Genetic analysis of the diversity and origin of hantaviruses in Peromyscus leucopus mice in North America

Abstract

Nucleotide sequences were determined for the complete M genome segments of two distinct hantavirus genetic lineages which were detected in hantavirus antibody- and PCR-positive white-footed mice (Peromyscus leucopus) from Indiana and Oklahoma. Phylogenetic analyses indicated that although divergent from each other, the virus lineages in Indiana and Oklahoma were monophyletic and formed a newly identified unique ancestral branch within the clade of Sin Nombre-like viruses found in Peromyscus mice. Interestingly, P. leucopus-borne New York virus was found to be most closely related to the P. maniculatus-borne viruses, Sin Nombre and Monongahela, and monophyletic with Monongahela virus. In parallel, intraspecific phylogenetic relationships of P. leucopus were also determined, based on the amplification, sequencing, and analysis of the DNA fragment representing the replication control region of the rodent mitochondrial genome. P. leucopus mitochondrial DNA haplotypes were found to form four separate genetic clades, referred to here as Eastern, Central, Northwestern, and Southwestern groups. The distinct Indiana and Oklahoma virus lineages were detected in P. leucopus of the Eastern and Southwestern mitochondrial DNA haplotypes, respectively. Taken together, our current data suggests that both cospeciation of Peromyscus-borne hantaviruses with their specific rodent hosts and biogeographic factors (such as allopatric migrations, geographic separation, and isolation) have played important roles in establishment of the current genetic diversity and geographic distribution of Sin Nombre-like hantaviruses. In particular, the unusual position of New York virus on the virus phylogenetic tree is most consistent with an historically recent host-switching event.

FIG. 1

Linear map of the P. leucopus 1.8-kb mitochondrial genome fragment containing the replication control region. Directions of primers used are shown with arrows. Grey bars represent fragments selected for amplification, sequencing, and phylogenetic analyses.

FIG. 2

Phylogenetic relationships of the IN and OK hantavirus lineages to previously known hantaviruses, based on sequence differences of the 1,141-nucleotide fragment of the M genome RNAs. Sequences were aligned with BR IN and OK M genome RNA sequences and then edited to match the length of the shortest sequence which was the partial-length sequence of MGL. (A) NJ analysis was performed with MEGA, using the Tamura algorithm with options of using both transversional and transitional changes and complete deletion of gaps. Bootstrap values were calculated by 1,000 replicates of the analysis. (B) MP analysis was performed with PAUP, version 3.1.1, using the branch-and-bound search option and a 4:1 weighting of transversions over transitions. Bootstrap analysis was carried out by using 1,000 heuristic search replicates with the aforementioned weighting of transversions. Numbers above horizontal branches indicate distances (NJ) or nucleotide step differences (MP). The percentage of bootstrap support exceeding 50% is indicated by numbers in parentheses below corresponding branches near the appropriate branching point. Vertical branches are for visual clarity only. Previously published hantavirus sequences (for abbreviations not provided below, see the text and Table 2, footnote a) used in the analysis include the following: HTN virus strain 76118 (49), GenBank accession no. M14627; SEO virus strain SR-11 (3), M34882; PH virus strain PHV-1 (42), X55129; TUL virus strain Moravia (43), Z66538; PUU virus strain CG1820 (16), M29979; BAY virus (36), L36930; BCC virus (46), L39950; ELMC virus strain RM-97 (56), U26828; NY virus strains RI1, NY-1, and NY-2 (24), U36801, U36802, and U36803, respectively; SN virus strains New Mexico h10 (NMh10) (52), L25783; Convict Creek 74 (CC74) and Convict Creek 107 (CC107) (30), L33684 and L33474; and MGL virus strain Monongahela-2 (50), U32653.

FIG. 3

Phylogeny of P. leucopus inferred from NJ analysis of combined 333- and 380-nucleotide fragments of the mtDNA replication control region. NJ analysis was performed with MEGA, using the Jukes-Cantor model. Bootstrap values were obtained by 1,000 repetitions of the analysis. The standard error test support numbers and bootstrap support numbers (in parentheses) for major clades are indicated below the corresponding branches near the appropriate branching point. The horizontal scale bar indicates a distance of 0.01. Vertical branches are for visual clarity only. Prefixes: Pl, P. leucopus; Pg, P. gossypinus. States of origin are indicated by two-letter postal code. Four clades or haplotypes are indicated. The first clade contains mtDNA sequences from the eastern United States including East Coast (Maine, Massachusetts, New York, Pennsylvania, Rhode Island, Maryland, and District of Columbia), Appalachian Mountain region (West Virginia, Virginia, Tennessee, Kentucky, South Carolina, and Georgia), and areas between the Appalachians and Great Lakes (Indiana and Ohio). The second clade is comprised of mtDNA sequences from the northern region of the Central Plains (Illinois, Wisconsin, Iowa, Missouri, and North Dakota). The third clade contains mtDNA sequences from Kansas and Arkansas, while the fourth clade is comprised of mtDNA sequences from Texas and Oklahoma.

FIG. 4

Geographic distribution of mtDNA haplotypes of P. leucopus and P. leucopus-borne hantaviruses. The shaded area represents the geographic distribution of P. leucopus according to Hall (17). White, dotted, grey, and black mouse figures designate localities containing Eastern, Northwestern, Central, and Southwestern mtDNA haplotypes, respectively. Black squares, triangles, and diamonds indicate localities containing northeastern, southwestern, and “hybrid” karyotypes, respectively, according to Baker et al. (5). White virion figures indicate localities where IN and OK hantavirus lineages were recovered from P. leucopus. The grey virion figure shows NY hantavirus. Mice from northern Ohio, southwestern Kentucky, and Colorado were assigned to mtDNA haplotype groups based on phylogenetic analysis of the fragment 1 only and therefore were not included in Fig. 3.