Presence and Diversity of Different Enteric Viruses in Wild Norway Rats (Rattus norvegicus)

Investigation of caliciviruses and astroviruses in Gabonese rodents: A possible influence of national and international trade on the spread of enteric viruses

Caliciviruses (Caliciviridae) and astroviruses (Astroviridae) are among the leading cause of non-bacterial foodborne disease and gastroenteritis in human. These non-enveloped RNA viruses infect a wide range of vertebrate species including rodents. Rodents are among the most important hosts of infectious diseases globally and are responsible for over 80 zoonotic pathogens that affect humans. Therefore, screening pathogens in rodents will be is necessary to prevent cross-species transmission to prevent zoonotic outbreaks. In the present study, we screened caliciviruses and astroviruses in order to describe their diversity and whether they harbor strains that can infect humans. RNA was then extracted from intestine samples of 245 rodents and retrotranscribed in cDNA to screen caliciviruses and astroviruses by PCRs. All the samples tested negative for caliciviruses and while astroviruses were detected in 18 (7.3%) samples of Rattus rattus species. Phylogenetic analyses based on the RdRp gene showed that all the sequences belonged to Mamastrovirus genus in which they were genetically related to R. rattus related AstVs previously detected in Gabon or in Rattus spp. AstV from Kenya and Asia. These findings suggested that transportation such as land and railway, as well national and international trade, are likely to facilitate spread of AstVs by the dissemination of rodents.

Exploring the Potential of Muridae as Sentinels for Human and Zoonotic Viruses

In recent years, the transmission of viruses from wildlife to humans has raised significant public health concerns, exemplified by the COVID-19 pandemic caused by the betacoronavirus SARS-CoV-2. Human activities play a substantial role in increasing the risk of zoonotic virus transmission from wildlife to humans. Rats and mice are prevalent in urban environments and may act as reservoirs for various pathogens. This study aimed to evaluate the presence of zoonotic viruses in wild rats and mice in both urban and rural areas, focusing on well-known zoonotic viruses such as betacoronavirus, hantavirus, arenavirus, kobuvirus, and monkeypox virus, along with other viruses occasionally detected in rats and mice, including rotavirus, norovirus, and astrovirus, which are known to infect humans at a high rate. A total of 128 animals were captured, including 70 brown rats (Rattus norvegicus), 45 black rats (Rattus rattus), and 13 house mice (Mus musculus), and feces, lung, and liver were collected. Among brown rats, one fecal sample tested positive for astrovirus RNA. Nucleotide sequencing revealed high sequence similarity to both human and rat astrovirus, suggesting co-presence of these viruses in the feces. Murine kobuvirus (MuKV) was detected in fecal samples from both black (n = 7) and brown (n = 6) rats, primarily from urban areas, as confirmed by sequence analysis. These findings highlight the importance of surveillance and research to understand and mitigate the risks associated with the potential transmission of pathogens by rodents.

Detection of multiple human enteropathogens in Norway rats (Rattus norvegicus) from an under-resourced neighborhood of Vancouver, British Columbia

Urban Norway rats (Rattus norvegicus) can carry various human pathogens, and may be involved in pathogen propagation and transmission to humans. From January 31-August 14, 2021, a community outbreak of Shigella flexneri serotype 2a occurred among unhoused or poorly housed people in the Downtown Eastside neighborhood of Vancouver, British Columbia, Canada. The source could not be identified; however, patients reported contact with rats, and previous studies indicated transmission of rat-associated zoonotic pathogens among the unhoused or poorly housed residents of this neighborhood. The study objective was to determine if rats trapped in the outbreak area were carriers of Shigella spp. and other zoonotic enteric pathogens. From March 23-April 9, 2021, 22 rats were lethally trapped within the outbreak area. Colonic content was analyzed using the BioFire FilmArray Gastrointestinal (multiplex PCR) panel for human enteropathogens, which detected: Campylobacter spp. (9/22), Clostridioides difficile (3/22), Yersinia enterocolitica (5/22), Cryptosporidium spp. (8/22), Giardia duodenalis (5/22), Rotavirus A (1/22), enteroaggressive Escherichia coli (2/22), enteropathogenic E. coli (10/22), and Shigella spp. or enteroinvasive E. coli (EIEC) (3/22). An ipaH PCR assay was used for targeted detection of Shigella spp./EIEC, with five rats positive. Two samples contained insertion sites unique to S. flexneri isolated from the human outbreak. This study highlights the potential for rats to carry a broad range of human pathogens, and their possible role in pathogen maintenance and/or transmission.

