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
Citation: 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

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

doi: 10.24272/j.issn.2095-8137.2022.535
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
  • 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.
  • 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.
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  • [1]
    Abdool Karim SS, de Oliveira T. 2021. New SARS-CoV-2 variants — clinical, public health, and vaccine implications. New England Journal of Medicine, 384(19): 1866−1868. doi: 10.1056/NEJMc2100362
    Bandelt HJ, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16(1): 37−48. doi: 10.1093/oxfordjournals.molbev.a026036
    Burki T. 2021. Understanding variants of SARS-CoV-2. The Lancet, 397(10273): 462. doi: 10.1016/S0140-6736(21)00298-1
    Chan JFW, Kok KH, Zhu Z, et al. 2020. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerging Microbes & Infections, 9(1): 221−236.
    Cheng CY, Zhang ZB. 2023. SARS-CoV-2 shows a much earlier divergence in the world than in the Chinese mainland. Science China Life Sciences,doi: 10.1007/s11427-023-2294-5.
    Delaune D, Hul V, Karlsson EA, et al. 2021. A novel SARS-CoV-2 related coronavirus in bats from Cambodia. Nature Communications, 12(1): 6563. doi: 10.1038/s41467-021-26809-4
    Deng SQ, Peng HJ. 2020. Characteristics of and public health responses to the coronavirus disease 2019 outbreak in China. Journal of Clinical Medicine, 9(2): 575. doi: 10.3390/jcm9020575
    Duchene S, Lemey P, Stadler T, et al. 2020. Bayesian evaluation of temporal signal in measurably evolving populations. Molecular Biology and Evolution, 37(11): 3363−3379. doi: 10.1093/molbev/msaa163
    Ellis NA, Ciocci S, German J. 2001. Back mutation can produce phenotype reversion in Bloom syndrome somatic cells. Human Genetics, 108(2): 167−173. doi: 10.1007/s004390000447
    Fan Y, Zhao K, Shi ZL, et al. 2019. Bat coronaviruses in China. Viruses, 11(3): 210. doi: 10.3390/v11030210
    Forster P, Forster L, Renfrew C, et al. 2020. Phylogenetic network analysis of SARS-CoV-2 genomes. Proceedings of the National Academy of Sciences of the United States of America, 117(17): 9241−9243. doi: 10.1073/pnas.2004999117
    Giovanetti M, Benvenuto D, Angeletti S, et al. 2020. The first two cases of 2019-nCoV in Italy: where they come from?. Journal of Medical Virology, 92(5): 518−521. doi: 10.1002/jmv.25699
    Hill V, Rambaut A. 2020[2021-02-17]. Phylodynamic analysis of SARS-CoV-2 | Update 2020-03-06.https://virological.org/t/phylodynamic-analysis-of-sars-cov-2-update-2020-03-06/420.
    Holmes EC, Nee S, Rambaut A, et al. 1995. Revealing the history of infectious disease epidemics through phylogenetic trees. Philosophical Transactions of the Royal Society B:Biological Sciences, 349(1327): 33−40. doi: 10.1098/rstb.1995.0088
    Kong S, Sánchez-Pacheco SJ, Murphy RW. 2016. On the use of median-joining networks in evolutionary biology. Cladistics, 32(6): 691−699. doi: 10.1111/cla.12147
    Lam TTY, Jia N, Zhang YW, et al. 2020. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature, 583(7815): 282−285. doi: 10.1038/s41586-020-2169-0
    Lanciotti RS, Ebel GD, Deubel V, et al. 2002. Complete genome sequences and phylogenetic analysis of west Nile virus strains isolated from the United States, Europe, and the Middle East. Virology, 298(1): 96−105. doi: 10.1006/viro.2002.1449
    Lau SKP, Luk HKH, Wong ACP, et al. 2020. Possible bat origin of severe acute respiratory syndrome coronavirus 2. Emerging Infectious Diseases, 26(7): 1542−1547. doi: 10.3201/eid2607.200092
    Lauring AS, Hodcroft EB. 2021. Genetic variants of SARS-CoV-2—What do they mean?. JAMA, 325(6): 529−531. doi: 10.1001/jama.2020.27124
    Li JG, Li Z, Cui XG, et al. 2020a. Bayesian phylodynamic inference on the temporal evolution and global transmission of SARS-CoV-2. Journal of Infection, 81(2): 318−356.
