Ecology, genetic diversity, and phylogeographic structure of andes virus in humans and rodents in Chile

Abstract

Andes virus (ANDV) is the predominant etiologic agent of hantavirus cardiopulmonary syndrome (HCPS) in southern South America. In Chile, serologically confirmed human hantavirus infections have occurred throughout a wide latitudinal distribution extending from the regions of Valparaíso (32 to 33 degrees S) to Aysén (46 degrees S) in southern Patagonia. In this study, we found seropositive rodents further north in the Coquimbo region (30 degrees S) in Chile. Rodent seroprevalence was 1.4%, with Oligoryzomys longicaudatus displaying the highest seroprevalence (5.9%), followed by Abrothrix longipilis (1.9%) and other species exhibiting </=0.6% seropositivity. We sequenced partial ANDV small (S) segment RNA from 6 HCPS patients and 32 rodents of four different species collected throughout the known range of hantavirus infection in Chile. Phylogenetic analyses showed two major ANDV South (ANDV Sout) clades, congruent with two major Chilean ecoregions, Mediterranean (Chilean matorral [shrubland]) and Valdivian temperate forest. Human and rodent samples grouped according to geographic location. Phylogenetic comparative analyses of portions of S and medium segments (encoding glycoproteins Gn and Gc) from a subset of rodent specimens exhibited similar topologies, corroborating two major ANDV Sout clades in Chile and suggesting that yet unknown factors influence viral gene flow and persistence throughout the two Chilean ecoregions. Genetic algorithms for recombination detection identified recombination events within the S segment. Molecular demographic analyses showed that the virus is undergoing purifying selection and demonstrated a recent exponential growth in the effective number of ANDV Sout infections in Chile that correlates with the increased number of human cases reported. Although we determined virus sequences from four rodent species, our results confirmed O. longicaudatus as the primary ANDV Sout reservoir in Chile. While evidence of geographic differentiation exists, a single cosmopolitan lineage of ANDV Sout remains the sole etiologic agent for HCPS in Chile.

FIG. 1.

Phylogenetic relationship and diversity of ANDV S-segment alleles in Chile. (A) Map of the sampled localities (numbers from Table 2) of the Andes virus in Chile and in the East Andes in Argentina). Black circles represent samples sequenced in this study, and black squares are samples obtained from GenBank. (B) Maximum likelihood tree obtained from aligned sequences (397 nt) of the S segment. Numbers above branches indicate pseudoreplicate bootstrap values obtained by maximum likelihood analysis (the first value [outside parentheses]) and maximum parsimony analysis (value in parentheses). Numbers below branches indicate posterior probabilities for Bayesian inference. The bar indicates 0.1 nucleotide substitution/site. Taxa shown in italic type are representatives of previously reported ANDV lineages as described in Table 2 and in Results. For further details, refer to Materials and Methods.

FIG. 2.

Unrooted network of ANDV Sout S segment using 397 nt with alleles depicted according to geographical distribution. The size of the circles represents the number of individuals per allele, and the designations represent alleles (Table 2). White and gray symbols represent alleles from the Chilean Mediterranean and temperate forest ecoregions, respectively. The origins of the samples are indicated as follows: squares, humans; circles, O. longicaudatus; rhombus, A. longipilis; pentagon, L. micropus; triangle, R. rattus. The circle and rhombus indicate that an allele was shared between O. longicaudatus and A. longipilis.

FIG. 3.

Phylogenetic comparison of the S and M segments of ANDV Sout in Chile. Maximum likelihood phylogenetic trees from aligned sequences of the pruned data set are shown. (A) S-segment phylogenetic tree partition 1 (1 to 333 nt), (B) S-segment phylogenetic tree partition 2 (600 nt), (C) M-Gn phylogenetic analysis (490 nt), and (D) M-Gc phylogenetic tree obtained using 577 nt. The numbers next to the branches are the pseudoreplicate bootstrap values obtained by maximum likelihood (first value) and maximum parsimony (second value) analyses and posterior probabilities obtained with Bayesian inference (third value) (−, no value). Names in italic type are previously reported ANDV lineages (Table 2). Recombining sequences are underlined in panels A and B. The bars indicate 0.05 or 0.1 nucleotide substitution/site.

FIG. 4.

Phylogenetic relationship of concatenated S- and M-segment sequences of ANDV Sout in Chile. Majority rule (50%) consensus tree for the 2Q+Γ model of concatenated M- and S-segment sequences (1,668 nt) using Bayesian inference. The consensus tree is based on 4,500 samples from a converged Markov chain. The numbers above branches are the posterior probability values. Sequence names shown in italic type indicate previously reported ANDV lineages (Table 2). The bar indicates 0.1 nucleotide substitution/site.

FIG. 5.

Number of ANDV infections estimated from genetic data. The Bayesian skyline plot is derived from S-segment (397-nt) sequences. The thick solid line is the median effective number of ANDV infections (left-hand y axis) and represents the product of effective population size and generation time (in years). The shaded area indicates the 95% highest posterior density (HPD) region interval. Bars represent the total number of human HCPS cases per year (1997 to 2004; right-hand y axis) as reported by the Chilean Ministry of Health.