Pathology

Disease

Coronavirus disease 2019 (COVID-19)

Infectious disease (medical specialty)

Biology

Gene

World Wide Web

Genome

Alternative medicine

Data sharing

Computer science

DNA sequencing

Computational biology

Genomic sequencing

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

Genetics

Medicine

Metadata

Nature Genetics

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.

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