Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases

BACKGROUND

Rodents represent around 43% of all mammalian species, are widely distributed, and are the natural reservoirs of a diverse group of zoonotic viruses, including hantaviruses, Lassa viruses, and tick-borne encephalitis viruses. Thus, analyzing the viral diversity harbored by rodents could assist efforts to predict and reduce the risk of future emergence of zoonotic viral diseases.

RESULTS

We used next-generation sequencing metagenomic analysis to survey for a range of mammalian viral families in rodents and other small animals of the orders Rodentia, Lagomorpha, and Soricomorpha in China. We sampled 3,055 small animals from 20 provinces and then outlined the spectra of mammalian viruses within these individuals and the basic ecological and genetic characteristics of novel rodent and shrew viruses among the viral spectra. Further analysis revealed that host taxonomy plays a primary role and geographical location plays a secondary role in determining viral diversity. Many viruses were reported for the first time with distinct evolutionary lineages, and viruses related to known human or animal pathogens were identified. Phylogram comparison between viruses and hosts indicated that host shifts commonly happened in many different species during viral evolutionary history.

CONCLUSIONS

These results expand our understanding of the viromes of rodents and insectivores in China and suggest that there is high diversity of viruses awaiting discovery in these species in Asia. These findings, combined with our previous bat virome data, greatly increase our knowledge of the viral community in wildlife in a densely populated country in an emerging disease hotspot.

Persistence of tick-borne virus in the presence of multiple host species: tick reservoirs and parasite mediated competition

Tick-borne viruses in tropical and temperate parts of the world have a significant impact on human, livestock and wildlife hosts both directly, through mortality/morbidity, and economically. Since the ticks have multiple life stages and can utilize a large range of host species our understanding of the dynamics of these infections is often not clear. In this paper we consider the impact of a population which is a tick host but non-viraemic on one which is both a tick host and viraemic. We present two simple deterministic models and use joint threshold density curves to illustrate the basic reproductive ratios of both the ticks and the virus. We find that the non-viraemic hosts can have considerable impact on the viraemic host. Either they amplify the tick population and cause the virus to persist, or they dilute the infection and cause it to die out. A general model framework is presented here but a special case of this model describes the red grouse-hare-Louping-ill system.

Detection and preliminary characterization of a new rabbit calicivirus related to rabbit hemorrhagic disease virus but nonpathogenic

A new rabbit calicivirus related to the rabbit hemorrhagic disease virus (RHDV) was identified. The new virus contains significant differences from the previously characterized RHDV isolates in terms of pathogenicity, viral titer, tropism, and primary sequence of the structural protein. Cross-protection experiments, antigenic data, and sequence comparisons demonstrate that the new virus is more closely related to RHDV than to the European brown hare syndrome virus, another member of the caliciviruses of the lagomorph group. The existence of a nonpathogenic calicivirus, which we propose to name rabbit calicivirus (RCV), provides an explanation for the early discrepancies found in the course of serological surveys of the rabbit population in European countries.

European brown hare syndrome virus: molecular cloning and sequencing of the genome

The genome of the European brown hare syndrome virus (EBHSV), a calicivirus related to rabbit haemorrhagic disease virus (RHDV), was fully sequenced. It was 7442 bases long and contained two ORFs. In RHDV, the 5' large ORF (ORF1) is predicted to encode a polyprotein precursor to the non-structural and capsid proteins. The small ORF (ORF2) encodes a predicted protein of 12 kDa. Alignment of sequences of EBHSV and RHDV showed 71% nucleotide identity; the changes were uniformly scattered over the whole genome. Minor differences could be detected when comparing two EBHSV sequences, indicating that EBHSV could vary to the same extent as RHDV. Four cleavage sites previously identified on the RHDV polyprotein were conserved in EBHSV. These sequencing data clearly show that EBHSV and RHDV share a similar genomic organization and confirm that EBHSV and RHDV are two distinct members within the family Caliciviridae.

