Global landscape of SARS-CoV-2 genomic surveillance and data sharing

Genomic surveillance has shaped our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. We performed a global landscape analysis on SARS-CoV-2 genomic surveillance and genomic data using a collection of country-specific data. Here, we characterize increasing circulation of the Alpha variant in early 2021, subsequently replaced by the Delta variant around May 2021. SARS-CoV-2 genomic surveillance and sequencing availability varied markedly across countries, with 45 countries performing a high level of routine genomic surveillance and 96 countries with a high availability of SARS-CoV-2 sequencing. We also observed a marked heterogeneity of sequencing percentage, sequencing technologies, turnaround time and completeness of released metadata across regions and income groups. A total of 37% of countries with explicit reporting on variants shared less than half of their sequences of variants of concern (VOCs) in public repositories. Our findings indicate an urgent need to increase timely and full sharing of sequences, the standardization of metadata files and support for countries with limited sequencing and bioinformatics capacity. Analyses on the global diversity of SARS-CoV-2 genomic surveillance across 118 countries and the extent of public availability of genomic data provide evidence to better inform SARS-CoV-2 surveillance policy.

Automated summary

This study analyzed global SARS-CoV-2 genomic surveillance and genomic data, finding significant variations in surveillance and sequencing capabilities among different countries. It also identified heterogeneity in sequencing percentage, sequencing technologies, turnaround time, and completeness of released metadata across regions and income groups. Moreover, it revealed a lack of proactive sharing of sequences related to variant of concerns (VOCs) in public repositories by some countries. Urgent actions are required to enhance timely and full sharing of sequences, standardize metadata files, and support countries with limited sequencing and bioinformatics capacity.