Phylogeny and origins of hantaviruses harbored by bats, insectivores, and rodents

Epidemiology and genetic diversity of pathogenic Leptospira among Rattus norvegicus in urban residential areas of Guangzhou, Southern China

Leptospirosis, a zoonotic disease caused by pathogenic Leptospira spirochetes, poses a significant global public health threat. Rodents, particularly those inhabiting urban environments, are recognized as the primary reservoirs for human infections. Therefore, conducting epidemiological studies on pathogenic Leptospira in urban rodent populations is essential for evaluating the risk of human leptospirosis. In this study, we captured 263 Rattus norvegicus from urban residential areas across five districts in Guangzhou to access the prevalence and genetic diversity of pathogenic Leptospira. Our findings revealed the presence of two pathogenic Leptospira species, L. interrogans and L. borgpetersenii, which are the primary pathogens responsible for human leptospirosis in China, in four of the five districts, with an overall prevalence of 10.3 %. Given the close proximity of R. norvegicus to human populations in urban areas, this significant prevalence of pathogenic Leptospira indicates an elevated risk of leptospirosis outbreaks among residents of Guangzhou. These results highlight the urgent need for ongoing monitoring of pathogenic Leptospira infections in urban rodent populations to prevent and control potential outbreaks of leptospirosis in the city.

Effect of Land-Use on Hantavirus Infection Among Introduced and Endemic Small Mammals of Madagascar

Hantaviruses are globally distributed zoonotic pathogens capable of causing fatal disease in humans. Addressing the risk of hantavirus spillover from animal reservoirs to humans requires identifying the local reservoirs (usually rodents and other small mammals) and the predictors of infection, such as habitat characteristics and human exposure. We screened a collection of 1663 terrestrial small mammals and 227 bats for hantavirus RNA, comprised of native and non-native species from northeastern Madagascar, trapped over 5 successive years. We specifically investigated the influence of diverse habitat types: villages, agricultural fields, regrowth areas, secondary and semi-intact forests on infection with hantaviruses. We detected Hantavirus RNA closely related to the previously described Anjozorobe virus in 9.5% of Rattus rattus sampled, with an absence of detection in other species. Land-use had a complex impact on hantavirus infections: intensive land-use positively correlated with the abundance of R. rattus and the average R. rattus body size varied between habitats. Larger individuals had a higher probability of infection, regardless of sex. Thus, villages and pristine forests which host the smallest, and hence, least infected rats, represent the lowest risk for hantavirus exposure to people while flooded rice fields which were home to the largest rats, and subsequently most infected rats, represent the greatest exposure risk. These findings provide new insights into the relationship between rat ecology and the gradients of hantavirus exposure risk for farmers in northeastern Madagascar as they work in different land-use types.

Detection of Brno loanvirus (Loanvirus brunaense) in common noctule bats (Nyctalus noctula) in Southern Russia

Hantaviruses that infect humans are rodent-derived viruses with zoonotic potential. Several studies show that before emerging in rodents hantaviruses could emerge in bats, which makes it important to study bat-derived hantaviruses. In this study, we performed PCR screening of hantaviruses in samples from common noctules (Nyctalus noctula [182 fecal and 81 blood serum samples]), parti-coloured bats (Vespertilio murinus [41 fecal samples]), Kuhl's pipistrelles (Pipistrellus kuhlii [15 fecal samples]), and serotine bats (Eptesicus serotinus [8 fecal samples]) from Rostov Bat Rehabilitation Center (Rostov-on-Don, Russia) and phylogenetic analysis of detected viruses. As a result, hantaviruses were detected in samples from N. noctula bats with an overall prevalence of 4.94% (4/81, 95% CI 0.22-9.66%) in blood serum samples and 1.1% (2/182, 95% CI 0-2.61%) in fecal samples. Phylogenetic analysis revealed that detected hantaviruses are highly homologic to Brno loanviruses (Loanvirus brunaense) previously discovered in N. noctula bats from Central Europe, which brings some evidence that these are the same bat-derived viruses. This study shows that Loanvirus brunaense could be species-specific to the host and has a wide area of habitat: from Central Europe to Southern Russia. These are the first findings of this virus in Southern Russia and Ciscaucasus/Fore-Caucasus. Further studies with wider screening and genomic assays of Loanvirus brunaense in bats could reveal trends in the molecular evolution of hantaviruses and provide valuable data for the control of potential spillovers.

Emergence of a novel porcine pestivirus with potential for cross-species transmission in China, 2023

Pestiviruses, RNA viruses belonging to the Flaviviridae family, have a broad host range. Their pathogenicity varies greatly and they have caused significant economic losses in animal husbandry. In this study, a novel pestivirus, porcine abortion-associated pestivirus (PAAPeV), was isolated from pigs in China in 2023. Clinically, PAAPeV causes abortions in sows and leads to congenital tremors and death in piglets. PAAPeV replicates efficiently in ST cells. Morphologically, PAAPeV virions are spherical particles with a diameter of approximately 80 nm. Phylogenetic analysis reveals that PAAPeV is closely related to Wenzhou Pipistrellus abramus pestivirus and clusters into a distinct branch, suggesting that it represents a new species: Pestivirus chinensis. Animal experiments demonstrated that PAAPeV-infected piglets and mice exhibit significant histopathological changes. In piglets, histopathological examination revealed myocarditis, hepatitis, glial vacuolation and cerebrovascular inflammation. In mice, findings included hepatic monocyte aggregation, glomerular atrophy, pulmonary edema, inflammatory cell infiltration, and capillary dilation. Viremia has been detected in both piglets and mice, with high viral genome loads found in various organs. In vitro results revealed that PAAPeV replicates in ST cells and, to a lesser extent, in human (A549 and HepG2) and monkey (Vero) cells. Overall, PAAPeV infects both pigs and mice and has the potential to infect other mammals, indicating its ability for cross-species transmission. This poses significant risks to the pig industry and public health. Strengthening monitoring and prevention efforts for PAAPeV is crucial. Our findings greatly increase the understanding of pestivirus diversity and its broader pathogen spectrum.

Epidemiological surveillance and phylogenetic diversity of Orthohantavirus hantanense using high-fidelity nanopore sequencing, Republic of Korea

BACKGROUND

Orthohantavirus hantanense (HTNV) poses a substantial global public health threat due to its role in causing hemorrhagic fever with renal syndrome (HFRS). HTNV outbreaks are particularly prevalent in the Gyeonggi and Gangwon Provinces of the Republic of Korea (ROK). This study aimed to evaluate the application of advanced nanopore sequencing and bioinformatics to generate complete genome sequences of HTNV, with the objective of accurately identifying infection sources and analyzing their genetic diversity.

METHODOLOGY/PRINCIPAL FINDINGS

In 2022 and 2023, we collected 579 small mammals from 11 distinct locations across Gyeonggi and Gangwon Provinces, as well as in Gwangju Metropolitan City, ROK. Among these, 498 Apodemus agrarius specimens were subjected to an epidemiological survey to investigate HTNV infections. The serological and molecular positivity of HTNV were found to be 65/498 (13.1%) and 17/65 (26.2%), respectively. Furthermore, 15 whole-genome sequences of HTNV were obtained from rodents in Gyeonggi and Gangwon Provinces. We developed a novel amplicon-based nanopore sequencing approach to acquire high-fidelity and precise genomic sequences of HTNV. Genome exchange analysis revealed three reassortant candidates, including heterogeneous L segments, from Paju-si and Yeoncheon-gun in Gyeonggi Province.

CONCLUSION/SIGNIFICANCE

Our findings enhance the resolution of the spatiotemporal genomic surveillance of HTNV by consistently providing new viral sequences and epidemiological data from HFRS-endemic regions in the ROK. This report signifies a notable advancement in nanopore sequencing techniques and bioinformatics, offering a robust platform for genome-based diagnostics and sophisticated phylogenetic analyses of orthohantaviruses, which are essential for public health strategies aimed at controlling HFRS.

Identification and epidemiological analysis of a putative novel hantavirus in Australian flying foxes

In July 2017, an investigation into the cause of neurological signs in a black flying fox (Pteropus alecto, family Pteropodidae) identified a putative novel hantavirus (Robina virus, ROBV, order Bunyavirales, family Hantaviridae, genus Mobatvirus) in its brain. Analysis of the evolutionary relationship between other hantaviruses using maximum-likelihood, a systematic Bayesian clustering approach, and a minimum spanning tree, all suggest that ROBV is most closely related to another Mobatvirus, Quezon virus, previously identified in the lung of a Philippine frugivorous bat (Rousettus amplexicaudatus, also family Pteropodidae). Subsequently, between March 2018 and October 2023, a total of 495 bats were opportunistically screened for ROBV with an experimental qRT-PCR. The total prevalence of ROBV RNA detected in Pteropus spp. was 4.2% (95% CI 2.8-6.4%). Binomial modelling identified that there was substantial evidence supporting an increase (P = 0.033) in the detection of ROBV RNA in bats in 2019 and 2020 suggesting of a possible transient epidemic. There was also moderate evidence to support the effect of season (P = 0.064), with peak detection in the cooler seasons, autumn, and winter, possibly driven by physiological and ecological factors similar to those already identified for other bat-borne viruses. This is Australia's first reported putative hantavirus and its identification could expand the southern known range of hantaviruses in Australasia.