An overview of the lagomorph immune system and its genetic diversity

Our knowledge of the lagomorph immune system remains largely based upon studies of the European rabbit (Oryctolagus cuniculus), a major model for studies of immunology. Two important and devastating viral diseases, rabbit hemorrhagic disease and myxomatosis, are affecting European rabbit populations. In this context, we discuss the genetic diversity of the European rabbit immune system and extend to available information about other lagomorphs. Regarding innate immunity, we review the most recent advances in identifying interleukins, chemokines and chemokine receptors, Toll-like receptors, antiviral proteins (RIG-I and Trim5), and the genes encoding fucosyltransferases that are utilized by rabbit hemorrhagic disease virus as a portal for invading host respiratory and gut epithelial cells. Evolutionary studies showed that several genes of innate immunity are evolving by strong natural selection. Studies of the leporid CCR5 gene revealed a very dramatic change unique in mammals at the second extracellular loop of CCR5 resulting from a gene conversion event with the paralogous CCR2. For the adaptive immune system, we review genetic diversity at the loci encoding antibody variable and constant regions, the major histocompatibility complex (RLA) and T cells. Studies of IGHV and IGKC genes expressed in leporids are two of the few examples of trans-species polymorphism observed outside of the major histocompatibility complex. In addition, we review some endogenous viruses of lagomorph genomes, the importance of the European rabbit as a model for human disease studies, and the anticipated role of next-generation sequencing in extending knowledge of lagomorph immune systems and their evolution.

European brown hare syndrome in England

The livers from 50 brown hares (Lepus europaeus) were examined by electron microscopy for calicivirus-like particles typical of the virus of European brown hare syndrome (EBHS). The virus was visible in 23 of the livers which included four taken from hares which died in 1982 and 1985 and which had been stored at -20 degrees C. The clinical histories, post mortem and other findings associated with these 23 hares were similar to those described in cases of European brown hare syndrome in other European countries. The findings were compared with those associated with viral haemorrhagic disease (VHD) of rabbits which, although it did not occur in the United Kingdom until 1992, is also caused by a calicivirus believed to be related to EBHS virus. The finding of the virus in hares which died from the disease in 1982 is the earliest recorded isolation of the organism and predates the description of VHD virus and VHD in China in 1984. A retrospective review of post mortem reports revealed cases of disease between 1976 and 1977 which may have been due to EBHS and it is considered that the disease has occurred sporadically in England for several years. The results from suspected and confirmed cases of EBHS in England between 1976 and 1990 are reported and the epidemiology and emergence of the disease is considered.

Shedding of a low pathogenic avian influenza virus in a common synanthropic mammal--the cottontail rabbit

BACKGROUND

Cottontails (Sylvilagus spp.) are common mammals throughout much of the U.S. and are often found in peridomestic settings, potentially interacting with livestock and poultry operations. If these animals are susceptible to avian influenza virus (AIV) infections and shed the virus in sufficient quantities they may pose a risk for movement of avian influenza viruses between wildlife and domestic animals in certain situations.

METHODOLOGY/PRINCIPAL FINDINGS

To assess the viral shedding potential of AIV in cottontails, we nasally inoculated fourteen cottontails with a low pathogenic AIV (H4N6). All inoculated cottontails shed relatively large quantities of viral RNA both nasally (≤ 10(6.94) PCR EID50 equivalents/mL) and orally (≤ 10(5.09) PCR EID50 equivalents/mL). However, oral shedding tended to decline more quickly than did nasal shedding. No animals showed any obvious signs of disease throughout the study. Evidence of a serological response was found in all infected rabbits at 22 days post infection in convalescent sera.

CONCLUSIONS/SIGNIFICANCE

To our knowledge, cottontails have not been previously assessed for AIV shedding. However, it was obvious that they shed AIV RNA extensively via the nasal and oral routes. This is significant, as cottontails are widely distributed throughout the U.S. and elsewhere. These mammals are often found in highly peridomestic situations, such as farms, parks, and suburban neighborhoods, often becoming habituated to human activities. Thus, if infected these mammals could easily transport AIVs short distances.

