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7. Author Correction: Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals

Author

Brizzi, Andrea, primary, Whittaker, Charles, additional, Servo, Luciana M. S., additional, Hawryluk, Iwona, additional, Prete, Carlos A., additional, de Souza, William M., additional, Aguiar, Renato S., additional, Araujo, Leonardo J. T., additional, Bastos, Leonardo S., additional, Blenkinsop, Alexandra, additional, Buss, Lewis F., additional, Candido, Darlan, additional, Castro, Marcia C., additional, Costa, Silvia F., additional, Croda, Julio, additional, de Souza Santos, Andreza Aruska, additional, Dye, Christopher, additional, Flaxman, Seth, additional, Fonseca, Paula L. C., additional, Geddes, Victor E. V., additional, Gutierrez, Bernardo, additional, Lemey, Philippe, additional, Levin, Anna S., additional, Mellan, Thomas, additional, Bonfim, Diego M., additional, Miscouridou, Xenia, additional, Mishra, Swapnil, additional, Monod, Mélodie, additional, Moreira, Filipe R. R., additional, Nelson, Bruce, additional, Pereira, Rafael H. M., additional, Ranzani, Otavio, additional, Schnekenberg, Ricardo P., additional, Semenova, Elizaveta, additional, Sonabend, Raphael, additional, Souza, Renan P., additional, Xi, Xiaoyue, additional, Sabino, Ester C., additional, Faria, Nuno R., additional, Bhatt, Samir, additional, and Ratmann, Oliver, additional

Published
2022
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8. Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe

Author

Flaxman, Seth, Mishra, Swapnil, Gandy, Axel, Unwin, H. Juliette T., Mellan, Thomas A., Coupland, Helen, Whittaker, Charles, Zhu, Harrison, Berah, Tresnia, Eaton, Jeffrey W., Monod, Mélodie, Perez-Guzman, Pablo N., Schmit, Nora, Cilloni, Lucia, Ainslie, Kylie E. C., Baguelin, Marc, Boonyasiri, Adhiratha, Boyd, Olivia, Cattarino, Lorenzo, Cooper, Laura V., Cucunubá, Zulma, Cuomo-Dannenburg, Gina, Dighe, Amy, Djaafara, Bimandra, Dorigatti, Ilaria, van Elsland, Sabine L., FitzJohn, Richard G., Gaythorpe, Katy A. M., Geidelberg, Lily, Grassly, Nicholas C., Green, William D., Hallett, Timothy, Hamlet, Arran, Hinsley, Wes, Jeffrey, Ben, Knock, Edward, Laydon, Daniel J., Nedjati-Gilani, Gemma, Nouvellet, Pierre, Parag, Kris V., Siveroni, Igor, Thompson, Hayley A., Verity, Robert, Volz, Erik, Walters, Caroline E., Wang, Haowei, Wang, Yuanrong, Watson, Oliver J., Winskill, Peter, Xi, Xiaoyue, Walker, Patrick G. T., Ghani, Azra C., Donnelly, Christl A., Riley, Steven, Vollmer, Michaela A. C., Ferguson, Neil M., Okell, Lucy C., Bhatt, Samir, Medical Research Council (MRC), and Wellcome Trust

Subjects
0301 basic medicine, medicine.medical_specialty, General Science & Technology, Population, Pooling, Psychological intervention, law.invention, 03 medical and health sciences, 0302 clinical medicine, law, Case fatality rate, Pandemic, Epidemiology, Imperial College COVID-19 Response Team, Medicine, 030212 general & internal medicine, education, education.field_of_study, Science & Technology, Multidisciplinary, business.industry, Multidisciplinary Sciences, 030104 developmental biology, Transmission (mechanics), Science & Technology - Other Topics, business, Basic reproduction number, Demography
Abstract

Following the detection of the new coronavirus1 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its spread outside of China, Europe has experienced large epidemics of coronavirus disease 2019 (COVID-19). In response, many European countries have implemented non-pharmaceutical interventions, such as the closure of schools and national lockdowns. Here we study the effect of major interventions across 11 European countries for the period from the start of the COVID-19 epidemics in February 2020 until 4 May 2020, when lockdowns started to be lifted. Our model calculates backwards from observed deaths to estimate transmission that occurred several weeks previously, allowing for the time lag between infection and death. We use partial pooling of information between countries, with both individual and shared effects on the time-varying reproduction number (Rt). Pooling allows for more information to be used, helps to overcome idiosyncrasies in the data and enables more-timely estimates. Our model relies on fixed estimates of some epidemiological parameters (such as the infection fatality rate), does not include importation or subnational variation and assumes that changes in Rt are an immediate response to interventions rather than gradual changes in behaviour. Amidst the ongoing pandemic, we rely on death data that are incomplete, show systematic biases in reporting and are subject to future consolidation. We estimate that-for all of the countries we consider here-current interventions have been sufficient to drive Rt below 1 (probability Rt

