Expanded host diversity and geographic distribution of hantaviruses in sub-Saharan Africa

Divergent Hantavirus in Somali Shrews (Crocidura somalica) in the Semi-Arid North Rift, Kenya

Hantaviruses are zoonotic rodent-borne viruses that are known to infect humans and cause various symptoms of disease, including hemorrhagic fever with renal and cardiopulmonary syndromes. They have a segmented single-stranded, enveloped, negative-sense RNA genome and are widely distributed. This study aimed to investigate the circulation of rodent-borne hantaviruses in peridomestic rodents and shrews in two semi-arid ecologies within the Kenyan Rift Valley. The small mammals were trapped using baited folding Sherman traps set within and around houses, then they were sedated and euthanatized through cervical dislocation before collecting blood and tissue samples (liver, kidney, spleen, and lungs). Tissue samples were screened with pan-hantavirus PCR primers, targeting the large genome segment (L) encoding the RNA-dependent RNA polymerase (RdRp). Eleven of the small mammals captured were shrews (11/489, 2.5%) and 478 (97.5%) were rodents. A cytochrome b gene-based genetic assay for shrew identification confirmed the eleven shrews sampled to be Crocidura somalica. Hantavirus RNA was detected in three (3/11, 27%) shrews from Baringo County. The sequences showed 93-97% nucleotide and 96-99% amino acid identities among each other, as well as 74-76% nucleotide and 79-83% amino acid identities to other shrew-borne hantaviruses, such as Tanganya virus (TNGV). The detected viruses formed a monophyletic clade with shrew-borne hantaviruses from other parts of Africa. To our knowledge, this constitutes the first report published on the circulation of hantaviruses in shrews in Kenya.

Pending Reorganization of Hantaviridae to Include Only Completely Sequenced Viruses: A Call to Action

The official classification of newly discovered or long-known unassigned viruses by the International Committee on Taxonomy of Viruses (ICTV) requires the deposition of coding-complete or -near-complete virus genome sequences in GenBank to fulfill a requirement of the taxonomic proposal (TaxoProp) process. However, this requirement is fairly new; thus, genomic sequence information is fragmented or absent for many already-classified viruses. As a result, taxon-wide modern phylogenetic analyses are often challenging, if not impossible. This problem is particularly eminent among viruses with segmented genomes, such as bunyavirals, which were frequently classified solely based on single-segment sequence information. To solve this issue for one bunyaviral family, Hantaviridae, we call on the community to provide additional sequence information for incompletely sequenced classified viruses by mid-June 2023. Such sequence information may be sufficient to prevent their possible declassification during the ongoing efforts to establish a coherent, consistent, and evolution-based hantavirid taxonomy.

Kiwira Virus, a Newfound Hantavirus Discovered in Free-tailed Bats (Molossidae) in East and Central Africa

A novel hantavirus, named Kiwira virus, was molecularly detected in six Angolan free-tailed bats (Mops condylurus, family Molossidae) captured in Tanzania and in one free-tailed bat in the Democratic Republic of Congo. Hantavirus RNA was found in different organs, with the highest loads in the spleen. Nucleotide sequences of large parts of the genomic S and L segments were determined by in-solution hybridisation capture and high throughput sequencing. Phylogenetic analyses placed Kiwira virus into the genus Mobatvirus of the family Hantaviridae, with the bat-infecting Quezon virus and Robina virus as closest relatives. The detection of several infected individuals in two African countries, including animals with systemic hantavirus infection, provides evidence of active replication and a stable circulation of Kiwira virus in M. condylurus bats and points to this species as a natural host. Since the M. condylurus home range covers large regions of Sub-Saharan Africa and the species is known to roost inside and around human dwellings, a potential spillover of the Kiwira virus to humans must be considered.

Multiple Mammarenaviruses Circulating in Angolan Rodents

Rodents are a speciose group of mammals with strong zoonotic potential. Some parts of Africa are still underexplored for the occurrence of rodent-borne pathogens, despite this high potential. Angola is at the convergence of three major biogeographical regions of sub-Saharan Africa, each harbouring a specific rodent community. This rodent-rich area is, therefore, strategic for studying the diversity and evolution of rodent-borne viruses. In this study we examined 290 small mammals, almost all rodents, for the presence of mammarenavirus and hantavirus RNA. While no hantavirus was detected, we found three rodent species positive for distinct mammarenaviruses with a particularly high prevalence in Namaqua rock rats (Micaelamys namaquensis). We characterised four complete virus genomes, which showed typical mammarenavirus organisation. Phylogenetic and genetic distance analyses revealed: (i) the presence of a significantly divergent strain of Luna virus in Angolan representatives of the ubiquitous Natal multimammate mouse (Mastomys natalensis), (ii) a novel Okahandja-related virus associated with the Angolan lineage of Micaelamys namaquensis for which we propose the name Bitu virus (BITV) and (iii) the occurrence of a novel Mobala-like mammarenavirus in the grey-bellied pygmy mouse (Mus triton) for which we propose the name Kwanza virus (KWAV). This high virus diversity in a limited host sample size and in a relatively small geographical area supports the idea that Angola is a hotspot for mammarenavirus diversity.

