Hokkaido genotype of Puumala virus in the grey red-backed vole (Myodes rufocanus) and northern red-backed vole (Myodes rutilus) in Siberia

Abstract

Three species of Myodes voles known to harbor hantaviruses include the bank vole (Myodes glareolus), which serves as the reservoir host of Puumala virus (PUUV), the prototype arvicolid rodent-borne hantavirus causing hemorrhagic fever with renal syndrome (HFRS) in Europe, and the grey red-backed vole (Myodes rufocanus) and royal vole (Myodes regulus) which carry two PUUV-like hantaviruses, designated Hokkaido virus (HOKV) and Muju virus (MUJV), respectively. To ascertain the hantavirus harbored by the northern red-backed vole (Myodes rutilus), we initially screened sera from 233 M. rutilus, as well as from 90 M. rufocanus and 110 M. glareolus, captured in western and eastern Siberia during June 2007 to October 2009, for anti-hantaviral antibodies. Thereafter, lung tissues from 44 seropositive voles were analyzed for hantavirus RNA by reverse transcription-polymerase chain reaction. Partial L-, M- and S-segment sequences, detected in M. rutilus and M. rufocanus, were closely related to HOKV, differing from previously published L-, M- and S-segment sequences of HOKV by 17.8-20.2%, 15.9-23.4% and 15.0-17.0% at the nucleotide level and 2.6-7.9%, 1.3-6.3% and 1.2-4.0% at the amino acid level, respectively. Alignment and comparison of hantavirus sequences from M. glareolus trapped in Tyumen Oblast showed very high sequence similarity to the Omsk lineage of PUUV. Phylogenetic analysis, using neighbor-joining, maximal likelihood and Bayesian methods, showed that HOKV strains shared a common ancestry with PUUV and exhibited geographic-specific clustering. This report provides the first molecular evidence that both M. rutilus and M. rufocanus harbor HOKV, which might represent a genetic variant of PUUV.

Keywords: Hantavirus; Myodes voles; Puumala virus; Siberia.

Fig. 1

Map of Russia, showing the locations of the rodent trapping sites: (1) Kuchuk, (2) Ust-Ishim, (3) Sukhorechie, (4) Balakhnino, (5) Parnaya, (6) Khmelevka, (7) Kolyvan, (8) Pokrovka, (9) Solton, (10) Kuzedeyevo, (11) Teletskoye Lake, (12) and Srednyaya Shush, as well as (13) Omsk region (Dekonenko et. al., 2003) and (14) Olhon district (Yashina et al., 2013). Sites where anti-hantavirus antibody-positive and hantavirus RNA-positive voles were captured are labeled with double and filled circles, respectively

