@article{86fabe03268f4ac08146851f5fc2d288,
title = "Global landscape of SARS-CoV-2 genomic surveillance and data sharing",
abstract = "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.",
author = "Zhiyuan Chen and Azman, {Andrew S.} and Xinhua Chen and Junyi Zou and Yuyang Tian and Ruijia Sun and Xiangyanyu Xu and Yani Wu and Wanying Lu and Shijia Ge and Zeyao Zhao and Juan Yang and Leung, {Daniel T.} and Domman, {Daryl B.} and Hongjie Yu",
note = "Funding Information: We gratefully acknowledge all authors from the originating and submitting laboratories who contributed to generating and sharing sequences to GISAID, GenBank, the National Genomics Data Center, the National Microbiology Data Center and China National GeneBank, as most of our analyses were made possible by the sharing of their work. An acknowledgements table listing all originating and submission laboratories is available in the Supplementary Information, and a table listing related accession numbers of sequences is available in GitHub ( https://github.com/zychenfd/Global-landscape-of-SARS-CoV-2-variants ). We thank all authors who contributed to generating and sharing aggregated data to the European Surveillance System. We thank L. Ma, Y. Bao and their team from China National Center for Bioinformation for building the 2019nCoVR dataset and kind discussions. We thank Q. Wang, Q. Wu, J. Chen, X. Deng, X. Yan, F. Hao and J. Dong from Fudan University for their comments. This study was funded by Key Program of the National Natural Science Foundation of China (grant 82130093 to H.Y.), Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response (grant 20dz2260100 to H.Y.), Key Discipline Construction Plan from Shanghai Municipal Health Commission (grant GWV-10.1-XK01 to H.Y.) and the National Institutes of Health (grant R01 AI135115 to D.T.L. and A.S.A.; grant KL2TR001448 to D.B.D.). The funders had no role in study design, data collection, data analysis, data interpretation or writing of the report. Funding Information: We gratefully acknowledge all authors from the originating and submitting laboratories who contributed to generating and sharing sequences to GISAID, GenBank, the National Genomics Data Center, the National Microbiology Data Center and China National GeneBank, as most of our analyses were made possible by the sharing of their work. An acknowledgements table listing all originating and submission laboratories is available in the Supplementary Information, and a table listing related accession numbers of sequences is available in GitHub (https://github.com/zychenfd/Global-landscape-of-SARS-CoV-2-variants). We thank all authors who contributed to generating and sharing aggregated data to the European Surveillance System. We thank L. Ma, Y. Bao and their team from China National Center for Bioinformation for building the 2019nCoVR dataset and kind discussions. We thank Q. Wang, Q. Wu, J. Chen, X. Deng, X. Yan, F. Hao and J. Dong from Fudan University for their comments. This study was funded by Key Program of the National Natural Science Foundation of China (grant 82130093 to H.Y.), Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response (grant 20dz2260100 to H.Y.), Key Discipline Construction Plan from Shanghai Municipal Health Commission (grant GWV-10.1-XK01 to H.Y.) and the National Institutes of Health (grant R01 AI135115 to D.T.L. and A.S.A.; grant KL2TR001448 to D.B.D.). The funders had no role in study design, data collection, data analysis, data interpretation or writing of the report. Funding Information: H.Y. has received research funding from Sanofi Pasteur, Shanghai Roche Pharmaceutical Company, and SINOVAC Biotech Ltd. None of those research funding is related to this work. All other authors report no competing interests. Publisher Copyright: {\textcopyright} 2022, The Author(s).",
year = "2022",
month = apr,
doi = "10.1038/s41588-022-01033-y",
language = "English (US)",
volume = "54",
pages = "499--507",
journal = "Nature Genetics",
issn = "1061-4036",
publisher = "Nature Publishing Group",
number = "4",
}