Genetic analysis of Thailand hantavirus in Bandicota indica trapped in Thailand

Abstract

Sixty one tissue samples from several rodent species trapped in five provinces of Thailand were examined for the presence of hantaviral markers by enzyme-immunoassay and immunoblotting. Four samples, all from the great bandicoot rat Bandicota indica, were confirmed positive for the hantaviral N-antigen. Two of them were trapped in Nakhon Pathom province, the other two in Nakhon Ratchasima province, approximately 250 km from the other trapping site. When analysed by RT-nested PCR, all four rodents were found positive for the hantaviral S- and M-segment nucleotide sequences. Genetic analysis revealed that the four newly described wild-type strains belong to Thailand hantavirus. On the phylogenetic trees they formed a well-supported cluster within the group of Murinae-associated hantaviruses and shared a recent common ancestor with Seoul virus.

Figure 1

Phylogenetic tree (ML-TreePuzzle) of hantaviruses based on the complete coding region of the S segment. Only bootstrap support values greater than 70% are shown. Complete S-segment sequences:Thottapalayam virus (TPLV) (GeneBank accession no. AY526097); Seoul virus (SEOV), strain SR11 (M34881); Thailand virus (THAIV), strain 741 (AB186420); Dobrava virus (DOBV), strain Dobrava (L41916); Saaremaa virus (SAAV), strain Saaremaa/160v (AJ009773); Hantaan virus (HTNV), strain 76–118 (M14626); Amur virus (AMRV), strain Solovey/AP63/1999 (AB071184); Soochong virus, strain SC-1 (AY675349); Muju virus, strain Muju99-28 (DQ138142); Puumala virus (PUUV), strain Sotkamo (X61035); Hokkaido virus (HOKV), strain Kamiiso-8-Cr-95 (AB010730); Topografov virus (TOPV), strain Ls136V (AJ011646); Khabarovsk virus (KHAV), strain MF-43 (U35255); Tula virus (TULV), strain Moravia/02v (Z69991); Isla Vista virus (ISLAV), strain MC-SB-47 (U19302); Prospect Hill virus (PHV), strain PH-1 (Z49098); Bloodland lake virus (BLLV), strain MO46 (U19303); Bayou virus (BAYV), strain Louisiana (L36929); Black Creek Canal (BCCV) (L39949); Muleshoe virus (MULV), strain SH-Tx-339 (U54575); Maporal virus, strain HV-97021050 (AY267347); Choclo virus (DQ285046); Maciel virus (MCLV), strain 13796 (AF482716); Pergamino virus (PRGV), strain 14403 (AF482717); Oran virus (ORNV), strain 22996 (AF482715); Hu39694 virus (AF482711); Lechiguanas virus (LECV), strain 22819 (AF482714); Bermejo virus (BMJV), strain Oc22531 (AF482713); Andes virus (ANDV), strain AH-1 (AF324902); Araucaria virus, strain HPR/02-72 (AY740625); Rio Mamore virus (RIOMV), strain Om-556 (U52136); Laguna Negra virus (LANV), strain 510B (AF005727); Rio Segundo virus (RIOSV), strain RMx-Costa-1 (U18100); El Moro Canyon (ELMCV), strain RM-97 (U11427); Sin Nombre virus (SNV), strain NM H10 (L25784); Monongahela virus (MGLV), strain Monongahela-1 (U32591); and New York virus (NYV), strain RI-1 (U09488).

Figure 2

Phylogenetic tree (ML-TreePuzzle) of hantaviruses based on partial sequence (nt 389–946) of the S segment. Only bootstrap support values greater than 70% are shown. Partial S-segment sequences:PUUV, strain Sotkamo (X61035); TULV, strain Moravia/02v (Z69991); SEOV, strains Gou3 (AF184988), Gou3v9 (AB027522), Hb8610 (AF288643), R22 (AF288295), L99 (AF288299), Z37 (AF187082), zy27 (AF406965), Pf26 (AY006465), IR461 (AF329388), SR11 (M34881), Tchoupitoulas (AF329389), Jakarta137 (AJ620583), Cambodia (Camb)41 (AJ427501), Camb32 (AJ427508), Camb58 (AJ427510), Camb180 (AJ427506), Camb174 (AJ427513), Camb96 (AJ427512), and Camb117 (AJ427511); THAIV virus, strain 741 (AB186420); SAAV, strain Saaremaa/160v (AJ009773); DOBV, strain Dobrava (L41916); Da Bie Shan virus (DBSV), strains NC167 (AB027523), AH211 (AF288647), and AH09 (AF285264); Amur virus (AMRV), strains Solovey/AP63/1999 (AB071184), and Solovey/AP61/1999 (AB071183); and HTNV, strains A16 (AB027099), A9 (AF329390), Maaji (AF321095), and 76–118 (M14626).

Figure 3

Phylogenetic tree (Fitch-Margoiliash) of hantaviruses based on partial sequence (nt 2021–2303) of the M segment. Only bootstrap support values greater than 70% are shown. Partial M-segment sequences:PUUV, strain Sotkamo (X61034); TULV, strain Moravia/02v (Z69993); DOBV, strain Dobrava (L33685); SAAV, strain Saaremaa/160v (AJ009774); DBSV, strain NC167 (AB027115); HTNV, strains 76–118 (M14627), HoJo (D00376), Lee (D00377), HV114 (L08753), and A9 (AF035831); THAIV, strain 749 (L08756); and SEOV, strains Gou3 (AB027521), SR11 (M34882), Tchoupitoulas (U00473), Hubei-1 (S72343), 80–39 (S47716), Girard Point (U00464), Egypt (U00463), SD227 (AB027091), CD10 (AB027092), Z37 (AF187081), Hebei4 (AB027089), c3 (AB027088), IR461 (AF458104), Brazil (U00460), Baltimore (U00151), B1 (X53861), France-Rn90 (AJ878418), Jakarta137 (AJ620583), Beijing-Rn (AB027087), HN71-L (AB027085), Houston (U00465), Shanxi (AB027084), Henan (AB027083), Wan (AB027081), NM39 (AB027080), and J12 (AB027082).