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.

Phylodynamics of deer tick virus in North America

“…Our phylogenetic analysis supported the presence of two geographically separated DTV sublineages, consistent with prior reports ( Pesko et al. 2010 ; Anderson and Armstrong 2012 ; Bondaryuk et al. 2021 ).…”

“…Time-scaled phylogenetic analysis of DTV sequences indicated that the Northeast and Midwest sublineages last shared an MRCA approximately 1,200 years ago. Our results (time to most recent common ancestor (TMRCA) 1,184 years ago, 95 per cent HPD 770–1,658) were consistent with the results from an analysis of twenty-six full-genome sequences in 2019 (TMRCA 1,160 years ago, 95 per cent HPD 760–1,750) ( Bondaryuk et al. 2021 ).…”

“…POWV is the only North American member of the Flavivirus tick-borne encephalitis serogroup, first identified in 1958 in a patient with encephalitis in Powassan, ON, Canada ( McLean and Donohue 1959 ). The canonical I POWV lineage has been estimated to diverge from the European tick-borne encephalitis complex between 2,000 and 6,000 years ago, around the time the Bering Land Bridge between Alaska and Far Eastern Russia disappeared, effectively limiting migration between Russia and North America ( Bondaryuk et al. 2021 ).…”

Phylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States

“…We estimate that the evolutionary rate of this clade is 8.25×10 −5 substitutions/site/year (95% highest posterior density [HPD] interval: [8.23-10.46×10 −5 ]; 95% HPD interval of the associated coefficient of variation: [0.48-0.75]). Our estimate is higher than previous estimated evolutionary rates for all Powassan viruses (3.3×10 −5 (23) ) and NS5 coding sequences (3.9×10 −5 -5.4×10 −5 (5, 24) ), but lower than previous estimates based on envelope coding sequences (2.2×10 −4 (5) ). This is likely a reflection of the recent emergence of lineage II in the region.…”

“…46 10 -5 ]). Our estimate is higher than previous estimated evolutionary rates for all × Powassan viruses (3.3 10 -5 ) 22 , and than previous estimates based on envelope (2.2 10 -4 ) 5 and × × NS5 coding sequences (3.9 10 -5 -5.4 10 -5 ) 5,23 , likely a reflection of the recent emergence of × × lineage II in the region. Our work increased the number of publicly available Powassan virus lineage II sequences by more than ten-fold, enabling us to better understand the patterns of emergence and spread in the northeastern United States.…”