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Wellcome open research · 2021

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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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 U G

Аннотация

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.