First Detection of Hepatitis E Virus (Rocahepevirus ratti Genotype C1) in Synanthropic Norway Rats (Rattus norvegicus) in Romania

Hepatitis E virus (HEV) is an emerging zoonotic pathogen with different viral genera and species reported in a wide range of animals. Rodents, particularly rats, carry the specific genus rat HEV (Rocahepevirus genus, genotype C1) and are exposed occasionally to HEV-3 (Paslahepevirus genus, genotype 3), a zoonotic genotype identified in humans and widely distributed in domestic and feral pigs. In this study, the presence of HEV was investigated in synanthropic Norway rats from Eastern Romania, in areas where the presence of HEV-3 was previously reported in pigs, wild boars and humans. Using methods capable of detecting different HEV species, the presence of HEV RNA was investigated in 69 liver samples collected from 52 rats and other animal species. Nine rat liver samples were identified as being positive for rat HEV RNA (17.3%). High sequence identity (85-89% nt) was found with other European Rocahepevirus. All samples tested from other animal species, within the same environment, were negative for HEV. This is the first study to demonstrate the presence of HEV in rats from Romania. Since rat HEV has been reported to cause zoonotic infections in humans, this finding supports the need to extend the diagnosis of Rocahepevirus in humans with suspicion of hepatitis.

Comparison of viral communities in the blood, feces and various tissues of wild brown rats (Rattus norvegicus)

Viral diseases caused by new outbreaks of viral infections pose a serious threat to human health. Wild brown rats (Rattus norvegicus), considered one of the world's largest and most widely distributed rodents, are host to various zoonotic pathogens. To further understand the composition of the virus community in wild brown rats and explore new types of potentially pathogenic viruses, viral metagenomics was conducted to investigate blood, feces, and various tissues of wild brown rats captured from Zhenjiang, China. Results indicated that the composition of the virus community in different samples showed significant differences. In blood and tissue samples, members of the Parvoviridae and Anelloviridae form the main body of the virus community. Picornaviridae, Picobirnaviridae, and Astroviridae made up a large proportion of fecal samples. Several novel genome sequences from members of different families, including Anelloviridae, Parvoviridae, and CRESS DNA viruses, were detected in both blood and other samples, suggesting that they have the potential to spread across organs to cause viremia. These viruses included not only strains closely related to human viruses, but also a potential recombinant virus. Multiple dual-segment picornaviruses were obtained from fecal samples, as well as virus sequences from the Astroviridae and Picornaviridae. Phylogenetic analysis showed that these viruses belonged to different genera, with multiple viruses clustered with other animal viruses. Whether they have pathogenicity and the ability to spread across species needs further study.

Lack of molecular evidence of fecal-borne viruses in capybaras from São Paulo state, Brazil, 2018-2020: a minor public health issue

