Phylogeny of Shrew- and Mole-Borne Hantaviruses in Poland and Ukraine

Abstract

Earlier, we demonstrated the co-circulation of genetically distinct non-rodent-borne hantaviruses, including Boginia virus (BOGV) in the Eurasian water shrew (Neomys fodiens), Seewis virus (SWSV) in the Eurasian common shrew (Sorex araneus) and Nova virus (NVAV) in the European mole (Talpa europaea), in central Poland. To further investigate the phylogeny of hantaviruses harbored by soricid and talpid reservoir hosts, we analyzed RNAlater^®-preserved lung tissues from 320 shrews and 26 moles, both captured during 1990-2017 across Poland, and 10 European moles from Ukraine for hantavirus RNA through RT-PCR and DNA sequencing. SWSV and Altai virus (ALTV) were detected in Sorex araneus and Sorex minutus in Boginia and the Białowieża Forest, respectively, and NVAV was detected in Talpa europaea in Huta Dłutowska, Poland, and in Lviv, Ukraine. Phylogenetic analyses using maximum-likelihood and Bayesian methods showed geography-specific lineages of SWSV in Poland and elsewhere in Eurasia and of NVAV in Poland and Ukraine. The ATLV strain in Sorex minutus from the Białowieża Forest on the Polish-Belarusian border was distantly related to the ATLV strain previously reported in Sorex minutus from Chmiel in southeastern Poland. Overall, the gene phylogenies found support long-standing host-specific adaptation.

Keywords: Hantaviridae; Poland; Ukraine; hantavirus; mole; shrew.

Figure 1

(A) Map of Poland showing the nine sites where shrews and moles were captured in the present study: (1) Białowieża Forest; (2) Boginia; (3) Chmiel; (4) Huta Dłutowska; (5) Kurowice; (6) Poznań, Morasko-Kampus; (7) Poznań, city center; (8) Zakulin; (9) Zielątkowo. Hantaviruses are color-coded: ALTV (green circle); SWSV (red circle); NVAV (black circle); hantavirus RNA not detected (white circle). (B) Map of Poland showing the 21 trap sites in eight provinces where shrews and moles were captured in all published studies. Red stars indicate the eight sites where hantavirus-infected shrews and/or moles were found. White circles indicate the 13 sites where hantavirus RNA was not detected in shrews and moles.

Figure 2

Phylogenetic trees generated by way of the maximum-likelihood method using PAUP* and based on the 698- and 707-nucleotide S-segment and the partial 353-nucleotide L-segment sequences of NVAV from European moles captured in Poland, Ukraine, Belgium, France and Hungary, showing geographic-specific clustering. Similarly, SWSV strains from Poland and elsewhere are grouped according to geography. Newfound sequences from Poland and Ukraine are shown in red lettering. SWSV, ALTV and NVAV strains show the year of capture of the host and the country of origin. GenBank numbers for all taxa are provided in Supplementary Table S2. The numbers at selected nodes are bootstrap support values of >70 (expressed as the percentage of replicates in which the node was recovered), which were determined for 100 maximum-likelihood iterations under the same model of evolution using PAUP* version 4.0a169 (http://phylosolutions.com/paup-test/, accessed on 15 February 2023). The scale bar indicates 0.1 nucleotide substitutions per site.

Figure 3

Phylogenetic trees generated by the Bayesian method, under the best-fit GTR+I+Γ model of evolution, based on the 698- and 707-nucleotide S-segment and the partial 353-nucleotide L-segment sequences of NVAV from European moles captured in Poland, Ukraine, Belgium, France and Hungary, showing geographic-specific clustering. Similarly, SWSV strains from Poland and elsewhere are grouped according to geography. Newfound sequences from Poland and Ukraine are shown in red lettering. SWSV, ALTV and NVAV strains show the year of capture of the host and the country of origin. GenBank numbers for all taxa are provided in Supplementary Table S2. The numbers at selected nodes are Bayesian posterior probabilities > 0.7 based on 150,000 trees; two replicate Markov chain Monte Carlo runs, consisting of six chains of 10 million generations, each sampled every 100 generations with a burn-in of 25,000 (25%). Scale bars indicate 0.1 nucleotide substitutions per site.