How accurately can we assess zoonotic risk?

Identifying the animal reservoirs from which zoonotic viruses will likely emerge is central to understanding the determinants of disease emergence. Accordingly, there has been an increase in studies attempting zoonotic “risk assessment.” Herein, we demonstrate that the virological data on which these analyses are conducted are incomplete, biased, and rapidly changing with ongoing virus discovery. Together, these shortcomings suggest that attempts to assess zoonotic risk using available virological data are likely to be inaccurate and largely only identify those host taxa that have been studied most extensively. We suggest that virus surveillance at the human–animal interface may be more productive.

Determining which organisms harbour viruses that could potentially infect humans is of great topical interest. This Essay demonstrates that the data on which such zoonotic risk assessments are conducted are incomplete, biased, and rapidly changing with ongoing virus discovery.

Genetic Diversity and Phylogeography of Thottapalayam thottimvirus (Hantaviridae) in Asian House Shrew (Suncus murinus) in Eurasia

Murid and cricetid rodents were previously believed to be the principal reservoir hosts of hantaviruses. Recently, however, multiple newfound hantaviruses have been discovered in shrews, moles, and bats, suggesting a complex evolutionary history. Little is known about the genetic diversity and geographic distribution of the prototype shrew-borne hantavirus, Thottapalayam thottimvirus (TPMV), carried by the Asian house shrew (Suncus murinus), which is widespread in Asia, Africa, and the Middle East. Comparison of TPMV genomic sequences from two Asian house shrews captured in Myanmar and Pakistan with TPMV strains in GenBank revealed that the Myanmar TPMV strain (H2763) was closely related to the prototype TPMV strain (VRC66412) from India. In the L-segment tree, on the other hand, the Pakistan TPMV strain (PK3629) appeared to be the most divergent, followed by TPMV strains from Nepal, then the Indian-Myanmar strains, and finally TPMV strains from China. The Myanmar strain of TPMV showed sequence similarity of 79.3-96.1% at the nucleotide level, but the deduced amino acid sequences showed a high degree of conservation of more than 94% with TPMV strains from Nepal, India, Pakistan, and China. Cophylogenetic analysis of host cytochrome b and TPMV strains suggested that the Pakistan TPMV strain was mismatched. Phylogenetic trees, based on host cytochrome b and cytochrome c oxidase subunit I genes of mitochondrial DNA, and on host recombination activating gene 1 of nuclear DNA, suggested that the Asian house shrew and Asian highland shrew (Suncus montanus) comprised a species complex. Overall, the geographic-specific clustering of TPMV strains in Asian countries suggested local host-specific adaptation. Additional in-depth studies are warranted to ascertain if TPMV originated in Asian house shrews on the Indian subcontinent.

Genetic diversity and evolution of Hantaan virus in China and its neighbors

BACKGROUND

Hantaan virus (HTNV; family Hantaviridae, order Bunyavirales) causes hemorrhagic fever with renal syndrome (HFRS), which has raised serious concerns in Eurasia, especially in China, Russia, and South Korea. Previous studies reported genetic diversity and phylogenetic features of HTNV in different parts of China, but the analyses from the holistic perspective are rare.

METHODOLOGY AND PRINCIPAL FINDINGS

To better understand HTNV genetic diversity and gene evolution, we analyzed all available complete sequences derived from the small (S) and medium (M) segments with bioinformatic tools. Eleven phylogenetic groups were defined and showed geographic clustering; 42 significant amino acid variant sites were found, and 19 of them were located in immune epitopes; nine recombinant events and eight reassortments with highly divergent sequences were found and analyzed. We found that sequences from Guizhou showed high genetic divergence, contributing to multiple lineages of the phylogenetic tree and also to the recombination and reassortment events. Bayesian stochastic search variable selection analysis revealed that Heilongjiang, Shaanxi, and Guizhou played important roles in HTNV evolution and migration; the virus may originate from Zhejiang Province in the eastern part of China; and the virus population size expanded from the 1980s to 1990s.

