayoade, additional, Sijuwola, Ayotunde Elijah, additional, Ibrahimi, Azeddine, additional, Marycelin, Baba, additional, Salako, Babatunde Lawal, additional, Oderinde, Bamidele S., additional, Bolajoko, Bankole, additional, Dhaala, Beatrice, additional, Herring, Belinda L., additional, Tsofa, Benjamin, additional, Mvula, Bernard, additional, Njanpop-Lafourcade, Berthe-Marie, additional, Marondera, Blessing T., additional, Khaireh, Bouh Abdi, additional, Kouriba, Bourema, additional, Adu, Bright, additional, Pool, Brigitte, additional, McInnis, Bronwyn, additional, Brook, Cara, additional, Williamson, Carolyn, additional, Anscombe, Catherine, additional, Pratt, Catherine B., additional, Scheepers, Cathrine, additional, Akoua-Koffi, Chantal G., additional, Agoti, Charles N., additional, Loucoubar, Cheikh, additional, Onwuamah, Chika Kingsley, additional, Ihekweazu, Chikwe, additional, Malaka, Christian Noël, additional, Peyrefitte, Christophe, additional, Omoruyi, Chukwuma Ewean, additional, Rafaï, Clotaire Donatien, additional, Morang’a, Collins M., additional, Nokes, D. James, additional, Lule, Daniel Bugembe, additional, Bridges, Daniel J., additional, Mukadi-Bamuleka, Daniel, additional, Park, Danny, additional, Baker, David, additional, Doolabh, Deelan, additional, Ssemwanga, Deogratius, additional, Tshiabuila, Derek, additional, Bassirou, Diarra, additional, Amuzu, Dominic S.Y., additional, Goedhals, Dominique, additional, Grant, Donald S., additional, Omuoyo, Donwilliams O., additional, Maruapula, Dorcas, additional, Wanjohi, Dorcas Waruguru, additional, Foster-Nyarko, Ebenezer, additional, Lusamaki, Eddy K., additional, Simulundu, Edgar, additional, Ong’era, Edidah M., additional, Ngabana, Edith N., additional, Abworo, Edward O., additional, Otieno, Edward, additional, Shumba, Edwin, additional, Barasa, Edwine, additional, Ahmed, El Bara, additional, Kampira, Elizabeth, additional, Fahime, Elmostafa El, additional, Lokilo, Emmanuel, additional, Mukantwari, Enatha, additional, Cyril, Erameh, additional, Philomena, Eromon, additional, Belarbi, Essia, additional, Simon-Loriere, Etienne, additional, Anoh, Etilé A., additional, Leendertz, Fabian, additional, Taweh, Fahn M., additional, Wasfi, Fares, additional, Abdelmoula, Fatma, additional, Takawira, Faustinos T., additional, Derrar, Fawzi, additional, Ajogbasile, Fehintola V, additional, Treurnicht, Florette, additional, Onikepe, Folarin, additional, Ntoumi, Francine, additional, Muyembe, Francisca M., additional, Ngiambudulu, Francisco, additional, Zongo Ragomzingba, Frank Edgard, additional, Dratibi, Fred Athanasius, additional, Iyanu, Fred-Akintunwa, additional, Mbunsu, Gabriel K., additional, Thilliez, Gaetan, additional, Kay, Gemma L., additional, Akpede, George O., additional, George, Uwem E., additional, van Zyl, Gert, additional, Awandare, Gordon A., additional, Schubert, Grit, additional, Maphalala, Gugu P., additional, Ranaivoson, Hafaliana C., additional, Lemriss, Hajar, additional, Omunakwe, Hannah E, additional, Onywera, Harris, additional, Abe, Haruka, additional, Karray, Hela, additional, Nansumba, Hellen, additional, Triki, Henda, additional, Adje Kadjo, Herve Albéric, additional, Elgahzaly, Hesham, additional, Gumbo, Hlanai, additional, mathieu, Hota, additional, Kavunga-Membo, Hugo, additional, Smeti, Ibtihel, additional, Olawoye, Idowu B., additional, Adetifa, Ifedayo, additional, Odia, Ikponmwosa, additional, Boubaker, Ilhem Boutiba-Ben, additional, Ssewanyana, Isaac, additional, Wurie, Isatta, additional, Konstantinus, Iyaloo