Thottapalayam virus is genetically distant to the rodent-borne hantaviruses, consistent with its isolation from the Asian house shrew (Suncus murinus)

Abstract

Thottapalayam (TPM) virus belongs to the genus Hantavirus, family Bunyaviridae. The genomes of hantaviruses consist of three negative-stranded RNA segments (S, M and L) encoding the virus nucleocapsid (N), glycoprotein (Gn, Gc), and polymerase (L) proteins, respectively. The genus Hantavirus contains predominantly rodent-borne viruses, with the prominent exception of TPM virus which was isolated in India in 1964 from an insectivore, Suncus murinus, commonly referred to as the Asian house shrew or brown musk shrew. Analysis of the available TPM virus S (1530 nt) RNA genome segment sequence and the newly derived M (3621 nt) and L (6581 nt) segment sequences demonstrate that the entire TPM virus genome is very unique. Remarkably high sequence differences are seen at the nucleotide (up to S - 47%, M - 49%, L - 38%) and protein (up to N - 54%, Gn/Gc - 57% and L - 39%) levels relative to the rodent-borne hantaviruses, consistent with TPM virus having a unique host association.

Figure 1

Phylogenetic relationship of TPM virus relative to representatives of the rodent-borne hantaviruses. Hantavirus sequences were aligned using the PILEUP program of the Wisconsin Package version 10.2 (Accelerys, Inc.) and phylogenetic analysis performed using PAUP 4.0b10 (Sinauer Association Inc., Sunderland, MA). Nucleotide sequences were analyzed by maximum likelihood method and maximum parsimony method was used for amino acids. Bootstrap confidence intervals were calculated using 500 heuristic search replicates. S segment sequence sources are: Hantaan (HTN) virus 76–118 M14626, Bayou (BAY) L36929, Black Creek Canal (BCC) virus l39949, Laguna Negra (LN) virus AF005727, Sin Nombre (SN) virus NM H10 L25784, New York (NY) virus RI-1 U09488, EI Moro Canyon (ELMC) virus RM97 U11427, Tula/Moravia/5302/95 Z69991, Puumala (PUU) virus Sotkamo X161036, PUU virus/Umea/hu NC_005224, Isla Vista (ISLA) virus U31534, Saaremaa virus 160V AJ009773, Dobrava (DOB) virus Ano-Poroia/Afl9/1999 AJ410615, Soochong virus SC-1 AY675349, Seoul (SEO) virus 80–39 AY273791, Hantavirus Thailand 741 AB288299, Topografov AJ011646, Andes virus CHI-7913 AY228237 and Thottapalayam (TPM) virus AY526097. M segment sources are: HTN virus 76–118, Bayou (BAY) L36930, BCC virus l39950, LN virus AF005728, SN virus NM H10 L25783, NY virus RI-1 U36801, ELMC virus RM97 U11428, Tula/Moravia/5302/95 Z69993, PUU virus Sotkamo X161034, PUU virus/Umea/hu NC_005223, Saaremaa virus160V AJ009774, DOB virus Ano-Poroia/Afl9/1999 AJ410616, Soochong virus SC-1 AY675353, SEO virus 80–39 S47716, Thailand 749 L08756, Topografov AJ011647, Andes virus CHI-7913 AY228238 and TPM virus. L segment sources are: HTN virus 76–118 X55901, SN virus NM H10 L37901, Tula/Moravia/5302/95 NC_005226, Puumala Sotkamo NC_005225, Puumala virus/Umea/hu AY526217, Saaremaa virus 160V AJ410618, DOB virus Ano-Poroia/Afl9/1999 AJ410617, Soochong virus SC-1 DQ056292, SEO virus 80–39 NC_005238, Andes virus CHI-7913 AY228239 and TPM virus.