CONCLUSIONS/SIGNIFICANCE

These findings revealed the original and evolutionary features of HTNV, which will help to illustrate hantavirus epidemic trends, thus aiding in disease control and prevention.

Highly Divergent Genetic Variants of Soricid-Borne Altai Virus (Hantaviridae) in Eurasia Suggest Ancient Host-Switching Events

With the recent discovery of genetically distinct hantaviruses (family Hantaviridae) in shrews (order Eulipotyphla, family Soricidae), the once-conventional view that rodents (order Rodentia) served as the primordial reservoir hosts now appears improbable. The newly identified soricid-borne hantaviruses generally demonstrate well-resolved lineages organized according to host taxa and geographic origin. However, beginning in 2007, we detected sequences that did not conform to the prototypic hantaviruses associated with their soricid host species and/or geographic locations. That is, Eurasian common shrews (Sorexaraneus), captured in Hungary and Russia, were found to harbor hantaviruses belonging to two separate and highly divergent lineages. We have since accumulated additional examples of these highly distinctive hantavirus sequences in the Laxmann's shrew (Sorexcaecutiens), flat-skulled shrew (Sorexroboratus) and Eurasian least shrew (Sorexminutissimus), captured at the same time and in the same location in the Sakha Republic in Far Eastern Russia. Pair-wise alignment and phylogenetic analysis of partial and full-length S-, M- and/or L-segment sequences indicate that a distinct hantavirus species related to Altai virus (ALTV), first reported in a Eurasian common shrew from Western Siberia, was being maintained in these closely related syntopic soricine shrew species. These findings suggest that genetic variants of ALTV might have resulted from ancient host-switching events with subsequent diversification within the Soricini tribe in Eurasia.

Tigray Orthohantavirus Infects Two Related Rodent Species Adapted to Different Elevations in Ethiopia

Orthohantaviruses are RNA viruses that some members are known to cause severe zoonotic diseases in humans. Orthohantaviruses are hosted by rodents, soricomorphs (shrews and moles), and bats. Only two orthohantaviruses associated with murid rodents are known in Africa, Sangassou orthohantavirus (SANGV) in two species of African wood mice (Hylomyscus), and Tigray orthohantavirus (TIGV) in the Ethiopian white-footed rat (Stenocephalemys albipes). In this article, we report evidence that, like SANGV, two strains of TIGV occur in two genetically related rodent species, S. albipes and S. sp. A, occupying different elevational zones in the same mountain. Investigating the other members of the genus Stenocephalemys for TIGV could reveal the real diversity of TIGV in the genus.

Molecular taxonomy of Crocidura species (Eulipotyphla: Soricidae) in a key biogeographical region for African shrews, Nigeria

The taxonomy of African shrew species is still unresolved due to their conserved morphology. This also affects knowledge concerning their geographic distribution. In Nigeria, using mitochondrial Cytochrome b gene sequences, we carried out a survey for shrews from the genus Crocidura across various ecological zones to determine taxa that are present and also to assess their phylogeographic structure. Our analyses include 183 specimens collected with Sherman traps from 19 localities around the country. We detected six taxa: Crocidura olivieri lineages II, III and IV, C. hildegardeae, C. jouvenetae, and C. foxi. Among these, C. hildegardeae and C. jouvenetae are reported in Nigeria for the first time. Phylogenetic comparison of our genetic sequences to those generated from other parts of Africa demonstrate that all species in our study, as currently defined, are in need of taxonomic revision. Geographically, Nigeria seems to represent the easternmost boundary for C. olivieri lineage II and C. jouvenetae, and the western distribution limit of C. olivieri lineage IV and C. hildegardeae. The Niger River appears to be the most significant topographical barrier restricting these taxa. This information is vital to preserving the diversity but also managing the epidemiological potential of these small mammals.