S, additional, Afiwa Halatoko, Jacqueline Wemboo, additional, Ayei, James, additional, Sonoo, Janaki, additional, Lekana-Douki, Jean Bernard, additional, Makangara, Jean-Claude C., additional, Tamfum, Jean-Jacques M., additional, Heraud, Jean-Michel, additional, Shaffer, Jeffrey G., additional, Giandhari, Jennifer, additional, Musyoki, Jennifer, additional, Uwanibe, Jessica N., additional, Bhiman, Jinal N., additional, Yasuda, Jiro, additional, Morais, Joana, additional, Mends, Joana Q., additional, Kiconco, Jocelyn, additional, Sandi, John Demby, additional, Huddleston, John, additional, Odoom, John Kofi, additional, Morobe, John M., additional, Gyapong, John O., additional, Kayiwa, John T., additional, Okolie, Johnson C., additional, Xavier, Joicymara Santos, additional, Gyamfi, Jones, additional, Kofi Bonney, Joseph Humphrey, additional, Nyandwi, Joseph, additional, Everatt, Josie, additional, Farah, Jouali, additional, Nakaseegu, Joweria, additional, Ngoi, Joyce M., additional, Namulondo, Joyce, additional, Oguzie, Judith U., additional, Andeko, Julia C., additional, Lutwama, Julius J., additional, O’Grady, Justin, additional, Siddle, Katherine J, additional, Victoir, Kathleen, additional, Adeyemi, Kayode T., additional, Tumedi, Kefentse A., additional, Carvalho, Kevin Sanders, additional, Mohammed, Khadija Said, additional, Musonda, Kunda G., additional, Duedu, Kwabena O., additional, Belyamani, Lahcen, additional, Fki-Berrajah, Lamia, additional, Singh, Lavanya, additional, Biscornet, Leon, additional, de Oliveira Martins, Leonardo, additional, Chabuka, Lucious, additional, Olubayo, Luicer, additional, Deng, Lul Lojok, additional, Ochola-Oyier, Lynette Isabella, additional, Mine, Madisa, additional, Ramuth, Magalutcheemee, additional, Mastouri, Maha, additional, ElHefnawi, Mahmoud, additional, Mbanne, Maimouna, additional, Matsheka, Maitshwarelo I., additional, Kebabonye, Malebogo, additional, Diop, Mamadou, additional, Momoh, Mambu, additional, Lima Mendonça, Maria da Luz, additional, Venter, Marietjie, additional, Paye, Marietou F, additional, Faye, Martin, additional, Nyaga, Martin M., additional, Mareka, Mathabo, additional, Damaris, Matoke-Muhia, additional, Mburu, Maureen W., additional, Mpina, Maximillian, additional, Claujens Chastel, Mfoutou Mapanguy, additional, Owusu, Michael, additional, Wiley, Michael R., additional, Tatfeng, Mirabeau Youtchou, additional, Ayekaba, Mitoha Ondo’o, additional, Abouelhoda, Mohamed, additional, Beloufa, Mohamed Amine, additional, Seadawy, Mohamed G, additional, Khalifa, Mohamed K., additional, Dellagi, Mohammed Koussai, additional, Matobo, Mooko Marethabile, additional, Kane, Mouhamed, additional, Ouadghiri, Mouna, additional, Salou, Mounerou, additional, Mbulawa, Mphaphi B., additional, Saibu, Mudashiru Femi, additional, Mwenda, Mulenga, additional, Kaba, Muluken, additional, Phan, My V.T., additional, Abid, Nabil, additional, Touil, Nadia, additional, Rujeni, Nadine, additional, Ismael, Nalia, additional, Top, Ndeye Marieme, additional, Dia, Ndongo, additional, Mabunda, Nédio, additional, Hsiao, Nei-yuan, additional, Silochi, Nelson Boricó, additional, Saasa, Ngonda, additional, Bbosa, Nicholas, additional, Murunga, Nickson, additional, Gumede, Nicksy, additional, Wolter, Nicole, additional, Sitharam, Nikita, additional, Ndodo, Nnaemeka, additional, Ajayi, Nnennaya A., additional, Tordo, Noël, additional, Mbhele, Nokuzola, additional, Razanajatovo, Norosoa