Divergent ancestral lineages of newfound hantaviruses harbored by phylogenetically related crocidurine shrew species in Korea

Abstract

Spurred by the recent isolation of a novel hantavirus, named Imjin virus (MJNV), from the Ussuri white-toothed shrew (Crocidura lasiura), targeted trapping was conducted for the phylogenetically related Asian lesser white-toothed shrew (Crocidura shantungensis). Pair-wise alignment and comparison of the S, M and L segments of a newfound hantavirus, designated Jeju virus (JJUV), indicated remarkably low nucleotide and amino acid sequence similarity with MJNV. Phylogenetic analyses, using maximum likelihood and Bayesian methods, showed divergent ancestral lineages for JJUV and MJNV, despite the close phylogenetic relationship of their reservoir soricid hosts. Also, no evidence of host switching was apparent in tanglegrams, generated by TreeMap 2.0β.

Fig. 1

(A) Geographic distribution, shaded in green (Bannikova et al., 2009; Ohdachi et al., 2004), of the Asian lesser white-toothed shrew, showing the locations of Jeju and Ulleung Islands. (B) Map of the Republic of Korea, showing locations of trap sites on Jeju Island, where hantavirus-infected shrews were captured.

Fig. 2

Phylogenetic trees generated by the maximum-likelihood method, using the GTR+I+Γ model of evolution as estimated from the data, based on the alignment of the coding regions of the entire (S) 1,287-nucleotide S segment, (M) 3,432-nucleotide M segment and (L) 6,474-nucleotide L genomic segment of JJUV strain 10–11 (S: HQ834695, M: HQ834696, L: HQ834697). The phylogenetic positions of JJUV strain 10–11 are shown in relationship to representative Murinae rodent-borne hantaviruses, including Hantaan virus (HTNV 76–118, S: NC_005218, M: NC_005219, L: NC_005222), Soochong virus (SOOV SOO-1, S: AY675349, M: AY675353, L: DQ056292), Dobrava-Belgrade virus (DOB/BGDV Greece, S: NC_005233, M: NC_005234, L: NC_005235) and Seoul virus (SEOV HR80-39, S: NC_005236, M: NC_005237, L: NC_005238); Arvicolinae rodent-borne hantaviruses, including Tula virus (TULV M5302v, S: NC_005227, M: NC_005228, L: NC_005226), Puumala virus (PUUV Sotkamo, S: NC_005224, M: NC_005223, L: NC_005225) and Prospect Hill virus (PHV PH-1, S: Z49098, M: X55129, L: EF646763); and Neotominae rodent-borne hantaviruses, Sin Nombre virus (SNV NMH10, S: NC_005216, M: NC_005215, L: NC_005217) and Andes virus (ANDV Chile9717869, S: AF291702, M: AF291703, L: AF291704). Also shown are Thottapalayam virus (TPMV VRC66412, S: AY526097, M: EU001329, L: EU001330), Imjin virus (MJNV Cl05-11, S: EF641804, M: EF641798, L: EF641806), Cao Bang virus (CBNV CBN-3, S: EF543524, M: EF543526, L: EF543525), Ash River virus (ARRV MSB 73418, S: EF650086, L: EF619961), Jemez Springs virus (JMSV MSB144475, S: FJ593499, M: FJ593500, L: FJ593501), Seewis virus (SWSV mp70, S: EF636024, M: EF636025, L: EF636026), Qiandao Lake virus (QDLV YN05-284, S: GU566023, M: GU566022, L: GU566021), Oxbow virus (OXBV Ng1453, S: FJ5339166, M: FJ539167, L: FJ593497), Tanganya virus (TGNV Tan826, S: EF050455, L: EF050454), Nova virus (NVAV MSB95703, S: FJ539168, M: HQ840957, L: FJ593498), Asama virus (ASAV N10, S: EU929072, M: EU929075, L: EU929078), Azagny virus (AZGV KBM15, S: JF276226, M: JF276227, L: JF276228) and JJUV strain SH42 (S: HQ663933, M: HQ663934, L: HQ663935). The numbers at each node are posterior node probabilities based on 150,000 trees (left) and bootstrap values of 100 ML replicates executed on the RAxML BlackBox web server (right), respectively. The scale bars indicate nucleotide substitutions per site.

Fig. 3

Tanglegrams, generated by TreeMap 2.0β, using consensus ML topologies based on the amino acid sequences of the nucleocapsid protein (labeled Saa), Gn and Gc glycoproteins (labeled Maa) and viral RNA-dependent RNA-polymerase (labeled Laa) of JJUV 10–11 and JJUV SH42, and representative rodent-, shrew- and mole-borne hantaviruses and cytochrome b mtDNA sequences of the respective reservoir host species. Node support was derived from 100 ML bootstrap replicates executed on the RAxML BlackBox web server. Virus and host names are provided in the legend to Fig. 2.

Fig. 4

Bayesian phylogenetic tree, based on the 1,140-nucleotide cytochrome b region of mtDNA of small mammals within the Order Soricomorpha, Family Talpidae and Soricidae and the Order Rodentia, Family Muridae and Cricetidae. The tree was rooted using Elephantulus (Order Macroscelidea, GenBank accession numbers DQ901019, DQ901206 and DQ901201) as the outgroup. Numbers at nodes indicate posterior probability values.