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

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,6799 transmission chains and 1766 transmission networks were reconstructed,with chain lengths ranging from 1-9 nodes.The root node samples of the 1766 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.