    Li WD, Shi ZL, Yu M, et al. 2005. Bats are natural reservoirs of SARS-like coronaviruses. Science, 310(5748): 676−679. doi: 10.1126/science.1118391
    Li XG, Wang W, Zhao XF, et al. 2020b. Transmission dynamics and evolutionary history of 2019-nCoV. Journal of Medical Virology, 92(5): 501−511. doi: 10.1002/jmv.25701
    Li XG, Zai JJ, Wang XM, et al. 2020c. Potential of large “first generation” human-to-human transmission of 2019-nCoV. Journal of Medical Virology, 92(4): 448−454. doi: 10.1002/jmv.25693
    Li XG, Zai JJ, Zhao Q, et al. 2020d. Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2. Journal of Medical Virology, 92(6): 602−611. doi: 10.1002/jmv.25731
    Liu Q, Zhao SL, Shi CM, et al. 2020. Population genetics of SARS-CoV-2: disentangling effects of sampling bias and infection clusters. Genomics, Proteomics & Bioinformatics, 18(6): 640−647.
    Lu RJ, Zhao X, Li J, et al. 2020. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. The Lancet, 395(10224): 565−574. doi: 10.1016/S0140-6736(20)30251-8
    Lundstrom K, Seyran M, Pizzol D, et al. 2020. The importance of research on the origin of SARS-CoV-2. Viruses, 12(11): 1203. doi: 10.3390/v12111203
    Mallapaty S. 2020. Coronaviruses closely related to the pandemic virus discovered in Japan and Cambodia. Nature, 588(7836): 15−16. doi: 10.1038/d41586-020-03217-0
    Morel B, Barbera P, Czech L, et al. 2021. Phylogenetic analysis of SARS-CoV-2 data is difficult. Molecular Biology and Evolution, 38(5): 1777−1791. doi: 10.1093/molbev/msaa314
    Nabil B, Sabrina B, Abdelhakim B. 2021. Transmission route and introduction of pandemic SARS-CoV-2 between China, Italy, and Spain. Journal of Medical Virology, 93(1): 564−568. doi: 10.1002/jmv.26333
    Nie Q, Li XG, Chen W, et al. 2020. Phylogenetic and phylodynamic analyses of SARS-CoV-2. Virus Research, 287: 198098. doi: 10.1016/j.virusres.2020.198098
    Paraskevis D, Kostaki EG, Magiorkinis G, et al. 2020. Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event. Infection, Genetics and Evolution, 79: 104212. doi: 10.1016/j.meegid.2020.104212
    Patwardhan A, Ray S, Roy A. 2014. Molecular markers in phylogenetic studies-a review. Journal of Phylogenetics & Evolutionary Biology, 2(2): 1000131.
    Peng MS, Li JB, Cai ZF, et al. 2021. The high diversity of SARS-CoV-2-related coronaviruses in pangolins alerts potential ecological risks. Zoological Research, 42(6): 834−844.
    Pipes L, Wang HR, Huelsenbeck JP, et al. 2021. Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny. Molecular Biology and Evolution, 38(4): 1537−1543. doi: 10.1093/molbev/msaa316
    Poon AFY, Walker LW, Murray H, et al. 2013. Mapping the shapes of phylogenetic trees from human and zoonotic RNA viruses. PLoS One, 8(11): e78122. doi: 10.1371/journal.pone.0078122
    Ruan YS, Wen HJ, Hou M, et al. 2022. The twin-beginnings of COVID-19 in Asia and Europe - one prevails quickly. National Science Review, 9(4): nwab223. doi: 10.1093/nsr/nwab223
    Sekizuka T, Itokawa K, Kageyama T, et al. 2020. Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak. Proceedings of the National Academy of Sciences of the United States of America, 117(33): 20198−20201. doi: 10.1073/pnas.2006824117
    Shan KJ, Wei CS, Wang Y, et al. 2021. Host-specific asymmetric accumulation of mutation types reveals that the origin of SARS-CoV-2 is consistent with a natural process. The Innovation, 2(4): 100159. doi: 10.1016/j.xinn.2021.100159
    Song SH, Ma LN, Zou D, et al. 2020. The global landscape of SARS-CoV-2 genomes, variants, and haplotypes in 2019nCoVR. Genomics, Proteomics & Bioinformatics, 18(6): 749−759.
