Phylogenetic and phylodynamic analyses of SARS-CoV-2

Abstract

To investigate the evolutionary and epidemiological dynamics of the current COVID-19 outbreak, a total of 112 genomes of SARS-CoV-2 strains sampled from China and 12 other countries with sampling dates between 24 December 2019 and 9 February 2020 were analyzed. We performed phylogenetic, split network, likelihood-mapping, model comparison, and phylodynamic analyses of the genomes. Based on Bayesian time-scaled phylogenetic analysis with the best-fitting combination models, we estimated the time to the most recent common ancestor (TMRCA) and evolutionary rate of SARS-CoV-2 to be 12 November 2019 (95 % BCI: 11 October 2019 and 09 December 2019) and 9.90 × 10^-4 substitutions per site per year (95 % BCI: 6.29 × 10^-4-1.35 × 10^-3), respectively. Notably, the very low R_e estimates of SARS-CoV-2 during the recent sampling period may be the result of the successful control of the pandemic in China due to extreme societal lockdown efforts. Our results emphasize the importance of using phylodynamic analyses to provide insights into the roles of various interventions to limit the spread of SARS-CoV-2 in China and beyond.

Keywords: COVID-19; Evolutionary rate; Lockdown; Re; SARS-CoV-2; TMRCA.

Fig. 1

Likelihood-mapping and split network analyses of SARS-CoV-2. Likelihood-mapping (A) and split network (B) analyses of SARS-CoV-2 for “dataset_112” are shown. For likelihood-mapping analysis, corners represent tree-like phylogenetic signals and those at sides represent network-like signals. Central area of likelihood map represents star-like signals of unresolved phylogenetic information.

Fig. 2

Estimated maximum-likelihood phylogenetic tree of SARS-CoV-2. Maximum-likelihood phylogenetic tree of SARS-CoV-2 for “dataset_112” is shown. Tree is midpoint rooted. Colors indicate different sampling locations. Scale bar at bottom indicates 0.0003 nucleotide substitutions per site.

Fig. 3

Root-to-tip genetic divergence plot of SARS-CoV-2. Root-to-tip plot shows regression of genetic divergence against sampling dates. Colors indicate different sampling locations. Gray color indicates linear regression line.

Fig. 4

Estimated maximum-clade-credibility tree of SARS-CoV-2. Circle at tip is colored according to sampling location.

Fig. 5

R_e estimates over time of SARS-CoV-2. R_e estimates obtained using Bayesian birth-death skyline model over five equidistant intervals. Horizontal red dotted line represents epidemiological threshold (R_e = 1). Shaded area represents 95 % BCI.