Reconstructing early transmission networks of SARS-CoV-2 using a genomic mutation model

Chao-Yuan Cheng; Zhi-Bin Zhang

doi:10.24272/j.issn.2095-8137.2022.535

Volume 44 Issue 3

May 2023

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Chao-Yuan Cheng, Zhi-Bin Zhang. Reconstructing early transmission networks of SARS-CoV-2 using a genomic mutation model. Zoological Research, 2023, 44(3): 494-504. doi: 10.24272/j.issn.2095-8137.2022.535

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Chao-Yuan Cheng, Zhi-Bin Zhang. Reconstructing early transmission networks of SARS-CoV-2 using a genomic mutation model. Zoological Research, 2023, 44(3): 494-504. doi: 10.24272/j.issn.2095-8137.2022.535

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Reconstructing early transmission networks of SARS-CoV-2 using a genomic mutation model

doi: 10.24272/j.issn.2095-8137.2022.535

Chao-Yuan Cheng¹,
Zhi-Bin Zhang^{1, 2
,
,}

1.
State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
2.
CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China

All SARS-CoV-2 sequences used in this study were downloaded from the GISAID database (https://www.gisaid.org/). The accession numbers of each genomic sequence of this study are available in the ScienceDB (https://www.scidb.cn/en) repository at https://dx.doi.org/10.57760/sciencedb.01771.

Funds: This study was supported by the Ministry of Science and Technology of the People’s Republic of China (2021YFC0863400) and Institute of Zoology, Chinese Academy of Sciences (E0517111, E122G611)

More Information

Corresponding author: E-mail: zhangzb@ioz.ac.cn
Received Date: 2023-03-17
Accepted Date: 2023-03-31

Published Online: 2023-03-31

Publish Date: 2023-05-18

Abstract

Abstract

The coronavirus disease 2019 (COVID-19) pandemic has greatly damaged human society, but the origins and early transmission patterns of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogen remain unclear. Here, we reconstructed the transmission networks of SARS-CoV-2 during the first three and six months since its first report based on ancestor-offspring relationships using BANAL-52-referenced mutations. We explored the position (i.e., root, middle, or tip) of early detected samples in the evolutionary tree of SARS-CoV-2. In total, 6 799 transmission chains and 1 766 transmission networks were reconstructed, with chain lengths ranging from 1–9 nodes. The root node samples of the 1 766 transmission networks were from 58 countries or regions and showed no common ancestor, indicating the occurrence of many independent or parallel transmissions of SARS-CoV-2 when first detected (i.e., all samples were located at the tip position of the evolutionary tree). No root node sample was found in any sample (n=31, all from the Chinese mainland) collected in the first 15 days from 24 December 2019. Results using six-month data or RaTG13-referenced mutation data were similar. The reconstruction method was verified using a simulation approach. Our results suggest that SARS-CoV-2 may have already been spreading independently worldwide before the outbreak of COVID-19 in Wuhan, China. Thus, a comprehensive global survey of human and animal samples is essential to explore the origins of SARS-CoV-2 and its natural reservoirs and hosts.
- SARS-CoV-2,
- Transmission chain,
- Transmission network,
- Ancestor-offspring relationship,
- De novo mutation,
- Back mutation,
- Secondary mutation

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References(59)

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