    Tang XL, Wu CC, Li X, et al. 2020. On the origin and continuing evolution of SARS-CoV-2. National Science Review, 7(6): 1012−1023. doi: 10.1093/nsr/nwaa036
    Tang XL, Ying RC, Yao XM, et al. 2021. Evolutionary analysis and lineage designation of SARS-CoV-2 genomes. Science Bulletin, 66(22): 2297−2311. doi: 10.1016/j.scib.2021.02.012
    Temmam S, Vongphayloth K, Baquero E, et al. 2022. Bat coronaviruses related to SARS-CoV-2 and infectious for human cells. Nature, 604(7905): 330−336. doi: 10.1038/s41586-022-04532-4
    Tong YG, Liu WL, Liu PP, et al. 2021. The origins of viruses: discovery takes time, international resources, and cooperation. The Lancet, 398(10309): 1401−1402. doi: 10.1016/S0140-6736(21)02180-2
    Turakhia Y, de Maio N, Thornlow B, et al. 2020. Stability of SARS-CoV-2 phylogenies. PLoS Genetics, 16(11): e1009175. doi: 10.1371/journal.pgen.1009175
    van Dorp L, Acman M, Richard D, et al. 2020. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. Infection, Genetics and Evolution, 83: 104351. doi: 10.1016/j.meegid.2020.104351
    Wacharapluesadee S, Tan CW, Maneeorn P, et al. 2021. Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in southeast Asia. Nature Communications, 12(1): 972. doi: 10.1038/s41467-021-21240-1
    Wang HJ, Zhao W. 2021. WHO-convened global study of origins of SARS-CoV-2: China part (text extract). Infectious Diseases & Immunity, 1(3): 125−132.
    WHO Team. 2023. Weekly epidemiological update on COVID-19 - 16 March 2023. https://www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19---16-march-2023.
    Wong G, Bi YH, Wang QH, et al. 2020. Zoonotic origins of human coronavirus 2019 (HCoV-19 / SARS-CoV-2): why is this work important?. Zoological Research, 41(3): 213−219. doi: 10.24272/j.issn.2095-8137.2020.031
    Wu CI, Wen HJ, Lu J, et al. 2021. On the origin of SARS-CoV-2—the blind watchmaker argument. Science China Life Sciences, 64(9): 1560−1563. doi: 10.1007/s11427-021-1972-1
    Wu F, Zhao S, Yu B, et al. 2020. A new coronavirus associated with human respiratory disease in China. Nature, 579(7798): 265−269. doi: 10.1038/s41586-020-2008-3
    Xiao KP, Zhai JQ, Feng YY, et al. 2020. Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins. Nature, 583(7815): 286−289. doi: 10.1038/s41586-020-2313-x
    Yu D, Zhu J, Yang J, et al. 2022. Global cold-chain related SARS-CoV-2 transmission identified by pandemic-scale phylogenomics. Zoological Research, 43(5): 871−874. doi: 10.24272/j.issn.2095-8137.2022.238
    Yu WB, Tang GD, Zhang L, et al. 2020. Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data. Zoological Research, 41(3): 247−257. doi: 10.24272/j.issn.2095-8137.2020.022
    Zhang YZ, Holmes EC. 2020. A genomic perspective on the origin and emergence of SARS-CoV-2. Cell, 181(2): 223−227. doi: 10.1016/j.cell.2020.03.035
    Zhou H, Chen X, Hu T, et al. 2020a. A novel bat coronavirus closely related to SARS-CoV-2 contains natural insertions at the S1/S2 cleavage site of the spike protein. Current Biology, 30(11): 2196−2203.e3. doi: 10.1016/j.cub.2020.05.023
    Zhou H, Ji JK, Chen X, et al. 2021. Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses. Cell, 184(17): 4380−4391.e14. doi: 10.1016/j.cell.2021.06.008
    Zhou P, Yang XL, Wang XG, et al. 2020b. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798): 270−273. doi: 10.1038/s41586-020-2012-7
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