Molecular Characterization of Equine Rotavirus Group A Detected in Argentinean Foals During 2009–2014

Genetic and antigenic characterization of two diarrhoeicdominant rotavirus A genotypes G3P[12] and G14P[12] circulating in the global equine population

Equine rotavirus species A (ERVA) G3P[12] and G14P[12] are two dominant genotypes that cause foal diarrhoea with a significant economic impact on the global equine industry. ERVA can also serve as a source of novel (equine-like) rotavirus species A (RVA) reassortants with zoonotic potential as those identified previously in 2013-2019 when equine G3-like RVA was responsible for worldwide outbreaks of severe gastroenteritis and hospitalizations in children. One hurdle to ERVA research is that the standard cell culture system optimized for human rotavirus replication is not efficient for isolating ERVA. Here, using an engineered cell line defective in antiviral innate immunity, we showed that both equine G3P[12] and G14P[12] strains can be rapidly isolated from diarrhoeic foals. The genome sequence analysis revealed that both G3P[12] and G14P[12] strains share the identical genotypic constellation except for VP7 and VP6 segments in which G3P[12] possessed VP7 of genotype G3 and VP6 of genotype I6 and G14P[12] had the combination of VP7 of genotype G14 and VP6 of genotype I2. Further characterization demonstrated that two ERVA genotypes have a limited cross-neutralization. The lack of an in vitro broad cross-protection between both genotypes supported the increased recent diarrhoea outbreaks due to equine G14P[12] in foals born to dams immunized with the inactivated monovalent equine G3P[12] vaccine. Finally, using the structural modelling approach, we provided the genetic basis of the antigenic divergence between ERVA G3P[12] and G14P[12] strains. The results of this study will provide a framework for further investigation of infection biology, pathogenesis and cross-protection of equine rotaviruses.

Equine Rotavirus A under the One Health Lens: Potential Impacts on Public Health

Group A rotaviruses are a well-known cause of viral gastroenteritis in infants and children, as well as in many mammalian species and birds, affecting them at a young age. This group of viruses has a double-stranded, segmented RNA genome with high genetic diversity linked to point mutations, recombination, and, importantly, reassortment. While initial molecular investigations undertaken in the 1900s suggested host range restriction among group A rotaviruses based on the fact that different gene segments were distributed among different animal species, recent molecular surveillance and genome constellation genotyping studies conducted by the Rotavirus Classification Working Group (RCWG) have shown that animal rotaviruses serve as a source of diversification of human rotavirus A, highlighting their zoonotic potential. Rotaviruses occurring in various animal species have been linked with contributing genetic material to human rotaviruses, including horses, with the most recent identification of equine-like G3 rotavirus A infecting children. The goal of this article is to review relevant information related to rotavirus structure/genomic organization, epidemiology (with a focus on human and equine rotavirus A), evolution, inter-species transmission, and the potential zoonotic role of equine and other animal rotaviruses. Diagnostics, surveillance and the current status of human and livestock vaccines against RVA are also reviewed.

Quadruplex Real-Time TaqMan® RT-qPCR Assay for Differentiation of Equine Group A and B Rotaviruses and Identification of Group A G3 and G14 Genotypes

Equine rotavirus A (ERVA) is the leading cause of diarrhea in foals, with G3P[12] and G14P[12] genotypes being the most prevalent. Recently, equine G3-like RVA was recognized as an emerging infection in children, and a group B equine rotavirus (ERVB) was identified as an emergent cause of foal diarrhea in the US. Thus, there is a need to adapt molecular diagnostic tools for improved detection and surveillance to identify emerging strains, understand their molecular epidemiology, and inform future vaccine development. We developed a quadruplex TaqMan® RT-qPCR assay for differentiation of ERVA and ERVB and simultaneous G-typing of ERVA strains, evaluated its analytical and clinical performance, and compared it to (1) a previously established ERVA triplex RT-qPCR assay and (2) standard RT-PCR assay and Sanger sequencing of PCR products. This quadruplex RT-qPCR assay demonstrated high sensitivity (>90%)/specificity (100%) for every target and high overall agreement (>96%). Comparison between the triplex and quadruplex assays revealed only a slightly higher sensitivity for the ERVA NSP3 target using the triplex format (p-value 0.008) while no significant differences were detected for other targets. This quadruplex RT-qPCR assay will significantly enhance rapid surveillance of both ERVA and ERVB circulating and emerging strains with potential for interspecies transmission.