H, additional, Iguosadolo, Nosamiefan, additional, Mba, Nwando, additional, Kingsley, Ojide C., additional, Sylvanus, Okogbenin, additional, Peter, Okokhere, additional, Femi, Oladiji, additional, Testimony, Olumade, additional, Ogunsanya, Olusola Akinola, additional, Fakayode, Oluwatosin, additional, Ogah, Onwe E., additional, Faye, Ousmane, additional, Smith-Lawrence, Pamela, additional, Ondoa, Pascale, additional, Combe, Patrice, additional, Nabisubi, Patricia, additional, Semanda, Patrick, additional, Oluniyi, Paul E., additional, Arnaldo, Paulo, additional, Quashie, Peter Kojo, additional, Bejon, Philip, additional, Dussart, Philippe, additional, Bester, Phillip A., additional, Mbala, Placide K., additional, Kaleebu, Pontiano, additional, Abechi, Priscilla, additional, El-Shesheny, Rabeh, additional, Joseph, Rageema, additional, Aziz, Ramy Karam, additional, Essomba, René Ghislain, additional, Ayivor-Djanie, Reuben, additional, Njouom, Richard, additional, Phillips, Richard O., additional, Gorman, Richmond, additional, Kingsley, Robert A., additional, Audu, Rosemary, additional, Carr, Rosina A.A., additional, Kabbaj, Saâd El, additional, Gargouri, Saba, additional, Masmoudi, Saber, additional, Sankhe, Safietou, additional, Mohamed, Sahra Isse, additional, Mhalla, Salma, additional, Hosch, Salome, additional, Kassim, Samar Kamal, additional, Metha, Samar, additional, Trabelsi, Sameh, additional, Lemriss, Sanaâ, additional, Agwa, Sara Hassan, additional, Mwangi, Sarah Wambui, additional, Doumbia, Seydou, additional, Makiala-Mandanda, Sheila, additional, Aryeetey, Sherihane, additional, Ahmed, Shymaa S., additional, Ahmed, Sidi Mohamed, additional, Elhamoumi, Siham, additional, Moyo, Sikhulile, additional, Lutucuta, Silvia, additional, Gaseitsiwe, Simani, additional, Jalloh, Simbirie, additional, Andriamandimby, Soafy, additional, Oguntope, Sobajo, additional, Grayo, Solène, additional, Lekana-Douki, Sonia, additional, Prosolek, Sophie, additional, Ouangraoua, Soumeya, additional, van Wyk, Stephanie, additional, Schaffner, Stephen F., additional, Kanyerezi, Stephen, additional, Ahuka-Mundeke, Steve, additional, Rudder, Steven, additional, Pillay, Sureshnee, additional, Nabadda, Susan, additional, Behillil, Sylvie, additional, Budiaki, Sylvie L., additional, van der Werf, Sylvie, additional, Mashe, Tapfumanei, additional, Aanniz, Tarik, additional, Mohale, Thabo, additional, Le-Viet, Thanh, additional, Velavan, Thirumalaisamy P., additional, Schindler, Tobias, additional, Maponga, Tongai, additional, Bedford, Trevor, additional, Anyaneji, Ugochukwu J., additional, Chinedu, Ugwu, additional, Ramphal, Upasana, additional, Enouf, Vincent, additional, Nene, Vishvanath, additional, Gorova, Vivianne, additional, Roshdy, Wael H., additional, Karim, Wasim Abdul, additional, Ampofo, William K., additional, Preiser, Wolfgang, additional, Choga, Wonderful T., additional, Ahmed, Yahaya Ali, additional, Ramphal, Yajna, additional, Bediako, Yaw, additional, Naidoo, Yeshnee, additional, Butera, Yvan, additional, de Laurent, Zaydah R., additional, Ouma, Ahmed E.O., additional, von Gottberg, Anne, additional, Githinji, George, additional, Moeti, Matshidiso, additional, Tomori, Oyewale, additional, Sabeti, Pardis C., additional, Sall, Amadou A., additional, Oyola, Samuel O., additional, Tebeje, Yenew K., additional, Tessema, Sofonias K., additional, de Oliveira, Tulio, additional, Happi, Christian, additional, Lessells, Richard, additional, Nkengasong, John, additional, and Wilkinson, Eduan, additional