Fig. 2

Phylogenetic trees, generated by the maximum-likelihood and Bayesian methods, using the GTR+I+Γ model of evolution as estimated from the data, were based on the alignment of the coding regions of the (S) partial S segment (position 43–1251), (M) partial M segment (position 2764–3004) and (L) partial L segment (position 180–522) of Myodes vole-borne hantaviruses and other representative hantaviruses. Because the unrooted phylogenetic trees using these methods were very similar, the trees generated by MrBayes were displayed. The phylogenetic positions of the newfound Myodes vole-borne hantaviruses from Siberia are shown in relationship to PUUV CG215 (AF367066); PUUV CRF161 (AF367069, AF367061); PUUV CRF308 (AF367070); PUUV Virrat/25Cg (Z69985, Z70201); PUUV Pallasjarvi/63Cg/98 (AJ314597); PUUV Sotkamo (NC_005224, NC_005223, NC_005225); PUUV Pieksamaki/Mg4/2008 (JN831946); PUUV Pieksamaki/Mg7/2008 (JN831945); PUUV Kazan (Z84204, Z84205, EF405801); PUUV Udmurtia/338Cg (Z30708); PUUV CG1820 (M32750, M29979, M63194); PUUV Samara/147Cg (AB433855); PUUV Samara/49Cg/2005 (AB433850, AB574183); PUUV Samara/94Cg/2005 (AB574184); PUUV DTK/Ufa-97 (AB297667); PUUV Couvin/59Cg/97 (AJ277034, AJ277040); PUUV Cg-Erft (AJ238779, AJ238778); PUUV Omsk222 (AF442616); PUUV Opina916 (AF294652); PUUV Cg13891 (U22418); PUUV Balkan-2 (AJ314601); PUUV Klippitztoerl (AJ888751); PUUV Vranica (U14137); PUUV Vindeln/L20 (Z48586); PUUV Mellansel/Cg47 (AJ223374); PUUV Umea (AY526219, AY526218, AY526217); PUUV Fyn (AJ238791); PUUV Fyn131 (AJ278092); PUUV Eidsvoll/Cg1138 (AJ223369); PUUV Solleftea/Cg6 (AJ223377); HOKV Kitahiyama128 (AB675463, AB676848, AB712372); HOKV Kamiiso-8Cr-95 (AB010730); HOKV Kamiiso-Crf (AB011631); HOKV Tobetsu27S/2004 (AB675465); HOKV Tobetsu35/2010 (AB675451, AB675452); HOKV Ishikari9S/2009 (AB675469); HOKV Kiritappu126S/2000 (AB675474); HOKV Sakhalin99/1998 (AB675453, AB675454, AB675455); HOKV Tunka227 (KP325675, KR072694); HOKV Muhorshibir767 (AM930972, AM930975); HOKV Muhorshibir791 (AM930976); HOKV Olhon109 (KP325674, KM245956, KM245961); HOKV Fusong 200-05 (EF211820); HOKV Fusong-247 (EF442087, EF442094); HOKV Fusong-302 (EF442095); HOKV Fusong8405 (EF422372); HOKV Khekhtsir3S/1998 (AB677476); HOKV Khekhtsir37/2002 (AB677484, AB677488); HOKV CRF74372 (AY491383); HOKV CRF74333 (AY491381); MUJV 11-1 (JX028273, JX028272, JX028271); MUJV 11-4 (JX046484, JX046483, JX046482); MUJV 11-5 (JX046487, JX046486, JX046485); TOPV Ls136v (AJ011646, AJ011647, AJ011649); KBRV MF-43 (U35255, AJ011648, AJ011650); TULV M5302v (NC_005227, NC_005228, NC_005226); PHV PH-1 (Z49098, X55129, EF646763); and LUXV LX309 (HM756286, HM756287, HQ404253). Other rodent-borne hantaviruses included ANDV Chile9717869 (NC_003466, NC_003467, NC_003468); SNV NMH10 (NC_005216, NC_005215, NC_005217); HTNV 76–118 (NC_005218, Y00386, NC_005222); SOOV SOO-1 (AY675349, AY675353, DQ562292); DOBV Greece (NC_005233, NC_005234, NC_005235); and SEOV 80-39 (NC_005236, NC_005237, NC_005238). Shrew- and mole-borne hantaviruses included MJNV Cl05–11 (EF641804, EF641798, EF641806); TPMV VRC66412 (AY526097, EU001329, EU001330); and NVAV MSB95703 (FJ539168, HQ840957, FJ593498). The corresponding geographic areas are indicated as BAL (Balkan), BEL (Belgium), BUR (Buryatia), CHN/RUS (China/Russia), DAN (Denmark), FIN (Finland), JPN/RUS (Japan/Russia), KOR (Korea), NSCA (Northern Scandinavia), OMSK (Omsk), RUS (Russia), SIB-1 (Siberia), SIB-2 (Siberia), and SSCA (Southern Scandinavia). The numbers at each node are posterior node probabilities based on 150,000 trees. The scale bar indicates nucleotide substitutions per site. The GenBank accession numbers for the newfound hantaviral sequences from Siberia are listed in Table 3.

