PT  - JOURNAL ARTICLE
AU  - Bin Fang
AU  - Linlin Liu
AU  - Xiao Yu
AU  - Xiang Li
AU  - Guojun Ye
AU  - Juan Xu
AU  - Ling Zhang
AU  - Faxian Zhan
AU  - Guiming Liu
AU  - Tao Pan
AU  - Yilin Shu
AU  - Yongzhong Jiang
TI  - Genome-wide data inferring the evolution and population demography of the novel pneumonia coronavirus (SARS-CoV-2)
AID  - 10.1101/2020.03.04.976662
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.03.04.976662
4099  - http://biorxiv.org/content/early/2020/03/11/2020.03.04.976662.short
4100  - http://biorxiv.org/content/early/2020/03/11/2020.03.04.976662.full
AB  - 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). The results showed that 80 haplotypes had 183 substitution sites, including 27 parsimony-informative and 156 singletons. Sliding window analyses of genetic diversity suggested a certain mutations abundance in the genomes of SARS-CoV-2, which may be explaining the existing widespread and high adaptation of the deadly virus. Phylogenetic analysis showed that the view, pangolin acted as an intermediate host, may be controversial. The network indicated that, in the original haplotype (H14), one patient sample lived near the Huanan seafood market (approximate 2 km), indicating high possibility of the patient having a history of unconscious contact with this market. However, based on this clue, we cannot accurately concluded 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 and then leading to the outbreak of SARS-CoV-2 in Wuhan and other areas. The EBSP results showed that the first estimated expansion date of SARS-CoV-2 began from 7 December 2019, which may indicated that the transmission could have begun from person to person in mid to late November.