Phylogenetic analyses of virus isolates in the genus Hantavirus, family Bunyaviridae

Abstract

We constructed a phylogenic tree by pairwise comparison of the deduced amino acid sequences encoded in the medium (M) genome segments of 13 hantaviruses. Five distinct branches were identified, four of which are represented by Hantaan, Seoul, Puumala, and Prospect Hill viruses. These groups corresponded to those previously established by serological and genetic means. In addition, we present sequence information for the M segment of Thailand virus and demonstrate that it represents a unique, fifth branch on the dendrogram. We show that a tree nearly identical to that constructed from the deduced amino acids encoded in the M segments of these viruses can be constructed by comparing nucleotide sequences of a 333-bp region of the M segments of the same hantaviruses. This region can be amplified, for most hantaviruses, by reverse transcriptase-polymerase chain reaction (RT-PCR) techniques, using a single primer pair. By using this method, we constructed a consensus tree for 30 hantaviruses, including 15 isolates for which we PCR-amplified and sequenced the 333-bp region. In addition to the five branches described above, we identified a sixth unique hantavirus group represented by Dobrava virus, an Apodemus isolate from Slovenia. Although we were unable to PCR-amplify the M segment of Thottapalayam virus, a distantly related hantavirus isolated from a shrew captured in India, we were able to amplify, clone, and sequence a portion of the small (S) segment of that virus. When we compared our Thottapalayam sequence to corresponding S segment sequences of other hantaviruses, the results indicated that this virus may represent a seventh, distinct group of hantaviruses.