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1. Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections

Author

Illingworth, Christopher J. R., Hamilton, William L., Warne, Ben, Routledge, Matthew, Popay, Ashley, Jackson, Chris, Fieldman, Tom, Meredith, Luke W., Houldcroft, Charlotte J., Hosmillo, Myra, Jahun, Aminu S., Caller, Laura G., Caddy, Sarah L., Yakovleva, Anna, Hall, Grant, Khokhar, Fahad A., Feltwell, Theresa, Pinckert, Malte L., Georgana, Iliana, Chaudhry, Yasmin, Curran, Martin D., Parmar, Surendra, Sparkes, Dominic, Rivett, Lucy, Jones, Nick K., Sridhar, Sushmita, Forrest, Sally, Dymond, Tom, Grainger, Kayleigh, Workman, Chris, Ferris, Mark, Gkrania-Klotsas, Effrossyni, Brown, Nicholas M., Weekes, Michael P., Baker, Stephen, Peacock, Sharon J., Goodfellow, Ian G., Gouliouris, Theodore, de Angelis, Daniela, Torok, M. Estee, Illingworth, Christopher J. R., Hamilton, William L., Warne, Ben, Routledge, Matthew, Popay, Ashley, Jackson, Chris, Fieldman, Tom, Meredith, Luke W., Houldcroft, Charlotte J., Hosmillo, Myra, Jahun, Aminu S., Caller, Laura G., Caddy, Sarah L., Yakovleva, Anna, Hall, Grant, Khokhar, Fahad A., Feltwell, Theresa, Pinckert, Malte L., Georgana, Iliana, Chaudhry, Yasmin, Curran, Martin D., Parmar, Surendra, Sparkes, Dominic, Rivett, Lucy, Jones, Nick K., Sridhar, Sushmita, Forrest, Sally, Dymond, Tom, Grainger, Kayleigh, Workman, Chris, Ferris, Mark, Gkrania-Klotsas, Effrossyni, Brown, Nicholas M., Weekes, Michael P., Baker, Stephen, Peacock, Sharon J., Goodfellow, Ian G., Gouliouris, Theodore, de Angelis, Daniela, and Torok, M. Estee

Abstract

SARS-CoV-2 is notable both for its rapid spread, and for the heterogeneity of its patterns of transmission, with multiple published incidences of superspreading behaviour. Here, we applied a novel network reconstruction algorithm to infer patterns of viral transmission occurring between patients and health care workers (HCWs) in the largest clusters of COVID-19 infection identified during the first wave of the epidemic at Cambridge University Hospitals NHS Foundation Trust, UK. Based upon dates of individuals reporting symptoms, recorded individual locations, and viral genome sequence data, we show an uneven pattern of transmission between individuals, with patients being much more likely to be infected by other patients than by HCWs. Further, the data were consistent with a pattern of superspreading, whereby 21% of individuals caused 80% of transmission events. Our study provides a detailed retrospective analysis of nosocomial SARS-CoV-2 transmission, and sheds light on the need for intensive and pervasive infection control procedures.