Complete Genome Sequencing Reveals Unusual Equine Rotavirus A of Bat Origin from India

Rotaviruses are the most common viral agents associated with foal diarrhea. Between 2014 and 2017, the annual prevalence of rotavirus in diarrheic foals ranged between 18 and 28% in Haryana (India). Whole-genome sequencing of two equine rotavirus A (ERVA) isolates (RVA/Horse-wt/IND/ERV4/2017 and RVA/Horse-wt/IND/ERV6/2017) was carried out to determine the genotypic constellations (GCs) of ERVAs. The GCs of both the isolates were G3-P[3]-I8-R3-C3-M3-A9-N3-T3-E3-H6, a unique combination reported for ERVAs so far. Both the isolates carried VP6 of genotype I8, previously unreported from equines. Upon comparison with RVAs of other species, the GC of both isolates was identical to that of a bat rotavirus strain, MSLH14, isolated from China in 2012. The nucleotide sequences of the genes encoding VP3, NSP2, and NSP3 shared >95.81% identity with bat RVA strains isolated from Africa (Gabon). The genes encoding VP1, VP2, VP7, NSP1, and NSP4 shared 94.82% to 97.12% nucleotide identities with the human strains which have zoonotic links to bats (RCH272 and MS2015-1-0001). The VP6 genes of both strains were distinct and had the highest similarity of only 87.08% with that of CMH222, a human strain of bat origin. The phylogenetic analysis and lineage studies revealed that VP7 of both isolates clustered in a new lineage (lineage X) of the G3 genotype with bat, human, and alpaca strains. Similarly, VP4 clustered in a distinct P[3] lineage. These unusual findings highlight the terra incognita of the genomic diversity of equine rotaviruses and support the need for the surveillance of RVAs in animals and humans with a "one health" approach. IMPORTANCE Rotaviruses are globally prevalent diarrheal pathogens in young animals including foals, piglets, calves, goats, sheep, cats, and dogs along with humans. The genome of rotaviruses consists of 11 segments, which enables them to undergo reshuffling by reassortment of segments from multiple species during mixed infections. In this study, the prevalence of equine rotaviruses was 32.11% in organized equine farms of North India. The complete genome analysis of two ERVA isolates revealed an unusual genomic constellation, which was previously reported only in a bat RVA strain. A segment-wise phylogenetic analysis revealed that most segments of both isolates were highly similar either to bat or to bat-like human rotaviruses. The occurrence of unusual bat-like rotaviruses in equines emphasizes the need of extensive surveillance of complete genomes of both animal and human rotaviruses with a "one health" approach.

Bacterial and viral enterocolitis in horses: a review

Enteritis, colitis, and enterocolitis are considered some of the most common causes of disease and death in horses. Determining the etiology of these conditions is challenging, among other reasons because different causes produce similar clinical signs and lesions, and also because some agents of colitis can be present in the intestine of normal animals. We review here the main bacterial and viral causes of enterocolitis of horses, including Salmonella spp., Clostridium perfringens type A NetF-positive, C. perfringens type C, Clostridioides difficile, Clostridium piliforme, Paeniclostridium sordellii, other clostridia, Rhodococcus equi, Neorickettsia risticii, Lawsonia intracellularis, equine rotavirus, and equine coronavirus. Diarrhea and colic are the hallmark clinical signs of colitis and enterocolitis, and the majority of these conditions are characterized by necrotizing changes in the mucosa of the small intestine, colon, cecum, or in a combination of these organs. The presumptive diagnosis is based on clinical, gross, and microscopic findings, and confirmed by detection of some of the agents and/or their toxins in the intestinal content or feces.

