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

O'Toole, Áine; Hill, Verity; Pybus, Oliver G; Watts, Alexander; Bogoch, Issac I; Khan, Kamran; Messina, Jane P; COVID-19 Genomics UK (COG-UK) consortium; Network for Genomic Surveillance in South Africa (NGS-SA); Brazil-UK CADDE Genomic Network; Tegally, Houriiyah; Lessells, Richard R; Giandhari, Jennifer; Pillay, Sureshnee; Tumedi, Kefentse Arnold; Nyepetsi, Gape; Kebabonye, Malebogo; Matsheka, Maitshwarelo; Mine, Madisa; Tokajian, Sima; Hassan, Hamad; Salloum, Tamara; Merhi, Georgi; Koweyes, Jad; Geoghegan, Jemma L; de Ligt, Joep; Ren, Xiaoyun; Storey, Matthew; Freed, Nikki E; Pattabiraman, Chitra; Prasad, Pramada; Desai, Anita S; Vasanthapuram, Ravi; Schulz, Thomas F; Steinbrück, Lars; Stadler, Tanja; Swiss Viollier Sequencing Consortium; Parisi, Antonio; Bianco, Angelica; García de Viedma, Darío; Buenestado-Serrano, Sergio; Borges, Vítor; Isidro, Joana; Duarte, Sílvia; Gomes, João Paulo; Zuckerman, Neta S; Mandelboim, Michal; Mor, Orna; Seemann, Torsten; Arnott, Alicia; Draper, Jenny; Gall, Mailie; Rawlinson, William; Deveson, Ira; Schlebusch, Sanmarié; McMahon, Jamie; Leong, Lex; Lim, Chuan Kok; Chironna, Maria; Loconsole, Daniela; Bal, Antonin; Josset, Laurence; Holmes, Edward; St George, Kirsten; Lasek-Nesselquist, Erica; Sikkema, Reina S; Oude Munnink, Bas; Koopmans, Marion; Brytting, Mia; Sudha Rani, V; Pavani, S; Smura, Teemu; Heim, Albert; Kurkela, Satu; Umair, Massab; Salman, Muhammad; Bartolini, Barbara; Rueca, Martina; Drosten, Christian; Wolff, Thorsten; Silander, Olin; Eggink, Dirk; Reusken, Chantal; Vennema, Harry; Park, Aekyung; Carrington, Christine; Sahadeo, Nikita; Carr, Michael; Gonzalez, Gabo; 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); de Oliveira, Tulio; Faria, Nuno; Rambaut, Andrew; Kraemer, Moritz UG

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

O'Toole, Áine ; Hill, Verity ; Pybus, Oliver G ; Watts, Alexander ; Bogoch, Issac I ; Khan, Kamran ; Messina, Jane P ; COVID-19 Genomics UK (COG-UK) consortium ; Network for Genomic Surveillance in South Africa (NGS-SA) ; Brazil-UK CADDE Genomic Network ; Tegally, Houriiyah ; Lessells, Richard R ; Giandhari, Jennifer ; Pillay, Sureshnee ; Tumedi, Kefentse Arnold ; Nyepetsi, Gape ; Kebabonye, Malebogo ; Matsheka, Maitshwarelo ; Mine, Madisa ; Tokajian, Sima ; Hassan, Hamad ; Salloum, Tamara ; Merhi, Georgi ; Koweyes, Jad ; Geoghegan, Jemma L ; de Ligt, Joep ; Ren, Xiaoyun ; Storey, Matthew ; Freed, Nikki E ; Pattabiraman, Chitra ; Prasad, Pramada ; Desai, Anita S ; Vasanthapuram, Ravi ; Schulz, Thomas F ; Steinbrück, Lars ; Stadler, Tanja ; Swiss Viollier Sequencing Consortium ; Parisi, Antonio ; Bianco, Angelica ; García de Viedma, Darío ; Buenestado-Serrano, Sergio ; Borges, Vítor ; Isidro, Joana ; Duarte, Sílvia ; Gomes, João Paulo ; Zuckerman, Neta S ; Mandelboim, Michal ; Mor, Orna ; Seemann, Torsten ; Arnott, Alicia ; Draper, Jenny ; Gall, Mailie ; Rawlinson, William ; Deveson, Ira ; Schlebusch, Sanmarié ; McMahon, Jamie ; Leong, Lex ; Lim, Chuan Kok ; Chironna, Maria ; Loconsole, Daniela ; Bal, Antonin ; Josset, Laurence ; Holmes, Edward ; St George, Kirsten ; Lasek-Nesselquist, Erica ; Sikkema, Reina S ; Oude Munnink, Bas ; Koopmans, Marion ; Brytting, Mia ; Sudha Rani, V ; Pavani, S ; Smura, Teemu ; Heim, Albert ; Kurkela, Satu ; Umair, Massab ; Salman, Muhammad ; Bartolini, Barbara ; Rueca, Martina ; Drosten, Christian ; Wolff, Thorsten ; Silander, Olin ; Eggink, Dirk ; Reusken, Chantal ; Vennema, Harry ; Park, Aekyung ; Carrington, Christine ; Sahadeo, Nikita ; Carr, Michael ; Gonzalez, Gabo ; 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) ; de Oliveira, Tulio ; Faria, Nuno ; Rambaut, Andrew ; Kraemer, Moritz UG

Identifier: https://hdl.handle.net/2292/66420

Issue Date: 2021-01

Reference: (2021). Wellcome Open Research, 6, 121-.

Rights: Copyright: The authors

Rights (URI): https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm

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.

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