Persistence of multiple genetic lineages within intrahost populations of Ross River virus

Abstract

We examined the structure and extent of genetic diversity in intrahost populations of Ross River virus (RRV) in samples from six human patients, focusing on the nonstructural (nsP3) and structural (E2) protein genes. Strikingly, although the samples were collected from contrasting ecological settings 3,000 kilometers apart in Australia, we observed multiple viral lineages in four of the six individuals, which is indicative of widespread mixed infections. In addition, a comparison with previously published RRV sequences revealed that these distinct lineages have been in circulation for at least 5 years, and we were able to document their long-term persistence over extensive geographical distances.

Fig. 1.

Distribution of variable sites across the E2 (a) and nsP3 (b) nucleotide and amino acid sequences of Ross River virus.

Fig. 2.

Phylogenetic relationships between E2 (a) and nsP3 (b) genes from intrahost samples of Ross River virus from patients from urban and rural settings in Australia. Note the presence of two clearly distinct lineages. RRV (consensus) sequences generated from previous studies are in red. Individuals that harbor each of the phylogenetically distinct lineages are marked with an asterisk. The phylogenetic position of strain QML1 is also indicated. Both trees are mid-point rooted for purposes of clarity only, and all horizontal branch lengths are drawn to a scale of nucleotide substitutions per site. Bootstrap support values (>70%) are shown for key nodes.

Fig. 2.

Phylogenetic relationships between E2 (a) and nsP3 (b) genes from intrahost samples of Ross River virus from patients from urban and rural settings in Australia. Note the presence of two clearly distinct lineages. RRV (consensus) sequences generated from previous studies are in red. Individuals that harbor each of the phylogenetically distinct lineages are marked with an asterisk. The phylogenetic position of strain QML1 is also indicated. Both trees are mid-point rooted for purposes of clarity only, and all horizontal branch lengths are drawn to a scale of nucleotide substitutions per site. Bootstrap support values (>70%) are shown for key nodes.