Published
2022
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41. Associations Between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants and Risk of Coronavirus Disease 2019 (COVID-19) Hospitalization Among Confirmed Cases in Washington State: A Retrospective Cohort Study

Author

Paredes, Miguel I, primary, Lunn, Stephanie M, additional, Famulare, Michael, additional, Frisbie, Lauren A, additional, Painter, Ian, additional, Burstein, Roy, additional, Roychoudhury, Pavitra, additional, Xie, Hong, additional, Mohamed Bakhash, Shah A, additional, Perez, Ricardo, additional, Lukes, Maria, additional, Ellis, Sean, additional, Sathees, Saraswathi, additional, Mathias, Patrick C, additional, Greninger, Alexander, additional, Starita, Lea M, additional, Frazar, Chris D, additional, Ryke, Erica, additional, Zhong, Weizhi, additional, Gamboa, Luis, additional, Threlkeld, Machiko, additional, Lee, Jover, additional, McDermot, Evan, additional, Truong, Melissa, additional, Nickerson, Deborah A, additional, Bates, Daniel L, additional, Hartman, Matthew E, additional, Haugen, Eric, additional, Nguyen, Truong N, additional, Richards, Joshua D, additional, Rodriguez, Jacob L, additional, Stamatoyannopoulos, John A, additional, Thorland, Eric, additional, Melly, Geoff, additional, Dykema, Philip E, additional, MacKellar, Drew C, additional, Gray, Hannah K, additional, Singh, Avi, additional, Peterson, JohnAric M, additional, Russell, Denny, additional, Torres, Laura Marcela, additional, Lindquist, Scott, additional, Bedford, Trevor, additional, Allen, Krisandra J, additional, and Oltean, Hanna N, additional

Published
2022
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43. Diagnostic Accuracy of an At-Home, Rapid Self-test for Influenza: Prospective Comparative Accuracy Study

Author

Geyer, Rachel E, primary, Kotnik, Jack Henry, additional, Lyon, Victoria, additional, Brandstetter, Elisabeth, additional, Zigman Suchsland, Monica, additional, Han, Peter D, additional, Graham, Chelsey, additional, Ilcisin, Misja, additional, Kim, Ashley E, additional, Chu, Helen Y, additional, Nickerson, Deborah A, additional, Starita, Lea M, additional, Bedford, Trevor, additional, Lutz, Barry, additional, and Thompson, Matthew J, additional

Published
2022
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44. 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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46. Comparison of Symptoms and RNA Levels in Children and Adults With SARS-CoV-2 Infection in the Community Setting

Author

Chung, Erin, primary, Chow, Eric J., additional, Wilcox, Naomi C., additional, Burstein, Roy, additional, Brandstetter, Elisabeth, additional, Han, Peter D., additional, Fay, Kairsten, additional, Pfau, Brian, additional, Adler, Amanda, additional, Lacombe, Kirsten, additional, Lockwood, Christina M., additional, Uyeki, Timothy M., additional, Shendure, Jay, additional, Duchin, Jeffrey S., additional, Rieder, Mark J., additional, Nickerson, Deborah A., additional, Boeckh, Michael, additional, Famulare, Michael, additional, Hughes, James P., additional, Starita, Lea M., additional, Bedford, Trevor, additional, Englund, Janet A., additional, and Chu, Helen Y., additional

Published
2021
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47. Remote Household Observation for Noninfluenza Respiratory Viral Illness.