Epidemiological characteristics and genetic diversity of Bartonella species from rodents in Guangxi Zhuang autonomous region, Southwestern China

Bartonella spp. are gram-negative bacteria recognized as zoonotic pathogens of wide spectrum mammals. Rodents are recognized as a natural reservoir of pathogens, and many Bartonella species transmitted by various blood-sucking arthropods have been detected in various rodents populations. In Guangxi Zhuang Autonomous Region, humans have a habit of preying on rodents, however, data on the genetic diversity of Bartonella are still absent. Investigating the epidemiological characteristics of Bartonella infection in rodents is of great significance for the prevention and control of human Bartonellosis. In this study, rodents were captured to monitor the prevalence of Bartonella in four cities in Guangxi Zhuang Autonomous Region, Southwestern China. Six species of Bartonella, including three confirmed zoonotic species, were detected based on the rrs gene with an overall prevalence of 11.5 % (32/278) in rodents. Bartonella tribocorum (21/32, 65.6 %) was the predominant species among the three zoonotic Bartonella species. In addition, phylogenetic and genetic analyses of the rrs, gltA, and rpoB genes indicated that the strains were divided into distinct clade within the same rodent, suggesting the co-circulating of diverse genetic genotypes of Bartonella species. These results provide insights into the prevalence and genetic diversity of Bartonella species circulating in rodents in Guangxi Zhuang Autonomous Region, and also urged the surveillance of rodent-associated Bartonella species in these areas.

Effects of climate change on the distribution of Molossus molossus and the potential risk of Orthohantavirus transmission in the Neotropical region

Molossus molossus is a widely distributed neotropical bat species in the Americas, often found in urban areas. This study evaluated climate change effects on the potential geographic distribution of M. molossus, a natural host of zoonotic pathogens such as Orthohantavirus, in the Neotropical region. Using ecological niche modeling (ENM), models were generated for current (1970-2000) and future (2070) climate scenarios based on two Shared Socioeconomic Pathways (SSP2-4.5 and SSP5-8.5) and two Global Circulation Models (MPI-ESM1-2-LR and IPSL-CM6A-LR). Results indicated that in the current scenario, warm and coastal areas of the Neotropics are suitable for M. molossus occurrence. Risk areas for Orthohantavirus transmission were mapped by overlapping the probability of urban expansion with projections of climatic suitability for the bat. For both future scenarios (2070), projections indicate an expansion of suitable climatic areas for M. molossus over urban expansion zones, specifically in Brazil, Paraguay, Peru, Ecuador, Costa Rica, Honduras, El Salvador, Guatemala, Belize, Mexico, the United States, Cuba, Haiti, the Dominican Republic, and Puerto Rico. However, projections also indicate the Lesser Antilles under climate threat, considering that no climatic suitability areas will remain. These findings provide important information for planning surveillance and mitigation actions for zoonotic risks associated with M. molossus, considering climate change impacts on its geographic distribution in the Neotropical region.

Comparative genomics and evolutionary analysis of dengue virus strains circulating in Pakistan

Dengue fever virus (DENV) poses a significant public health risk in tropical and subtropical regions across the world. Although the dengue fever virus (DENV) exhibits significant genetic diversity and has the potential to evolve, there is a lack of comprehensive research on the comparative genomics and evolutionary dynamics of the virus in Pakistan. Phylogenetic analysis demonstrated the circulation of all four dengue virus serotypes (DENV-1, - 2, - 3, and - 4) with prevalent genotypes III and V within DENV-1, cosmopolitan genotype within DENV-2, genotype III within DENV-3, and genotype I within DENV-4 during 2006-2014. Based on the complete envelope region, genome-wide residue signature and genetic diversity indicate that there is a high level of genetic diversity among DENV-1 strains, while DENV-3 strains exhibit the least genetic diversity. Comparative analysis of all four DENV serotypes revealed that certain codons in DENV-2 and -4 were subject to strong purifying selection, while a few codon sites in the envelope region showed evidence of positive selection. These findings provided valuable insights into the comparative genomics and evolutionary pattern of DENV strains reported from Pakistan. Whether those characteristics conferred a fitness advantage to DENV-1 genotypes within a specific geography and time interval warrants further investigations. The findings of the current study will contribute to tracking disease dynamics, understanding virus transmission and evolution, and formulating effective disease control strategies.

Integrating animal welfare into the WHO pandemic treaty: a thematic analysis of civil society perspectives and comparison with treaty drafting

The COVID-19 pandemic has exposed critical weaknesses in the global health system, highlighting the urgent need for a coordinated international approach to pandemic prevention and management. As negotiations for a new WHO pandemic treaty progress, the effective integration of animal welfare is crucial. This paper aims to investigate the perspectives of key civil society organizations on the integration of animal welfare provisions into the pandemic treaty. Through a thematic analysis of documents prepared by FOUR PAWS, Wildlife Conservation Society, and Action for Animal Health between 2020-2023, five major themes are identified: prevention of zoonotic spillover, One Health approach, animal health systems and infrastructure, sustainable and ethical animal management practices, and policy coherence and governance. A comparative analysis of these themes against the April 2024 draft of the pandemic treaty reveals areas of alignment and divergence. Due to the ongoing controversies and the need for further improvements, the WHO's intergovernmental negotiating body was unable to finalize the treaty text for the 77th World Health Assembly in May 2024, leading to an extended mandate until 2025. Based on the findings, the paper proposes recommendations to strengthen the integration of animal welfare into the treaty, arguing that incorporating these recommendations is critical for developing a transformative, equitable, and effective treaty that addresses the systemic drivers of pandemic risk.

Epidemiological Surveillance and Genomic Characterization of Soochong Virus From Apodemus Species Using Multiplex PCR-Based Next-Generation Sequencing, Republic of Korea

Orthohantavirus hantanense causes hemorrhagic fever with renal syndrome in Eurasia, posing a substantial public health threat. Although the Hantaan virus is the primary etiological agent in the Republic of Korea (ROK), evidence suggests the potential zoonotic transmission of the Amur virus (AMRV), closely related to the Soochong virus (SOOV), to humans in China and Russia. This study examined 31 Apodemus spp. captured from six regions in Gangwon Province, ROK, between 2015 and 2018. Of these, 5/31 (16.1%) tested positive for anti-SOOV immunoglobulin G and SOOV RNA, with 3/6 (50%) in Hongcheon-gun and 2/5 (40%) in Pyeongchang-gun. Utilizing a multiplex polymerase chain reaction-based next-generation sequencing approach, we achieved complete genomic sequencing of SOOV from rodent lung tissues, with coverage rates of 90.3%-98.2% for the S segment, 92.3%-98.1% for the M segment, and 88.1%-93.0% for the L segment. Five novel whole-genome sequences of SOOV were obtained from rodents in Hongcheon-gun and Pyeongchang-gun, representing the first documented SOOV in Pyeongchang-gun. The evolutionary rate analysis of SOOV tripartite genomes demonstrated lower divergence in the S segment. Phylogenetic analysis revealed a well-supported divergence of the SOOV and AMRV lineages across the ROK, China, and Russia, with incongruences suggesting differential segment evolution. Co-divergence analysis indicated the inter-species transmission of SOOV Aa18-104 from Apodemus agrarius in Pyeongchang-gun. The high zoonotic potential of all SOOV strains underscores the need for extensive monitoring and surveillance. This report provides crucial insights for the development of effective control strategies against hantaviral outbreaks in the ROK.

Seoul orthohantavirus evades innate immune activation by reservoir endothelial cells

Pathogenic hantaviruses are maintained world-wide within wild, asymptomatic rodent reservoir hosts, with increasingly frequent human spillover infections resulting in severe hemorrhagic fever or cardio-pulmonary disease. With no approved therapeutics or vaccines, research has, until recently, focused on understanding the drivers of immune-mediated pathogenesis. An emerging body of work is now investigating the mechanisms that allow for asymptomatic, persistent infections of mammalian reservoir hosts with highly pathogenic RNA viruses. Despite limited experimental data, several hypotheses have arisen to explain limited or absent disease pathology in reservoir hosts. In this study, we directly tested two leading hypotheses: 1) that reservoir host cells induce a generally muted response to viral insults, and 2) that these viruses employ host-specific mechanisms of innate antiviral antagonism to limit immune activation in reservoir cells. We demonstrate that, in contrast to human endothelial cells which mount a robust antiviral and inflammatory response to pathogenic hantaviruses, primary Norway rat endothelial cells do not induce antiviral gene expression in response to infection with their endemic hantavirus, Seoul orthohantavirus (SEOV). Reservoir rat cells do, however, induce strong innate immune responses to exogenous stimulatory RNAs, type I interferon, and infection with Hantaan virus, a closely related hantavirus for which the rat is not a natural reservoir. We also find that SEOV-infected rat endothelial cells remain competent for immune activation induced by exogenous stimuli or subsequent viral infection. Importantly, these findings support an alternative model for asymptomatic persistence within hantavirus reservoir hosts: that efficient viral replication within reservoir host cells may prevent the exposure of critical motifs for cellular antiviral recognition and thus limits immune activation that would otherwise result in viral clearance and/or immune-mediated disease. Defining the mechanisms that allow for infection tolerance and persistence within reservoir hosts will reveal novel strategies for viral countermeasures against these highly pathogenic zoonotic threats.

