Genetic Cluster Analysis of SARS-CoV-2 and the Identification of Those Responsible for the Major Outbreaks in Various Countries

Overview

Journal Emerg Microbes Infect

Specialty Infectious Diseases

Date 2020 Jun 12

PMID 32525765

Citations 32

Authors

Xuemei Yang

Ning Dong

Edward Wai-Chi Chan

Sheng Chen

Affiliations

Soon will be listed here.

Abstract

A newly emerged coronavirus, SARS-CoV-2, caused severe pneumonia outbreaks in China in December 2019 and has since spread to various countries around the world. To trace the evolution route and probe the transmission dynamics of this virus, we performed phylodynamic analysis of 247 high quality genomic sequences available in the GISAID platform as of 5 March 2020. Among them, four genetic clusters, defined as super-spreaders (SSs), could be identified and were found to be responsible for the major outbreaks that subsequently occurred in various countries. SS1 was widely disseminated in Asia and the US, and mainly responsible for outbreaks in the states of Washington and California as well as South Korea, whereas SS4 contributed to the pandemic in Europe. Using the signature mutations of each SS as markers, we further analysed 1539 genome sequences reported after 29 February 2020 and found that 90% of these genomes belonged to SSs, with SS4 being the most dominant. The relative degree of contribution of each SS to the pandemic in different continents was also depicted. Identification of these super-spreaders greatly facilitates development of new strategies to control the transmission of SARS-CoV-2.

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References

Lu R, Zhao X, Li J, Niu P, Yang B, Wu H . Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. 2020; 395(10224):565-574. PMC: 7159086. DOI: 10.1016/S0140-6736(20)30251-8. View

Letunic I, Bork P . Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016; 44(W1):W242-5. PMC: 4987883. DOI: 10.1093/nar/gkw290. View

Zhu N, Zhang D, Wang W, Li X, Yang B, Song J . A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med. 2020; 382(8):727-733. PMC: 7092803. DOI: 10.1056/NEJMoa2001017. View

Sagulenko P, Puller V, Neher R . TreeTime: Maximum-likelihood phylodynamic analysis. Virus Evol. 2018; 4(1):vex042. PMC: 5758920. DOI: 10.1093/ve/vex042. View

Forster P, Forster L, Renfrew C, Forster M . Phylogenetic network analysis of SARS-CoV-2 genomes. Proc Natl Acad Sci U S A. 2020; 117(17):9241-9243. PMC: 7196762. DOI: 10.1073/pnas.2004999117. View

Tang X, Wu C, Li X, Song Y, Yao X, Wu X . On the origin and continuing evolution of SARS-CoV-2. Natl Sci Rev. 2021; 7(6):1012-1023. PMC: 7107875. DOI: 10.1093/nsr/nwaa036. View

Chen N, Zhou M, Dong X, Qu J, Gong F, Han Y . Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. 2020; 395(10223):507-513. PMC: 7135076. DOI: 10.1016/S0140-6736(20)30211-7. View

Wu F, Zhao S, Yu B, Chen Y, Wang W, Song Z . A new coronavirus associated with human respiratory disease in China. Nature. 2020; 579(7798):265-269. PMC: 7094943. DOI: 10.1038/s41586-020-2008-3. View

Zhou P, Yang X, Wang X, Hu B, Zhang L, Zhang W . A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020; 579(7798):270-273. PMC: 7095418. DOI: 10.1038/s41586-020-2012-7. View

10.

Katoh K, Asimenos G, Toh H . Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol. 2009; 537:39-64. DOI: 10.1007/978-1-59745-251-9_3. View

11.

Stamatakis A . RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30(9):1312-3. PMC: 3998144. DOI: 10.1093/bioinformatics/btu033. View

12.

Tcherepanov V, Ehlers A, Upton C . Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome. BMC Genomics. 2006; 7:150. PMC: 1534038. DOI: 10.1186/1471-2164-7-150. View

13.

Hadfield J, Megill C, Bell S, Huddleston J, Potter B, Callender C . Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. 2018; 34(23):4121-4123. PMC: 6247931. DOI: 10.1093/bioinformatics/bty407. View

14.

Shu Y, McCauley J . GISAID: Global initiative on sharing all influenza data - from vision to reality. Euro Surveill. 2017; 22(13). PMC: 5388101. DOI: 10.2807/1560-7917.ES.2017.22.13.30494. View

15.

Sardar R, Satish D, Birla S, Gupta D . Integrative analyses of SARS-CoV-2 genomes from different geographical locations reveal unique features potentially consequential to host-virus interaction, pathogenesis and clues for novel therapies. Heliyon. 2020; 6(9):e04658. PMC: 7439967. DOI: 10.1016/j.heliyon.2020.e04658. View

16.

Cui J, Li F, Shi Z . Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol. 2018; 17(3):181-192. PMC: 7097006. DOI: 10.1038/s41579-018-0118-9. View

17.

Nguyen L, Schmidt H, von Haeseler A, Minh B . IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2014; 32(1):268-74. PMC: 4271533. DOI: 10.1093/molbev/msu300. View