Published
2020
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9. Estimating the COVID-19 infection fatality ratio accounting for seroreversion using statistical modelling

Author

Brazeau, Nicholas F., primary, Verity, Robert, additional, Jenks, Sara, additional, Fu, Han, additional, Whittaker, Charles, additional, Winskill, Peter, additional, Dorigatti, Ilaria, additional, Walker, Patrick G. T., additional, Riley, Steven, additional, Schnekenberg, Ricardo P., additional, Hoeltgebaum, Henrique, additional, Mellan, Thomas A., additional, Mishra, Swapnil, additional, Unwin, H. Juliette T., additional, Watson, Oliver J., additional, Cucunubá, Zulma M., additional, Baguelin, Marc, additional, Whittles, Lilith, additional, Bhatt, Samir, additional, Ghani, Azra C., additional, Ferguson, Neil M., additional, and Okell, Lucy C., additional

Published
2022
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10. Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals

Author

Brizzi, Andrea, primary, Whittaker, Charles, additional, Servo, Luciana M. S., additional, Hawryluk, Iwona, additional, Prete, Carlos A., additional, de Souza, William M., additional, Aguiar, Renato S., additional, Araujo, Leonardo J. T., additional, Bastos, Leonardo S., additional, Blenkinsop, Alexandra, additional, Buss, Lewis F., additional, Candido, Darlan, additional, Castro, Marcia C., additional, Costa, Silvia F., additional, Croda, Julio, additional, de Souza Santos, Andreza Aruska, additional, Dye, Christopher, additional, Flaxman, Seth, additional, Fonseca, Paula L. C., additional, Geddes, Victor E. V., additional, Gutierrez, Bernardo, additional, Lemey, Philippe, additional, Levin, Anna S., additional, Mellan, Thomas, additional, Bonfim, Diego M., additional, Miscouridou, Xenia, additional, Mishra, Swapnil, additional, Monod, Mélodie, additional, Moreira, Filipe R. R., additional, Nelson, Bruce, additional, Pereira, Rafael H. M., additional, Ranzani, Otavio, additional, Schnekenberg, Ricardo P., additional, Semenova, Elizaveta, additional, Sonabend, Raphael, additional, Souza, Renan P., additional, Xi, Xiaoyue, additional, Sabino, Ester C., additional, Faria, Nuno R., additional, Bhatt, Samir, additional, and Ratmann, Oliver, additional

Published
2022
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11. A dataset of non-pharmaceutical interventions on SARS-CoV-2 in Europe

Author

Altman, George, primary, Ahuja, Janvi, additional, Monrad, Joshua Teperowski, additional, Dhaliwal, Gurpreet, additional, Rogers-Smith, Charlie, additional, Leech, Gavin, additional, Snodin, Benedict, additional, Sandbrink, Jonas B., additional, Finnveden, Lukas, additional, Norman, Alexander John, additional, Oehm, Sebastian B., additional, Sandkühler, Julia Fabienne, additional, Kulveit, Jan, additional, Flaxman, Seth, additional, Gal, Yarin, additional, Mishra, Swapnil, additional, Bhatt, Samir, additional, Sharma, Mrinank, additional, Mindermann, Sören, additional, and Brauner, Jan Markus, additional

Published
2022
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12. Understanding the effectiveness of government interventions against the resurgence of COVID-19 in Europe

Author

Sharma, Mrinank, primary, Mindermann, Sören, additional, Rogers-Smith, Charlie, additional, Leech, Gavin, additional, Snodin, Benedict, additional, Ahuja, Janvi, additional, Sandbrink, Jonas B., additional, Monrad, Joshua Teperowski, additional, Altman, George, additional, Dhaliwal, Gurpreet, additional, Finnveden, Lukas, additional, Norman, Alexander John, additional, Oehm, Sebastian B., additional, Sandkühler, Julia Fabienne, additional, Aitchison, Laurence, additional, Gavenčiak, Tomáš, additional, Mellan, Thomas, additional, Kulveit, Jan, additional, Chindelevitch, Leonid, additional, Flaxman, Seth, additional, Gal, Yarin, additional, Mishra, Swapnil, additional, Bhatt, Samir, additional, and Brauner, Jan Markus, additional