Capybara (Hydrochoerus hydrochaeris) is the world's largest rodent species distributed throughout South America. These animals are incredibly tolerant to anthropogenic environments and are occupying large urban centers. Capybaras are known to carry potentially zoonotic agents, including R. rickettsia, Leishmania spp., Leptospira spp., Trypanosoma spp., Salmonella spp., Toxoplasma gondii, and rabies virus. Focusing on the importance of monitoring potential sources of emerging zoonotic viruses and new viral reservoirs, the aim of the present study was to assess the presence of fecal-borne viruses in the feces of capybaras living in urban parks in São Paulo state, Brazil. A total of 337 fecal samples were collected between 2018 and 2020 and screened for the following: (i) Rotavirus group A (RVA) by ELISA; (ii) non-RVA species and Picobirnavirus (PBV) using PAGE; (iii) Human Bocaparvovirus (HBoV), Bufavirus (BuV), Tusavirus (TuV), and Cutavirus (CuV) qPCR; (iv) Human Enterovirus (EV), Norovirus GII (NoV), and Hantavirus by in houses RT-qPCR; (v) SARS-CoV-2 via commercial RT-qPCR kit assay; and (vi) Astrovirus (AstV) and Adenovirus (AdV) using conventional nested (RT)-PCRs. All fecal samples tested were negative for fecal-borne viruses. This study adds further evidence that the fecal-borne viruses is a minor public health issue in Brazilian capybaras, at least during the surveillance period and surveyed areas. Continuous monitoring of sylvatic animals is essential to prevent and control the emergence or re-emergence of newly discovered virus as well as viruses with known zoonotic potential.

Rotaviruses in Wild Ungulates from Germany, 2019-2022

Rotavirus A (RVA) is an important cause of diarrhea in humans and animals. However, RVA in wild animals has only scarcely been investigated so far. Here, the presence of RVA in wild ungulates hunted between 2019 and 2022 in Brandenburg, Germany, was investigated using real-time RT-PCR and sequencing of RT-PCR products. By analyzing intestinal contents, RVA-RNA was detected in 1.0% (2/197) of wild boar (Sus scrofa), 1.3% (2/152) of roe deer (Capreolus capreolus), and 2.1% (2/95) of fallow deer (Dama dama) but not in 28 red deer (Cervus elaphus) samples. Genotyping identified G3P[13] strains in wild boar, which were closely related to previously described pig and wild boar strains. Genotype G10P[15] strains, closely related to strains from roe deer, sheep, or cattle, were found in roe deer. The strains of fallow deer represented genotype G3P[3], clustering in a group containing different strains from several hosts. The results indicated a low prevalence of RVA in wild ungulates in Germany. Associations of specific genotypes with certain ungulate species seem to exist but should be confirmed by analyses of more samples in the future.

Detection of Hepatitis E Virus Genotype 3 in Feces of Capybaras (Hydrochoeris hydrochaeris) in Brazil

Hepatitis E virus (HEV) is an emerging zoonotic pathogen associated with relevant public health issues. The aim of this study was to investigate HEV presence in free-living capybaras inhabiting urban parks in São Paulo state, Brazil. Molecular characterization of HEV positive samples was undertaken to elucidate the genetic diversity of the virus in these animals. A total of 337 fecal samples were screened for HEV using RT-qPCR and further confirmed by conventional nested RT-PCR. HEV genotype and subtype were determined using Sanger and next-generation sequencing. HEV was detected in one specimen (0.3%) and assigned as HEV-3f. The IAL-HEV_921 HEV-3f strain showed a close relationship to European swine, wild boar and human strains (90.7-93.2% nt), suggesting an interspecies transmission. Molecular epidemiology of HEV is poorly investigated in Brazil; subtype 3f has been reported in swine. This is the first report of HEV detected in capybara stool samples worldwide.

Genome sequence analysis of a novel rotavirus strain indicates a broad genetic diversity of rotavirus A in shrews

Rotavirus A (RVA) is an etiologic agent of diarrhea in humans and animals. It shows a high degree of genetic heterogeneity. Although distinct associations of RVA genotypes with certain host species are common, interspecies-transmission has also been described. Recently, RVA strains, which are genetically distinct and cluster basally to all other RVA strains in phylogenetic trees, have been identified in common shrews (Sorex araneus). Here, the genome sequence analysis of another RVA strain (RVA/Common Shrew-wt/GER/KS11-0893/2010/G42P[58]) from a common shrew from Germany is described. Generally, the strain shows low sequence identities to established strains, which is reflected by the assessment of the novel genotypes G42-P[58]-I32-R28-C24-M24-A39-N28-T28-E32-H28 to its genome segments. Specifically, the strain is phylogenetically distant from previously described RVA strains of common shrews, whereas it is more closely related to other avian and mammalian RVA strains including those from Asian house shrews (Suncus murinus). The results indicate that a broad variety of diverse RVA strains can be found in shrews suggesting a significant role of these animals in rotavirus evolution.