Apparent effect of rabbit endogenous lentivirus type K acquisition on retrovirus restriction by lagomorph Trim5αs

To test the hypothesis that rabbit endogenous lentivirus type K (RELIK) could play a role in shaping the evolution of TRIM5α, the susceptibility of viruses containing the RELIK capsid (CA) to TRIM5 restriction was evaluated. RELIK CA-containing viruses were susceptible to the TRIM5αs from Old World monkeys but were unaffected by most ape or New World monkey factors. TRIM5αs from various lagomorph species were also isolated and tested for anti-retroviral activity. The TRIM5αs from both cottontail rabbit and pika restrict a range of retroviruses, including HIV-1, HIV-2, FIV, EIAV and N-MLV. TRIM5αs from the European and cottontail rabbit, which have previously been found to contain RELIK, also restricted RELIK CA-containing viruses, whereas a weaker restriction was observed with chimeric TRIM5α containing the B30.2 domain from the pika, which lacks RELIK. Taken together, these results could suggest that the pika had not been exposed to exogenous RELIK and that endogenized RELIK might exert a selective pressure on lagomorph TRIM5α.

Colorimetric detection of lagomorphs' calicivirus genomic sequences by polymerase chain reaction incorporating digoxigenin dUTP

A method of reverse transcription followed by polymerase chain reaction (RT-PCR) has been implemented for the demonstration of the rabbit haemorrhagic disease virus (RHDV) genome in organ suspensions, leukocytes and excretions of infected rabbits. RT-PCR has been tested with 10 RHDV strains isolated at various geographic sites and times using a pair of primers coming from the gene region coding for the capsid protein VP60. The same primers were effective in the amplification of 4 of 5 European brown hare syndrome (EBHS) virus isolates. Non-radioactive labelling of PCR products with digoxigenin during the amplification and a system of colorimetric assessment of hybridization reactions between a biotin-labelled RHDV capture probe and the chains of labelled amplicons (PCR ELISA) were used for specific analyses of nucleic acid synthesis. The sensitivity of the alternative procedure of analysis of the dig-labelled PCR products with PCR ELISA was two logs10 higher than that of conventional electrophoresis in agarose gel stained with ethidium bromide. The results of the hybridization reactions, carried out under various stringency conditions, have confirmed the presumption that the genomic similarity between the amplified and the probed areas of the capsid protein VP60 gene was not uniform within all the tested caliciviruses. A higher degree of heterogeneity was observed between the isolates of EBHSV and RHDV.

Monitoring of Hepatitis E Virus in Wild Lagomorphs in Spanish Mediterranean Ecosystems

Hepatitis E virus (HEV) is an emerging zoonotic pathogen in Europe. Even though swine species are considered the main host of the zoonotic HEV-3 genotype, rabbits are recognized as the main reservoir of the divergent HEV-3ra subtype. However, the role of wild lagomorphs in the epidemiology of this virus in Mediterranean ecosystems is under debate. The aims of this study were to assess exposure of HEV in wild rabbit (Oryctolagus cuniculus) and Iberian hare (Lepus granatensis) populations in southern Spain and to determine potential risk factors associated with HEV exposure in these species. Between 2018 and 2021, blood and fecal samples from 370 wild rabbits and 60 Iberian hares were collected. A total of 29 (6.7%; 95%CI: 4.4-9.1) out of 430 sampled animals showed anti-HEV antibodies. By species, the seroprevalences in wild rabbit and Iberian hare were 6.8% (29/370; 95%CI: 4.2-9.3) and 6.7% (4/60; 95%CI: 0.4-13.0), respectively. Seropositive animals were detected on 17 (26.2%; 95%CI: 15.4-36.8) of the 65 sampled hunting estates. The generalized estimating equations model showed that geographical area was a risk factor potentially associated with HEV exposure in wild lagomorphs in the study region. HEV RNA was not detected in any of the 242 (0.0%; 95%CI: 0.0-1.5) fecal samples tested. This is the first large-scale serosurvey performed in wild rabbits in the Iberian Peninsula and in Iberian hares worldwide. Our results provide evidence of low, widespread, and heterogeneous distribution of HEV among wild rabbit and Iberian hare populations in Spanish Mediterranean ecosystems, which indicates a limited role of wild lagomorphs in the maintenance of the virus and a low risk of transmission of HEV to other species, including humans.

