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.

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.

Figure 1.

a) The cumulative number of countries with reports of lineage B.1.1.7 (grey line) and cumulative number of genomes of B.1.1.7 deposited in GISAID. b) Rolling seven-day average of the proportion of B.1.1.7 genomes in countries with more than ten sequences of the variant, and with more than ten days between the first B.1.1.7 sequence and the most recent one compared to all sampled genomes in that country. c) Number of sequences (log10) per country. Colour indicates the proportion of sequences that are classified as lineage B.1.1.7. d) Number of air travellers from major international London airports (Heathrow, Gatwick, Luton, City, Stansted, Southend) during October 2020. Colour indicates the number of sampled genomes of lineage B.1.1.7. Reported refers to countries that we found media reports stating there had been sequences of that particular lineage, but for which there were no sequences on GISAID. This is distinct from ‘not reported’ where there were no records found of that lineage in a given country. e) Map of international flights from major international London airports to countries with B.1.1.7 sequences. Colours indicate the date of earliest detection of B.1.1.7. in each country. The width of the lines indicates the number of flights. International Air Transport Association data used here account for ~90% of passenger travel itineraries on commercial flights, excluding transportation via unscheduled charter flights (the remainder is modelled using market intelligence). Data shown represents origin-destination journeys during October 2020. Routes to countries that have not yet detected B.1.1.7 and deposited data on GISAID are not included.

Figure 2.

a) Shows the cumulative number of countries with reports of lineage B.1.351 (black line) and cumulative number of genomes of B.1.351 deposited in GISAID. b) Rolling seven-day average of the proportion of B.1.351 genomes in countries with more than ten sequences of the variant, and with more than ten days between the first B.1.351 sequence and the most recent one compared to all sampled genomes in that country. c) Number of sequences (log10) per country. Colour indicates the proportion of sequences that are classified as lineage B.1.351 d) Number of air travellers from South Africa during October 2020. Colour indicates the number of sampled genomes of lineage B.1.351. Not reported refers to a given country having no record of B.1.351, and reported refers to countries that we found media reports but that country had no SARS-CoV-2 genomes shared on GISAID at that time. e) Map of international flights to countries with B.1.351 sequences. Colours indicate the date of earliest detection of B.1.351 in each country. The width of the lines indicates the number of flights. International Air Transport Association data used here account for ~90% of passenger travel itineraries on commercial flights, excluding transportation via unscheduled charter flights (the remainder is modelled using market intelligence). Data shown represents origin-destination journeys during October 2020. Routes to countries that have not yet detected B.1.351 and deposited data on GISAID are not included. >300 travellers from South Africa).