Genome-wide data inferring the evolution and population demography of the novel pneumonia coronavirus (SARS-CoV-2)

Since December 2019, coronavirus disease 2019 (COVID-19) emerged in Wuhan, Central China and rapidly spread throughout China. Up to March 3, 2020, SARS-CoV-2 has infected more than 89,000 people in China and other 66 countries across six continents. In this study, we used 10 new sequenced genomes of SARS-CoV-2 and combined 136 genomes from GISAID database to investigate the genetic variation and population demography through different analysis approaches (e.g. Network, EBSP, Mismatch, and neutrality tests) in the previous three months. The results showed that eighty haplotypes had 183 substitution sites, including 27 parsimony-informative and 156 singletons. Sliding window analyses of genetic diversity suggested a certain range in mutations and variation in genomic abundance of SARS-CoV-2, which could be explaining the existing widespread and high adaptation of the deadly virus. Phylogenetic analysis showed that pangolin may not be an intermediate host. The network indicated that, in the original haplotype (H14), one patient sample lived near the Huanan seafood market (approximately 2 km), which indicating high possibility of the patient having a history of unconscious contact with this market. However, based on this clue, we cannot accurately conclude that whether this market was the origin center of SARS-CoV-2. Additionally, 16 genomes, collected from this market, assigned to 10 haplotypes, indicated a circulating infection within the market in a short term, which would have led to the outbreak of SARS-CoV-2 in Wuhan and other areas. The EBSP results showed that the first estimated expansion date began from 7 December 2019, which indicated that the transmission of SARS-CoV-2 could have begun from person to person in mid to late November.