Epidemiology and genetic diversity of bocavirus in wild rodents in urban areas of Guangzhou, Southern China

Members of the genus Bocaparvovirus have a significant impact on human health and can infect a wide range of hosts, increasing the likelihood of crossing species barriers. Among the various mammalian hosts, rodents are widely recognized as important reservoirs for emerging and zoonotic viruses. However, despite recent reports of bocavirus infections in rodents, our current understanding of rat bocavirus (RBoV) genetic diversity and evolution is limited. In this study, rodent samples were collected from the urban areas of Guangzhou city, Southern China, to investigate the presence and genetic diversity of RBoV. Through PCR-based screening of 296 rodent spleens, 54 samples were determined to be positive for RBoV infection, and 12 nearly complete genome sequences of RBoV were recovered. Phylogenetic analysis revealed distinct lineages and sub-lineages of RBoV, and six recombination events with strong statistical support were identified, with five of these events involving sequences obtained from this study. These results highlight the genetic diversity of RBoV circulating in rodents in Guangzhou city and emphasize the importance of extensive surveillance to gain a better understanding of RBoV epidemiology, evolutionary characteristics, and potential for cross-species transmission.

Viruses Identified in Shrews (Soricidae) and Their Biomedical Significance

Shrews (Soricidae) are common small wild mammals. Some species of shrews, such as Asian house shrews (Suncus murinus), have a significant overlap in their habitats with humans and domestic animals. Currently, over 190 species of viruses in 32 families, including Adenoviridae, Arenaviridae, Arteriviridae, Astroviridae, Anelloviridae, Bornaviridae, Caliciviridae, Chuviridae, Coronaviridae, Filoviridae, Flaviviridae, Hantaviridae, Hepadnaviridae, Hepeviridae, Nairoviridae, Nodaviridae, Orthoherpesviridae, Orthomyxoviridae, Paramyxoviridae, Parvoviridae, Phenuiviridae, Picobirnaviridae, Picornaviridae, Polyomaviridae, Poxviridae, Rhabdoviridae, Sedoreoviridae, Spinareoviridae, and three unclassified families, have been identified in shrews. Diverse shrew viruses, such as Borna disease virus 1, Langya virus, and severe fever with thrombocytopenia syndrome virus, cause diseases in humans and/or domestic animals, posing significant threats to public health and animal health. This review compiled fundamental information about shrews and provided a comprehensive summary of the viruses that have been detected in shrews, with the aim of facilitating a deep understanding of shrews and the diversity, epidemiology, and risks of their viruses.

The discovery of novel variants reveals the genetic diversity and potential origin of Seoul orthohantavirus

Seoul orthohantavirus (SEOV) has been identified as one of the main causative agents of hemorrhagic fever with renal syndrome (HFRS) in China. The virus was found circulating in rodent populations in almost all provinces of the country, reflecting the wide distribution of HFRS. Here, using the direct immunofluorescence assay (DFA) and real-time quantitative reverse transcription PCR (qRT-PCR) approach, we performed screening in 1784 small mammals belonging to 14 species of three orders captured in the main areas of HFRS endemicity in Yunnan province (southwestern China) and identified 37 SEOV-positive rats (36 Rattus norvegicus and 1 Rattus tanezumi). A 3-year surveillance of HFRS epidemics and dynamics of rodent reservoir density and virus prevalence implied a potential correlation between them. The subsequent meta-transcriptomic sequencing and phylogenetic analyses revealed three SEOV variants, among which two are completely novel. The ancestral character state reconstruction (ACSR) analysis based on both novel variants and documented strains from 5 continents demonstrated that SEOV appeared to originate near the southwestern area (Yunnan-Kweichow Plateau) of China, then could spread to other regions and countries by their rodent carriers, resulting in a global distribution today. In summary, these data furthered the understanding regards genetic diversity and the potential origin for SEOV. However, the expanding endemic foci in the province suggest that the virus is spreading over a wider region and is much more diverse than previous depicted, which means that increased sampling is necessary.

The Risk of Virus Emergence in South America: A Subtle Balance Between Increasingly Favorable Conditions and a Protective Environment

South American ecosystems host astonishing biodiversity, with potentially great richness in viruses. However, these ecosystems have not yet been the source of any widespread, epidemic viruses. Here we explore a set of putative causes that may explain this apparent paradox. We discuss that human presence in South America is recent, beginning around 14,000 years ago; that few domestications of native species have occurred; and that successive immigration events associated with Old World virus introductions reduced the likelihood of spillovers and adaptation of local viruses into humans. Also, the diversity and ecological characteristics of vertebrate hosts might serve as protective factors. Moreover, although forest areas remained well preserved until recently, current brutal, sudden, and large-scale clear cuts through the forest have resulted in nearly no ecotones, which are essential for creating an adaptive gradient of microbes, hosts, and vectors. This may be temporarily preventing virus emergence. Nevertheless, the mid-term effect of such drastic changes in habitats and landscapes, coupled with explosive urbanization and climate changes, must not be overlooked by health authorities.

Human Orthohantavirus disease prevalence and genotype distribution in the U.S., 2008-2020: a retrospective observational study

Background

In the United States (U.S.), hantavirus pulmonary syndrome (HPS) and non-HPS hantavirus infection are nationally notifiable diseases. Criteria for identifying human cases are based on clinical symptoms (HPS or non-HPS) and acute diagnostic results (IgM+, rising IgG+ titers, RT-PCR+, or immunohistochemistry (IHC)+). Here we provide an overview of diagnostic testing and summarize human Hantavirus disease occurrence and genotype distribution in the U.S. from 2008 to 2020.

Methods

Epidemiological data from the national hantavirus registry was merged with laboratory diagnostic testing results performed at the CDC. Residual hantavirus-positive specimens were sequenced, and the available epidemiological and genetic data sets were linked to conduct a genomic epidemiological study of hantavirus disease in the U.S.

Findings

From 1993 to 2020, 833 human hantavirus cases have been identified, and from 2008 to 2020, 335 human cases have occurred. Among New World (NW) hantavirus cases detected at the CDC diagnostic laboratory (representing 29.2% of total cases), most (85.0%) were detected during acute disease, however, some convalescent cases were detected in states not traditionally associated with hantavirus infections (Connecticut, Missouri, New Jersey, Pennsylvania, Tennessee, and Vermont). From 1993 to 2020, 94.9% (745/785) of U.S. hantaviruses cases were detected west of the Mississippi with 45.7% (359/785) in the Four Corners region of the U.S. From 2008 to 2020, 67.7% of NW hantavirus cases were detected between the months of March and August. Sequencing of RT-PCR-positive cases demonstrates a geographic separation of Orthohantavirus sinnombreense species [Sin Nombre virus (SNV), New York virus, and Monongahela virus]; however, there is a large gap in viral sequence data from the Northwestern and Central U.S. Finally, these data indicate that commercial IgM assays are not concordant with CDC-developed assays, and that "concordant positive" (i.e., commercial IgM+ and CDC IgM+ results) specimens exhibit clinical characteristics of hantavirus disease.

Interpretation

Hantaviral disease is broadly distributed in the contiguous U.S, viral variants are localised to specific geographic regions, and hantaviral disease infrequently detected in most Southeastern states. Discordant results between two diagnostic detection methods highlight the need for an improved standardised testing plan in the U.S. Hantavirus surveillance and detection will continue to improve with clearly defined, systematic reporting methods, as well as explicit guidelines for clinical characterization and diagnostic criteria.

Funding

This work was funded by core funds provided to the Viral Special Pathogens Branch at CDC.

