tetano
Editor, Senior Moderator
Wellcome Open Res
. 2021 May 19;6:121.
doi: 10.12688/wellcomeopenres.16661.1. eCollection 2021.
Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2
Áine O'Toole[SUP] #[/SUP][SUP] 1 [/SUP], Verity Hill[SUP] #[/SUP][SUP] 1 [/SUP], Oliver G Pybus[SUP] 2 [/SUP], Alexander Watts[SUP] 3 4 [/SUP], Issac I Bogoch[SUP] 5 6 [/SUP], Kamran Khan[SUP] 3 4 5 [/SUP], Jane P Messina[SUP] 7 [/SUP], COVID-19 Genomics UK (COG-UK) consortium; Network for Genomic Surveillance in South Africa (NGS-SA); Brazil-UK CADDE Genomic Network; Houriiyah Tegally[SUP] 8 [/SUP], Richard R Lessells[SUP] 8 [/SUP], Jennifer Giandhari[SUP] 8 [/SUP], Sureshnee Pillay[SUP] 8 [/SUP], Kefentse Arnold Tumedi[SUP] 9 [/SUP], Gape Nyepetsi[SUP] 10 [/SUP], Malebogo Kebabonye[SUP] 11 [/SUP], Maitshwarelo Matsheka[SUP] 9 [/SUP], Madisa Mine[SUP] 10 [/SUP], Sima Tokajian[SUP] 12 [/SUP], Hamad Hassan[SUP] 13 [/SUP], Tamara Salloum[SUP] 12 [/SUP], Georgi Merhi[SUP] 12 [/SUP], Jad Koweyes[SUP] 12 [/SUP], Jemma L Geoghegan[SUP] 14 15 [/SUP], Joep de Ligt[SUP] 15 [/SUP], Xiaoyun Ren[SUP] 15 [/SUP], Matthew Storey[SUP] 15 [/SUP], Nikki E Freed[SUP] 16 [/SUP], Chitra Pattabiraman[SUP] 17 [/SUP], Pramada Prasad[SUP] 17 [/SUP], Anita S Desai[SUP] 17 [/SUP], Ravi Vasanthapuram[SUP] 17 [/SUP], Thomas F Schulz[SUP] 18 [/SUP], Lars Steinbrück[SUP] 18 [/SUP], Tanja Stadler[SUP] 19 [/SUP], Swiss Viollier Sequencing Consortium; Antonio Parisi[SUP] 20 [/SUP], Angelica Bianco[SUP] 20 [/SUP], Darío García de Viedma[SUP] 21 22 [/SUP], Sergio Buenestado-Serrano[SUP] 21 [/SUP], Vítor Borges[SUP] 23 [/SUP], Joana Isidro[SUP] 23 [/SUP], Sílvia Duarte[SUP] 24 [/SUP], João Paulo Gomes[SUP] 23 [/SUP], Neta S Zuckerman[SUP] 25 [/SUP], Michal Mandelboim[SUP] 25 [/SUP], Orna Mor[SUP] 25 [/SUP], Torsten Seemann[SUP] 26 [/SUP], Alicia Arnott[SUP] 27 [/SUP], Jenny Draper[SUP] 27 [/SUP], Mailie Gall[SUP] 27 [/SUP], William Rawlinson[SUP] 28 [/SUP], Ira Deveson[SUP] 29 [/SUP], Sanmarié Schlebusch[SUP] 30 [/SUP], Jamie McMahon[SUP] 30 [/SUP], Lex Leong[SUP] 31 [/SUP], Chuan Kok Lim[SUP] 31 [/SUP], Maria Chironna[SUP] 32 [/SUP], Daniela Loconsole[SUP] 32 [/SUP], Antonin Bal[SUP] 33 [/SUP], Laurence Josset[SUP] 33 [/SUP], Edward Holmes[SUP] 34 [/SUP], Kirsten St George[SUP] 35 [/SUP], Erica Lasek-Nesselquist[SUP] 35 [/SUP], Reina S Sikkema[SUP] 36 [/SUP], Bas Oude Munnink[SUP] 36 [/SUP], Marion Koopmans[SUP] 36 [/SUP], Mia Brytting[SUP] 37 [/SUP], V Sudha Rani[SUP] 38 [/SUP], S