Abstract
The outbreak of COVID-19 started in mid-December 2019 in Wuhan, China. Up to 29 February 2020, SARS-CoV-2 (HCoV-19 / 2019-nCoV) had infected more than 85 000 people in the world. In this study, we used 93 complete genomes of SARS-CoV-2 from the GISAID EpiFluTM database to investigate the evolution and human-to-human transmissions of SARS-CoV-2 in the first two months of the outbreak. We constructed haplotypes of the SARS-CoV-2 genomes, performed phylogenomic analyses and estimated the potential population size changes of the virus. The date of population expansion was calculated based on the expansion parameter tau (τ) using the formula t=τ/2u. A total of 120 substitution sites with 119 codons, including 79 non-synonymous and 40 synonymous substitutions, were found in eight coding-regions in the SARS-CoV-2 genomes. Forty non-synonymous substitutions are potentially associated with virus adaptation. No combinations were detected. The 58 haplotypes (31 found in samples from China and 31 from outside China) were identified in 93 viral genomes under study and could be classified into five groups. By applying the reported bat coronavirus genome (bat-RaTG13-CoV) as the outgroup, we found that haplotypes H13 and H38 might be considered as ancestral haplotypes, and later H1 was derived from the intermediate haplotype H3. The population size of the SARS-CoV-2 was estimated to have undergone a recent expansion on 06 January 2020, and an early expansion on 08 December 2019. Furthermore, phyloepidemiologic approaches have recovered specific directions of human-to-human transmissions and the potential sources for international infected cases.
Highlights
Betacoronaviruses are characterized by enveloped, positivesense, single-stranded RNA, and hosted in animals, mammals (Cui et al, 2019)
The genome EPI_ISL_402131 from Global Initiative on Sharing All Influenza Data (GISAID) was included as the outgroup, because it is the closest sister betacoronavirus available to SARS-CoV-2 (Zhou et al, 2020)
The coding sequence (CDS) regions contained 120 substitution sites (Supplementary Figure S1), which were classified as 58 haplotypes (Supplementary Table S2)
Summary
Betacoronaviruses are characterized by enveloped, positivesense, single-stranded RNA, and hosted in animals, mammals (Cui et al, 2019). Before December 2019, four species/strains of Betacoronavirus, HKU1, MERSCoV, OC43, and SARS-CoV, had been reported to cause severe human diseases (Cui et al, 2019). The fifth species/strain, a novel betacoronavirus SARS-CoV-2 / HCoV19 / 2019-nCoV (Gorbalenya et al, 2020; Jiang et al, 2020) causing human pneumonia (i.e., COVID-19), was first reported in Wuhan, Hubei, Central China (Wu et al, 2020a; Zhou et al, 2020; Zhu et al, 2020). Up to 29 February 2020, SARS-CoV-2 had infected more than 85 000 people in all provinces/regions of China, and another 59 countries/regions across Africa, Asia, Europe, North America, Oceania, and South America (Wikipedia, 2020). Confirmed infection cases were more than 2 000 between 30 January and 16 February, 2020, and the highest was more than 15 100 (Wikipedia, 2020), almost twice the total number for SARS-CoV (Chan-Yeung & Xu, 2003)
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