Genomic sequencing effort for SARS-CoV-2 by country during the pandemic

Abstract

Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), tremendous efforts have been made to sequence the viral genome from samples collected throughout the world. Here, we evaluate how various countries have performed in sequencing from the perspectives of "fraction", "timeliness", and "openness". We found that high proportions of samples were sequenced in the UK, the USA, Australia, and Iceland; sequencing was performed promptly in Iceland, the Netherlands, and the Democratic Republic of the Congo; and data were shared timely from the Netherlands, the USA, Iceland, and the UK. Although many developing countries have high numbers of SARS-CoV-2 infected cases but few published sequences, we observed good performance on sequencing efforts for some low- and middle-income countries. Further strengthening of the sequencing capacity at a global level would help in the fight against not only the current pandemic but also future outbreaks of viral diseases.

Keywords: COVID-19; Evolution; Genome; Global health; Molecular epidemiology; SARS-CoV-2; Sequencing.

Figure 1

Number of genomic sequences of SARS-CoV-2. Countries in which more than 100 genomic sequences had been published as of September 2020 are listed in order of the number of sequences. The number of SARS-CoV-2 genomic sequences per reported COVID-19 case in each country is also shown. UK, the United Kingdom; USA, the United States of America; DRC, the Democratic Republic of the Congo; UAE, the United Arab Emirates.

Figure 2

Sequencing effort for SARS-CoV-2. Countries are ranked by three indicators describing sequencing efforts. “Fraction” is the number of viral sequences of samples collected by the time the cumulative number of COVID-19 cases had reached 1000 in each country. Because samples were collected before disease confirmation and positive samples could be identified retrospectively, the value could be larger than 1000. “Timeliness” is the number of sequences that had been published by the time the cumulative number of COVID-19 cases had reached 1000 in each country. “Openness” is the time gap (days) between sample collection and sequence data submission for the first 100 sequences in each country. Sequence data for which the collection and submission dates are unknown were excluded from the analysis. Darker colors indicate better performances.