Phylogeography and Re-Evaluation of Evolutionary Rate of Powassan Virus Using Complete Genome Data

Abstract

In this paper, we revealed the genetic structure and migration history of the Powassan virus (POWV) reconstructed based on 25 complete genomes available in NCBI and ViPR databases (accessed in June 2021). The usage of this data set allowed us to perform a more precise assessment of the evolutionary rate of this virus. In addition, we proposed a simple Bayesian technique for the evaluation and visualization of 'temporal signal dynamics' along the phylogenetic tree. We showed that the evolutionary rate value of POWV is 3.3 × 10^-5 nucleotide substitution per site per year (95% HPD, 2.0 × 10^-5-4.7 × 10^-5), which is lower than values reported in the previous studies. Divergence of the most recent common ancestor (MRCA) of POWV into two independent genetic lineages most likely occurred in the period between 2600 and 6030 years ago. We assume that the divergence of the virus lineages happened due to the melting of glaciers about 12,000 years ago, which led to the disappearance of the Bering Land Bridge between Eurasia and North America (the modern Alaskan territory) and spatial division of the viral areal into two parts. Genomic data provide evidence of the virus migrations between two continents. The mean migration rate detected from the Far East of Russia to North America was one event per 1750 years. The migration to the opposite direction occurred approximately once per 475 years.

Keywords: Bayesian inference; Powassan virus; evolutionary rate; phylogenetics; phylogeography.

Figure 1

The time scaled phylogenetic tree of POWV in NA and FER: The color of tree branches and nodes represent a state/territory (see legend in the top left corner). The change in colors is a virus migration event between the states/territories. Numbers to the left from main nodes are node state/territory posterior probability. Black asterisks show clades with posterior probability less than 0.8 (please, do not confuse with node state/territory posterior probability). In the other cases, posterior probability is more than 0.8. An insert is the relative genetic diversity (effective population size (N_e) × generation time (τ—time between two successful infections in the chain of transmission).

Figure 2

The prior and posterior distributions of tMRCAs of root age and five main clades (clades (A–E)). An insert within the root plot is boxplots of 95% quantile width of the tree root height.

Figure 3

Date permutation test results: The boxplots present 95% HPD of (a) evolutionary rate and (b) tree root height parameters. Analysis with correct isolation dates is shown as the orange bar. Horizontal dashed lines demonstrate overlapping areas of the analysis using correct dates and permuted replicates.