Molecular insight into the neutralization mechanism of human-origin monoclonal antibody AH100 against Hantaan virus

Both Old World and New World hantaviruses are transmitted through rodents and can lead to hemorrhagic fever with renal syndrome or hantavirus cardiopulmonary syndrome in humans without the availability of specific therapeutics. The square-shaped surface spikes of hantaviruses consist of four Gn-Gc heterodimers that are pivotal for viral entry into host cells and serve as targets for the immune system. Previously, a human-derived neutralizing monoclonal antibody, AH100, demonstrated specific neutralization against the Old World hantavirus, Hantaan virus. However, the precise mode binding of this neutralizing monoclonal antibody remains unclear. In the present study, we determined the structure of the Hantaan virus Gn-AH100 antigen-binding fragment complex and identified its epitope. Crystallography revealed that AH100 targeted the epitopes on domain A and b-ribbon and E3-like domain. Epitope mapping onto a model of the higher order (Gn-Gc)4 spike revealed its localization between neighboring Gn protomers, distinguishing this epitope as a unique site compared to the previously reported monoclonal antibodies. This study provides crucial insights into the structural basis of hantavirus neutralizing antibody epitopes, thereby facilitating the development of therapeutic antibodies.IMPORTANCEHantaan virus (HTNV) poses a significant threat to humans by causing hemorrhagic fever with renal syndrome with high mortality rates. In the absence of FDA-approved drugs or vaccines, it is urgent to develop specific therapeutics. Here, we elucidated the epitope of a human-derived neutralizing antibody, AH100, by determining the HTNV glycoprotein Gn-AH100 antigen-binding fragment (Fab) complex structure. Our findings revealed that the epitopes situated on the domain A and b-ribbon and E3-like domain of the HTNV Gn head. By modeling the complex structure in the viral lattice, we propose that AH100 neutralizes the virus by impeding conformational changes of Gn protomer, which is crucial for viral entry. Additionally, sequence analysis of all reported natural isolates indicated the absence of mutations in epitope residues, suggesting the potential neutralization ability of AH100 in diverse isolates. Therefore, our results provide novel insights into the epitope and the molecular basis of AH100 neutralization.

Distribution and genetic characterization of hantaviruses in bats and rodents from Yunnan

Hemorrhagic fever with renal syndrome caused by hantaviruses has long been a serious public health issue in Yunnan Province. Hantaviruses exhibit a high extent of biodiversity in their natural hosts, particularly in mammalian hosts. This study was conducted to screen for hantaviruses in bats and rodents in Yunnan Province and elucidate their genetic characteristics and possible zoonotic disease risk. Hantaviruses were detected in 202 bats and 372 rodents with the positive rates 27.49% and 1.25% respectively. A novel lineage (named Lineage 10) of the Seoul virus (SEOV) from rodents and the geographic clustering of hantavirus in bats were identified using phylogenetic analyses of the full-length M- and S-segments. Our study suggest a high cross-species transmissibility of hantaviruses in bats and existence of a new lineage of SEOV in rodents differing significantly from other SEOVs. These results provide data to support the prevention and control of hantavirus-associated diseases in Yunnan Province.

Discovery and characterization of novel jeilongviruses in wild rodents from Hubei, China

The genus Jeilongvirus comprises non-segmented negative-stranded RNA viruses that are classified within the Paramyxoviridae family by phylogeny. Jeilongviruses are found in various reservoirs, including rodents and bats. Rodents are typical viral reservoirs with diverse spectra and zoonotic potential. Little is currently known about jeilongviruses in rodents from central China. The study utilized high-throughput and Sanger sequencing to obtain jeilongvirus genomes, including those of two novel strains (HBJZ120/CHN/2021 (17,468 nt) and HBJZ157/CHN/2021 (19,143 nt)) and three known viruses (HBXN18/CHN/2021 (19,212 nt), HBJZ10/CHN/2021 (19,700 nt), HBJM106/CHN/2021 (18,871 nt)), which were characterized by genome structure, identity matrix, and phylogenetic analysis. Jeilongviruses were classified into three subclades based on their topology, phylogeny, and hosts. Based on the amino acid sequence identities and phylogenetic analysis of the L protein, HBJZ120/CHN/2021 and HBJZ157/CHN/2021 were found to be strains rather than novel species. Additionally, according to specific polymerase chain reaction screening, the positive percentage of Beilong virus in Hubei was 6.38%, suggesting that Beilong virus, belonging to the Jeilongvirus genus, is likely to be widespread in wild rodents. The identification of novel strains further elucidated the genomic diversity of jeilongviruses. Additionally, the prevalence of jeilongviruses in Hubei, China, was profiled, establishing a foundation for the surveillance and early warning of emerging paramyxoviruses.

Great genetic diversity of vector-borne bacteria and protozoan in wild rodents from Guangxi, China

BACKGROUND

Rodents are recognized as the hosts of many vector-borne bacteria and protozoan parasites and play an important role in their transmission and maintenance. Intensive studies have focused on their infections in vectors, especially in ticks, however, vector-borne bacterial and protozoan infections in rodents are poorly understood although human cases presenting with fever may due to their infection have been found.

METHODS

From May to October 2019, 192 wild rodents were trapped in wild environment of Guangxi Province, and the spleen samples were collected to reveal the presence of vector-borne bacterial and protozoan infections in them. The microorganisms in rodents were identified by detecting their DNA using (semi-)nested PCR. All the PCR products of the expected size were subjected to sequencing, and then analyzed by BLASTn. Furthermore, all the recovered sequences were subjected to nucleotide identity and phylogenetic analyses.

RESULTS

As a result, 192 rodents representing seven species were captured, and Bandicota indica were the dominant species, followed by Rattus andamanensis. Based on the (semi-)nested PCR, our results suggested that Anaplasma bovis, Anaplasma capra, Anaplasma ovis, Anaplasma phagocytophilum, "Candidatus Neoehrlichia mikurensis", "Candidatus E. hainanensis", "Candidatus E. zunyiensis", three uncultured Ehrlichia spp., Bartonella coopersplainsensis, Bartonella tribocorum, Bartonella rattimassiliensis, Bartonella silvatica, two uncultured Bartonella spp., Babesia microti and diverse Hepatozoon were identified in six rodent species. More importantly, six species (including two Anaplasma, two Bartonella, "Ca. N. mikurensis" and Bab. microti) are zoonotic pathogens except Anaplasma bovis and Anaplasma ovis with zoonotic potential. Furthermore, dual infection was observed between different microorganisms, and the most common type of co-infection is between "Ca. N. mikurensis" and other microorganisms. Additionally, potential novel Bartonella species and Hepatozoon species demonstrated the presence of more diverse rodent-associated Bartonella and Hepatozoon.

CONCLUSIONS

The results in this work indicated great genetic diversity of vector-borne infections in wild rodents, and highlighted the potential risk of human pathogens transmitted from rodents to humans through vectors.

Discovery and genetic characterization of novel paramyxoviruses from small mammals in Hubei Province, Central China

Paramyxoviruses are a group of single-stranded, negative-sense RNA viruses, some of which are responsible for acute human disease, including parainfluenza virus, measles virus, Nipah virus and Hendra virus. In recent years, a large number of novel paramyxoviruses, particularly members of the genus Jeilongvirus, have been discovered in wild mammals, suggesting that the diversity of paramyxoviruses may be underestimated. Here we used hemi-nested reverse transcription PCR to obtain 190 paramyxovirus sequences from 969 small mammals in Hubei Province, Central China. These newly identified paramyxoviruses were classified into four clades: genera Jeilongvirus, Morbillivirus, Henipavirus and Narmovirus, with most of them belonging to the genus Jeilongvirus. Using Illumina sequencing and Sanger sequencing, we successfully recovered six near-full-length genomes with different genomic organizations, revealing the more complex genome content of paramyxoviruses. Co-divergence analysis of jeilongviruses and their known hosts indicates that host-switching occurred more frequently in the evolutionary histories of the genus Jeilongvirus. Together, our findings demonstrate the high prevalence of paramyxoviruses in small mammals, especially jeilongviruses, and highlight the diversity of paramyxoviruses and their genome content, as well as the evolution of jeilongviruses.

Genome sequencing identifies "Limestone Canyon virus" as Montaño virus (Hantaviridae: Orthohantavirus montanoense) circulating in brush deermice in New Mexico

Orthohantaviruses infect distinct eulipotyphlan and rodent reservoirs throughout the world; some rodent orthohantaviruses can cause disease in humans. In the United States, a primary rodent reservoir for the human-pathogenic Sin Nombre virus (SNV) is the western deermouse (Peromyscus sonoriensis; formerly included in Peromyscus maniculatus). Deermice (rodents of genus Peromyscus) carry presumably distinct orthohantaviruses but, although deermice of ten species have been recorded in New Mexico, only SNV has been reported in rodents from that state. Using a set of pan-orthohantavirus primers, we discovered a non-SNV orthohantavirus in a brush deermouse (P. boylii), trapped in central New Mexico in 2019. Sequencing enabled the generation of a consensus coding-complete genome sequence, revealing similarity to the known partial sequences of the unclassified "Limestone Canyon virus (LSCV)" in GenBank and aligning with the information in an unpublished study of wild-caught brush deermice trapped in southwestern New Mexico in 2006. Phylogenetic analysis of these combined data revealed geospatial clades and overall identity of "LSCV", uncovering its association with the classified Montaño virus (MTNV), which is known to infect Aztec and Orizaba deermice in central Mexico. Our work emphasizes the importance of determining coding-complete viral genome sequences as a framework for rigorous virus classification as the basis for epidemiological studies.

