Short report: Genetic diversity of Thottapalayam virus, a Hantavirus harbored by the Asian house shrew (Suncus murinus) in Nepal

Abstract

Despite the recent discovery of genetically divergent hantaviruses in shrews of multiple species in widely separated geographic regions, data are unavailable about the genetic diversity and phylogeography of Thottapalayam virus (TPMV), a hantavirus originally isolated from an Asian house shrew (Suncus murinus) captured in southern India more than four decades ago. To bridge this knowledge gap, the S, M, and L segments of hantavirus RNA were amplified by reverse transcription polymerase chain reaction from archival lung tissues of Asian house shrews captured in Nepal from January to September 1996. Pair-wise alignment and comparison revealed approximately 80% nucleotide and > 94% amino acid sequence similarity to prototype TPMV. Phylogenetic analyses, generated by maximum likelihood and Bayesian methods, showed geographic-specific clustering of TPMV, similar to that observed for rodent- and soricid-borne hantaviruses. These findings confirm that the Asian house shrew is the natural reservoir of TPMV and suggest a long-standing virus-host relationship.

Figure 1.

Map of Nepal showing metropolitan centers (black dots) in Kathmandu, Bhaktapur, and Lalitpur districts where Asian house shrews were captured in 1996.

Figure 2.

Phylogenetic trees generated by the ML and Bayesian methods under the best-fit GTR+I+Γ model of evolution based on partial sequences of the S-, M-, and L-genomic segments of TPMV strains from Nepal and other well-characterized hantaviruses. The phylogenetic positions of TPMV strains from Nepal are shown in relationship to prototype TPMV VRC66412 (AY526097, EU001329, and EU001330) from India. Also shown are Imjin virus (MJNV Cl05–11: EF641804, EF641798, and EF641806) from the Ussuri white-toothed shrew (Crocidura lasiura), Seewis virus (SWSV mp70: EF636024, EF636025, and EF636026) from the Eurasian common shrew (Sorex araneus), Ash River virus (ARRV MSB73418: EF650086 and EF619961) from the masked shrew (Sorex cinereus), Qiandao Lake virus (QDLV YN05-284: GU566023, GU566022, and GU566021) from the stripe-backed shrew (Sorex cylindricauda), Jemez Springs virus (JMSV MSB144475: FJ593499, FJ593500, and FJ593501) from the dusky shrew (Sorex monticolus), Kenkeme virus (KKMV MSB148794: GQ306148, GQ306149, and GQ306150) from flat-skulled shrew (Sorex roboratus), Cao Bang virus (CBNV CBN-3: EF543524, EF543526, and EF543525) from the Chinese mole shrew (Anourosorex squamipes), Camp Ripley virus (RPLV MSB89863: FJ790772, EF540774, and EF540771) from the northern short-tailed shrew (Blarina brevicauda), Asama virus (ASAV N10: EU929072, EU929075, and EU929078) from the Japanese shrew mole (Urotrichus talpoides), Oxbow virus (OXBV Ng1453: FJ539166, FJ539167, and FJ593497) from the American shrew mole (Neurotrichus gibbsii), and Nova virus (NVAV MSB95703: FJ539168, HQ840957, and FJ593498) from the European common mole (Talpa europaea). Representative rodent-borne hantaviruses are shown, including Hantaan virus (HTNV 76–118: NC_005218, NC_005219, and NC_005222), Soochong virus (SOOV SOO-1: AY675349, AY675353, and DQ056292), Dobrava virus (DOBV Greece: NC_005233, NC_005234, and NC_005235), Seoul virus (SEOV 80–39: NC_005236, NC_005237, and NC_005238), Tula virus (TULV 5302v: NC_005227, NC_005228, and NC_005226), Puumala virus (PUUV Sotkamo: NC_005224, NC_005223, and NC_005225), Prospect Hill (PHV PH-1: Z49098, X55129, and EF646763), Sin Nombre virus (SNV NMH10: NC_00521, NC_005215, and NC_005217), and Andes virus (ANDV Chile9717869: NC_003466, NC_003467, and NC_003468). All tree topologies were very similar using MrBayes, RAxML, and PAUP. Therefore, trees generated by PAUP* were selected. The numbers at each node are posterior probabilities (above) based on 2 million generations with estimated sample sizes well over 100 (implemented in MrBayes) and bootstrap values (below) from 1,000 ML replicates (implemented in RAxML), respectively. The scale bars indicate nucleotide substitutions per site.

Figure 3.

Phylogenetic networks based on partial nucleotide (nt) and amino acid (aa) sequences of the S, M, and L segments constructed by the median-joining algorithm using Network 4.6. The numbers on the branches are proportional to the number of allele differences, and the sizes of the circles are proportional to the number of virus strains. Black and gray circles represent TPMV and MJNV strains, respectively. The small white circles are hypothetical median vectors created to connect existing strains within the network by maximum parsimony.