Evidence of increasing diversification of emerging Severe Acute Respiratory Syndrome Coronavirus 2 strains

Abstract

On 30th January 2020, an outbreak of atypical pneumonia caused by a novel betacoronavirus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared a public health emergency of international concern by the World Health Organization. For this reason, a detailed evolutionary analysis of SARS-CoV-2 strains currently circulating in different geographic regions of the world was performed. A compositional analysis as well as a Bayesian coalescent analysis of complete genome sequences of SARS-CoV-2 strains recently isolated in Europe, North America, South America, and Asia was performed. The results of these studies revealed a diversification of SARS-CoV-2 strains in three different genetic clades. Co-circulation of different clades in different countries, as well as different genetic lineages within different clades were observed. The time of the most recent common ancestor was established to be around 1st November 2019. A mean rate of evolution of 6.57 × 10^-4 substitutions per site per year was found. A significant migration rate per genetic lineage per year from Europe to South America was also observed. The results of these studies revealed an increasing diversification of SARS-CoV-2 strains. High evolutionary rates and fast population growth characterizes the population dynamics of SARS-CoV-2 strains.

Keywords: SARS-CoV-2; coalescent; coronavirus; evolution.

Figure 1

PCA of A, U, C, and G nucleotide frequencies in SARS‐CoV‐2 genomes. Position of the strains in the plane conformed by the first two major axes of PCA is shown. SVD was used to calculate principal components and unit variance was applied. The proportion of variance explained by each axis is shown between parentheses. Strain Wuhan/WH01/2019, isolated 26th December 2019 is indicated by a black arrow. Strains isolated in Europe, North America, South America, and South East Asia are shown in red, blue, green, and violet, respectively. N = 64 datapoints. PCA, principal component analysis; SARS‐CoV‐2, severe acute respiratory syndrome coronvirus 2; SVD, singular value decomposition

Figure 2

Marginal probability distribution of R ₀ values. The marginal probability distribution for Europe, North America, South America, and South East Asia are shown in gray, blue, red, and yellow, respectively

Figure 3

DensiTree analysis of complete genome sequences of SARS‐CoV‐2 strains recently isolated in four different geographic regions of the world. The results obtained using the HKY model, a relaxed exponential clock and a structured coalescent population model is shown. 5000 trees were drawn, shown in green. Root channel is shown in blue. The scale at the bottom is in units of evolutionary time and represents the years before the last sampling date. Strains in the tree are shown by name, followed by date of isolation (day/month/year). SARS‐C oV‐2, severe acute respiratory syndrome coronvirus 2