Fig. 2

Phylogenetic trees, generated by the maximum-likelihood and Bayesian methods, using the GTR+I+Γ model of evolution as estimated from the data, were based on the alignment of the coding regions of the (S) partial S segment (position 43–1251), (M) partial M segment (position 2764–3004) and (L) partial L segment (position 180–522) of Myodes vole-borne hantaviruses and other representative hantaviruses. Because the unrooted phylogenetic trees using these methods were very similar, the trees generated by MrBayes were displayed. The phylogenetic positions of the newfound Myodes vole-borne hantaviruses from Siberia are shown in relationship to PUUV CG215 (AF367066); PUUV CRF161 (AF367069, AF367061); PUUV CRF308 (AF367070); PUUV Virrat/25Cg (Z69985, Z70201); PUUV Pallasjarvi/63Cg/98 (AJ314597); PUUV Sotkamo (NC_005224, NC_005223, NC_005225); PUUV Pieksamaki/Mg4/2008 (JN831946); PUUV Pieksamaki/Mg7/2008 (JN831945); PUUV Kazan (Z84204, Z84205, EF405801); PUUV Udmurtia/338Cg (Z30708); PUUV CG1820 (M32750, M29979, M63194); PUUV Samara/147Cg (AB433855); PUUV Samara/49Cg/2005 (AB433850, AB574183); PUUV Samara/94Cg/2005 (AB574184); PUUV DTK/Ufa-97 (AB297667); PUUV Couvin/59Cg/97 (AJ277034, AJ277040); PUUV Cg-Erft (AJ238779, AJ238778); PUUV Omsk222 (AF442616); PUUV Opina916 (AF294652); PUUV Cg13891 (U22418); PUUV Balkan-2 (AJ314601); PUUV Klippitztoerl (AJ888751); PUUV Vranica (U14137); PUUV Vindeln/L20 (Z48586); PUUV Mellansel/Cg47 (AJ223374); PUUV Umea (AY526219, AY526218, AY526217); PUUV Fyn (AJ238791); PUUV Fyn131 (AJ278092); PUUV Eidsvoll/Cg1138 (AJ223369); PUUV Solleftea/Cg6 (AJ223377); HOKV Kitahiyama128 (AB675463, AB676848, AB712372); HOKV Kamiiso-8Cr-95 (AB010730); HOKV Kamiiso-Crf (AB011631); HOKV Tobetsu27S/2004 (AB675465); HOKV Tobetsu35/2010 (AB675451, AB675452); HOKV Ishikari9S/2009 (AB675469); HOKV Kiritappu126S/2000 (AB675474); HOKV Sakhalin99/1998 (AB675453, AB675454, AB675455); HOKV Tunka227 (KP325675, KR072694); HOKV Muhorshibir767 (AM930972, AM930975); HOKV Muhorshibir791 (AM930976); HOKV Olhon109 (KP325674, KM245956, KM245961); HOKV Fusong 200-05 (EF211820); HOKV Fusong-247 (EF442087, EF442094); HOKV Fusong-302 (EF442095); HOKV Fusong8405 (EF422372); HOKV Khekhtsir3S/1998 (AB677476); HOKV Khekhtsir37/2002 (AB677484, AB677488); HOKV CRF74372 (AY491383); HOKV CRF74333 (AY491381); MUJV 11-1 (JX028273, JX028272, JX028271); MUJV 11-4 (JX046484, JX046483, JX046482); MUJV 11-5 (JX046487, JX046486, JX046485); TOPV Ls136v (AJ011646, AJ011647, AJ011649); KBRV MF-43 (U35255, AJ011648, AJ011650); TULV M5302v (NC_005227, NC_005228, NC_005226); PHV PH-1 (Z49098, X55129, EF646763); and LUXV LX309 (HM756286, HM756287, HQ404253). Other rodent-borne hantaviruses included ANDV Chile9717869 (NC_003466, NC_003467, NC_003468); SNV NMH10 (NC_005216, NC_005215, NC_005217); HTNV 76–118 (NC_005218, Y00386, NC_005222); SOOV SOO-1 (AY675349, AY675353, DQ562292); DOBV Greece (NC_005233, NC_005234, NC_005235); and SEOV 80-39 (NC_005236, NC_005237, NC_005238). Shrew- and mole-borne hantaviruses included MJNV Cl05–11 (EF641804, EF641798, EF641806); TPMV VRC66412 (AY526097, EU001329, EU001330); and NVAV MSB95703 (FJ539168, HQ840957, FJ593498). The corresponding geographic areas are indicated as BAL (Balkan), BEL (Belgium), BUR (Buryatia), CHN/RUS (China/Russia), DAN (Denmark), FIN (Finland), JPN/RUS (Japan/Russia), KOR (Korea), NSCA (Northern Scandinavia), OMSK (Omsk), RUS (Russia), SIB-1 (Siberia), SIB-2 (Siberia), and SSCA (Southern Scandinavia). The numbers at each node are posterior node probabilities based on 150,000 trees. The scale bar indicates nucleotide substitutions per site. The GenBank accession numbers for the newfound hantaviral sequences from Siberia are listed in Table 3.

