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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2022-03-28

AUTHORS

Zhiyuan Chen, Andrew S. Azman, Xinhua Chen, Junyi Zou, Yuyang Tian, Ruijia Sun, Xiangyanyu Xu, Yani Wu, Wanying Lu, Shijia Ge, Zeyao Zhao, Juan Yang, Daniel T. Leung, Daryl B. Domman, Hongjie Yu

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. More... »

PAGES

499-507

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s41588-022-01033-y

DOI

http://dx.doi.org/10.1038/s41588-022-01033-y

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1146619737

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/35347305


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23 schema:description 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.
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31 Delta variant
32 SARS-CoV-2 genomic surveillance
33 SARS-CoV-2 sequencing
34 analysis
35 availability
36 bioinformatics capacity
37 capacity
38 circulation
39 collection
40 completeness
41 concern
42 countries
43 country-specific data
44 data
45 data sharing
46 explicit reporting
47 files
48 findings
49 full sharing
50 genomic data
51 genomic surveillance
52 global landscape
53 global landscape analysis
54 group
55 half
56 heterogeneity
57 high availability
58 high levels
59 income groups
60 landscape
61 landscape analysis
62 levels
63 limited sequencing
64 marked heterogeneity
65 metadata
66 metadata files
67 need
68 percentage
69 public repositories
70 region
71 reporting
72 repository
73 routine genomic surveillance
74 sequence
75 sequences of variants
76 sequencing
77 sequencing technologies
78 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants
79 sharing
80 standardization
81 support
82 surveillance
83 technology
84 time
85 total
86 turnaround time
87 understanding
88 urgent need
89 variants
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