Dataset Information

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch.

ABSTRACT: Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

SUBMITTER: O'Toole A

PROVIDER: S-EPMC8176267 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Publications

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch.

O'Toole Áine Á Hill Verity V Pybus Oliver G OG Watts Alexander A Bogoch Issac I II Khan Kamran K Messina Jane P JP Tegally Houriiyah H Lessells Richard R RR Giandhari Jennifer J Pillay Sureshnee S Tumedi Kefentse Arnold KA Nyepetsi Gape G Kebabonye Malebogo M Matsheka Maitshwarelo M Mine Madisa M Tokajian Sima S Hassan Hamad H Salloum Tamara T Merhi Georgi G Koweyes Jad J Geoghegan Jemma L JL de Ligt Joep J Ren Xiaoyun X Storey Matthew M Freed Nikki E NE Pattabiraman Chitra C Prasad Pramada P Desai Anita S AS Vasanthapuram Ravi R Schulz Thomas F TF Steinbrück Lars L Stadler Tanja T Parisi Antonio A Bianco Angelica A García de Viedma Darío D Buenestado-Serrano Sergio S Borges Vítor V Isidro Joana J Duarte Sílvia S Gomes João Paulo JP Zuckerman Neta S NS Mandelboim Michal M Mor Orna O Seemann Torsten T Arnott Alicia A Draper Jenny J Gall Mailie M Rawlinson William W Deveson Ira I Schlebusch Sanmarié S McMahon Jamie J Leong Lex L Lim Chuan Kok CK Chironna Maria M Loconsole Daniela D Bal Antonin A Josset Laurence L Holmes Edward E St George Kirsten K Lasek-Nesselquist Erica E Sikkema Reina S RS Oude Munnink Bas B Koopmans Marion M Brytting Mia M Sudha Rani V V Pavani S S Smura Teemu T Heim Albert A Kurkela Satu S Umair Massab M Salman Muhammad M Bartolini Barbara B Rueca Martina M Drosten Christian C Wolff Thorsten T Silander Olin O Eggink Dirk D Reusken Chantal C Vennema Harry H Park Aekyung A Carrington Christine C Sahadeo Nikita N Carr Michael M Gonzalez Gabo G de Oliveira Tulio T Faria Nuno N Rambaut Andrew A Kraemer Moritz U G MUG

Wellcome open research 20210917

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes fro ...[more]

PMID: 34095513

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Project description:BackgroundIn December 2020, the United Kingdom (UK) reported a SARS-CoV-2 Variant of Concern (VoC) which is now named B.1.1.7. Based on initial data from the UK and later data from other countries, this variant was estimated to have a transmission fitness advantage of around 40-80 % (Volz et al., 2021; Leung et al., 2021; Davies et al., 2021).AimThis study aims to estimate the transmission fitness advantage and the effective reproductive number of B.1.1.7 through time based on data from Switzerland.MethodsWe generated whole genome sequences from 11.8 % of all confirmed SARS-CoV-2 cases in Switzerland between 14 December 2020 and 11 March 2021. Based on these data, we determine the daily frequency of the B.1.1.7 variant and quantify the variant's transmission fitness advantage on a national and a regional scale.ResultsWe estimate B.1.1.7 had a transmission fitness advantage of 43-52 % compared to the other variants circulating in Switzerland during the study period. Further, we estimate B.1.1.7 had a reproductive number above 1 from 01 January 2021 until the end of the study period, compared to below 1 for the other variants. Specifically, we estimate the reproductive number for B.1.1.7 was 1.24 [1.07-1.41] from 01 January until 17 January 2021 and 1.18 [1.06-1.30] from 18 January until 01 March 2021 based on the whole genome sequencing data. From 10 March to 16 March 2021, once B.1.1.7 was dominant, we estimate the reproductive number was 1.14 [1.00-1.26] based on all confirmed cases. For reference, Switzerland applied more non-pharmaceutical interventions to combat SARS-CoV-2 on 18 January 2021 and lifted some measures again on 01 March 2021.ConclusionThe observed increase in B.1.1.7 frequency in Switzerland during the study period is as expected based on observations in the UK. In absolute numbers, B.1.1.7 increased exponentially with an estimated doubling time of around 2-3.5 weeks. To monitor the ongoing spread of B.1.1.7, our plots are available online.

Dataset Information

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch.

Publications

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch.

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