Published
2021

2. Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections

Author

Illingworth, Christopher J. R., Hamilton, William L., Warne, Ben, Routledge, Matthew, Popay, Ashley, Jackson, Chris, Fieldman, Tom, Meredith, Luke W., Houldcroft, Charlotte J., Hosmillo, Myra, Jahun, Aminu S., Caller, Laura G., Caddy, Sarah L., Yakovleva, Anna, Hall, Grant, Khokhar, Fahad A., Feltwell, Theresa, Pinckert, Malte L., Georgana, Iliana, Chaudhry, Yasmin, Curran, Martin D., Parmar, Surendra, Sparkes, Dominic, Rivett, Lucy, Jones, Nick K., Sridhar, Sushmita, Forrest, Sally, Dymond, Tom, Grainger, Kayleigh, Workman, Chris, Ferris, Mark, Gkrania-Klotsas, Effrossyni, Brown, Nicholas M., Weekes, Michael P., Baker, Stephen, Peacock, Sharon J., Goodfellow, Ian G., Gouliouris, Theodore, de Angelis, Daniela, Torok, M. Estee, Illingworth, Christopher J. R., Hamilton, William L., Warne, Ben, Routledge, Matthew, Popay, Ashley, Jackson, Chris, Fieldman, Tom, Meredith, Luke W., Houldcroft, Charlotte J., Hosmillo, Myra, Jahun, Aminu S., Caller, Laura G., Caddy, Sarah L., Yakovleva, Anna, Hall, Grant, Khokhar, Fahad A., Feltwell, Theresa, Pinckert, Malte L., Georgana, Iliana, Chaudhry, Yasmin, Curran, Martin D., Parmar, Surendra, Sparkes, Dominic, Rivett, Lucy, Jones, Nick K., Sridhar, Sushmita, Forrest, Sally, Dymond, Tom, Grainger, Kayleigh, Workman, Chris, Ferris, Mark, Gkrania-Klotsas, Effrossyni, Brown, Nicholas M., Weekes, Michael P., Baker, Stephen, Peacock, Sharon J., Goodfellow, Ian G., Gouliouris, Theodore, de Angelis, Daniela, and Torok, M. Estee

Abstract

SARS-CoV-2 is notable both for its rapid spread, and for the heterogeneity of its patterns of transmission, with multiple published incidences of superspreading behaviour. Here, we applied a novel network reconstruction algorithm to infer patterns of viral transmission occurring between patients and health care workers (HCWs) in the largest clusters of COVID-19 infection identified during the first wave of the epidemic at Cambridge University Hospitals NHS Foundation Trust, UK. Based upon dates of individuals reporting symptoms, recorded individual locations, and viral genome sequence data, we show an uneven pattern of transmission between individuals, with patients being much more likely to be infected by other patients than by HCWs. Further, the data were consistent with a pattern of superspreading, whereby 21% of individuals caused 80% of transmission events. Our study provides a detailed retrospective analysis of nosocomial SARS-CoV-2 transmission, and sheds light on the need for intensive and pervasive infection control procedures.

Published
2021

3. A million deaths from coronavirus: seven experts consider key questions

Author

Caddy, Sarah L, Moore, Anne, Bamford, Connor, Hunter, David, Gatherer, Derek, West, Robert, Michie, Susan, Caddy, Sarah L, Moore, Anne, Bamford, Connor, Hunter, David, Gatherer, Derek, West, Robert, and Michie, Susan

Abstract

The pandemic has reached a grim milestone: one million people have now died of COVID-19, according to Worldometers. On January 13, we published “Mystery China pneumonia outbreak likely caused by new human coronavirus” by Connor Bamford, a virologist at Queen’s University Belfast. Since then, we have published more than 3,500 articles on the now not-so-novel coronavirus, officially named Sars-CoV-2. Despite this huge output from the world’s leading experts, we have merely skimmed the surface of all there is to know about this perplexing pathogen. So much remains a mystery. At this important juncture, we asked several experts from different fields what their burning question about the coronavirus is. Here is what they said

Published
2020

4. A million deaths from coronavirus: seven experts consider key questions

Author

Caddy, Sarah L, Moore, Anne, Bamford, Connor, Hunter, David, Gatherer, Derek, West, Robert, Michie, Susan, Caddy, Sarah L, Moore, Anne, Bamford, Connor, Hunter, David, Gatherer, Derek, West, Robert, and Michie, Susan

Abstract

The pandemic has reached a grim milestone: one million people have now died of COVID-19, according to Worldometers. On January 13, we published “Mystery China pneumonia outbreak likely caused by new human coronavirus” by Connor Bamford, a virologist at Queen’s University Belfast. Since then, we have published more than 3,500 articles on the now not-so-novel coronavirus, officially named Sars-CoV-2. Despite this huge output from the world’s leading experts, we have merely skimmed the surface of all there is to know about this perplexing pathogen. So much remains a mystery. At this important juncture, we asked several experts from different fields what their burning question about the coronavirus is. Here is what they said

Published
2020

5. Virus genomes reveal factors that spread and sustained the Ebola epidemic.

Author

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

Abstract

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

Published
2017

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