Global landscape of SARS-CoV-2 genomic surveillance, public availability extent of genomic data, and epidemic shaped by variants

Abstract

Genomic surveillance has shaped our understanding of SARS-CoV-2 variants, which have proliferated globally in 2021.We collected country-specific data on SARS-CoV-2 genomic surveillance, sequencing capabilities, public genomic data from multiple public repositories, and aggregated publicly available variant data. Then, different proxies were used to estimate the sequencing coverage and public availability extent of genomic data, in addition to describing the global dissemination of variants. We found that the COVID-19 global epidemic clearly featured increasing circulation of Alpha since the start of 2021, which was rapidly replaced by the Delta variant starting around May 2021. SARS-CoV-2 genomic surveillance and sequencing availability varied markedly across countries, with 63 countries performing routine genomic surveillance and 79 countries with high availability of SARS-CoV-2 sequencing. We also observed a marked heterogeneity of sequenced coverage across regions and countries. Across different variants, 21-46% of countries with explicit reporting on variants shared less than half of their variant sequences in public repositories. Our findings indicated an urgent need to expand sequencing capacity of virus isolates, enhance the sharing of sequences, the standardization of metadata files, and supportive networks for countries with no sequencing capability.

Figure 1

Global SARS-CoV-2 genomic surveillance, sequencing availability, and publicly deposited genomic data. (A) The global distribution of three strategies of SARS-CoV-2 genomic surveillance. (B) The global availability of SARS-CoV-2 sequencing, countries with a high level of availability represent the ability to perform in-country SARS-CoV-2 sequencing alone. (C) The weekly number of publicly deposited SARS-CoV-2 genomic data by region. (D) Cumulative number of publicly deposited SARS-CoV-2 genomic data by countries as of 15 September 2021. (E) The weekly proportion of infections sequenced by region. (F) Cumulative proportion of infections sequenced by countries as of 15 September 2021, defined as the proportion of cumulative isolates sequences to the cumulative confirmed cases. The number of sequences for the most recent weeks might be incomplete due to a time delay between collecting specimens and sequencing submission. Data unavailable, includes those locations that not belonged to 194 Member States or had not applicable data.

Figure 2

The public availability extent of SARS-CoV-2 genomic data to publicly repositories by country and the variants of concern. The public availability extent was defined as the ratio of the cumulative number of variants in publicly repositories to the official reported number of variants within the same period. The ratio of exceed 100% in some countries might be due to the delay in the official report of the sequencing results or the incomplete official reporting system. In view of the availability of official data, the cumulative number of variants in different countries corresponds to different time periods, with detailed information in Table S6. Sequence without date of specimen collection in publicly repositories is not included in our analysis. The variant data for China only includes cases reported by mainland China. The officially reported number of Alpha variants might contain those confirmed by the PCR screen assay. The values beneath the country names show numbers of cumulative variant as of one specific week: variants in publicly repositories/official reported variants.

Figure 3

The earliest identification of Alpha, Beta, Gamma, and Delta variant in each country. If information about the earliest sampling date was unavailable but that of the earliest reporting date was available, we extrapolated the sampling date by using a fixed three-week lag from sample collection to reporting. Countries with darker red indicate earlier samples, and with darker blue refers to later samples. The white areas represent countries with variants unreported or data unavailable.

Figure 4

The prevalence and temporal dynamics of reference strains and four SARS-CoV-2 VOCs by country. The date presented in the top refers to the range of date of specimen collection. The prevalence was defined as the proportion of the strain number (reference strains or variants) to the total number of sequences generated in the same unit of time. Reference strains includes lineage A, A.1, B, and B.1; the sub-lineages of four VOCs are aggregated with the parent lineages. The grey areas represent countries with no COVID-19 epidemic, or no performing sequencing, or no uploading genomic data to publicly repositories.

Figure 5

The number and proportion of SARS-CoV-2 variants by region and time. The line and point in the left figure correspond to the y-axis on the right. The sub-lineages of four VOCs are aggregated with the parent lineages; designated Variants of Interest (VOIs) included lineage B.1.525, B.1.526, B.1.617.1, C.37, B.1.621 and their sub-lineages; other lineages included reference strains and other variants. Data used here are derived from the publicly repositories and aggregated dataset, with priority given to the one with highest sequenced numbers in a specific week.