Author

Emanuels, Anne, Heimonen, Jessica, O'Hanlon, Jessica, Kim, Ashley E, Wilcox, Naomi, McCulloch, Denise J, Brandstetter, Elisabeth, Wolf, Caitlin R, Logue, Jennifer K, Han, Peter D, Pfau, Brian, Newman, Kira L, Hughes, James P, Jackson, Michael L, Uyeki, Timothy M, Boeckh, Michael, Starita, Lea M, Nickerson, Deborah A, Bedford, Trevor, and Englund, Janet A

Subjects
VIRAL transmission, PUBLIC health surveillance
Abstract

Background Noninfluenza respiratory viruses are responsible for a substantial burden of disease in the United States. Household transmission is thought to contribute significantly to subsequent transmission through the broader community. In the context of the coronavirus disease 2019 (COVID-19) pandemic, contactless surveillance methods are of particular importance. Methods From November 2019 to April 2020, 303 households in the Seattle area were remotely monitored in a prospective longitudinal study for symptoms of respiratory viral illness. Enrolled participants reported weekly symptoms and submitted respiratory samples by mail in the event of an acute respiratory illness (ARI). Specimens were tested for 14 viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), using reverse-transcription polymerase chain reaction. Participants completed all study procedures at home without physical contact with research staff. Results In total, 1171 unique participants in 303 households were monitored for ARI. Of participating households, 128 (42%) included a child aged <5 years and 202 (67%) included a child aged 5–12 years. Of the 678 swabs collected during the surveillance period, 237 (35%) tested positive for 1 or more noninfluenza respiratory viruses. Rhinovirus, common human coronaviruses, and respiratory syncytial virus were the most common. Four cases of SARS-CoV-2 were detected in 3 households. Conclusions This study highlights the circulation of respiratory viruses within households during the winter months during the emergence of the SARS-CoV-2 pandemic. Contactless methods of recruitment, enrollment, and sample collection were utilized throughout this study and demonstrate the feasibility of home-based, remote monitoring for respiratory infections. [ABSTRACT FROM AUTHOR]

Published
2021
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48. Specific allelic discrimination of N501Y and other SARS‐CoV‐2 mutations by ddPCR detects B.1.1.7 lineage in Washington State.

Author

Perchetti, Garrett A., Zhu, Haiying, Mills, Margaret G., Shrestha, Lasata, Wagner, Cassia, Bakhash, Shah Mohamed, Lin, Michelle J., Xie, Hong, Huang, Meei‐Li, Mathias, Patrick, Bedford, Trevor, Jerome, Keith R., Greninger, Alexander L., and Roychoudhury, Pavitra