Landscape of IGH germline genes of Chiroptera and the pattern of Rhinolophus affinis bat IGH CDR3 repertoire

The emergence and re-emergence of abundant viruses from bats that impact human and animal health have resulted in a resurgence of interest in bat immunology. Characterizing the immune receptor repertoire is critical to understanding how bats coexist with viruses in the absence of disease and developing new therapeutics to target viruses in humans and susceptible livestock. In this study, IGH germline genes of Chiroptera including Rhinolophus ferrumequinum, Phyllostomus discolor, and Pipistrellus pipistrellus were annotated, and we profiled the characteristics of Rhinolophus affinis (RA) IGH CDR3 repertoire. The germline genes of Chiroptera are quite different from those of human, mouse, cow, and dog in evolution, but the three bat species have high homology. The CDR3 repertoire of RA is unique in many aspects including CDR3 subclass, V/J genes access and pairing, CDR3 clones, and somatic high-frequency mutation compared with that of human and mouse, which is an important point in understanding the asymptomatic nature of viral infection in bats. This study unveiled a detailed map of bat IGH germline genes on chromosome level and provided the first immune receptor repertoire of bat, which will stimulate new avenues of research that are directly relevant to human health and disease.IMPORTANCEThe intricate relationship between bats and viruses has been a subject of study since the mid-20th century, with more than 100 viruses identified, including those affecting humans. While preliminary investigations have outlined the innate immune responses of bats, the role of adaptive immunity remains unclear. This study presents a pioneering contribution to bat immunology by unveiling, for the first time, a detailed map of bat IGH germline genes at the chromosome level. This breakthrough not only provides a foundation for B cell receptor research in bats but also contributes to primer design and sequencing of the CDR3 repertoire. Additionally, we offer the first comprehensive immune receptor repertoire of bats, serving as a crucial library for future comparative analyses. In summary, this research significantly advances the understanding of bats' immune responses, providing essential resources for further investigations into viral tolerance and potential zoonotic threats.

Anaplasma, Bartonella, and Rickettsia infections in Daurian ground squirrels (Spermophilus dauricus), Hebei, China

Rodents have been confirmed as hosts of various vector-borne zoonotic pathogens and are important for the maintenance of these microbes in nature. However, surveillance for zoonotic pathogens is limited for many wild rodent species in China, so our knowledge of pathogen ecology, genetic diversity, and the risk of cross-species transmission to humans is limited. In this study, 165 spleen samples of Daurian ground squirrels (Spermophilus dauricus) were collected from Weichang Manchu and the Mongolian Autonomous County of Hebei Province, China, and Rickettsia, Bartonella, and Anaplasma were identified by DNA detection using polymerase chain reaction (PCR). Sequence analysis identified eight bacterial pathogens: R. raoultii, R. sibirica, Candidatus R. longicornii, B. washoensis, B. grahamii, B. jaculi, A. capra, and Candidatus Anaplasma cinensis. Co-infection of B. grahamii and R. raoultii in one sample was observed. Our results demonstrated the genetic diversity of bacteria in Daurian ground squirrels and contributed to the distribution of these pathogens. Six species, A. capra, R. raoultii, R. sibirica, Candidatus R. longicornii, B. washoensis, and B. grahamii, are known to be pathogenic to humans, indicating a potential public health risk to the local human population, especially to herders who frequently have close contact with Daurian ground squirrels and are thus exposed to their ectoparasites.

A novel hantavirus identified in bats (Carollia perspicillata) in Brazil

Bats play an essential role in maintaining ecosystems. Their unique characteristics increase the likelihood of interactions with various species, making them a potential source for the emergence and spread of infectious diseases. Hantaviruses are continuously expanding their range of hosts. This study presents the identification of a partial genome associated with Hantavirus in samples collected from neotropical bats. We conducted a metagenomic study using samples from Carollia perspicillata in Maranhão, Brazil. Tissue fragments were used for RNA extraction and subsequent sequencing. The resulting data was subjected to bioinformatic analysis. A sequence showing an identity of 72.86% with the L gene in the reference genome was obtained. The phylogenetic analysis revealed the study sequence, denoted as Buritiense, clustering within the Mobatvirus clade. The intragroup analysis showed a broader dispersion and were markedly asymmetric. This observation suggests the possibility that Buritiense could potentially represent a new species within the bat-borne hantaviruses, but further analyses are needed to provide additional insights if bats plays a role as reservoirs and the potential for transmission to human populations.

Species-specific responses during Seoul orthohantavirus infection in human and rat lung microvascular endothelial cells

Seoul orthohantavirus (SEOV) is a rat-borne zoonotic virus that is transmitted via inhalation of aerosolized infectious excreta, and can cause hemorrhagic fever with renal syndrome (HFRS) in humans worldwide. In rats, SEOV predominantly exists as a persistent infection in the absence of overt clinical signs. Lack of disease in rats is attributed to downregulation of pro-inflammatory and upregulation of regulatory host responses. As lung microvascular endothelial cells (LMECs) represent a primary target of infection in both human and rats, infections in these cells provide a unique opportunity to study the central role of LMECs in the dichotomy between pathogenicity in both species. In this study, host responses to SEOV infection in primary human and rat LMECs were directly compared on a transcriptional level. As infection of rat LMECs was more efficient than human LMECs, the majority of anti-viral defense responses were observed earlier in rat LMECs. Most prominently, SEOV-induced processes in both species included responses to cytokine stimulus, negative regulation of innate immune responses, responses to type I and II interferons, regulation of pattern recognition receptor signaling and MHC-I signaling. However, over time, in the rat LMECs, responses shifted from an anti-viral state towards a more immunotolerant state displayed by a PD-L1, B2M-, JAK2-focused interaction network aiding in negative regulation of cytotoxic CD8-positive T cell activation. This suggests a novel mechanism by which species-specific orthohantavirus-induced endothelium and T cell crosstalk may play a crucial role in the development of acute disease in humans and persistence in rodents.

Interferon-induced protein with tetratricopeptide repeats 5 of black fruit bat (Pteropus alecto) displays a broad inhibition of RNA viruses

Bats are natural host reservoirs and have adapted a unique innate immune system that permits them to host many viruses without exhibiting symptoms. Notably, bat interferon stimulated genes (ISGs) have been shown to play antiviral roles. Interferon induced protein with tetratricopeptide repeats 5 (IFIT5) is a well-characterised ISG in humans with antiviral activities against negative-sense RNA viruses via inhibiting viral transcription. Here, we aim to investigate if Pteropus alecto (pa) IFIT5 (paIFIT5) possess the ability to inhibit negative-sense RNA viruses. Initially, gene syntenic and comparative structural analyses of multiple animals highlighted a high level of similarity between Pteropus alecto and human IFIT5 proteins. Our results showed that paIFIT5 was significantly inducible by viral and dsRNA stimulation. Transient overexpression of paIFIT5 inhibited the replication of vesicular stomatitis virus (VSV). Using minireplicon and transcription reporter assays, we demonstrated the ability of paIFIT5 specifically to inhibit H17N10 polymerase activity. Mechanistically, we noticed that the antiviral potential of paIFIT5 against negative sense RNA viruses was retributed to its interaction with 5'ppp containing RNA. Taken together, these findings highlight the genetic and functional conservation of IFIT5 among mammals.

Genome-wide support for incipient Tula hantavirus species within a single rodent host lineage

Evolutionary divergence of viruses is most commonly driven by co-divergence with their hosts or through isolation of transmission after host shifts. It remains mostly unknown, however, whether divergent phylogenetic clades within named virus species represent functionally equivalent byproducts of high evolutionary rates or rather incipient virus species. Here, we test these alternatives with genomic data from two widespread phylogenetic clades in Tula orthohantavirus (TULV) within a single evolutionary lineage of their natural rodent host, the common vole Microtus arvalis. We examined voles from forty-two locations in the contact region between clades for TULV infection by reverse transcription (RT)-PCR. Sequencing yielded twenty-three TULV Central North and twenty-one TULV Central South genomes, which differed by 14.9-18.5 per cent at the nucleotide and 2.2-3.7 per cent at the amino acid (AA) level without evidence of recombination or reassortment between clades. Geographic cline analyses demonstrated an abrupt (<1 km wide) transition between the parapatric TULV clades in continuous landscape. This transition was located within the Central mitochondrial lineage of M. arvalis, and genomic single nucleotide polymorphisms showed gradual mixing of host populations across it. Genomic differentiation of hosts was much weaker across the TULV Central North to South transition than across the nearby hybrid zone between two evolutionary lineages in the host. We suggest that these parapatric TULV clades represent functionally distinct, incipient species, which are likely differently affected by genetic polymorphisms in the host. This highlights the potential of natural viral contact zones as systems for investigating the genetic and evolutionary factors enabling or restricting the transmission of RNA viruses.