Pavani[SUP] 38 [/SUP], Teemu Smura[SUP] 39 [/SUP], Albert Heim[SUP] 18 [/SUP], Satu Kurkela[SUP] 40 [/SUP], Massab Umair[SUP] 41 [/SUP], Muhammad Salman[SUP] 41 [/SUP], Barbara Bartolini[SUP] 42 [/SUP], Martina Rueca[SUP] 42 [/SUP], Christian Drosten[SUP] 43 [/SUP], Thorsten Wolff[SUP] 44 [/SUP], Olin Silander[SUP] 16 [/SUP], Dirk Eggink[SUP] 45 [/SUP], Chantal Reusken[SUP] 45 [/SUP], Harry Vennema[SUP] 45 [/SUP], Aekyung Park[SUP] 46 [/SUP], Christine Carrington[SUP] 47 [/SUP], Nikita Sahadeo[SUP] 47 [/SUP], Michael Carr[SUP] 48 [/SUP], Gabo Gonzalez[SUP] 48 [/SUP], SEARCH Alliance San Diego; National Virus Reference Laboratory; SeqCOVID-Spain; Danish Covid-19 Genome Consortium (DCGC); Communicable Diseases Genomic Network (CDGN); Dutch National SARS-CoV-2 surveillance program; Division of Emerging Infectious Diseases (KDCA); Tulio de Oliveira[SUP] 8 [/SUP], Nuno Faria[SUP] 2 49 [/SUP], Andrew Rambaut[SUP] 1 [/SUP], Moritz U G Kraemer[SUP] 2 [/SUP]
Affiliations
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.
Keywords: B.1.1.7; B.1.351; N501Y; SARS-CoV-2; air travel; coronavirus; genome sequencing; genomic epidemiology; genomic surveillance; genomics; pandemic; sequencing; surveillance; virus.
. 2021 May 19;6:121.
doi: 10.12688/wellcomeopenres.16661.1. eCollection 2021.
Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2
Áine O'Toole[SUP] #[/SUP][SUP] 1 [/SUP], Verity Hill[SUP] #[/SUP][SUP] 1 [/SUP], Oliver G Pybus[SUP] 2 [/SUP], Alexander Watts[SUP] 3 4 [/SUP], Issac I Bogoch[SUP] 5 6 [/SUP], Kamran Khan[SUP] 3 4 5 [/SUP], Jane P Messina[SUP] 7 [/SUP], COVID-19 Genomics UK (COG-UK) consortium; Network for Genomic Surveillance in South Africa (NGS-SA); Brazil-UK CADDE Genomic Network; Houriiyah Tegally[SUP] 8 [/SUP], Richard R Lessells[SUP] 8 [/SUP], Jennifer Giandhari[SUP] 8 [/SUP], Sureshnee Pillay[SUP] 8 [/SUP], Kefentse Arnold Tumedi[SUP] 9 [/SUP], Gape Nyepetsi[SUP] 10 [/SUP], Malebogo Kebabonye[SUP] 11 [/SUP], Maitshwarelo Matsheka[SUP] 9 [/SUP], Madisa Mine[SUP] 10 [/SUP], Sima Tokajian[SUP] 12 [/SUP], Hamad Hassan[SUP] 13 [/SUP], Tamara Salloum[SUP] 12 [/SUP], Georgi Merhi[SUP] 12 [/SUP], Jad Koweyes[SUP] 12 [/SUP], Jemma L Geoghegan[SUP] 14 15 [/SUP], Joep de Ligt[SUP] 15 [/SUP], Xiaoyun Ren[SUP] 15 [/SUP], Matthew Storey[SUP] 15 [/SUP], Nikki E Freed[SUP] 16 [/SUP], Chitra Pattabiraman[SUP] 17 [/SUP], Pramada Prasad[SUP] 17 [/SUP], Anita S Desai[SUP] 17 [/SUP], Ravi Vasanthapuram[SUP] 17 [/SUP], Thomas F