Molecular Phylogeny of Mobatviruses (Hantaviridae) in Myanmar and Vietnam

The discovery of highly divergent lineages of hantaviruses (family Hantaviridae) in shrews, moles, and bats of multiple species raises the possibility that non-rodent hosts may have played a significant role in their evolutionary history. To further investigate this prospect, total RNA was extracted from RNAlater®-preserved lung tissues of 277 bats (representing five families, 14 genera and 40 species), captured in Myanmar and Vietnam during 2013⁻2016. Hantavirus RNA was detected in two of 15 black-bearded tomb bats (Taphozous melanopogon) and two of 26 Pomona roundleaf bats (Hipposideros pomona) in Myanmar, and in three of six ashy leaf-nosed bats (Hipposideros cineraceus) in Vietnam. Pair-wise alignment and comparison of coding regions of the S, M, and L segments of hantaviruses from Taphozous and Hipposideros bats revealed high nucleotide and amino acid sequence similarities to prototype Láibīn virus (LAIV) and Xuân Sơn virus (XSV), respectively. Phylogenetic analyses, generated by maximum-likelihood and Bayesian methods, showed a geographic clustering of LAIV strains from China and Myanmar, but not of XSV strains from China and Vietnam. These findings confirm that the black-bearded tomb bat is the natural reservoir of LAIV, and that more than one species of Hipposideros bats can host XSV.

Complete genome characterisation and phylogenetic position of Tigray hantavirus from the Ethiopian white-footed mouse, Stenocephalemys albipes

Hantaviruses, well-known human pathogens, have only recently been identified on the African continent. Tigray virus (TIGV) was found in Ethiopia in 2012 in a Murinae species, Stenocephalemys albipes, but the genetic data obtained at that time were too limited to correctly assess its phylogenetic position within the hantavirus tree. We used high throughput sequencing to determine the complete genome of TIGV, which showed a typical hantavirus organisation. The large (L), medium (M), and small (S) genome segments were found to be 6532, 3594 and 1908 nucleotides long, respectively, and the 5' and 3' termini for all three segments were predicted to form the panhandle-like structure typical for bunyaviruses. Nucleotide-based phylogenetic analyses revealed that all three coding segments cluster in the phylogroup III sensu Guo et al. (2013). However, while TIGV S segment is basal to the Murinae-associated hantaviruses, the M and L segments are basal to the Soricomorpha-associated hantaviruses. TIGV is the first Murinae-borne hantavirus showing this inconsistent segmental clustering in the hantavirus phylogenetic tree. We finally propose non-exclusive scenarios that could explain the original phylogenetic position of TIGV.

Human Infections by Non-Rodent-Associated Hantaviruses in Africa

Various hantaviruses have been discovered in unconventional hosts (shrews and bats) in Africa. Up to now, it was unknown whether these viruses pose a threat for human health. In this study, using newly established serological assays, we demonstrated evidence of shrew-borne hantavirus infections in humans from Côte d'Ivoire and Gabon.

Molecular phylogeny of a genetically divergent hantavirus harbored by the Geoffroy's rousette (Rousettus amplexicaudatus), a frugivorous bat species in the Philippines

The recent discovery of genetically distinct hantaviruses in multiple species of shrews and moles (order Eulipotyphla, families Soricidae and Talpidae) prompted a further exploration of their host diversification and geographic distribution by analyzing lung tissues from 376 fruit bats representing six genera (order Chiroptera, suborder Yinpterochiroptera, family Pteropodidae), collected in the Republic of the Philippines during 2008 to 2013. Hantavirus RNA was detected by RT-PCR in one of 15 Geoffroy's rousettes (Rousettus amplexicaudatus), captured in Quezon Memorial National Park on Luzon Island in 2009. Phylogenetic analyses of the S, M and L segments, using maximum-likelihood and Bayesian methods, showed that the newfound hantavirus, designated Quezon virus (QZNV), shared a common ancestry with hantaviruses hosted by insectivorous bats, in keeping with their evolutionary relationships and suggests that ancestral bats may have served as the early or original mammalian hosts of primordial hantaviruses. As the first hantavirus detected in a megabat or flying fox species, QZNV extends our knowledge about the reservoir host range.

Dahonggou Creek virus, a divergent lineage of hantavirus harbored by the long-tailed mole (Scaptonyx fusicaudus)

Novel hantaviruses, recently detected in moles (order Eulipotyphla, family Talpidae) from Europe, Asia, and North America would predict a broader host range and wider ecological diversity. Employing RT-PCR, archival frozen tissues from the Chinese shrew mole (Uropsilus soricipes), broad-footed mole (Scapanus latimanus), coast mole (Scapanus orarius), Townsend’s mole (Scapanus townsendii), and long-tailed mole (Scaptonyx fusicaudus) were analyzed for hantavirus RNA. Following multiple attempts, a previously unrecognized hantavirus, designated Dahonggou Creek virus (DHCV), was detected in a long-tailed mole, captured in Shimian County, Sichuan Province, People’s Republic of China, in August 1989. Analyses of a 1058-nucleotide region of the RNA-dependent RNA polymerase-encoding L segment indicated that DHCV was genetically distinct from other rodent-, shrew-, mole-, and bat-borne hantaviruses. Phylogenetic trees, using maximum likelihood and Bayesian methods, showed that DHCV represented a divergent lineage comprising crocidurine and myosoricine shrew-borne hantaviruses. Although efforts to obtain the S- and M-genomic segments failed, the L-segment sequence analysis, reported here, expands the genetic database of non-rodent-borne hantaviruses. Also, by further mining natural history collections of archival specimens, the genetic diversity of hantaviruses will elucidate their evolutionary origins.