A Quadruplex qPCR for Detection and Differentiation of Classic and Natural Recombinant Myxoma Virus Strains of Leporids

A natural recombinant myxoma virus (referred to as ha-MYXV or MYXV-Tol08/18) emerged in the Iberian hare (Lepus granatensis) and the European rabbit (Oryctolagus cuniculus) in late 2018 and mid-2020, respectively. This new virus is genetically distinct from classic myxoma virus (MYXV) strains that caused myxomatosis in rabbits until then, by acquiring an additional 2.8 Kbp insert within the m009L gene that disrupted it into ORFs m009L-a and m009L-b. To distinguish ha-MYXV from classic MYXV strains, we developed a robust qPCR multiplex technique that combines the amplification of the m000.5L/R duplicated gene, conserved in all myxoma virus strains including ha-MYXV, with the amplification of two other genes targeted by the real-time PCR systems designed during this study, specific either for classic MYXV or ha-MYXV strains. The first system targets the boundaries between ORFs m009L-a and m009L-b, only contiguous in classic strains, while the second amplifies a fragment within gene m060L, only present in recombinant MYXV strains. All amplification reactions were validated and normalized by a fourth PCR system directed to a housekeeping gene (18S rRNA) conserved in eukaryotic organisms, including hares and rabbits. The multiplex PCR (mPCR) technique described here was optimized for Taqman^® and Evagreen^® systems allowing the detection of as few as nine copies of viral DNA in the sample with an efficiency > 93%. This real-time multiplex is the first fast method available for the differential diagnosis between classic and recombinant MYXV strains, also allowing the detection of co-infections. The system proves to be an essential and effective tool for monitoring the geographical spread of ha-MYXV in the hare and wild rabbit populations, supporting the management of both species in the field.

Exposure to West Nile Virus in Wild Lagomorphs in Spanish Mediterranean Ecosystems

BACKGROUND

West Nile virus (WNV) is the most widely distributed mosquito-borne flavivirus. Over the past decade, its spread across Europe has raised significant concerns for both public and animal health. Although WNV exposure has been evidenced in various wild mammal species in Spain, no seroepidemiological studies have been conducted on this flavivirus in wild lagomorphs so far.

AIM

This study aimed to assess WNV exposure in European wild rabbit (Oryctolagus cuniculus) and Iberian hare (Lepus granatensis) populations inhabiting Spanish Mediterranean ecosystems.

METHODS

Sera from 540 wild lagomorphs (399 European wild rabbit and 141 Iberian hares), from 106 hunting grounds distributed throughout Andalusia (southern Spain), were collected between the 2018/2019 and 2022/2023 hunting seasons.

RESULTS

Antibodies against flavivirus were detected by blocking enzyme-linked immunosorbent assay (bELISA) in 5.0% (27/540; 95% CI: 3.2-6.8) of the wild lagomorphs. Exposure to WNV was confirmed in 4.8% (19/394; 95% CI: 2.7-6.9) of wild rabbits and 0.7% (1/141; 95% CI: 0.0-2.1) of Iberian hares by virus microneutralisation test. Anti-WNV antibodies were found in wild lagomorphs sampled from three (2.8%) hunting grounds located in western Andalusia during the seasons 2020-2021 and 2021-2022. Remarkably, this spatiotemporal distribution overlaps with the largest outbreak of WNV in Spain. Antibodies against Usutu virus and Bagaza virus were not detected in the wild lagomorph populations analysed.

CONCLUSIONS

This study constitutes the first report of WNV exposure in wild rabbit in Spain and in Iberian hare worldwide. While these species seem not play a primary role in the epidemiology of the virus, they could serve as sentinel for monitoring WNV in Iberian Mediterranean ecosystems.