Diversity of human astroviruses in Germany 2018 and 2019

Aim of this study was to investigate the molecular diversity of human astroviruses (HAstV) in Germany. A follow-up study was performed with human stool samples collected in 2018-2019, which were genotyped retrospectively. A total of 2645 stool samples, collected between January 2018 and December 2019 from sporadic cases and outbreaks of acute gastroenteritis were analyzed. An algorithm of PCR systems was used to characterize human astrovirus. Human astroviruses were found in 40 samples (positive rate: 1.6%). During the study period, children aged 1-2 years (48%) were most affected by HAstV. Genotyping revealed a number of nine circulating genotypes representing four human Mamastrovirus species. Strain MLB1 was predominant in the study population with a detection rate of 25% followed by HAstV1 with a positive rate of 20%. The diversity of astrovirus genotypes seems to be rather stable in Germany in the last years. A clustering of regionally and/or temporally linked human astroviruses in Germany was not detectable.

Screen the unforeseen: Microbiome-profiling for detection of zoonotic pathogens in wild rats

Wild rats can host various zoonotic pathogens. Detection of these pathogens is commonly performed using molecular techniques targeting one or a few specific pathogens. However, this specific way of surveillance could lead to (emerging) zoonotic pathogens staying unnoticed. This problem may be overcome by using broader microbiome-profiling techniques, which enable broad screening of a sample's bacterial or viral composition. In this study, we investigated if 16S rRNA gene amplicon sequencing would be a suitable tool for the detection of zoonotic bacteria in wild rats. Moreover, we used virome-enriched (VirCapSeq) sequencing to detect zoonotic viruses. DNA from kidney samples of 147 wild brown rats (Rattus norvegicus) and 42 black rats (Rattus rattus) was used for 16S rRNA gene amplicon sequencing of the V3-V4 hypervariable region. Blocking primers were developed to reduce the amplification of rat host DNA. The kidney bacterial composition was studied using alpha- and beta-diversity metrics and statistically assessed using PERMANOVA and SIMPER analyses. From the sequencing data, 14 potentially zoonotic bacterial genera were identified from which the presence of zoonotic Leptospira spp. and Bartonella tribocorum was confirmed by (q)PCR or Sanger sequencing. In addition, more than 65% of all samples were dominated (>50% reads) by one of three bacterial taxa: Streptococcus (n = 59), Mycoplasma (n = 39) and Leptospira (n = 25). These taxa also showed the highest contribution to the observed differences in beta diversity. VirCapSeq sequencing in rat liver samples detected the potentially zoonotic rat hepatitis E virus in three rats. Although 16S rRNA gene amplicon sequencing was limited in its capacity for species level identifications and can be more difficult to interpret due to the influence of contaminating sequences in these low microbial biomass samples, we believe it has potential to be a suitable pre-screening method in the future to get a better overview of potentially zoonotic bacteria that are circulating in wildlife.

