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

• Published in: Nature genetics Vol. 54; no. 4; pp. 499 - 507
• Main Authors: Chen, Zhiyuan, Azman, Andrew S., Chen, Xinhua, Zou, Junyi, Tian, Yuyang, Sun, Ruijia, Xu, Xiangyanyu, Wu, Yani, Lu, Wanying, Ge, Shijia, Zhao, Zeyao, Yang, Juan, Leung, Daniel T., Domman, Daryl B., Yu, Hongjie
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.04.2022; Nature Publishing Group
• Subjects: 692/699/255; 692/700/478/174; Agriculture; Analysis; Animal Genetics and Genomics; Availability; Bioinformatics; Biomedical and Life Sciences; Biomedicine; Cancer Research; Coronaviruses; COVID-19; COVID-19 - epidemiology; COVID-19 - genetics; Data retrieval; Disease transmission; Gene Function; Genomes; Genomic analysis; Genomics; Health surveillance; Heterogeneity; High income; Human Genetics; Humans; Information Dissemination; Metadata; Mutation; Pandemics; SARS-CoV-2 - genetics; Severe acute respiratory syndrome coronavirus 2; Standardization; Vaccines; United Kingdom > UK; East Asia; Mediterranean Area
• ISSN: 1061-4036; 1546-1718; 1546-1718
• DOI: 10.1038/s41588-022-01033-y

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.