Subjects
SARS-CoV-2, COVID-19, POLYMERASE chain reaction
Abstract

Real‐time epidemiological tracking of variants of concern (VOCs) can help limit the spread of more contagious forms of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), such as those containing the N501Y mutation. Typically, genetic sequencing is required to be able to track VOCs in real‐time. However, sequencing can take time and may not be accessible in all laboratories. Genotyping by RT‐ddPCR offers an alternative to rapidly detect VOCs through discrimination of specific alleles such as N501Y, which is associated with increased transmissibility and virulence. Here we describe the first cases of the B.1.1.7 lineage of SARS‐CoV‐2 detected in Washington State by using a combination of reverse‐transcription polymerase chain reaction (RT‐PCR), RT‐ddPCR, and next‐generation sequencing. We initially screened 1035 samples positive for SARS‐CoV‐2 by our CDC‐based laboratory‐developed assay using ThermoFisher's multiplex RT‐PCR COVID‐19 assay over four weeks from late December 2020 to early January 2021. S gene target failures (SGTF) were subsequently assayed by RT‐ddPCR to confirm four mutations within the S gene associated with the B.1.1.7 lineage: a deletion at amino acid (AA) 69‐70 (ACATGT), deletion at AA 145, (TTA), N501Y mutation (TAT), and S982A mutation (GCA). All four targets were detected in two specimens; follow‐up sequencing revealed a total of 9 mutations in the S gene and phylogenetic clustering within the B.1.1.7 lineage. Next, we continued screening samples for SGTF detecting 23 additional B.1.1.7 variants by RT‐ddPCR and confirmed by sequencing. As VOCs become increasingly prevalent, molecular diagnostic tools like RT‐ddPCR can be utilized to quickly, accurately, and sensitively distinguish more contagious lineages of SARS‐CoV‐2. Highlights: ‐B.1.1.7 (alpha) lineage of SARS‐CoV‐2 was detected in Washington State using RT‐ddPCR.‐Specific allelic discrimination can be used to distinguish SARS‐CoV‐2 variants of concern.‐Allelic discrimination can identify variants of concern more rapidly than conventional sequencing techniques.‐S‐gene target failures can be used to screen for certain SARS‐CoV‐2 variants. [ABSTRACT FROM AUTHOR]

Published
2021
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49. Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States.

Author

Perofsky AC, Huddleston J, Hansen CL, Barnes JR, Rowe T, Xu X, Kondor R, Wentworth DE, Lewis N, Whittaker L, Ermetal B, Harvey R, Galiano M, Daniels RS, McCauley JW, Fujisaki S, Nakamura K, Kishida N, Watanabe S, Hasegawa H, Sullivan SG, Barr IG, Subbarao K, Krammer F, Bedford T, and Viboud C

Subjects
United States epidemiology, Humans, Child, Adult, Neuraminidase genetics, Neuraminidase immunology, Adolescent, Child, Preschool, Antigens, Viral immunology, Antigens, Viral genetics, Young Adult, Evolution, Molecular, Seasons, Middle Aged, Influenza A Virus, H3N2 Subtype genetics, Influenza A Virus, H3N2 Subtype immunology, Influenza, Human epidemiology, Influenza, Human virology, Influenza, Human immunology, Hemagglutinin Glycoproteins, Influenza Virus genetics, Hemagglutinin Glycoproteins, Influenza Virus immunology, Epidemics, Antigenic Drift and Shift genetics
Abstract