Diversity and genetic characterization of orthohantavirus from small mammals and humans during 2012-2022 in Hubei Province, Central China

Hemorrhagic fever with renal syndrome (HFRS) is a significant public health problem in Hubei Province, China, where a novel strain of orthohantavirus, HV004, was reported in 2012. However, no systematic study has investigated the prevalence and variation of orthohantavirus in rodents and humans. Herein, 2137 small mammals were collected from ten HFRS epidemic areas in Hubei Province from 2012 to 2022, and 143 serum samples from patients with suspected hemorrhagic fever were collected from two hospitals from 2017 to 2021. Orthohantavirus RNA was recovered from 134 lung tissue samples from five rodent species, with a 6.27 % prevalence, and orthohantavirus was detected in serum samples from 25 patients. Genetic analyses revealed that orthohantavirus hantanense (HTNV), orthohantavirus seoulense (SEOV), and orthohantavirus dabieshanense (DBSV) are co-circulating in rodents in Hubei, and HTNV and SEOV were identified in patient serum. Phylogenetic analysis showed that most of the HTNV sequences were clustered with HV004, indicating that HV004-like orthohantavirus was the main HNTV subtype in rodents. Two genetic reassortments and six recombination events were observed in Hubei orthohantaviruses. In summary, this study identified the diversity of orthohantaviruses circulating in Hubei over the past decade, with the HV004-like subtype being the main genotype in rodents and patients. These findings highlight the need for continued attention and focus on orthohantaviruses, especially concerning newly identified strains.

High-resolution phylogeographical surveillance of Hantaan orthohantavirus using rapid amplicon-based Flongle sequencing, Republic of Korea

Orthohantaviruses, etiological agents of hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome, pose a critical public health threat worldwide. Hantaan orthohantavirus (HTNV) outbreaks are particularly endemic in Gyeonggi Province in northern area of the Republic of Korea (ROK). Small mammals were collected from three regions in the Gyeonggi Province during 2017 and 2018. Serological and molecular prevalence of HTNV was 25/201 (12.4%) and 10/25 (40%), respectively. A novel nanopore-based diagnostic assay using a cost-efficient Flongle chip was developed to rapidly and sensitively detect HTNV infection in rodent specimens within 3 h. A rapid phylogeographical surveillance of HTNV at high-resolution phylogeny was established using the amplicon-based Flongle sequencing. In total, seven whole-genome sequences of HTNV were newly obtained from wild rodents collected in Paju-si (Gaekhyeon-ri) and Yeoncheon-gun (Hyeonga-ri and Wangnim-ri), Gyeonggi Province. Phylogenetic analyses revealed well-supported evolutionary divergence and genetic diversity, enhancing the resolution of the phylogeographic map of orthohantaviruses in the ROK. Incongruences in phylogenetic patterns were identified among HTNV tripartite genomes, suggesting differential evolution for each segment. These findings provide crucial insights into on-site diagnostics, genome-based surveillance, and the evolutionary dynamics of orthohantaviruses to mitigate hantaviral outbreaks in HFRS-endemic areas in the ROK.

Effect of habitat degradation on hantavirus infection among introduced and endemic small mammals of Madagascar

Hantaviruses are globally distributed zoonotic pathogens capable of causing fatal disease in humans. Rodents and other small mammals are the typical reservoirs of hantaviruses, though the particular host varies regionally. Addressing the risk of hantavirus spillover from animal reservoirs to humans requires identifying the local mammal reservoirs and the predictors of infection in those animals, such as their population density and habitat characteristics. We screened native and non-native small mammals and bats in northeastern Madagascar for hantavirus infection to investigate the influence of habitat, including effects of human land use on viral prevalence. We trapped 227 bats and 1663 small mammals over 5 successive years in and around Marojejy National Park across a range of habitat types including villages, agricultural fields, regrowth areas, and secondary and semi-intact forests. Animals sampled included endemic tenrecs (Tenrecidae), rodents (Nesomyidae) and bats (6 families), along with non-native rodents (Muridae) and shrews (Soricidae). A hantavirus closely related to the previously described Anjozorobe virus infected 9.5% of Rattus rattus sampled. We did not detect hantaviruses in any other species. Habitat degradation had a complex impact on hantavirus prevalence in our study system: more intensive land use increase the abundance of R. rattus. The average body size of individuals varied between agricultural and nonagricultural land-use types, which in turn affected infection prevalence. Smaller R.rattus had lower probability of infection and were captured more commonly in villages and forests. Thus, infection prevalence was highest in agricultural areas. These findings provide new insights to the gradients of hantavirus exposure risk for humans in areas undergoing rapid land use transformations associated with agricultural practices.

First Molecular Evidence of Seewis Virus in Croatia

Orthohantaviruses are mainly carried and transmitted by wild rodents, although during the last decade, they have also been identified in multiple species of shrews and moles. Orthohantavirus, Orthohantavirus seewisense (Seewis virus, SWSV), first detected in Switzerland in a single Sorex araneus (Eurasian common shrew) specimen, has been further described in several European countries, including Croatia's neighboring Slovenia and Hungary. Croatia is a well-known endemic region for several zoonotic agents including three different orthohantaviruses: Orthohantavirus puumalaense (PUUV), Orthohantavirus dobravaense (DOBV), and Orthohantavirus tulaense (TULV). In this study, nine shrews were tested and SWSV RNA was detected in liver, lung, and kidney belonging to two shrews (22.22%), one collected on Medvednica mountain in Zagreb County, and the other in the Stara Gradiška area in lowland Croatia. The phylogenetic analysis of the complete S segment's open reading frame (ORF) and partial L-segment revealed that the Croatian sequences, when compared to sequences from the adjacent geographic regions, form a specific genetic lineage. Two SWSV-positive shrew species-Sorex araneus and Neomys milleri (Mediterranean water shrew)-were identified using barcode-based sequence analysis. Therefore, the SWSV detection in N. milleri throughout the course of this study is seen as a rare find in this shrew species. To our knowledge, this is the first molecular and phylogenetic analysis of SWSV in Croatia.

Recently Emerged Novel Henipa-like Viruses: Shining a Spotlight on the Shrew

Henipaviruses are zoonotic viruses, including some highly pathogenic and capable of serious disease and high fatality rates in both animals and humans. Hendra virus and Nipah virus are the most notable henipaviruses, resulting in significant outbreaks across South Asia, South-East Asia, and Australia. Pteropid fruit bats have been identified as key zoonotic reservoirs; however, the increased discovery of henipaviruses outside the geographic distribution of Pteropid fruit bats and the detection of novel henipa-like viruses in other species such as the shrew, rat, and opossum suggest that Pteropid bats are not the sole reservoir for henipaviruses. In this review, we provide an update on henipavirus spillover events and describe the recent detection of novel unclassified henipaviruses, with a strong focus on the shrew and its emerging role as a key host of henipaviruses.

RNA virus diversity in rodents

Many zoonotic disease emergencies are associated with RNA viruses in rodents that substantially impact public health. With the widespread application of meta-genomics and meta-transcriptomics for virus discovery over the last decade, viral sequences deposited in public databases have expanded rapidly, and the number of novel viruses discovered in rodents has increased. As important reservoirs of zoonotic viruses, rodents have attracted increasing attention for the risk of potential spillover of rodent-borne viruses. However, knowledge of rodent viral diversity and the major factors contributing to the risk of zoonotic epidemic outbreaks remains limited. Therefore, this study analyzes the diversity and composition of rodent RNA viruses using virus records from the Database of Rodent-associated Viruses (DRodVir/ZOVER), which covers the published literatures and records in GenBank database, reviews the main rodent RNA virus-induced human infectious diseases, and discusses potential challenges in this field.

Genetic variants associated with hantavirus infection in a reservoir host are related to regulation of inflammation and immune surveillance

The immunogenetics of wildlife populations influence the epidemiology and evolutionary dynamic of the host-pathogen system. Profiling immune gene diversity present in wildlife may be especially important for those species that, while not at risk of disease or extinction themselves, are host to diseases that are a threat to humans, other wildlife, or livestock. Hantaviruses (genus: Orthohantavirus) are globally distributed zoonotic RNA viruses with pathogenic strains carried by a diverse group of rodent hosts. The marsh rice rat (Oryzomys palustris) is the reservoir host of Orthohantavirus bayoui, a hantavirus that causes fatal cases of hantavirus cardiopulmonary syndrome in humans. We performed a genome wide association study (GWAS) using the rice rat "immunome" (i.e., all exons related to the immune response) to identify genetic variants associated with infection status in wild-caught rice rats naturally infected with their endemic strain of hantavirus. First, we created an annotated reference genome using 10× Chromium Linked Reads sequencing technology. This reference genome was used to create custom baits which were then used to target enrich prepared rice rat libraries (n = 128) and isolate their immunomes prior to sequencing. Top SNPs in the association test were present in four genes (Socs5, Eprs, Mrc1, and Il1f8) which have not been previously implicated in hantavirus infections. However, these genes correspond with other loci or pathways with established importance in hantavirus susceptibility or infection tolerance in reservoir hosts: the JAK/STAT, MHC, and NFκB. These results serve as informative markers for future exploration and highlight the importance of immune pathways that repeatedly emerge across hantavirus systems. Our work aids in creating cross-species comparisons for better understanding mechanisms of genetic susceptibility and host-pathogen coevolution in hantavirus systems.

