Spread dynamics of SARS-CoV-2 epidemic in China: a phylogenetic analysis

BackgroundSince December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a pandemic and infected millions of people. As the first country proclaimed the SARS-CoV-2 outbreak, China implemented travel ban measure, and curbed the epidemic quickly. We performed a phylogenetic analysis to reveal the spread dynamics detail of SARS-CoV-2 in China and the impact of travel ban on SARS-CoV-2. MethodFocusing on SARS-CoV-2 sequences collected from China in public database released as of March 31, 2020, we performed a Bayesian inference phylogenetic analyses to estimate the effective population size (Ne) curve of SARS-CoV-2 epidemic. Furthermore, we displayed the geographic spread mode of SARS-CoV-2 among different China regions by using Bayesian stochastic search variable selection (BSSVS) method. ResultsThe most recent common ancestor (tMRCA) of SARS-CoV-2 in China was traced back to December 9, 2019. According the Ne estimation and geographic spread reconstruction, January 25, 2020 was considered as the crucial time point during the SARS-CoV-2 epidemic in China,which was 2 days after the travel ban implemented. On the point, the tendency of viral population size changed from ascending to decreasing, and the cross-regional spread paths were blocked. ConclusionsTravel ban is an effective measure to intervene in the spread of SARS-CoV-2, It is necessary to continue efforts in research for prevention and control measures.