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

Molecular evolution of Hokkaido virus, a genotype of Orthohantavirus puumalaense, among Myodes rodents

Viruses in the genus Orthohantavirus within the family Hantaviridae cause human hantavirus infections and represent a threat to public health. Hokkaido virus (HOKV), a genotype of Orthohantavirus puumalaense (Puumala virus; PUUV), was first identified in Tobetsu, Hokkaido, Japan. Although it is genetically related to the prototype of PUUV, the evolutionary pathway of HOKV is unclear. We conducted a field survey in a forest in Tobetsu in 2022 and captured 44 rodents. Complete coding genome sequences of HOKVs were obtained from five viral-RNA-positive rodents (four Myodes rufocanus bedfordiae and one Apodemus speciosus). Phylogenetic analysis revealed a close relationship between the phylogenies and geographical origins of M. rufocanus-related orthohantaviruses. Comparison of the phylogenetic trees of the S segments of orthohantaviruses and the cytochrome b genes of Myodes species suggested that Myodes-related orthohantaviruses evolved in Myodes rodent species as a result of genetic isolation and host switching.

Rodent-Borne Orthohantaviruses in Vietnam, Madagascar and Japan

Hantaviruses are harbored by multiple small mammal species in Asia, Europe, Africa, and the Americas. To ascertain the geographic distribution and virus-host relationships of rodent-borne hantaviruses in Japan, Vietnam, Myanmar, and Madagascar, RNAlater™-preserved lung tissues of 981 rodents representing 40 species, collected in 2011-2017, were analyzed for hantavirus RNA by RT-PCR. Our data showed Hantaan orthohantavirus Da Bie Shan strain in the Chinese white-bellied rat (Niviventer confucianus) in Vietnam, Thailand; orthohantavirus Anjo strain in the black rat (Rattus rattus) in Madagascar; and Puumala orthohantavirus Hokkaido strain in the grey-sided vole (Myodes rufocanus) in Japan. The Hokkaido strain of Puumala virus was also detected in the large Japanese field mouse (Apodemus speciosus) and small Japanese field mouse (Apodemus argenteus), with evidence of host-switching as determined by co-phylogeny mapping.

Orthohantaviruses, Emerging Zoonotic Pathogens

Orthohantaviruses give rise to the emerging infections such as of hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS) in Eurasia and the Americas, respectively. In this review we will provide a comprehensive analysis of orthohantaviruses distribution and circulation in Eurasia and address the genetic diversity and evolution of Puumala orthohantavirus (PUUV), which causes HFRS in this region. Current data indicate that the geographical location and migration of the natural hosts can lead to the orthohantaviruses genetic diversity as the rodents adapt to the new environmental conditions. The data shows that a high level of diversity characterizes the genome of orthohantaviruses, and the PUUV genome is the most divergent. The reasons for the high genome diversity are mainly caused by point mutations and reassortment, which occur in the genome segments. However, it still remains unclear whether this diversity is linked to the disease's severity. We anticipate that the information provided in this review will be useful for optimizing and developing preventive strategies of HFRS, an emerging zoonosis with potentially very high mortality rates.

Characterization of the Puumala orthohantavirus Strains in the Northwestern Region of the Republic of Tatarstan in Relation to the Clinical Manifestations in Hemorrhagic Fever With Renal Syndrome Patients

Over 1,000 cases of hemorrhagic fever with renal syndrome (HFRS) were recorded in the Republic of Tatarstan (RT) in 2015. HFRS is a zoonotic disease caused by several different Old World hantaviruses. In RT, Puumala orthohantavirus (PUUV) is a prevalent etiological agent of HFRS. We looked for the genetic link between the PUUV strains isolated from the bank voles and from the infected humans. In addition, possible correlation between the genetic makeup of the PUUV strain involved and different clinical picture of HFRS was investigated. Partial PUUV small (S) genome segment sequences were retrieved from 37 small animals captured in the northwestern region of RT in 2015. Phylogenetic analysis revealed that 34 PUUV sequences clustered with strains of the previously identified “Russia” (RUS) genetic lineage, while 3 remaining PUUV sequences clustered with the known lineage from Finland (FIN). Sequence comparisons showed that the majority of the S-segment sequences isolated in the current study displayed 98.2–100.0% sequence identity when compared with the strains isolated earlier from the HFRS patients hospitalized in Kazan city. HFRS patients infected with PUUV strains of either RUS or FIN genetic lineages were observed to have consistent differences in clinical presentation of the disease and laboratory findings. These findings indicated a strong genetic link between the infected bank voles and human HFRS cases from the same localities. Thus, S-segment sequences of the PUUV strains isolated from HFRS patients could serve as a molecular marker for determining the likely geographic area where infection occurred.

