Identification of astroviruses in bovine and buffalo calves with enteritis

Metatranscriptomic assessment of diarrhoeic faeces reveals diverse RNA viruses in rotavirus group A infected piglets and calves from India

RNA viruses are a major group contributing to emerging infectious diseases and neonatal diarrhoea, causing morbidity and mortality in humans and animals. Hence, the present study investigated the metatranscriptomic-derived faecal RNA virome in rotavirus group A (RVA)-infected diarrheic piglets and calves from India. The viral genomes retrieved belonged to Astroviridae in both species, while Reoviridae and Picornaviridae were found only in piglets. The nearly complete genomes of porcine RVA (2), astrovirus (AstV) (6), enterovirus G (EVG) (2), porcine sapelovirus (PSV) (2), Aichivirus C (1), and porcine teschovirus (PTV) (1) were identified and characterised. In the piglet, AstVs of PAstV2 (MAstV-26) and PAstV4 (MAstV-31) lineages were predominant, followed by porcine RVA, EVG, PSV, Aichivirus C, teschovirus (PTV-17) in decreasing order of sequence reads. In contrast, AstV accounted for the majority of reads in bovines and belonged to MAstV-28 and a proposed MAstV-35. Both RVA G4P[6] strains exhibited prototype Gottfried strains like a genotypic constellation of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. Ten out of eleven genes were of porcine origin, while the VP7 gene clustered with G4-lineage-1, consisting of human strains, suggesting a natural porcine-human reassortant. In the recombination analysis, multiple recombination events were detected in the PAstV4 and PAstV2 genomes, pointing out that these viruses were potential recombinants. Finally, the study finds diverse RNA virome in Indian piglets and calves for the first time, which may have contributed to diarrhoea. In the future, the investigation of RNA virome in animals will help in revealing pathogen diversity in multifactorial diseases, disease outbreaks, monitoring circulating viruses, viral discovery, and evaluation of their zoonotic potential.

Genetic characterization of canine astrovirus in non-diarrhea dogs and diarrhea dogs in Vietnam and Thailand reveals the presence of a unique lineage

The role of canine astrovirus (CaAstV) in canine gastrointestinal disease (GID) is unknown. In this study, a total of 327 fecal swab (FS) samples were collected, including 113 FSs in Vietnam (46 samples from healthy dogs and 67 samples from GID dogs) and 214 FSs in Thailand (107 samples from healthy dogs and 107 samples from GID dogs). Overall, the prevalence of CaAstV in Vietnam and Thailand was 25.7% (29/113) and 8.9% (19/214), respectively. CaAstV was detected in both non-diarrhea dogs (21.7 and 7.5%) and diarrhea dogs (28.4% and 10.3%), respectively, in Vietnam and Thailand. In both countries, CaAstV was frequently detected in puppies under 6 months of age (23.3%) (p = 0.02). CaAstV-positive samples in Vietnam and Thailand were identified as co-infected with canine parvovirus, canine enteric coronavirus, canine distemper virus, and canine kobuvirus. The complete coding sequence of seven Vietnamese CaAstV and two Thai CaAstV strains were successfully characterized. Phylogenetic analyses showed that Vietnamese and Thai CaAstV strains were genetically close to each other and related to the Chinese strains. Furthermore, analysis of complete coding sequences indicated that the OR220030_G21/Thailand/2021 strain formed a unique lineage, whereas no recombination event was found in this study, suggesting that this strain might be an original lineage. In summary, this is the first study to report the presence of CaAstV in dogs with and without diarrhea in Vietnam and Thailand, and it was most often found in puppies with diarrhea. Our results highlight the importance of the CaAstV in dog populations and the need for continued surveillance of these emerging pathogens.