Published
2021
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14. Comparing the responses of the UK, Sweden and Denmark to COVID-19 using counterfactual modelling

Author

Mishra, Swapnil, primary, Scott, James A., additional, Laydon, Daniel J., additional, Flaxman, Seth, additional, Gandy, Axel, additional, Mellan, Thomas A., additional, Unwin, H. Juliette T., additional, Vollmer, Michaela, additional, Coupland, Helen, additional, Ratmann, Oliver, additional, Monod, Melodie, additional, Zhu, Harrison H., additional, Cori, Anne, additional, Gaythorpe, Katy A. M., additional, Whittles, Lilith K., additional, Whittaker, Charles, additional, Donnelly, Christl A., additional, Ferguson, Neil M., additional, and Bhatt, Samir, additional

Published
2021
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15. Maps and metrics of insecticide-treated net access, use, and nets-per-capita in Africa from 2000-2020

Author

Bertozzi-Villa, Amelia, primary, Bever, Caitlin A., additional, Koenker, Hannah, additional, Weiss, Daniel J., additional, Vargas-Ruiz, Camilo, additional, Nandi, Anita K., additional, Gibson, Harry S., additional, Harris, Joseph, additional, Battle, Katherine E., additional, Rumisha, Susan F., additional, Keddie, Suzanne, additional, Amratia, Punam, additional, Arambepola, Rohan, additional, Cameron, Ewan, additional, Chestnutt, Elisabeth G., additional, Collins, Emma L., additional, Millar, Justin, additional, Mishra, Swapnil, additional, Rozier, Jennifer, additional, Symons, Tasmin, additional, Twohig, Katherine A., additional, Hollingsworth, T. Deirdre, additional, Gething, Peter W., additional, and Bhatt, Samir, additional

Published
2021
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17. Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo’

Author

Lavezzo, Enrico, Franchin, Elisa, Ciavarella, Constanze, Cuomo-Dannenburg, Gina, Barzon, Luisa, Del Vecchio, Claudia, Rossi, Lucia, Manganelli, Riccardo, Loregian, Arianna, Navarin, Nicolò, Abate, Davide, Sciro, Manuela, Merigliano, Stefano, De Canale, Ettore, Vanuzzo, Maria Cristina, Besutti, Valeria, Saluzzo, Francesca, Onelia, Francesco, Pacenti, Monia, Parisi, Saverio G., Carretta, Giovanni, Donato, Daniele, Flor, Luciano, Cocchio, Silvia, Masi, Giulia, Sperduti, Alessandro, Cattarino, Lorenzo, Salvador, Renato, Nicoletti, Michele, Caldart, Federico, Castelli, Gioele, Nieddu, Eleonora, Labella, Beatrice, Fava, Ludovico, Drigo, Matteo, Gaythorpe, Katy A. M., Brazzale, Alessandra R., Toppo, Stefano, Trevisan, Marta, Baldo, Vincenzo, Donnelly, Christl A., Ferguson, Neil M., Dorigatti, Ilaria, Crisanti, Andrea, Ainslie, Kylie E. C., Baguelin, Marc, Bhatt, Samir, Boonyasiri, Adhiratha, Boyd, Olivia, Coupland, Helen L., Cucunubá, Zulma, Djafaara, Bimandra A., van Elsland, Sabine L., FitzJohn, Rich, Flaxman, Seth, Green, Will D., Hallett, Timothy, Hamlet, Arran, Haw, David, Imai, Natsuko, Jeffrey, Benjamin, Knock, Edward, Laydon, Daniel J., Mellan, Thomas, Mishra, Swapnil, Nedjati-Gilani, Gemma, Nouvellet, Pierre, Okell, Lucy C., Parag, Kris V., Riley, Steven, Thompson, Hayley A., Unwin, H. Juliette T., Verity, Robert, Vollmer, Michaela A. C., Walker, Patrick G. T., Walters, Caroline E., Wang, Haowei, Wang, Yuanrong, Watson, Oliver J., Whittaker, Charles, Whittles, Lilith K., Xi, Xiaoyue, Medical Research Council (MRC), Medical Research Council, The Royal Society, Bill & Melinda Gates Foundation, Imperial College Healthcare NHS Trust- BRC Funding, The Academy of Medical Sciences, National Institute for Health Research, UK Research and Innovation, and Wellcome Trust