Fig. 2

Phylogenetic trees, generated by the maximum-likelihood and Bayesian methods, using the GTR+I+Γ model of evolution as estimated from the data, were based on the alignment of the coding regions of the (S) partial S segment (position 43–1251), (M) partial M segment (position 2764–3004) and (L) partial L segment (position 180–522) of Myodes vole-borne hantaviruses and other representative hantaviruses. Because the unrooted phylogenetic trees using these methods were very similar, the trees generated by MrBayes were displayed. The phylogenetic positions of the newfound Myodes vole-borne hantaviruses from Siberia are shown in relationship to PUUV CG215 (AF367066); PUUV CRF161 (AF367069, AF367061); PUUV CRF308 (AF367070); PUUV Virrat/25Cg (Z69985, Z70201); PUUV Pallasjarvi/63Cg/98 (AJ314597); PUUV Sotkamo (NC_005224, NC_005223, NC_005225); PUUV Pieksamaki/Mg4/2008 (JN831946); PUUV Pieksamaki/Mg7/2008 (JN831945); PUUV Kazan (Z84204, Z84205, EF405801); PUUV Udmurtia/338Cg (Z30708); PUUV CG1820 (M32750, M29979, M63194); PUUV Samara/147Cg (AB433855); PUUV Samara/49Cg/2005 (AB433850, AB574183); PUUV Samara/94Cg/2005 (AB574184); PUUV DTK/Ufa-97 (AB297667); PUUV Couvin/59Cg/97 (AJ277034, AJ277040); PUUV Cg-Erft (AJ238779, AJ238778); PUUV Omsk222 (AF442616); PUUV Opina916 (AF294652); PUUV Cg13891 (U22418); PUUV Balkan-2 (AJ314601); PUUV Klippitztoerl (AJ888751); PUUV Vranica (U14137); PUUV Vindeln/L20 (Z48586); PUUV Mellansel/Cg47 (AJ223374); PUUV Umea (AY526219, AY526218, AY526217); PUUV Fyn (AJ238791); PUUV Fyn131 (AJ278092); PUUV Eidsvoll/Cg1138 (AJ223369); PUUV Solleftea/Cg6 (AJ223377); HOKV Kitahiyama128 (AB675463, AB676848, AB712372); HOKV Kamiiso-8Cr-95 (AB010730); HOKV Kamiiso-Crf (AB011631); HOKV Tobetsu27S/2004 (AB675465); HOKV Tobetsu35/2010 (AB675451, AB675452); HOKV Ishikari9S/2009 (AB675469); HOKV Kiritappu126S/2000 (AB675474); HOKV Sakhalin99/1998 (AB675453, AB675454, AB675455); HOKV Tunka227 (KP325675, KR072694); HOKV Muhorshibir767 (AM930972, AM930975); HOKV Muhorshibir791 (AM930976); HOKV Olhon109 (KP325674, KM245956, KM245961); HOKV Fusong 200-05 (EF211820); HOKV Fusong-247 (EF442087, EF442094); HOKV Fusong-302 (EF442095); HOKV Fusong8405 (EF422372); HOKV Khekhtsir3S/1998 (AB677476); HOKV Khekhtsir37/2002 (AB677484, AB677488); HOKV CRF74372 (AY491383); HOKV CRF74333 (AY491381); MUJV 11-1 (JX028273, JX028272, JX028271); MUJV 11-4 (JX046484, JX046483, JX046482); MUJV 11-5 (JX046487, JX046486, JX046485); TOPV Ls136v (AJ011646, AJ011647, AJ011649); KBRV MF-43 (U35255, AJ011648, AJ011650); TULV M5302v (NC_005227, NC_005228, NC_005226); PHV PH-1 (Z49098, X55129, EF646763); and LUXV LX309 (HM756286, HM756287, HQ404253). Other rodent-borne hantaviruses included ANDV Chile9717869 (NC_003466, NC_003467, NC_003468); SNV NMH10 (NC_005216, NC_005215, NC_005217); HTNV 76–118 (NC_005218, Y00386, NC_005222); SOOV SOO-1 (AY675349, AY675353, DQ562292); DOBV Greece (NC_005233, NC_005234, NC_005235); and SEOV 80-39 (NC_005236, NC_005237, NC_005238). Shrew- and mole-borne hantaviruses included MJNV Cl05–11 (EF641804, EF641798, EF641806); TPMV VRC66412 (AY526097, EU001329, EU001330); and NVAV MSB95703 (FJ539168, HQ840957, FJ593498). The corresponding geographic areas are indicated as BAL (Balkan), BEL (Belgium), BUR (Buryatia), CHN/RUS (China/Russia), DAN (Denmark), FIN (Finland), JPN/RUS (Japan/Russia), KOR (Korea), NSCA (Northern Scandinavia), OMSK (Omsk), RUS (Russia), SIB-1 (Siberia), SIB-2 (Siberia), and SSCA (Southern Scandinavia). The numbers at each node are posterior node probabilities based on 150,000 trees. The scale bar indicates nucleotide substitutions per site. The GenBank accession numbers for the newfound hantaviral sequences from Siberia are listed in Table 3.