Molecular evolution of Puumala hantavirus

Abstract

Puumala virus (PUUV) is a negative-stranded RNA virus in the genus Hantavirus, family Bunyaviridae. In this study, detailed phylogenetic analysis was performed on 42 complete S segment sequences of PUUV originated from several European countries, Russia, and Japan, the largest set available thus far for hantaviruses. The results show that PUUV sequences form seven distinct and well-supported genetic lineages; within these lineages, geographical clustering of genetic variants is observed. The overall phylogeny of PUUV is star-like, suggesting an early split of genetic lineages. The individual PUUV lineages appear to be independent, with the only exception to this being the Finnish and the Russian lineages that are closely connected to each other. Two strains of PUUV-like virus from Japan form the most ancestral lineage diverging from PUUV. Recombination points within the S segment were searched for and evidence for intralineage recombination events was seen in the Finnish, Russian, Danish, and Belgian lineages of PUUV. Molecular clock analysis showed that PUUV is a stable virus, evolving slowly at a rate of 0.7 x 10(-7) to 2.2 x 10(-6) nt substitutions per site per year.

FIG. 1

Map of Europe showing the distribution of the bank vole (40). PUUV sequences analyzed in this paper belong to the following seven distinct lineages: FIN (1), NSCA (2), SSCA (3) (sequences are from Sweden [A] and Norway [B]), DAN (4), BEL (5) (sequences are from Belgium [A] and Germany [B]), BAL (6), and RUS (7) (sequences are from Russia [A] and the Baltics [B]).

FIG. 2

A phylogenetic tree of hantavirus N protein sequences calculated using TreePuzzle (55). An enlarged phylogenetic tree of PUUV S-segment coding sequences created using FITCH of the PHYLIP package (15) is shown. The bootstrap support values for the PUUV lineages are given in Table 2.

FIG. 3

Likelihood mapping of PUUV nucleotide (A) and amino acid (B) sequences. Dots in the corners of triangles represent fully resolved tree topologies and dots in the center represent unresolved ones.

FIG. 4

A phylogenetic tree of PUUV with contemporary tips and estimates of dates of divergence of the host rodents (9, 10, 30).

FIG. 5

Similarity analysis based on consensus sequences of distinct PUUV lineages. The query sequence is the Balkan consensus sequence (A) or the Baltic consensus sequence (B).

FIG. 6

(A) Splitstree based on the complete S-segment coding sequence of all PUUV strains. (B to D) Splitstrees based on partial sequences. (B) nt 1 to 400. (C) nt 401 to 1100. (D) nt 1101 to 1344. Two strains of each PUUV lineage are included together with two Baltic PUUV strains.