Influenza viruses continually evolve new antigenic variants, through mutations in epitopes of their major surface proteins, hemagglutinin (HA) and neuraminidase (NA). Antigenic drift potentiates the reinfection of previously infected individuals, but the contribution of this process to variability in annual epidemics is not well understood. Here, we link influenza A(H3N2) virus evolution to regional epidemic dynamics in the United States during 1997-2019. We integrate phenotypic measures of HA antigenic drift and sequence-based measures of HA and NA fitness to infer antigenic and genetic distances between viruses circulating in successive seasons. We estimate the magnitude, severity, timing, transmission rate, age-specific patterns, and subtype dominance of each regional outbreak and find that genetic distance based on broad sets of epitope sites is the strongest evolutionary predictor of A(H3N2) virus epidemiology. Increased HA and NA epitope distance between seasons correlates with larger, more intense epidemics, higher transmission, greater A(H3N2) subtype dominance, and a greater proportion of cases in adults relative to children, consistent with increased population susceptibility. Based on random forest models, A(H1N1) incidence impacts A(H3N2) epidemics to a greater extent than viral evolution, suggesting that subtype interference is a major driver of influenza A virus infection ynamics, presumably via heterosubtypic cross-immunity., Competing Interests: AP, JH, JB, TR, XX, RK, DW, NL, LW, BE, RH, MG, RD, SF, KN, NK, SW, HH, TB No competing interests declared, CH Received personal fees from Sanofi outside the submitted work, JM Received consulting fees, honoraria, and travel support from Sanofi Pasteur and Sequris, SS The WHO Collaborating Centre for Reference and Research on Influenza in Melbourne has a collaborative research and development agreement (CRADA) with CSL Seqirus for isolation of candidate vaccine viruses in cells and an agreement with IFPMA for isolation of candidate vaccine viruses in eggs. SGS reports honoraria from CSL Seqirus, Moderna, Pfizer, and Evo Health, IB, KS The WHO Collaborating Centre for Reference and Research on Influenza in Melbourne has a collaborative research and development agreement (CRADA) with CSL Seqirus for isolation of candidate vaccine viruses in cells and an agreement with IFPMA for isolation of candidate vaccine viruses in eggs, FK The Icahn School of Medicine at Mount Sinai has filed patent applications relating to influenza virus vaccines (U.S. patent numbers: 12030928, 11865173, 11266734, 11254733, 10736956, 10583188, 10137189, 10131695, 9968670, 9371366; publication numbers: 20230181715, 20220403358, 20220249652, 20220242935, 20220153873, 20210260179, 20190125859, 20190106461, 20180333479), SARS-CoV-2 serological assays (publication number: 20240210415), and SARS-CoV-2 vaccines (publication numbers: 20230310583, 20230226171), which list FK as co-inventor. FK has consulted for Merck and Pfizer (before 2020), and is currently consulting for Pfizer, Seqirus, 3rd Rock Ventures, GSK and Avimex. The Krammer laboratory is also collaborating with Pfizer on animal models of SARS‐CoV‐2 and with Dynavax on universal influenza virus vaccines, CV Received honoraria for serving as an Editor in Chief of the journal Epidemics (Elsevier)

Published
2024
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50. High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains.

Author

Loes AN, Tarabi RAL, Huddleston J, Touyon L, Wong SS, Cheng SMS, Leung NHL, Hannon WW, Bedford T, Cobey S, Cowling BJ, and Bloom JD

Abstract

The high genetic diversity of influenza viruses means that traditional serological assays have too low throughput to measure serum antibody neutralization titers against all relevant strains. To overcome this challenge, we developed a sequencing-based neutralization assay that simultaneously measures titers against many viral strains using small serum volumes using a workflow similar to traditional neutralization assays. The key innovation is to incorporate unique nucleotide barcodes into the hemagglutinin (HA) genomic segment, and then pool viruses with numerous different barcoded HA variants and quantify the infectivity of all of them simultaneously using next-generation sequencing. With this approach, a single researcher performed the equivalent of 2,880 traditional neutralization assays (80 serum samples against 36 viral strains) in approximately 1 month. We applied the sequencing-based assay to quantify the impact of influenza vaccination on neutralization titers against recent human H1N1 strains for individuals who had or had not also received a vaccine in the previous year. We found that the viral strain specificities of the neutralizing antibodies elicited by vaccination vary among individuals and that vaccination induced a smaller increase in titers for individuals who had also received a vaccine the previous year-although the titers 6 months after vaccination were similar in individuals with and without the previous-year vaccination. We also identified a subset of individuals with low titers to a subclade of recent H1N1 even after vaccination. We provide an experimental protocol (dx.doi.org/10.17504/protocols.io.kqdg3xdmpg25/v1) and computational pipeline (https://github.com/jbloomlab/seqneut-pipeline) for the sequencing-based neutralization assays to facilitate the use of this method by others., Importance: We describe a new approach that can rapidly measure how the antibodies in human serum inhibit infection by many different influenza strains. This new approach is useful for understanding how viral evolution affects antibody immunity. We apply the approach to study the effect of repeated influenza vaccination.

Published
2024
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