Pathogenicity of novel hantavirus isolate and antigenicity and immunogenicity of novel strain-based inactivated vaccine

BACKGROUND

Hantaan virus (HTNV, Orthohantavirus hantanensae species, Hantaviridae family) is the main etiological agent responsible for hemorrhagic fever with renal syndrome (HFRS). The novel HTNV may pose a potential danger to the control and prevention of HFRS in China, which highlights the importance of vaccine development in public health management. In previous studies, our laboratory discovered and successfully isolated a new HTNV strain, HV004 strain, from Apodemus agrarius captured in an epidemic area in Hubei, China.

METHODS

An initial biological and pathogenicity characterization of HTNV 76-118 (standard train), HV114 strain (a clinical isolate from Hubei province in 1986), and the novel isolate HV004 strain from the epidemic areas of Hubei province were performed in susceptible cells and in vivo. An experimental HV004 strain inactivated vaccine was prepared, and its corresponding immunogenicity was analyzed in BALB/c mice.

RESULTS

HV004 strain had a similar but higher pathogenicity than HTNV 76-118 and HV114 in suckling mice. A subcutaneous vaccination (s.c.) with the inactivated HTNV vaccine adjuvanted with aluminum, followed by a challenge intraperitoneally with 106 FFU/ml HTNV, afforded full protection against an HTNV challenge. All immunized mice in every group elicited serum neutralizing antibodies with increasing dosages, which may protect mice from HTNV infection. A dose-dependent stimulation index of splenocytes was also observed in immunized mice. The percentage of IFN-γ-producing CD3+CD8+ T cells was significantly higher in the spleens of immunized mice than in those of control mice.

CONCLUSIONS

These findings suggest that the inactivated HTNV vaccine may stimulate mice to produce high levels of antibodies with neutralization activity and elicit specific anti-HTNV humoral and cellular immune responses in BALB/c mice against the prevalent strain of HTNV in south central China.

Host traits shape virome composition and virus transmission in wild small mammals

Bats, rodents, and shrews are the most important animal sources of human infectious diseases. However, the evolution and transmission of viruses among them remain largely unexplored. Through the meta-transcriptomic sequencing of internal organ and fecal samples from 2,443 wild bats, rodents, and shrews sampled from four Chinese habitats, we identified 669 viruses, including 534 novel viruses, thereby greatly expanding the mammalian virome. Our analysis revealed high levels of phylogenetic diversity, identified cross-species virus transmission events, elucidated virus origins, and identified cases of invertebrate viruses in mammalian hosts. Host order and sample size were the most important factors impacting virome composition and patterns of virus spillover. Shrews harbored a high richness of viruses, including many invertebrate-associated viruses with multi-organ distributions, whereas rodents carried viruses with a greater capacity for host jumping. These data highlight the remarkable diversity of mammalian viruses in local habitats and their ability to emerge in new hosts.

Diversity and independent evolutionary profiling of rodent-borne viruses in Hainan, a tropical island of China

The risk of emerging infectious diseases (EID) is increasing globally. More than 60% of EIDs worldwide are caused by animal-borne pathogens. This study aimed to characterize the virome, analyze the phylogenetic evolution, and determine the diversity of rodent-borne viruses in Hainan Province, China. We collected 682 anal and throat samples from rodents, combined them into 28 pools according to their species and location, and processed them for next-generation sequencing and bioinformatics analysis. The diverse viral contigs closely related to mammals were assigned to 22 viral families. Molecular clues of the important rodent-borne viruses were further identified by polymerase chain reaction for phylogenetic analysis and annotation of genetic characteristics such as arenavirus, coronavirus, astrovirus, pestivirus, parvovirus, and papillomavirus. We identified pestivirus and bocavirus in Leopoldoms edwardsi from Huangjinjiaoling, and bocavirus in Rattus andamanensis from the national nature reserves of Bangxi with low amino acid identity to known pathogens are proposed as the novel species, and their rodent hosts have not been previously reported to carry these viruses. These results expand our knowledge of viral classification and host range and suggest that there are highly diverse, undiscovered viruses that have evolved independently in their unique wildlife hosts in inaccessible areas.

Clinical and Molecular Epidemiology of Hemorrhagic Fever with Renal Syndrome Caused by Orthohantaviruses in Xiangyun County, Dali Prefecture, Yunnan Province, China

Hemorrhagic fever with renal syndrome (HFRS) is a zoonotic disease transmitted by several rodent species. We obtained clinical data of HFRS patients from the medical records of the People's Hospital of Xiangyun County in Dali Prefecture from July 2019 to August 2021. We collected epidemiological data of HFRS patients through interviews and investigated host animals using the night clip or night cage method. We systematically performed epidemiological analyses of patients and host animals. The differences in the presence of rodent activity at home (χ2 = 8.75, p = 0.031 < 0.05), of rodent-proof equipment in the food (χ2 = 9.19, p = 0.025 < 0.05), and of rodents or rodent excrement in the workplace (χ2 = 10.35, p = 0.014 < 0.05) were statistically different in the four clinical types, including mild, medium, severe, and critical HFRS-associated diseases. Furthermore, we conducted molecular detection of orthohantavirus in host animals. The total orthohantavirus infection rate of rodents was 2.72% (9/331); the specific infection rate of specific animal species was 6.10% (5/82) for the Apodemus chevrieri, 100% (1/1) for the Rattus nitidus, 3.77% (2/53) for the Rattus norvegicus, and 12.50% (1/8) for the Crocidura dracula. In this study, a total of 21 strains of orthohantavirus were detected in patients and rodents. The 12 orthohantavirus strains from patients showed a closer relationship with Seoul orthohantavirus (SEOOV) L0199, DLR2, and GZRn60 strains; the six orthohantavirus strains from Rattus norvegicus and Apodemus chevrieri were closely related to SEOOV GZRn60 strain. One strain (XYRn163) from Rattus norvegicus and one strain (XYR.nitidus97) from Rattus nitidus were closely related to SEOOV DLR2 strain; the orthohantavirus strain from Crocidura dracula was closely related to the Luxi orthohantavirus (LUXV) LX309 strain. In conclusion, patients with HFRS in Xuangyun County of Dali Prefecture are predominantly affected by SEOOV, with multiple genotypes of orthohantavirus in host animals, and, most importantly, these orthohantavirus strains constantly demonstrated zoonotic risk in humans.

Lessons Learned From the U.S. Military Experience With Hantavirus During the Korean War

INTRODUCTION

The Korean War (1950-1953) consisted of two phases. The first was a rapid mobile phase, and the second was a slow and stationary phase. During the stationary phase, approximately 3,000 UN troops became infected with a then unknown agent. The resulting illness began with flu-like symptoms and often progressed to a severe hemorrhagic fever leading to kidney failure and death. However, the cause was not to be identified until well over 20 years following the conclusion of the war when Dr. Ho Wang Lee succeeded in isolating Hantavirus from field rodents. The U.S. Military experience with Hantavirus during the Korean War is a case study of the potential impact of war-related environmental change on disease transmission. The lessons learned from this experience should inform future military medical planning and serve as a reminder of the impact that an unknown agent can have on military operations.

MATERIALS AND METHODS

A literature review of all available records with respect to the U.S. Military experience with Hantavirus was conducted. PubMed was the primary search engine used for this review. However, primary literature and historical accounts were also evaluated. All records were examined for environmental, epidemiological, and public health data regarding hemorrhagic fever outbreaks among U.S. forces during the Korean War. The quantitative and qualitative data from these sources were analyzed and evaluated within the context of military medical planning and force health protection to derive lessons learned that should be applied to the management and mitigation of viral disease in future wars.

RESULTS

Widespread deforestation resulting from war-related efforts most likely played a significant role in the outbreaks of Hantavirus among UN forces during the war. A lack of cultural literacy and an overreliance on erroneous assumptions most likely delayed the identification of the true causative agent. It is conceivable that these delays led to an increased casualty rate and that they had a negative impact on military operations during the war.

CONCLUSIONS

A basic understanding of the ecological mechanisms that maintain species diversity in the local environment coupled with an appreciation for the impact of environmental change on this diversity is of paramount importance for the prevention and mitigation of viral disease outbreaks in the deployed setting. Military medical planners should become familiar with the medical literature of the region in which they will be operating as this literature often describes the agents that will most likely be encountered by U.S. forces.