Subjects
0301 basic medicine, Male, CORONAVIRUS, Viral Nonstructural Proteins, medicine.disease_cause, Disease Outbreaks, 0302 clinical medicine, Viral Envelope Proteins, Prevalence, 030212 general & internal medicine, Child, Asymptomatic Infections, Coronavirus, Aged, 80 and over, education.field_of_study, Coronavirus RNA-Dependent RNA Polymerase, Multidisciplinary, Middle Aged, Viral Load, 3. Good health, Multidisciplinary Sciences, Policy, Italy, Child, Preschool, Science & Technology - Other Topics, Female, medicine.symptom, Coronavirus Infections, Viral load, Serial interval, Adult, medicine.medical_specialty, Adolescent, General Science & Technology, Population, Pneumonia, Viral, Policy and public health in microbiology, Asymptomatic, 03 medical and health sciences, Betacoronavirus, Coronavirus Envelope Proteins, Young Adult, Internal medicine, medicine, Imperial College COVID-19 Response Team, Humans, Author Correction, education, Pandemics, Aged, Science & Technology, business.industry, SARS-CoV-2, Infant, Newborn, Outbreak, COVID-19, Infant, medicine.disease, RNA-Dependent RNA Polymerase, Confidence interval, Pneumonia, 030104 developmental biology, business
Abstract

On 21 February 2020, a resident of the municipality of Vo', a small town near Padua (Italy), died of pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection1. This was the first coronavirus disease 19 (COVID-19)-related death detected in Italy since the detection of SARS-CoV-2 in the Chinese city of Wuhan, Hubei province2. In response, the regional authorities imposed the lockdown of the whole municipality for 14 days3. Here we collected information on the demography, clinical presentation, hospitalization, contact network and the presence of SARS-CoV-2 infection in nasopharyngeal swabs for 85.9% and 71.5% of the population of Vo' at two consecutive time points. From the first survey, which was conducted around the time the town lockdown started, we found a prevalence of infection of 2.6% (95% confidence interval (CI): 2.1-3.3%). From the second survey, which was conducted at the end of the lockdown, we found a prevalence of 1.2% (95% CI: 0.8-1.8%). Notably, 42.5% (95% CI: 31.5-54.6%) of the confirmed SARS-CoV-2 infections detected across the two surveys were asymptomatic (that is, did not have symptoms at the time of swab testing and did not develop symptoms afterwards). The mean serial interval was 7.2 days (95% CI: 5.9-9.6). We found no statistically significant difference in the viral load of symptomatic versus asymptomatic infections (P = 0.62 and 0.74 for E and RdRp genes, respectively, exact Wilcoxon-Mann-Whitney test). This study sheds light on the frequency of asymptomatic SARS-CoV-2 infection, their infectivity (as measured by the viral load) and provides insights into its transmission dynamics and the efficacy of the implemented control measures.

Published
2020
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18. Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions

Author

Ragonnet-Cronin, Manon, primary, Boyd, Olivia, additional, Geidelberg, Lily, additional, Jorgensen, David, additional, Nascimento, Fabricia F., additional, Siveroni, Igor, additional, Johnson, Robert A., additional, Baguelin, Marc, additional, Cucunubá, Zulma M., additional, Jauneikaite, Elita, additional, Mishra, Swapnil, additional, Watson, Oliver J., additional, Ferguson, Neil, additional, Cori, Anne, additional, Donnelly, Christl A., additional, and Volz, Erik, additional

Published
2021
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22. State-level tracking of COVID-19 in the United States

Author

Unwin, H. Juliette T., primary, Mishra, Swapnil, additional, Bradley, Valerie C., additional, Gandy, Axel, additional, Mellan, Thomas A., additional, Coupland, Helen, additional, Ish-Horowicz, Jonathan, additional, Vollmer, Michaela A. C., additional, Whittaker, Charles, additional, Filippi, Sarah L., additional, Xi, Xiaoyue, additional, Monod, Mélodie, additional, Ratmann, Oliver, additional, Hutchinson, Michael, additional, Valka, Fabian, additional, Zhu, Harrison, additional, Hawryluk, Iwona, additional, Milton, Philip, additional, Ainslie, Kylie E. C., additional, Baguelin, Marc, additional, Boonyasiri, Adhiratha, additional, Brazeau, Nick F., additional, Cattarino, Lorenzo, additional, Cucunuba, Zulma, additional, Cuomo-Dannenburg, Gina, additional, Dorigatti, Ilaria, additional, Eales, Oliver D., additional, Eaton, Jeffrey W., additional, van Elsland, Sabine L., additional, FitzJohn, Richard G., additional, Gaythorpe, Katy A. M., additional, Green, William, additional, Hinsley, Wes, additional, Jeffrey, Benjamin, additional, Knock, Edward, additional, Laydon, Daniel J., additional, Lees, John, additional, Nedjati-Gilani, Gemma, additional, Nouvellet, Pierre, additional, Okell, Lucy, additional, Parag, Kris V., additional, Siveroni, Igor, additional, Thompson, Hayley A., additional, Walker, Patrick, additional, Walters, Caroline E., additional, Watson, Oliver J., additional, Whittles, Lilith K., additional, Ghani, Azra C., additional, Ferguson, Neil M., additional, Riley, Steven, additional, Donnelly, Christl A., additional, Bhatt, Samir, additional, and Flaxman, Seth, additional

