Complete genome sequence and molecular phylogeny of a newfound hantavirus harbored by the Doucet's musk shrew (Crocidura douceti) in Guinea

Abstract

Elucidation of the molecular phylogeny of shrew-borne hantaviruses in sub-Saharan Africa has been hampered by the lack of full-length viral genomes. In this report, we present the complete genome analysis of a newfound hantavirus, designated Bowé virus, detected in ethanol-fixed intercostal muscle of a Doucet's musk shrew (Crocidura douceti), captured in southwestern Guinea in February 2012. Full-length amino acid sequence comparison of the S-, M- and L-segment gene products revealed that Bowé virus differed by 24.1-53.4%, 17.0-59.9% and 14.6-39.7%, respectively, from all other representative rodent-, shrew- and mole-borne hantaviruses. Phylogenetic analysis, using maximum-likelihood and Bayesian methods, under the GTR+I+Γ model of evolution, showed that Bowé virus shared a common ancestry with Tanganya virus, a hantavirus detected in the Therese's shrew (Crocidura theresae) in Guinea. Whole genome analysis of many more hantaviruses from sub-Saharan Africa are needed to better clarify how the radiation of African shrews might have contributed to the phylogeography of hantaviruses.

Keywords: Crocidura; Guinea; Hantavirus; Phylogeny; Shrew.

Fig. 1

(A) Map of Guinea, showing the locations of the four trap sites. A single Doucet’s musk shrew captured in Bowé was found to be infected with a previously unrecognized hantavirus. (B) Schematic comparison of consensus secondary structures of the full-length N protein of TPMV, MJNV, JJUV and BOWV, with the partial N protein of AZGV and TGNV. N protein structures for the crocidurine shrew-borne hantaviruses from Africa and Asia were predicted using several methods, including HNN, DSC, PHD, PREDATOR and MLRC, available at the NPS@ structure server (Combet et al., 2000). Alpha helices are represented by purple bars, beta-strand by yellow-green bars, and random coil and unclassified structure by red and gray bars, respectively.

Fig. 2

Phylogenetic trees were generated by the maximum-likelihood and Bayesian methods, using the GTR+I+Γ model of evolution, based on the alignment of the S-, M- and L-segment sequences of BOWV strain VN1512. Since tree topologies were very similar using RAxML and MrBayes, the trees generated by MrBayes were displayed. The phylogenetic positions of BOWV are shown in relationship to crocidurine shrew-borne hantaviruses, including Tanganya virus (TGNV Tan826: EF050455, EF050454), Azagny virus (AZGV KBM15: JF276226, JF276227, JF276228), Jeju virus (JJUV 10–11: HQ834695, HQ834696, HQ834697), Thottapalayam virus (TPMV VRC66412: AY526097, EU001329, EU001330) and Imjin virus (MJNV Cl05–11: EF641804, EF641798, EF641806). Soricine shrew-borne hantaviruses included Cao Bang virus (CBNV CBN-3: EF543524, EF543526, EF543525), Ash River virus (ARRV MSB73418: EF650086, EF619961), Jemez Springs virus (JMSV MSB144475: FJ593499, FJ593500, FJ593501), Kenkeme virus (KKMV MSB148794: GQ306148, GQ306149, GQ306150), Qiandao Lake virus (QDLV YN05-284: GU566023, GU566022, GU566021) and Seewis virus (SWSV mp70: EF636024, EF636025, EF636026). Also shown are mole-borne hantaviruses, including Asama virus (ASAV N10: EU929072, EU929075, EU929078), Nova virus (NVAV MSB95703: FJ539168, HQ840957, FJ593498), Oxbow virus (OXBV Ng1453: FJ539166, FJ539167, FJ593497) and Rockport virus (RKPV MSB57412: HM015223, HM015219, HM015221). Rodent-borne hantaviruses included Hantaan virus (HTNV 76–118: NC_005218, Y00386, NC_005222), Soochong virus (SOOV SOO-1: AY675349, AY675353, DQ562292), Dobrava virus (DOBV Greece: NC_005233, NC_005234, NC_005235), Seoul virus (SEOV 80–39: NC_005236, NC_005237, NC_005238), Sangassou virus (SANGV SA14: JQ082300, JQ082301, JQ082302), Tula virus (TULV M5302v: NC_005227, NC_005228, NC_005226), Puumala virus (PUUV Sotkamo: NC_005224, NC_005223, NC_005225), Prospect Hill virus (PHV PH-1: Z49098, X55129, EF646763), Andes virus (ANDV Chile9717869: NC_003466, NC_003467, NC_003468) and Sin Nombre virus (SNV NMH10: NC_005216, NC_005215, NC_005217). The numbers at each node are posterior node probabilities based on 150,000 trees (left) and bootstrap values of 1,000 replicates executed on the RAxML BlackBox web server (right), respectively. The scale bars indicate nucleotide substitutions per site.