Identification of new astroviruses in synanthropic squamates

Astroviruses have been identified in a wide variety of animal species and are associated with gastro-intestinal disease in humans. Pathologies due to extra-intestinal localization are known in different hosts. We report the detection of astroviruses in synanthropic squamate reptile species (Podercis siculus and Tarentola mauritanica). Fecal samples were collected from 100 squamates from urban and peri-urban areas of three regions in South Italy and tested for the presence of astroviruses using a broadly reactive (pan-astrovirus) RT-PCR protocol targeting the RNA-dependent RNA polymerase. Astrovirus RNA was detected in 11% of the samples and for six strains a 3 kb-long fragment at the 3' end of the genome was sequenced, obtaining information on the complete capsid-encoding ORF2 sequence. Viral RNA was also detected in the brain of one of the positive animals. The sequences generated from the astrovirus strains shared low nucleotide identities in the ORF2 (< 43.7%) with other known reptilian astrovirus sequences, hinting to the massive genetic diversity of members of this viral family. Based on the partial RdRp gene of the sequenced strains, however, we observed species-specific patterns, regardless of the geographic origin of the animals, and we also identified a possible inter-species transmission event between geckoes and lizards.

An outbreak of neonatal enteritis in buffalo calves associated with astrovirus

Background

Enteritis of an infectious origin is a major cause of productivity and economic losses to cattle producers worldwide. Several pathogens are believed to cause or contribute to the development of calf diarrhea. Astroviruses (AstVs) are neglected enteric pathogens in ruminants, but they have recently gained attention because of their possible association with encephalitis in humans and various animal species, including cattle.

Objectives

This paper describes a large outbreak of neonatal diarrhea in buffalo calves (Bubalus bubalis), characterized by high mortality, which was associated with an AstV infection.

Methods

Following an enteritis outbreak characterized by high morbidity (100%) and mortality (46.2%) in a herd of Mediterranean buffaloes (B. bubalis) in Italy, 16 samples from buffalo calves were tested with the molecular tools for common and uncommon enteric pathogens, including AstV, kobuvirus, and torovirus.

Results

The samples tested negative for common enteric viral agents, including Rotavirus A, coronavirus, calicivirus, pestivirus, kobuvirus, and torovirus, while they tested positive for AstV. Overall, 62.5% (10/16) of the samples were positive in a single round reverse transcription polymerase chain reaction (PCR) assay for AstV, and 100% (16/16) were positive when nested PCR was performed. The strains identified in the outbreak showed a clonal origin and shared the closest genetic relationship with bovine AstVs (up to 85% amino acid identity in the capsid).

Conclusions

This report indicates that AstVs should be included in a differential diagnosis of infectious diarrhea in buffalo calves.

Comparison of gut viral communities in diarrhoea and healthy dairy calves

Calf diarrhoea has been a major cause of economic losses in the global dairy industry. Many factors, including multiple pathogen infections, can directly or indirectly cause calf diarrhoea. This study compared the faecal virome between 15 healthy calves and 15 calves with diarrhoea. Significantly lower diversity of viruses was found in samples from animals with diarrhoea than those in the healthy ones, and this feature may also be related to the age of the calves. Viruses belonging to the families Astroviridae and Caliciviridae that may cause diarrhoea in dairy calves have been characterized, which revealed that reads of caliciviruses and astroviruses in diarrhoea calves were much higher than those in healthy calves. Five complete genomic sequences closely related to Smacoviridae have been identified, which may participate in the regulation of the gut virus community ecology of healthy hosts together with bacteriophages. This research provides a theoretical basis for further understanding of known or potential enteric pathogens related to calf diarrhoea.

Genomic features of first bovine astrovirus detected in Egypt

Bovine astrovirus (BAstV) is a small single-stranded RNA virus, which belongs taxonomically to genus Mamastrovirus under the family Astroviridae. The BAstV is strongly linked to neonatal diarrhea of calves. A few studies are available on BAstV, mainly from Asia, and to a lesser extent from Europe, South America, and Africa. There is only one report from Egypt, in which BAstV was found in diarrheic calves, either in single- or co-infections, based on reverse transcription polymerase chain reaction (RT-PCR) and BAstV-polymerase enzyme targeting primers. One of the samples was further subjected to genomic characterization using Illumina platform for next generation sequencing (NGS). After being processed, the returned BAstV complete genome was subjected to sequence and phylogenetic analysis in comparison to reference strains. The BAstV open reading frames (ORF1a, ORF1b, and ORF2) followed a nearly similar genetic topology, as they belonged to the same unclassified lineage, which was earlier proposed as BAstV-lineage 1, and is known to be disseminated worldwide. This close phylogenetic relationship between the study strain and other members of this lineage was further confirmed by high nucleotide and amino acid (aa) identities. Additionally, a total of 24 unique aa residues were found through the entire BAstV genome. As being the first report in Egypt, indeed Africa, we believe that this record shall be useful in either taxonomic classification or epidemiological tracking of BAstV. The status of BAstV in Egypt should be carefully investigated with possible to-be-implemented precautions for the protection of animal-raising industries.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-021-00668-5.

