Phylodynamics of deer tick virus in North America

Abstract

The burden of ticks and the pathogens they carry is increasing worldwide. Powassan virus (POWV; Flaviviridae: Flavivirus), the only known North American tick-borne flavivirus, is of particular concern due to rising cases and the severe morbidity of POWV encephalitis. Here, we use a multifaceted approach to evaluate the emergence of the II POWV lineage, known as deer tick virus (DTV), in parts of North America where human cases occur. We detected DTV-positive ticks from eight of twenty locations in the Northeast USA with an average infection rate of 1.4 per cent. High-depth, whole-genome sequencing of eighty-four POWV and DTV samples allowed us to assess geographic and temporal phylodynamics. We observed both stable infection in the Northeast USA and patterns of geographic dispersal within and between regions. A Bayesian skyline analysis demonstrated DTV population expansion over the last 50 years. This is concordant with the documented expansion of Ixodes scapularis tick populations and suggests an increasing risk of human exposure as the vector spreads. Finally, we isolated sixteen novel viruses in cell culture and demonstrated limited genetic change after passage, a valuable resource for future studies investigating this emerging virus.

Keywords: Powassan virus; deer tick virus; emerging virus; phylodynamics; tick-borne flavivirus.

Figure 1.

2019 Spring tick collection sites. I. scapularis ticks were collected from twenty locations in the Northeast USA (light gray) and Ontario, Canada (dark gray). Powassan-positive locations are indicated by an X. Figure created with biorender.com.

Figure 2.

Comparison of DTV population from tick homogenate and virus isolated in cell culture. (A) Consensus-level, SNPs in DTV sequences after one passage in BHK cells. (B) The average Shannon entropy for six paired samples, calculated based on iSNVs from two independent libraries.

Figure 3.

ML phylogenetic tree of 108 POWV genome sequences. Sequence names indicate location, unique identifier, and year. GenBank accession numbers are included for previously reported sequences. Circles indicated nodes with ultrafast bootstrap support of 99 per cent or greater. The location strip plot indicates the US state (with colors matching the map and map legend) or Canada (designated with ‘CAN’), Russia (‘RUS’), or unknown location (‘UNK’). The year strip plot is in grayscale as indicated by the year legend. Labeled branches indicate the two major lineages (I and II) and the Northeast sublineage of the II lineage. Specific clades of interest are marked with brackets. The map was created with mapchart.net.

Figure 4.

Time-scaled analysis of seventy-five deer tick virus genome sequences from the Northeast USA using a relaxed log-normal clock model and CEBS tree prior. (A) Maximum-clade credibility tree. Sequence names indicate the location, unique identifier, and year. GenBank accession numbers are included for previously reported sequences. Nodes with a posterior probability of 0.95 or higher are marked with circles. Nodes of interest are labeled with their TMRCA (95 per cent HPD). (B) The extended Bayesian skyline plot shows the estimated population size over time since present.