Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch
Open Access
- 17 September 2021
- journal article
- Published by F1000 Research Ltd in Wellcome Open Research
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.Funding Information
- European Research Council (725422)
- Medical Research Council
- Branco Weiss Fellowship – Society in Science
- Wellcome Trust (grant.203783/Z/16/Z, 206298/Z/17/Z)
- Instituto de Salud Carlos III (COV0020/00140)
- South African Medical Research Council
- Fast Grants (2236)
- Wellcome Trust and Royal Society Sir Henry Dale Fellowship (204311/Z/16/Z)
- EU Grant (874850 MOOD)
- National Institute of Health Research
- Deutsche Forschungsgemeinschaft (SFB900, EXC2155 RESIST)
- UK Research & Innovation
- MRC SHIP
- Wellcome Trust (206298)
- Department of Science and Innovation (DSI) of South Africa
- Genome Research Limited
- Oxford Martin School
- BlueDot
- Canadian Institutes of Health Research, COVID-19 Rapid Research Funding Opportunity (02179-000)
- Biotechnology and Biological Sciences Research Council (BB/M010996/1)
- Medical Research Council-São Paulo Research Foundation CADDE partnership award (MR/S0195/1,FAPESP 18/14389-0)
This publication has 11 references indexed in Scilit:
- Science, 2021
- Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic dataPublished by Cold Spring Harbor Laboratory ,2021
- Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South AfricaPublished by Cold Spring Harbor Laboratory ,2020
- Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020Published by Cold Spring Harbor Laboratory ,2020
- A cross-country database of COVID-19 testingScientific Data, 2020
- A genomics network established to respond rapidly to public health threats in South AfricaThe Lancet Microbe, 2020
- A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiologyNature Microbiology, 2020
- An integrated national scale SARS-CoV-2 genomic surveillance networkThe Lancet Microbe, 2020
- An interactive web-based dashboard to track COVID-19 in real timeThe Lancet Infectious Diseases, 2020
- Data, disease and diplomacy: GISAID's innovative contribution to global healthGlobal Challenges, 2017