Genetic Diversity of Artybash Virus in the Laxmann's Shrew (Sorex caecutiens)

Although based on very limited M and L segment sequences, Artybash virus (ARTV) was proposed previously as a unique hantavirus harbored by the Laxmann's shrew (Sorex caecutiens). To verify this conjecture, lung tissues from 68 Laxmann's shrews, captured during 2006 to 2014 in eastern Siberia, Russia, and Hokkaido, Japan, were analyzed for ARTV RNA using reverse transcription polymerase chain reaction (RT-PCR). ARTV RNA was detected in six Laxmann's shrews. Pairwise alignment and comparison of partial- and full-length S, M, and L segment sequences from these Laxmann's shrews, as well as phylogenetic analyses, using maximum likelihood and Bayesian methods indicated that ARTV was distinct from other soricine shrew-borne hantaviruses and representative hantaviruses harbored by rodents, moles, and bats. Taxonomic identity of the ARTV-infected Laxmann's shrews was confirmed by full-length cytochrome b mitochondrial DNA sequence analysis. Our data indicate that the hantavirus previously known as Amga virus (MGAV) represents genetic variants of ARTV. Thus, the previously proposed designation of ARTV/MGAV should be replaced by ARTV.

Genetic variants of Cao Bang hantavirus in the Chinese mole shrew (Anourosorex squamipes) and Taiwanese mole shrew (Anourosorex yamashinai)

To determine the genetic diversity and geographic distribution of Cao Bang virus (CBNV) and to ascertain the existence of CBNV-related hantaviruses, natural history collections of archival tissues from Chinese mole shrews (Anourosorex squamipes) and Taiwanese mole shrews (Anourosorex yamashinai), captured in Guizho Province, People's Republic of China, and in Nantou County, Taiwan, in 2006 and 1989, respectively, were analyzed for hantavirus RNA by RT-PCR. Pair-wise alignment and comparison of the S-, M- and L-segment sequences indicated CBNV in two of five Chinese mole shrews and a previously unrecognized hantavirus, named Xinyi virus (XYIV), in seven of 15 Taiwanese mole shrews. XYIV was closely related to CBNV in Vietnam and China, as well as to Lianghe virus (LHEV), recently reported as a distinct hantavirus species in Chinese mole shrews from Yunnan Province in China. Phylogenetic analyses, using maximum-likelihood and Bayesian methods, showed that XYIV shared a common ancestry with CBNV and LHEV, in keeping with the evolutionary relationship between Anourosorex mole shrews. Until such time that tissue culture isolates of CBNV, LHEV and XYIV can be fully analyzed, XYIV and LHEV should be regarded as genetic variants, or genotypes, of CBNV.

Complete mitochondrial genome of the gray red-backed vole (Myodes rufocanus) and a complete estimate of the phylogenetic relationships in Cricetidae

Myodes rufocanus belongs to the genera Myodes within the subfamily Cricetidae, its complete mitochondrial genome is 16 487 bp in length, containing 12S rRNA gene, 16S rRNA gene, 22 tRNA genes, 13 protein-coding genes and 1 control region as other Cricetidae species. Results of phylogenetic analysis showed that Myodes had close relationship with Eothenomys, and had distant relationship with Microtus, Cricetulus, Wiedomys, Akodon and other genera. This study verifies the evolutionary status of Myodes rufocanus in Myodes at the molecular level. The mitochondrial genome would be a significant supplement for the M. rufocanus genetic background analysis and experimental animalization.