Schulz[SUP] 18 [/SUP], Lars Steinbrück[SUP] 18 [/SUP], Tanja Stadler[SUP] 19 [/SUP], Swiss Viollier Sequencing Consortium; Antonio Parisi[SUP] 20 [/SUP], Angelica Bianco[SUP] 20 [/SUP], Darío García de Viedma[SUP] 21 22 [/SUP], Sergio Buenestado-Serrano[SUP] 21 [/SUP], Vítor Borges[SUP] 23 [/SUP], Joana Isidro[SUP] 23 [/SUP], Sílvia Duarte[SUP] 24 [/SUP], João Paulo Gomes[SUP] 23 [/SUP], Neta S Zuckerman[SUP] 25 [/SUP], Michal Mandelboim[SUP] 25 [/SUP], Orna Mor[SUP] 25 [/SUP], Torsten Seemann[SUP] 26 [/SUP], Alicia Arnott[SUP] 27 [/SUP], Jenny Draper[SUP] 27 [/SUP], Mailie Gall[SUP] 27 [/SUP], William Rawlinson[SUP] 28 [/SUP], Ira Deveson[SUP] 29 [/SUP], Sanmarié Schlebusch[SUP] 30 [/SUP], Jamie McMahon[SUP] 30 [/SUP], Lex Leong[SUP] 31 [/SUP], Chuan Kok Lim[SUP] 31 [/SUP], Maria Chironna[SUP] 32 [/SUP], Daniela Loconsole[SUP] 32 [/SUP], Antonin Bal[SUP] 33 [/SUP], Laurence Josset[SUP] 33 [/SUP], Edward Holmes[SUP] 34 [/SUP], Kirsten St George[SUP] 35 [/SUP], Erica Lasek-Nesselquist[SUP] 35 [/SUP], Reina S Sikkema[SUP] 36 [/SUP], Bas Oude Munnink[SUP] 36 [/SUP], Marion Koopmans[SUP] 36 [/SUP], Mia Brytting[SUP] 37 [/SUP], V Sudha Rani[SUP] 38 [/SUP], S Pavani[SUP] 38 [/SUP], Teemu Smura[SUP] 39 [/SUP], Albert Heim[SUP] 18 [/SUP], Satu Kurkela[SUP] 40 [/SUP], Massab Umair[SUP] 41 [/SUP], Muhammad Salman[SUP] 41 [/SUP], Barbara Bartolini[SUP] 42 [/SUP], Martina Rueca[SUP] 42 [/SUP], Christian Drosten[SUP] 43 [/SUP], Thorsten Wolff[SUP] 44 [/SUP], Olin Silander[SUP] 16 [/SUP], Dirk Eggink[SUP] 45 [/SUP], Chantal Reusken[SUP] 45 [/SUP], Harry Vennema[SUP] 45 [/SUP], Aekyung Park[SUP] 46 [/SUP], Christine Carrington[SUP] 47 [/SUP], Nikita Sahadeo[SUP] 47 [/SUP], Michael Carr[SUP] 48 [/SUP], Gabo Gonzalez[SUP] 48 [/SUP], SEARCH Alliance San Diego; National Virus Reference Laboratory; SeqCOVID-Spain; Danish Covid-19 Genome Consortium (DCGC); Communicable Diseases Genomic Network (CDGN); Dutch National SARS-CoV-2 surveillance program; Division of Emerging Infectious Diseases (KDCA); Tulio de Oliveira[SUP] 8 [/SUP], Nuno Faria[SUP] 2 49 [/SUP], Andrew Rambaut[SUP] 1 [/SUP], Moritz U G Kraemer[SUP] 2 [/SUP]
Affiliations
- PMID: 34095513
- PMCID: PMC8176267
- DOI: 10.12688/wellcomeopenres.16661.1
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.
Keywords: B.1.1.7; B.1.351; N501Y; SARS-CoV-2; air travel; coronavirus; genome sequencing; genomic epidemiology; genomic surveillance; genomics; pandemic; sequencing; surveillance; virus.