Identification of a Ruminant Origin Group B Rotavirus Associated with Diarrhea Outbreaks in Foals

Equine rotavirus group A (ERVA) is one of the most common causes of foal diarrhea. Starting in February 2021, there was an increase in the frequency of severe watery to hemorrhagic diarrhea cases in neonatal foals in Central Kentucky. Diagnostic investigation of fecal samples failed to detect evidence of diarrhea-causing pathogens including ERVA. Based on Illumina-based metagenomic sequencing, we identified a novel equine rotavirus group B (ERVB) in fecal specimens from the affected foals in the absence of any other known enteric pathogens. Interestingly, the protein sequence of all 11 segments had greater than 96% identity with group B rotaviruses previously found in ruminants. Furthermore, phylogenetic analysis demonstrated clustering of the ERVB with group B rotaviruses of caprine and bovine strains from the USA. Subsequent analysis of 33 foal diarrheic samples by RT-qPCR identified 23 rotavirus B-positive cases (69.69%). These observations suggest that the ERVB originated from ruminants and was associated with outbreaks of neonatal foal diarrhea in the 2021 foaling season in Kentucky. Emergence of the ruminant-like group B rotavirus in foals clearly warrants further investigation due to the significant impact of the disease in neonatal foals and its economic impact on the equine industry.

Genetic diversity and molecular epidemiological characterization of group A rotaviruses in raw sewage in Jinan by next generation sequencing

OBJECTIVE

To understand the genetic diversity and molecular epidemiology characteristics of group A Rotavirus (RVA) in domestic sewage through next generation sequencing (NGS), and to explore the feasibility and necessity of NGS method for RVA environmental surveillance.

METHODS

In this study, two sewage samples from Jinan each quarter in 2019 were selected for concentration, RNA extraction, and then RT-PCR reaction. The amplified positive products were subjected to NGS. Finally, the results were analyzed for diversity and phylogeny.

RESULTS

A total of 9 G-genotypes and 13 P-genotypes were detected. The Simpson diversity indices in autumn and winter were relatively high. Phylogenetic analysis showed that the dominant types G9 and P[8] were closely related to human-derived sequences.

CONCLUSIONS

This study proves that environmental surveillance as a means to understand the prevalence of RVA in the population is not only feasible but necessary. NGS based environmental surveillance greatly improves our understanding on RVA genetic diversity, and should be encouraged as a sensitive surveillance tool.

Equine rotavirus infection

This review briefly describes the virus classification, clinical signs, epidemiology, diagnosis, disinfection, and vaccines related equine group A rotavirus (RVA) infection. Equine RVA is one of the most important pathogens causing diarrhoea in foals. The main transmission route is faecal–oral, and the clinical signs are diarrhoea, fever, lethargy, and anorexia (decreased suckling). Some human RVA rapid antigen detection kits based on the principles of the immunochromatographic assay are useful for the diagnosis of equine RVA infection. The kits are used in daily clinical practice because of their rapidity and ease of handling. Equine RVA is a non-enveloped virus and is more resistant to disinfectants than enveloped viruses such as equine influenza virus and equine herpesvirus. Although amphoteric soaps and quaternary ammonium compounds are commonly used in veterinary hygiene, they are generally ineffective against equine RVA. Alcohol products, aldehydes, and chlorine- and iodine-based compounds are effective against equine RVA. Inactivated vaccines have been used for equine RVA infection in some countries. Pregnant mares are intramuscularly inoculated with a vaccine, and thus their colostrum has abundant antibodies against RVA at the time of birth. According to G and P classification defined in accordance with the VP7 and VP4 genes, respectively, the predominant equine RVAs circulating in horse populations globally are G3P[12] and G14P[12] equine RVAs, but the vaccines contain only the G3P[12] equine RVA strain. Ideally, a G14P[12] equine RVA should be added as a vaccine strain to obtain a better vaccine effect.