OUP accepted manuscript

Species A rotaviruses (RVAs) are important aetiological agents of severe diarrhoea in young children. They are also widely distributed in mammals and birds, and increasing evidence indicates the possibility of zoonotic transmission of RVA strains between animals and humans. Moreover, reassortment of the eleven segments of the RVA genome can result in rapid biological changes and may influence pathogenic properties. Here, the nearly complete genome of an RVA strain from a common shrew (Sorex araneus) was sequenced, which showed high nucleotide sequence similarity to additionally determined partial sequences from common shrew RVAs but only very low identity (below 68 per cent) to RVAs from other animal species and humans. New genotypes were assigned to most genome segments of the novel common shrew RVA strain KS14/269, resulting in the genome constellation G39-P[55]-I27-R26-C22-M22-A37-N26-T26-E30-H26. Phylogenetic analyses clustered the common shrew RVAs as ancestral branches of other mammalian and avian RVAs for most of the genome segments, which is in contrast to the phylogeny of the hosts. Nevertheless, conserved sequences typical for all RVAs were identified at the 5ʹ- and 3ʹ- non-coding segment termini. To explore whether the common shrew RVA can exchange genetic material with other mammalian RVAs by reassortment, a reverse genetics system based on the simian RVA strain SA11 was used. However, no viable reassortants could be rescued by exchanging the VP4-, VP6-, or VP7-encoding genome segment alone or in combinations. It can be concluded that highly divergent RVAs are present in common shrews, indicating an evolution of these viruses largely separated from other mammalian and avian RVAs. The zoonotic potential of the virus seems to be low but needs to be further analysed in future.

Serological Evidence of Hepatitis E Virus Infection in Semi-Domesticated Eurasian Tundra Reindeer (Rangifer tarandus tarandus) in Norway

Hepatitis E virus (HEV) is a common cause of viral hepatitis in humans. In developing countries, HEV-infections seem to be mainly associated with pigs, but other animal species may be involved in viral transmission. Recently, anti-HEV antibodies were detected in Norwegian wild reindeer. Here, we investigated anti-HEV seroprevalence in Norwegian semi-domesticated reindeer, animals in closer contact with humans than their wild counterparts. Blood samples (n = 516) were obtained from eight reindeer herds during the period 2013–2017 and analysed with a commercial enzyme-linked immunosorbent assay designed for detecting anti-HEV antibodies in livestock. Antibodies were found in all herds and for all sampling seasons. The overall seroprevalence was 15.7% (81/516), with adults showing a slightly higher seroprevalence (18.0%, 46/256) than calves (13.5%, 35/260, p = 0.11). The seroprevalence was not influenced by gender or latitude, and there was no temporal trend (p > 0.15). A positive association between the presence of anti-HEV antibodies and antibodies against alphaherpesvirus and pestivirus, detected in a previous screening, was found (p < 0.05). We conclude that Norwegian semi-domesticated reindeer are exposed to HEV or an antigenically similar virus. Whether the virus is affecting reindeer health or infects humans and poses a threat for human health remains unknown and warrants further investigations.

Gut microbiota dysbiosis associated with plasma levels of Interferon-γ and viral load in patients with acute hepatitis E infection

Few studies have focused on the effect of hepatitis E virus (HEV) infection on gut microbiota. To explore the relationship between changes in gut microbiota and inflammatory factors and viral load, we conducted a comparative study of 33 patients with acute hepatitis E (AHE) patients and 25 healthy controls (HCs) using high-throughput 16S ribosomal ribonucleic acid gene sequencing. Shannon and Simpson's indices showed no significant differences in bacterial diversity between the AHE and HCs groups. Proteobacteria, Gammaproteobacteria, and Enterobacteriaceae were most abundant in the AHE group, which contributed to the difference between the gut microbiota of the AHE and HCs groups, and the same difference between the HEV-RNA-positive and HEV-RNA-negative groups. Functional prediction analysis showed that ribosome, purine metabolism, and two-component system were the top three pathways. Compared with the AHE group with normal interferon (IFN)-γ, Proteobacteria, Gammaproteobacteria, Xanthomonadaceae, and Enterobacteriaceae were more abundant in the high-IFN-γ group. The abundance of Gammaproteobacteria was positively correlated with the level of serum alanine transaminase and total bilirubin. The abundance of Gammaproteobacteria could discriminate AHE patients from HCs, and could better predict the severity of AHE patients. We believe that our findings will contribute toward a novel treatment strategy for AHE.