tetano
Editor, Senior Moderator
Zool Res
. 2023 May 18;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
Chao-Yuan Cheng[SUP] 1 [/SUP], Zhi-Bin Zhang[SUP] 1 2 [/SUP]
Affiliations
Abstract
in English, Chinese
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.
Keywords: Ancestor-offspring relationship; Back mutation; De novo mutation; SARS-CoV-2; Secondary mutation; Transmission chain; Transmission network.
. 2023 May 18;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
Chao-Yuan Cheng[SUP] 1 [/SUP], Zhi-Bin Zhang[SUP] 1 2 [/SUP]
Affiliations
- PMID: 36999549
- DOI: 10.24272/j.issn.2095-8137.2022.535
Abstract
in English, Chinese
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.
Keywords: Ancestor-offspring relationship; Back mutation; De novo mutation; SARS-CoV-2; Secondary mutation; Transmission chain; Transmission network.