Rabbit Hemorrhagic Disease Virus in Mexico in 2020-2021: Risk Areas and Climatic Distribution

Mexico is home to 14 species of lagomorphs, 6 of which are endemic. Studies on diseases affecting native lagomorphs are scarce, and in most cases, the impact on their populations remains largely unknown. Rabbit hemorrhagic disease virus (RHDV), especially the RHDV2 variant, causes a serious and extremely contagious disease, resulting in high mortality rates and major declines in wild lagomorph populations. The objectives of this study were to identify disease hotspots and critical biodiversity regions in Mexico through the combined use of disease information and lagomorph distribution maps and to determine the areas of greatest concern. In total, 19 states of Mexico recorded RHDV2 from April 2020 to August 2021, and 12 of them reported the wild species Sylvilagus audubonii, Lepus californicus, and unidentified Leporidae species. The distribution of RHDV2 in Mexico can be closely predicted from climatic variables. RHDV2 hotspots are located in the central-southern area of the Mexican Highlands and the Trans-Mexican Volcanic Belt, where the virus affects multiple species. This knowledge is essential for proposing specific actions to manage and preserve lagomorph populations at risk and address these issues as soon as possible.

[The role of small terrestrial mammals in the epidemiology of rabies]

The examination should help to elucidate the possibility of virus occurrence in free living small terrestrial rodents. The examination was oriented on the following: 1. Animals living in natural surroundings. 2. Rodents examined after injuring man. The examination was carried out by means of the direct immunofluorescent test and, partially, also by biological assay on suckling laboratory mice. In the first part of experiment, more than 10,000 small terrestrial mammals were entrapped, belonging to 16 species. In the second part of experiment, 1,969 rodents, belonging to 12 species, were examined after injuring humans. In these cases, a biological test was also carried out to demonstrate the occurrence of the virus. In neither of the above mentioned experiment the occurrence of rabies was proved.

Detections of Rabbit Hemorrhagic Disease Virus 2 (RHDV2) Following the 2020 Outbreak in Wild Lagomorphs across the Western United States

Rabbit hemorrhagic disease virus 2 (RHDV2) is a highly infectious, often fatal viral disease that affects both domestic and wild lagomorph species. In the United States (U.S.), the virus first was detected in wild lagomorph populations in the southwest in March 2020 and has continued to be detected in native North American lagomorph species over several years. The susceptibility of host species and exact mechanisms of environmental transmission across the U.S. landscape remain poorly understood. Our study aims to increase the understanding of RHDV2 in wild lagomorph populations by providing a history of detection. We present and summarize results from all RHDV2-suspect wild lagomorph morbidity and mortality samples submitted for diagnostic testing in the U.S. from March 2020 to March 2024. Samples were submitted from 916 wild lagomorphs across eight native North American species in 14 western states, of which 313 (34.2%) tested positive by RHDV2 RT-qPCR. Detections of RHDV2 in pygmy rabbits (Brachylagus idahoensis) and riparian brush rabbits (Sylvilagus bachmani riparius) suggest that the risk to threatened and endangered species warrants more attention. Continuing to investigate wild lagomorph morbidity and mortality events and tracking RHDV2 detections over time can help inform on disease epidemiology and wild lagomorph population trends.

Practical Suggestions for Assessing Rabbit Haemorrhagic Disease Virus 2 Risk to Endangered Native Lagomorphs in North America and Southern Africa

A new form of the rabbit haemorrhagic disease virus, RHDV2, first observed in European rabbits, has spread widely among different species of hares in Europe, jackrabbits and cottontails in North America, and hares in southern Africa. However, only limited surveillance studies have been undertaken so far. It is suggested that methods developed for controlling the disease in farmed rabbits in Europe and studying the efficacy of RHDV as a biological control agent in Australia could facilitate epidemiological research on those recently affected lagomorph species. This would enable the assessment of the risk of RHDV2 to native lagomorphs, including endangered species, and the determination of the main host species of RHDV2. Because RHDV2 has not spread equally through all lagomorph species, epidemiological studies could give insights into factors important for determining host susceptibility.

Domestic European Rabbits Oryctolagus cuniculus: A Super-Highway for the Spread of Emergent Viral Diseases to Other Lagomorphs?

