Journal
BRIEFINGS IN BIOINFORMATICS
Volume 22, Issue 2, Pages 631-641Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbaa386
Keywords
SARS-CoV-2; COVID-19; pathogen discovery; bioinformatics; phylogenetic analysis; next-generation sequencing
Funding
- Key research and development project of Shandong province [2020SFXGFY01, 2020SFXGFY08]
- National Major Project for Control and Prevention of Infectious Disease in China [2018ZX10101004, 2017ZX10104001]
- Academic Promotion Programme of Shandong First Medical University [2019QL006]
- National Key Research and Development Programme of China [2020YFC0840800]
- Taishan Scholars Programme of Shandong Province [ts201511056]
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In early 2020, the novel coronavirus responsible for the pneumonia outbreak in Wuhan was identified using NGS and bioinformatics pipelines. These technologies are now being used globally for genomic surveillance of SARS-CoV-2, tracking its spread, evolution, and global variation patterns, with a focus on technical advancements needed for future infectious disease outbreaks.
In early January 2020, the novel coronavirus (SARS-CoV-2) responsible for a pneumonia outbreak in Wuhan, China, was identified using next-generation sequencing (NGS) and readily available bioinformatics pipelines. In addition to virus discovery, these NGS technologies and bioinformatics resources are currently being employed for ongoing genomic surveillance of SARS-CoV-2 worldwide, tracking its spread, evolution and patterns of variation on a global scale. In this review, we summarize the bioinformatics resources used for the discovery and surveillance of SARS-CoV-2. We also discuss the advantages and disadvantages of these bioinformatics resources and highlight areas where additional technical developments are urgently needed. Solutions to these problems will be beneficial not only to the prevention and control of the current COVID-19 pandemic but also to infectious disease outbreaks of the future.
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