Prevalence of bovine astroviruses and their genotypes in sampled Chinese calves with and without diarrhoea

Bovine astrovirus (BoAstV) belongs to genus Mamastravirus (MAstV). It can be detected in the faeces of both diarrhoeal and healthy calves. However, its prevalence, genetic diversity, and association with cattle diarrhoea are poorly understood. In this study, faecal samples of 87 diarrhoeal and 77 asymptomatic calves from 20 farms in 12 provinces were collected, and BoAstV was detected with reverse transcription-polymerase chain reaction (RT-PCR). The overall prevalence rate of this virus in diarrhoeal and asymptomatic calves was 55.17 % (95 % CI: 44.13, 65.85 %) and 36.36 % (95 % CI: 25.70, 48.12 %), respectively, indicating a correlation between BoAstV infection and calf diarrhoea (OR=2.15, P=0.024). BoAstV existed mainly in the form of co-infection (85.53 %) with one to five of nine viruses, and there was a strong positive correlation between BoAstV co-infection and calf diarrhoea (OR=2.83, P=0.004). Binary logistic regression analysis confirmed this correlation between BoAstV co-infection and calf diarrhoea (OR=2.41, P=0.038). The co-infection of BoAstV and bovine rotavirus (BRV) with or without other viruses accounted for 70.77 % of all the co-infection cases. The diarrhoea risk for the calves co-infected with BoAstV and BRV was 8.14-fold higher than that for the calves co-infected with BoAstV and other viruses (OR=8.14, P=0.001). Further, the co-infection of BoAstV/BRV/bovine kobuvirus (BKoV) might increase the risk of calf diarrhoea by 14.82-fold, compared with that of BoAstV and other viruses (OR=14.82, P <0.001). Then, nearly complete genomic sequences of nine BoAstV strains were assembled by using next-generation sequencing (NGS) method. Sequence alignment against known astrovirus (AstV) strains at the levels of both amino acids and nucleotides showed a high genetic diversity. Four genotypes were identified, including two known genotypes MAstV-28 (n=3) and MAstV-33 (n=2) and two novel genotypes designated tentatively as MAstV-34 (n=1) and MAstV-35 (n=3). In addition, seven out of nine BoAstV strains showed possible inter-genotype recombination and cross-species recombination. Therefore, our results increase the knowledge about the prevalence and the genetic evolution of BoAstV and provide evidence for the association between BoAstV infection and calf diarrhoea.

Detection of mink astrovirus in Poland and further phylogenetic comparison with other European and Canadian astroviruses

Mink astrovirus infection remains a poorly understood disease entity, and the aetiological agent itself causes disease with a heterogeneous course, including gastrointestinal and neurological symptoms. This paper presents cases of astrovirus infection in mink from continental Europe. RNA was isolated from the brains and intestines of animals showing symptoms typical of shaking mink syndrome (n = 6). RT-PCR was used to amplify astrovirus genetic material, and the reaction products were separated on a 1% agarose gel. The specificity of the reaction was confirmed by sequencing fragment coding RdRP protein (length of sequencing product 170 bp) from all samples. The presence of astrovirus RNA was detected in each of the samples tested. Sequencing and bioinformatic analysis indicated the presence of the same variant of the virus in all samples. Comparison of the variant with the sequences available in bioinformatics databases confirmed that the Polish isolates form a separate clade, closely related to Danish isolates. The dissimilarity of the Polish variant to those isolated in other countries ranged from 2.4% (in relation to Danish isolates) to 7.1% (in relation to Canadian isolates). Phylogenetic relationships between variants appear to be associated with the geographic distances between them. To our knowledge, this work describes the first results on the molecular epidemiology of MAstV in continental Europe. The detection of MAstV in Central Europe indicates the need for further research to broaden our understanding of the molecular epidemiology of MAstV in Europe.