Isolation and characterization of a rare group A rotavirus G13P[18] strain from a diarrhoeic foal in Japan

A rare genotype G13P[18] group A rotavirus (RVA/Horse-tc/JPN/MK9/2019/G13P[18]) was isolated from a diarrhoeic foal for the first time in 28 years. The genotype constellation of the virus was assigned to G13-P[18]-I6-R9-C9-M6-A6-N9-T12-E14-H11 and was the same as that of the first isolated strain, RVA/Horse-tc/GBR/L338/1991/G13P[18]. Phylogenetic analysis suggests that the virus is related to RVA/Horse-tc/GBR/L338/1991/G13P[18] and is distant from typical equine rotaviruses of the G3P[12] and G14P[12] genotypes.

Molecular analyses of G3A/G3B and G14 equine group A rotaviruses detected between 2012 and 2018 in Japan

Equine group A rotaviruses (RVAs) cause diarrhoea in foals. We investigated the G genotypes of 360 RVA-positive samples obtained from diarrhoeic foals between 2012 and 2018 in the Hidaka district of Hokkaido, Japan, through sequence analysis of VP7. All samples were classified into genotypes G3A, G3B and G14. G3B RVAs were detected until 2016, and G3A RVAs were detected from 2016 to 2018. G14 RVAs were detected from 2012 to 2018. Although G3B RVAs had been circulating in Japan for a long time, G3A RVAs suddenly emerged in 2016, and have replaced G3B RVAs since 2017. Molecular analyses of VP7 and VP4 showed that these Japanese G3A RVAs are closely related to North American G3A RVAs detected in 2017. Additionally, whole-genome analyses suggested that genetic reassortments occurred between G3A and G14 RVAs in NSP1, NSP2, NSP4 and NSP5.

Development and evaluation of a one-step multiplex real-time TaqMan® RT-qPCR assay for the detection and genotyping of equine G3 and G14 rotaviruses in fecal samples

BACKGROUND

Equine rotavirus A (ERVA) is the leading cause of diarrhea in neonatal foals and has a negative impact on equine breeding enterprises worldwide. Among ERVA strains infecting foals, the genotypes G3P[12] and G14P[12] are the most prevalent, while infections by strains with other genomic arrangements are infrequent. The identification of circulating strains of ERVA is critical for diagnostic and surveillance purposes, as well as to understand their molecular epidemiology. Current genotyping methods available for ERVA and rotaviruses affecting other animal species rely on Sanger sequencing and are significantly time-consuming, costly and labor intensive. Here, we developed the first one-step multiplex TaqMan® real-time reverse transcription polymerase chain reaction (RT-qPCR) assay targeting the NSP3 and VP7 genes of ERVA G3 and G14 genotypes for the rapid detection and G-typing directly from fecal specimens.

METHODS

A one-step multiplex TaqMan® RT-qPCR assay targeting the NSP3 and VP7 genes of ERVA G3 and G14 genotypes was designed. The analytical sensitivity was assessed using serial dilutions of in vitro transcribed RNA containing the target sequences while the analytical specificity was determined using RNA and DNA derived from a panel of group A rotaviruses along with other equine viruses and bacteria. The clinical performance of this multiplex assay was evaluated using a panel of 177 fecal samples and compared to a VP7-specific standard RT-PCR assay and Sanger sequencing. Limits of detection (LOD), sensitivity, specificity, and agreement were determined.