Deep Sequencing to Reveal Phylo-Geographic Relationships of Juquitiba Virus in Paraguay

Several hantaviruses result in zoonotic infections of significant public health concern, causing hemorrhagic fever with renal syndrome (HFRS) or hantavirus cardiopulmonary syndrome (HCPS) in the Old and New World, respectively. Given a 35% case fatality rate, disease-causing New World hantaviruses require a greater understanding of their biology, genetic diversity, and geographical distribution. Juquitiba hantaviruses have been identified in Oligoryzomys nigripes in Brazil, Paraguay, and Uruguay. Brazil has reported the most HCPS cases associated with this virus. We used a multiplexed, amplicon-based PCR strategy to screen and deep-sequence the virus harbored within lung tissues collected from Oligoryzomys species during rodent field collections in southern (Itapúa) and western (Boquerón) Paraguay. No Juquitiba-like hantaviruses were identified in Boquerón. Herein, we report the full-length S and M segments of the Juquitiba hantaviruses identified in Paraguay from O. nigripes. We also report the phylogenetic relationships of the Juquitiba hantaviruses in rodents collected from Itapúa with those previously collected in Canindeyú. We showed, using the TN93 nucleotide substitution model, the coalescent (constant-size) population tree model, and Bayesian inference implemented in the Bayesian evolutionary analysis by sampling trees (BEAST) framework, that the Juquitiba virus lineage in Itapúa is distinct from that in Canindeyú. Our spatiotemporal analysis showed significantly different time to the most recent ancestor (TMRA) estimates between the M and S segments, but a common geographic origin. Our estimates suggest the additional geographic diversity of the Juquitiba virus within the Interior Atlantic Forest and highlight the need for more extensive sampling across this biome.

Zoonotic Hantaviridae with Global Public Health Significance

Hantaviridae currently encompasses seven genera and 53 species. Multiple hantaviruses such as Hantaan virus, Seoul virus, Dobrava-Belgrade virus, Puumala virus, Andes virus, and Sin Nombre virus are highly pathogenic to humans. They cause hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome or hantavirus pulmonary syndrome (HCPS/HPS) in many countries. Some hantaviruses infect wild or domestic animals without causing severe symptoms. Rodents, shrews, and bats are reservoirs of various mammalian hantaviruses. Recent years have witnessed significant advancements in the study of hantaviruses including genomics, taxonomy, evolution, replication, transmission, pathogenicity, control, and patient treatment. Additionally, new hantaviruses infecting bats, rodents, shrews, amphibians, and fish have been identified. This review compiles these advancements to aid researchers and the public in better recognizing this zoonotic virus family with global public health significance.

Two point mutations in protocadherin-1 disrupt hantavirus recognition and afford protection against lethal infection

Andes virus (ANDV) and Sin Nombre virus (SNV) are the etiologic agents of severe hantavirus cardiopulmonary syndrome (HCPS) in the Americas for which no FDA-approved countermeasures are available. Protocadherin-1 (PCDH1), a cadherin-superfamily protein recently identified as a critical host factor for ANDV and SNV, represents a new antiviral target; however, its precise role remains to be elucidated. Here, we use computational and experimental approaches to delineate the binding surface of the hantavirus glycoprotein complex on PCDH1's first extracellular cadherin repeat domain. Strikingly, a single amino acid residue in this PCDH1 surface influences the host species-specificity of SNV glycoprotein-PCDH1 interaction and cell entry. Mutation of this and a neighboring residue substantially protects Syrian hamsters from pulmonary disease and death caused by ANDV. We conclude that PCDH1 is a bona fide entry receptor for ANDV and SNV whose direct interaction with hantavirus glycoproteins could be targeted to develop new interventions against HCPS.

Forecasting Outbreaks of Hantaviral Disease: Future Directions in Geospatial Modeling

Hantaviral diseases have been recognized as 'place diseases' from their earliest identification and, epidemiologically, are tied to single host species with transmission occurring from infectious hosts to humans. As such, human populations are most at risk when they are in physical proximity to suitable habitats for reservoir populations, when numbers of infectious hosts are greatest. Because of the lags between improving habitat conditions and increasing infectious host abundance and spillover to humans, it should be possible to anticipate (forecast) where and when outbreaks will most likely occur. Most mammalian hosts are associated with specific habitat requirements, so identifying these habitats and the ecological drivers that impact population growth and the dispersal of viral hosts should be markers of the increased risk for disease outbreaks. These regions could be targeted for public health and medical education. This paper outlines the rationale for forecasting zoonotic outbreaks, and the information that needs to be clarified at various levels of biological organization to make the forecasting of orthohantaviruses successful. Major challenges reflect the transdisciplinary nature of forecasting zoonoses, with needs to better understand the implications of the data collected, how collections are designed, and how chosen methods impact the interpretation of results.

Structural and mechanistic basis of neutralization by a pan-hantavirus protective antibody

Emerging rodent-borne hantaviruses cause severe diseases in humans with no approved vaccines or therapeutics. We recently isolated a monoclonal broadly neutralizing antibody (nAb) from a Puumala virus-experienced human donor. Here, we report its structure bound to its target, the Gn/Gc glycoprotein heterodimer comprising the viral fusion complex. The structure explains the broad activity of the nAb: It recognizes conserved Gc fusion loop sequences and the main chain of variable Gn sequences, thereby straddling the Gn/Gc heterodimer and locking it in its prefusion conformation. We show that the nAb's accelerated dissociation from the divergent Andes virus Gn/Gc at endosomal acidic pH limits its potency against this highly lethal virus and correct this liability by engineering an optimized variant that sets a benchmark as a candidate pan-hantavirus therapeutic.

Hantavirus Brno loanvirus is highly specific to the common noctule bat (Nyctalus noctula) and widespread in Central Europe

Bat-associated hantaviruses have been detected in Asia, Africa and Europe. Recently, a novel hantavirus (Brno loanvirus, BRNV) was identified in common noctule bats (Nyctalus noctula) in the Czech Republic, but nothing is known about its geographical range and prevalence. The objective of this study was to evaluate the distribution and host specificity of BRNV by testing bats from neighbouring countries Germany, Austria and Poland. One thousand forty-seven bats representing 21 species from Germany, 464 bats representing 18 species from Austria and 77 bats representing 12 species from Poland were screened by L segment broad-spectrum nested reverse transcription-polymerase chain reaction (RT-PCR) or by BRNV-specific real-time RT-PCR. Three common noctules from Germany, one common noctule from Austria and three common noctules from Poland were positive in the hantavirus RNA screening. Conventional RT-PCR and primer walking resulted in the amplification of partial L segment and (almost) complete S and M segment coding sequences for samples from Germany and partial L segment sequences for samples from Poland. Phylogenetic analysis of these nucleotide sequences showed highest similarity to BRNV from Czech Republic. The exclusive detection of BRNV in common noctules from different countries suggests high host specificity. The RNA detection rate in common noctules ranged between 1 of 207 (0.5%; Austria), 3 of 245 (1.2%; Germany) and 3 of 20 (15%; Poland). In conclusion, this study demonstrates a broader distribution of BRNV in common noctules in Central Europe, but at low to moderate prevalence. Additional studies are needed to prove the zoonotic potential of this hantavirus and evaluate its transmission within bat populations.

[Shrew-borne hantaviruses (Hantaviridae: Orthohantavirus) in the Far East of Russia]

INTRODUCTION

Insectivores are newly recognized hantaviral reservoir worldwide. Four distinct shrew-borne hantaviruses (family Hantaviridae) have been identified in two regions located in southern and northern part of the Russian Far East, two genetic variants of Seewis virus (SWSV), Lena River virus (LENV), Kenkeme virus (KKMV) and Yakeshi virus (YKSV). Here, we describe geographic distribution of shrew-borne hantaviruses in southern part of the Russian Far East: Jewish Autonomous region, Khabarovsk Krai, Primorsky Krai and Sakhalin region.

MATERIALS AND METHODS

Lung samples from shrews of genus Sorex, captured in the four regions of Far Eastern Russia, were examined for hantavirus RNA using reverse transcription polymerase chain reaction (RT-PCR). Phylogenetic analysis of the partial nucleotide sequences of viral genome was conducted using MEGA X software.

RESULTS

New genetic variant of YKSV was identified in new reservoir host, long-clawed shrew (S. ungiuculatus) from Sakhalin Island. Genetic variant of SWSV, ARTV-Sc, has been found to circulate among S. caecutiens on the seacoast of Khabarovsk and Primorsky Krai. KKMV virus and second genetic variant of SWSV, ARTV-St, were found in S. roboratus and S. tundrensis, respectively from Jewish Autonomous region.

CONCLUSION

Sorex-borne hantaviruses were found in all studied regions of Far Eastern Russia. Our results demonstrated co-evolution of SWSV, KKMV, and YKSV viruses throughout the geographic distribution of its hosts.

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.

A Brief History of Bunyaviral Family Hantaviridae

The discovery of Hantaan virus as an etiologic agent of hemorrhagic fever with renal syndrome in South Korea in 1978 led to identification of related pathogenic and nonpathogenic rodent-borne viruses in Asia and Europe. Their global distribution was recognized in 1993 after connecting newly discovered relatives of these viruses to hantavirus pulmonary syndrome in the Americas. The 1971 description of the shrew-infecting Hantaan-virus-like Thottapalayam virus was long considered an anomaly. Today, this virus and many others that infect eulipotyphlans, bats, fish, rodents, and reptiles are classified among several genera in the continuously expanding family Hantaviridae.