Sin Nombre hantavirus nucleocapsid protein exhibits a metal-dependent DNA-specific endonucleolytic activity

We demonstrate that the nucleocapsid protein of Sin Nombre hantavirus (SNV-N) has a DNA-specific endonuclease activity. Upon incubation of SNV-N with DNA in the presence of magnesium or manganese, we observed DNA digestion in sequence-unspecific manner. In contrast, RNA was not affected under the same conditions. Moreover, pre-treatment of SNV-N with RNase before DNA cleavage increased the endonucleolytic activity. Structure-based protein fold prediction using known structures from the PDB database revealed that Asp residues in positions 88 and 103 of SNV-N show sequence similarity with the active site of the restriction endonuclease HindIII. Crystal structure of HindIII predicts that residues Asp93 and Asp108 are essential for coordination of the metal ions required for HindIII DNA cleavage. Therefore, we hypothesized that homologous residues in SNV-N, Asp88 and Asp103, may have a similar function. Replacing Asp88 and Asp103 by alanine led to an SNV-N protein almost completely abrogated for endonuclease activity.

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.

Isolation and partial characterization of a highly divergent lineage of hantavirus from the European mole (Talpa europaea)

Genetically distinct hantaviruses have been identified in five species of fossorial moles (order Eulipotyphla, family Talpidae) from Eurasia and North America. Here, we report the isolation and partial characterization of a highly divergent hantavirus, named Nova virus (NVAV), from lung tissue of a European mole (Talpa europaea), captured in central Poland in August 2013. Typical hantavirus-like particles, measuring 80-120 nm in diameter, were found in NVAV-infected Vero E6 cells by transmission electron microscopy. Whole-genome sequences of the isolate, designated NVAV strain Te34, were identical to that amplified from the original lung tissue, and phylogenetic analysis of the full-length L, M and S segments, using maximum-likelihood and Bayesian methods, showed that NVAV was most closely related to hantaviruses harbored by insectivorous bats, consistent with an ancient evolutionary origin. Infant Swiss Webster mice, inoculated with NVAV by the intraperitoneal route, developed weight loss and hyperactivity, beginning at 16 days, followed by hind-limb paralysis and death. High NVAV RNA copies were detected in lung, liver, kidney, spleen and brain by quantitative real-time RT-PCR. Neuropathological examination showed astrocytic and microglial activation and neuronal loss. The first mole-borne hantavirus isolate will facilitate long-overdue studies on its infectivity and pathogenic potential in humans.

The evolution and emergence of hantaviruses

Hantaviruses are a major class of zoonotic pathogens and cause a variety of severe diseases in humans. For most of the last 50 years rodents have been considered to be the primary hosts of hantaviruses, with hantavirus evolution thought to reflect a process of virus-rodent co-divergence over a time-scale of millions of years, with occasional spill-over into humans. However, recent discoveries have revealed that hantaviruses infect a more diverse range of mammalian hosts, particularly Chiroptera (bats) and Soricomorpha (moles and shrews), and that cross-species transmission at multiple scales has played an important role in hantavirus evolution. As a consequence, the evolution and emergence of hantaviruses is more complex than previously anticipated, and may serve as a realistic model for other viral groups.

Reconstructing the evolutionary origins and phylogeography of hantaviruses

Rodents have long been recognized as the principal reservoirs of hantaviruses. However, with the discovery of genetically distinct and phylogenetically divergent lineages of hantaviruses in multiple species of shrews, moles, and insectivorous bats from widely separated geographic regions, a far more complex landscape of hantavirus host distribution, evolution, and phylogeography is emerging. Detailed phylogenetic analyses, based on partial and full-length genomes of previously described rodent-borne hantaviruses and newly detected non-rodent-borne hantaviruses, indicate an Asian origin and support the emerging concept that ancestral non-rodent mammals may have served as the hosts of primordial hantaviruses.