We propose that the worldwide spread of several viral diseases in European rabbits (Oryctolagus cuniculus) is facilitated by domestic rabbit meat production and associated international trade. This view is based on published records of the transfer of rabbit haemorrhagic disease viruses (RHDV/RHDV2) between countries and supported by data from the Food and Agriculture Organization (FAO) and the World Animal Health Information System (WAHIS) correlating the amount of rabbit meat produced and the number of rabbit haemorrhagic disease (RHD) outbreaks reported. Although RHDV was mainly confined to European rabbits, outbreak reporting rose after RDHV2 emerged and spread into many other lagomorph species. More than 80 species of native lagomorphs are now at risk from the disease in countries reporting RHD outbreaks. Our findings have implications for the maintenance of both industrial-scale cuniculture and village-scale production to combat poverty, for the future use of viruses for the biological control of pest rabbits and the conservation of native lagomorphs. Greater awareness of the risks of virus transfer in both directions between domestic rabbits and wild lagomorphs is important for future management of domestic rabbits and the conservation of native lagomorphs.

Absence of Crimean-Congo hemorrhagic fever virus in wild lagomorphs and their ticks in Spanish Mediterranean ecosystems

Crimean-Congo hemorrhagic fever virus (CCHFV) is an emerging tick-borne pathogen in different European countries. Since 2013, clinical and fatality cases associated with CCHFV infection have been reported in humans in Spain. During the last few years, endemic circulation of this virus has been detected in ticks and wild ungulates in this country, but the role of other sympatric wild species in the sylvatic cycle of this multi-host virus remains poorly understood. The aims of the present study were to assess exposure to CCHFV in wild lagomorphs in southern Spain, a CCHFV endemic area, and to determine the presence of the virus in ticks feeding on these species. Serum samples from 473 European wild rabbits (Oryctolagus cuniculus) and 162 Iberian hares (Lepus granatensis), and 120 ticks feeding on 85 of these wild lagomorphs were collected on 133 hunting grounds between 2018/2019 and 2021/2022 hunting seasons. The presence of antibodies against CCHFV was assessed in all serum samples using a commercial ELISA, whereas ticks were tested for the presence of CCHFV-RNA by a multiplex RT-qPCR that detects all known genotypes of this virus. None of the 635 (0.0 %; 95 %CI: 0.0-0.6) lagomorphs tested had anti-CCHFV antibodies and CCHFV-RNA was not found in any of the 120 (0.0 %; 95 %CI: 0.0-3.0) ticks analyzed. To the best of the authors knowledge, this is the first epidemiological study conducted on CCHFV in Iberian hare worldwide. Our findings indicate absence of exposure to CCHFV in European wild rabbit and Iberian hare populations, as well as in their ticks, which suggests that they do not seem to play a relevant role in the epidemiology of CCHFV in Mediterranean ecosystems of southern Spain.

Five-year longitudinal surveillance reveals the continual circulation of both alpha- and beta-coronaviruses in Plateau and Gansu pikas (Ochotona spp.) at Qinghai Lake, China1

The discovery of alphacoronaviruses and betacoronaviruses in plateau pikas (Ochotona curzoniae) expanded the host range of mammalian coronavirus (CoV) to a new order - Lagomorpha. However, the diversity and evolutionary relationships of CoVs in these plateau-region-specific animal population remains uncertain. We conducted a five-year longitudinal surveillance of CoVs harboured by pikas around Qinghai Lake, China. CoVs were identified in 33 of 236 plateau pikas and 2 of 6 Gansu pikas (Ochotona cansus), with a total positivity rate of 14.5%, and exhibiting a wide spatiotemporal distribution across seven sampling sites and six time points. Through meta-transcriptomic sequencing and RT-PCR, we recovered 16 near-complete viral genome sequences. Phylogenetic analyses classified the viruses as variants of either pika alphacoronaviruses or betacoronaviruses endemic to plateau pikas from the Qinghai-Tibet Plateau region. Of particular note, the pika-associated betacoronaviruses may represent a novel subgenus within the genus Betacoronavirus. Tissue tropism, evaluated using quantitative real-time PCR, revealed the presence of CoV in the rectal and/or lung tissues, with the highest viral loads at 103.55 or 102.80 RNA copies/μL. Surface plasmon resonance (SPR) assays indicated that the newly identified betacoronavirus did not bind to human or pika Angiotensin-converting enzyme 2 (ACE2) or Dipeptidyl peptidase 4 (DPP4). The findings highlight the ongoing circulation and broadening host spectrum of CoVs among pikas, emphasizing the necessity for further investigation to evaluate their potential public health risks.