Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data

Wen-Bin Yu; Guang-Da Tang; Li Zhang; Richard T. Corlett

doi:10.24272/j.issn.2095-8137.2020.022

Volume 41 Issue 3

May 2020

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Wen-Bin Yu, Guang-Da Tang, Li Zhang, Richard T. Corlett. Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data. Zoological Research, 2020, 41(3): 247-257. doi: 10.24272/j.issn.2095-8137.2020.022

Citation:

Wen-Bin Yu, Guang-Da Tang, Li Zhang, Richard T. Corlett. Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data. Zoological Research, 2020, 41(3): 247-257. doi: 10.24272/j.issn.2095-8137.2020.022

Citation:

Wen-Bin Yu, Guang-Da Tang, Li Zhang, Richard T. Corlett. Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data. Zoological Research, 2020, 41(3): 247-257. doi: 10.24272/j.issn.2095-8137.2020.022

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Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data

doi: 10.24272/j.issn.2095-8137.2020.022

Wen-Bin Yu^{1, 2
,
,},
Guang-Da Tang^{3, 4},
Li Zhang⁵,
Richard T. Corlett^{1, 2}

1.
Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
2.
Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
3.
Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong 512005, China
4.
College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, Guangdong 510642, China
5.
Chinese Institute for Brain Research, Beijing 102206, China

Funds: This study was supported by grants from Ten Thousand Talents Program of Yunnan for Top-notch Young Talents, and the open research project of “Cross-Cooperative Team” of the Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences

More Information

Corresponding author: E-mail: yuwenbin@xtbg.ac.cn
Received Date: 2020-03-01
Accepted Date: 2020-04-27

Published Online: 2020-04-30

Publish Date: 2020-05-18

Abstract

Abstract

The outbreak of COVID-19 started in mid-December 2019 in Wuhan, China. Up to 29 February 2020, SARS-CoV-2 (HCoV-19 / 2019-nCoV) had infected more than 85 000 people in the world. In this study, we used 93 complete genomes of SARS-CoV-2 from the GISAID EpiFlu^TM database to investigate the evolution and human-to-human transmissions of SARS-CoV-2 in the first two months of the outbreak. We constructed haplotypes of the SARS-CoV-2 genomes, performed phylogenomic analyses and estimated the potential population size changes of the virus. The date of population expansion was calculated based on the expansion parameter tau (τ) using the formula t=τ/2u. A total of 120 substitution sites with 119 codons, including 79 non-synonymous and 40 synonymous substitutions, were found in eight coding-regions in the SARS-CoV-2 genomes. Forty non-synonymous substitutions are potentially associated with virus adaptation. No combinations were detected. The 58 haplotypes (31 found in samples from China and 31 from outside China) were identified in 93 viral genomes under study and could be classified into five groups. By applying the reported bat coronavirus genome (bat-RaTG13-CoV) as the outgroup, we found that haplotypes H13 and H38 might be considered as ancestral haplotypes, and later H1 was derived from the intermediate haplotype H3. The population size of the SARS-CoV-2 was estimated to have undergone a recent expansion on 06 January 2020, and an early expansion on 08 December 2019. Furthermore, phyloepidemiologic approaches have recovered specific directions of human-to-human transmissions and the potential sources for international infected cases.
- COVID-19,
- HCoV-19,
- SARS-CoV-2,
- Novel pneumonia outbreak,
- Human-to-human transmission,
- Phyloepidemiology

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References(52)

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