RESULTS

The multiplex G3 and G14 VP7 assays demonstrated high specificity and efficiency, with perfect linearity. A 100-fold difference in their analytical sensitivity was observed when compared to the singleplex assays; however, this difference did not have an impact on the clinical performance. Clinical performance of the multiplex RT-qPCR assay demonstrated that this assay had a high sensitivity/specificity for every target (100% for NSP3, > 90% for G3 VP7 and > 99% for G14 VP7, respectively) and high overall agreement (> 98%) compared to conventional RT-PCR and sequencing.

CONCLUSIONS

This new multiplex RT-qPCR assay constitutes a useful, very reliable tool that could significantly aid in the rapid detection and G-typing of ERVA strains circulating in the field.

Evaluation of inactivated vaccines against equine group A rotaviruses by use of a suckling mouse model

BACKGROUND

Equine group A rotaviruses (RVAs) cause diarrhea in suckling foals. The dominant RVAs circulating among horses worldwide, including Japan, are G3P[12] and/or G14P[12] genotypes. Inactivated vaccines containing a G3P[12] RVA are commercially available in some countries for prevention of diarrhea caused by equine RVAs. However, there is no reported evidence whether vaccines containing a G3P[12] RVA are effective against G14P[12] RVAs or whether using a G14P[12] RVA results in a more effective vaccine. This study used a suckling mouse model to evaluate the effectiveness of inactivated vaccines containing G3P[12] (G3 vaccine) or G14P[12] (G14 vaccine) RVAs against G3P[12] and G14P[12] RVAs.

METHODS

Female mice were inoculated twice with G3 or G14 vaccines, and were then mated. After parturition, suckling mice were challenged with one of either two G3P[12] RVAs, two G14P[12] RVAs, or one G13P[18] RVA. After virus inoculation, suckling mice were observed for diarrhea, and the incidence rates of diarrhea in the vaccinated groups were compared with those in the non-vaccinated groups.

RESULTS

Following G3P[12] RVA challenge, suckling mice in the G3 and G14 vaccinated groups had significantly lower rates of diarrhea incidence than did those in the non-vaccinated group, and the rates in the G3 vaccinated group tended to be lower than in the G14 vaccinated group. Following G14P[12] RVA challenge, suckling mice in the G14 vaccinated group had significantly lower rates of diarrhea incidence than did those in the non-vaccinated and G3 vaccinated groups. The G3 and G14 vaccines did not reduce the rate when challenged with the G13P[18] RVA.

CONCLUSION

The mouse model showed that the G3 and G14 vaccines were both effective against G3P[12] RVAs, and that the G14 vaccine was effective against G14P[12] RVAs. These results suggest that at least a G14 RVA strain should be included in as a vaccine strain.

Detection, molecular characterization and phylogenetic analysis of G3P[12] and G14P[12] equine rotavirus strains co-circulating in central Kentucky

Equine rotavirus A (ERVA) is the leading cause of diarrhea in neonatal foals and a major health problem to the equine breeding industry worldwide. The G3P[12] and G14P[12] ERVA genotypes are the most prevalent in foals with diarrhea. Control and prevention strategies include vaccination of pregnant mares with an inactivated vaccine containing a prototype ERVA G3P[12] strain with limited and controversial field efficacy. Here, we performed the molecular characterization of ERVA strains circulating in central Kentucky using fecal samples collected during the 2017 foaling season. The data indicated for the first time that the G14P[12] genotype is predominant in this region in contrast to a previous serotyping study where only G3 genotype strains were reported. Overall, analysis of antigenic sites in the VP7 protein demonstrated the presence of several amino acid substitutions in the epitopes exposed on the surface including a non-conserved N-linked glycosylation site (D123N) in G14P[12] strains, while changes in antigenic sites of VP8* were minor. Also, we report the successful isolation of three ERVA G14P[12] strains which presented a high identity with other G14 strains from around the world. These may constitute ideal reference strains to comparatively study the molecular biology of G3 and G14 strains and perform vaccine efficacy studies following heterologous challenge in the future.