Published
2020
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23. Response to COVID-19 in South Korea and implications for lifting stringent interventions

Author

Dighe, Amy, primary, Cattarino, Lorenzo, additional, Cuomo-Dannenburg, Gina, additional, Skarp, Janetta, additional, Imai, Natsuko, additional, Bhatia, Sangeeta, additional, Gaythorpe, Katy A. M., additional, Ainslie, Kylie E. C., additional, Baguelin, Marc, additional, Bhatt, Samir, additional, Boonyasiri, Adhiratha, additional, Brazeau, Nicholas F., additional, Cooper, Laura V., additional, Coupland, Helen, additional, Cucunuba, Zulma, additional, Dorigatti, Ilaria, additional, Eales, Oliver D., additional, van Elsland, Sabine L., additional, FitzJohn, Richard G., additional, Green, William D., additional, Haw, David J., additional, Hinsley, Wes, additional, Knock, Edward, additional, Laydon, Daniel J., additional, Mellan, Thomas, additional, Mishra, Swapnil, additional, Nedjati-Gilani, Gemma, additional, Nouvellet, Pierre, additional, Pons-Salort, Margarita, additional, Thompson, Hayley A., additional, Unwin, H. Juliette T., additional, Verity, Robert, additional, Vollmer, Michaela A. C., additional, Walters, Caroline E., additional, Watson, Oliver J., additional, Whittaker, Charles, additional, Whittles, Lilith K., additional, Ghani, Azra C., additional, Donnelly, Christl A., additional, Ferguson, Neil M., additional, and Riley, Steven, additional

Published
2020
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26. Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

Author

Volz, Erik, Mishra, Swapnil, Chand, Meera, Barrett, Jeffrey C, Johnson, Robert, Geidelberg, Lily, Hinsley, Wes R, Laydon, Daniel J, Dabrera, Gavin, O'Toole, Áine, Amato, Robert, Ragonnet-Cronin, Manon, Harrison, Ian, Jackson, Ben, Ariani, Cristina V, Boyd, Olivia, Loman, Nicholas J, McCrone, John T, Gonçalves, Sónia, Jorgensen, David, Myers, Richard, Hill, Verity, Jackson, David K, Gaythorpe, Katy, Groves, Natalie, Sillitoe, John, Kwiatkowski, Dominic P, COVID-19 Genomics UK (COG-UK) Consortium, Flaxman, Seth, Ratmann, Oliver, Bhatt, Samir, Hopkins, Susan, Gandy, Axel, Rambaut, Andrew, and Ferguson, Neil M

Subjects
Adult, Aged, 80 and over, Time Factors, Adolescent, SARS-CoV-2, Basic Reproduction Number, Infant, Newborn, COVID-19, Infant, Genome, Viral, Middle Aged, 3. Good health, Evolution, Molecular, Young Adult, Age Distribution, England, Child, Preschool, Spike Glycoprotein, Coronavirus, Humans, Child, Phylogeny, Aged
Abstract

The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England1, was first identified in the UK in late summer to early autumn 20202. Whole-genome SARS-CoV-2 sequence data collected from community-based diagnostic testing for COVID-19 show an extremely rapid expansion of the B.1.1.7 lineage during autumn 2020, suggesting that it has a selective advantage. Here we show that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S gene target failures (SGTF) in community-based diagnostic PCR testing. Analysis of trends in SGTF and non-SGTF case numbers in local areas across England shows that B.1.1.7 has higher transmissibility than non-VOC lineages, even if it has a different latent period or generation time. The SGTF data indicate a transient shift in the age composition of reported cases, with cases of B.1.1.7 including a larger share of under 20-year-olds than non-VOC cases. We estimated time-varying reproduction numbers for B.1.1.7 and co-circulating lineages using SGTF and genomic data. The best-supported models did not indicate a substantial difference in VOC transmissibility among different age groups, but all analyses agreed that B.1.1.7 has a substantial transmission advantage over other lineages, with a 50% to 100% higher reproduction number.

27. Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

Author

Daniel Mair, Adrian Signell, Daniel Laydon, Nadua Bayzid, Clare M McCann, Flavia Flaviani, Thomas Connor, Samir Bhatt, Catherine Moore, Dr Benjamin Lindsey, Malte Pinckert, Jane Masoli, Rachel Blacow, Jacqui Prieto, Ian Harrison, Scott Thurston, Lance Turtle, Thushan De Silva, Gregory Young, Natalie Groves, Andrew Nelson, Angie Lackenby, Lily Geidelberg, Mili Estee Torok, Brendan Payne, Katy Gaythorpe, Sonia Goncalves, Ewan Harrison, Andrew Rambaut, Angela Beckett, David Partridge, Swapnil Mishra, Dimitris Grammatopoulos, Judith Breuer, Jenna Nichols, Erik Volz, Sharon Glaysher, Harry David Wilson, Jack Lee, Marta Gallis, Christophe Fraser, Susan Hopkins, Patrick McClure, Derrick Crook, Juan Ledesma, Theocharis Tsoleridis, Natasha Palmalux, Matthew Dorman, Helen Lowe, Kordo Saeed, Oliver Ratmann, Darren Smith, Gilberto Betancor Quintana, Alan McNally, Matthew Bashton, Steven Rudder, Dennis Wang, Joseph Chappell, Elias Allara, Volz, Erik [0000-0001-6268-8937], Mishra, Swapnil [0000-0002-8759-5902], Geidelberg, Lily [0000-0002-8057-1844], Laydon, Daniel J [0000-0003-4270-3321], Jackson, Ben [0000-0002-9981-0649], Gaythorpe, Katy [0000-0003-3734-9081], Kwiatkowski, Dominic P [0000-0002-5023-0176], Flaxman, Seth [0000-0002-2477-4217], Gandy, Axel [0000-0002-6777-0451], Rambaut, Andrew [0000-0003-4337-3707], Ferguson, Neil M [0000-0002-1154-8093], Apollo - University of Cambridge Repository, Medical Research Council, Bill & Melinda Gates Foundation, and Medical Research Council (MRC)

Subjects
The COVID-19 Genomics UK (COG-UK) consortium, Adult, 0301 basic medicine, Time Factors, Adolescent, General Science & Technology, Lineage (evolution), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Basic Reproduction Number, Population genetics, Genome, Viral, Biology, law.invention, Evolution, Molecular, Young Adult, 03 medical and health sciences, Age Distribution, 0302 clinical medicine, law, Phylogenetics, Humans, 030212 general & internal medicine, Child, Phylogeny, Aged, Aged, 80 and over, COVID-19 Genomics UK (COG-UK) consortium, Science & Technology, Multidisciplinary, Generation time, SARS-CoV-2, Infant, Newborn, COVID-19, Infant, Middle Aged, Transmissibility (vibration), 3. Good health, Multidisciplinary Sciences, 030104 developmental biology, Transmission (mechanics), England, Evolutionary biology, Child, Preschool, Spike Glycoprotein, Coronavirus, Science & Technology - Other Topics, Basic reproduction number
Abstract

The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England1, was first identified in the UK in late summer to early autumn 20202. Whole-genome SARS-CoV-2 sequence data collected from community-based diagnostic testing for COVID-19 show an extremely rapid expansion of the B.1.1.7 lineage during autumn 2020, suggesting that it has a selective advantage. Here we show that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S gene target failures (SGTF) in community-based diagnostic PCR testing. Analysis of trends in SGTF and non-SGTF case numbers in local areas across England shows that B.1.1.7 has higher transmissibility than non-VOC lineages, even if it has a different latent period or generation time. The SGTF data indicate a transient shift in the age composition of reported cases, with cases of B.1.1.7 including a larger share of under 20-year-olds than non-VOC cases. We estimated time-varying reproduction numbers for B.1.1.7 and co-circulating lineages using SGTF and genomic data. The best-supported models did not indicate a substantial difference in VOC transmissibility among different age groups, but all analyses agreed that B.1.1.7 has a substantial transmission advantage over other lineages, with a 50% to 100% higher reproduction number.

Published
2021
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