Population Genetics of SARS-CoV-2:Disentangling Effects of Sampling Bias and Infection Clusters
- Author:
Liu QI
1
,
2
,
3
;
Zhao SHILEI
;
Shi CHENG-MIN
;
Song SHUHUI
;
Zhu SIHUI
;
Su YANKAI
;
Zhao WENMING
;
Li MINGKUN
;
Bao YIMING
;
Xue YONGBIAO
;
Chen HUA
Author Information
1. Beijing Institute of Genomics,Chinese Academy of Sciences,Beijing 100101,China
2. China National Center for Bioinformation,Beijing 100101,China
3. University of Chinese Academy of Sciences,Beijing 100049,China
- Keywords:
COVID-19;
SARS-CoV-2;
Phylogenetic divergence;
Infection cluster;
Sampling bias
- From:
Genomics, Proteomics & Bioinformatics
2020;18(6):640-647
- CountryChina
- Language:Chinese
-
Abstract:
A novel RNA virus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is responsible for the ongoing outbreak of coronavirus disease 2019 (COVID-19). Population genetic analysis could be useful for investigating the origin and evolutionary dynamics of COVID-19. However, due to extensive sampling bias and existence of infection clusters during the epidemic spread, direct applications of existing approaches can lead to biased parameter estima-tions and data misinterpretation. In this study, we first present robust estimator for the time to the most recent common ancestor (TMRCA) and the mutation rate, and then apply the approach to analyze 12,909 genomic sequences of SARS-CoV-2. The mutation rate is inferred to be 8.69 × 10-4 per site per year with a 95％ confidence interval (CI) of [8.61 × 10-4, 8.77 × 10-4], and the TMRCA of the samples inferred to be Nov 28, 2019 with a 95％ CI of [Oct 20, 2019, Dec 9, 2019]. The results indicate that COVID-19 might originate earlier than and outside of Wuhan Seafood Market. We further demonstrate that genetic polymorphism patterns, including the enrichment of specific haplotypes and the temporal allele frequency trajectories generated from infection clusters, are similar to those caused by evolutionary forces such as natural selection. Our results show that population genetic methods need to be developed to efficiently detangle the effects of sampling bias and infection clusters to gain insights into the evolutionary mechanism ofSARS-CoV-2. Software for implementing VirusMuT can be downloaded at https://bigd.big.ac.cn/biocode/tools/BT007081.
