Genetic characterization and phylogenetic analysis of feline astrovirus from Anhui province in eastern China

Monitoring and characterization of canine and feline astroviruses in domestic dogs and cats in Thailand

Astrovirus (AstV) is an RNA virus that causes gastroenteritis in humans and various mammal species, including dogs and cats. In this study, we conducted a survey of canine and feline astroviruses in domestic dogs and cats in Bangkok and its vicinity in Thailand. From January 2022 to December 2023, we collected a total of 1,498 rectal swab samples from domestic dogs (n = 862) and cats (n = 636) at private small animal hospitals in Bangkok, Nonthaburi, and Samut Prakran, Thailand. The positive rate for canine astrovirus (CaAstV) was 4.2% (36/862), while that of feline astrovirus (FeAstV) in cats was 10.8% (69/636). We performed complete genome sequencing of Thai-CaAstVs (n = 11) and Thai-FeAstVs (n = 12). Phylogenetic analysis revealed that Thai-CaAstVs were clustered into lineages 1, 3, and 4, while Thai-FeAstVs were grouped within FeAstV group 1. This study identifies novel CaAstV lineages in domestic dogs and represents the first molecular detection of FeAstV in cats in Thailand. Our findings provide detailed information on the genetic characteristics of CaAstVs and FeAstVs currently circulating in Thailand, highlighting challenges for potential diagnostics and future control strategies.

Mamastrovirus species are shaped by recombination and can be reliably distinguished in ORF1b genome region

Astroviruses are a diverse group of small non-enveloped positive sense single-stranded RNA viruses that infect animals and birds. More than half of all known genome sequences of mammalian astroviruses are not assigned to provisional species, and the biological mechanisms that could support segregation of astroviruses into species are not well understood. The systematic analysis of recombination in Mamastrovirus genomes available in GenBank was done to identify mechanisms providing genetic distinction between astroviruses. Recombination breakpoints were present in all Mamastrovirus genome regions, but occurred most commonly at the ORF1b/ORF2 junction. Recombination was ubiquitous within, but never between established and putative new species, and may be suggested as an additional species criterion. The current species criterion for the genus Mamastrovirus based on ORF2 amino acid sequence p-distances did not reliably distinguish several established species and was of limited use to identify distinct groups among unclassified astroviruses that were isolated recently, predominantly from cattle and pigs. A 17% nucleotide sequence distance cut-off in ORF1b fairly distinguished the established species and several groups among the unclassified viruses, providing better correspondence between phylogenetic grouping, reproductive isolation and the virus hosts. Sequence distance criteria (17% in nucleotide sequence of ORF1b and 25% in amino acid sequence of ORF2) and the recombination pattern corresponded fairly well as species criteria, but all had minor exclusions among mammalian astroviruses. A combination of these taxonomic criteria supported the established Mamastrovirus species and suggested redefining a few provisional species that were proposed earlier and introducing at least six novel species among recently submitted rat and bovine astroviruses.

Mamastrovirus spike protein: Sequence and structural characterization as a basis for understanding cross-species transmission

Astroviruses (AstVs) are notable for their propensity for cross-species transmission; however, the molecular determinants underlying this phenomenon remain poorly understood. The spike protein, which is responsible for host cell entry and is a major antigenic determinant, is hypothesized to play a pivotal role. In this study, we observed high sequence variability in the spike region of AstV. Structural analyses have revealed variability, arising from diverse evolutionary relationships, among AstVs of the same host origin. AstV spike proteins can be categorized into six groups, each of which encompasses AstVs from diverse hosts that exhibit high degrees of structural similarity. These six groups correspond to branches observed in the phylogenetic tree. Notably, the spike surface-exposed loops emerged as focal hotspots for B-cell epitopes across groups, with sequence variability that may contribute to immune evasion upon host switching. Differences in the spike structures of AstVs infecting the same host raise the possibility of distinct tissue tropisms and corresponding clinical manifestations. Collectively, our findings provide insights into the roles of spike protein similarities and immune epitope diversity in driving AstV cross-species transmission. Understanding these molecular mechanisms is crucial to predicting and mitigating the emergence of novel AstV strains.

Emergence of Multiple Novel Inter-Genotype Recombinant Strains of Human Astroviruses Detected in Pediatric Patients With Acute Gastroenteritis in Thailand

Objective: Human astrovirus (HAstV) is recognized as an important cause of acute gastroenteritis in children. Recombination between different genotypes of HAstV can contribute to diversity and evolution of the virus. This study aimed to investigate the emergence of HAstV recombinant strains in pediatric patients hospitalized with acute gastroenteritis in Chiang Mai, Thailand, spanning 2011–2020.

Methods: A total of 92 archival HAstV strains collected from pediatric patients with acute gastroenteritis during 2011–2020 were further characterized to identify the recombinant strains. The ORF1b and ORF2 junction region of each strain was amplified and sequenced. The obtained sequences were analyzed in comparison with the reference sequences retrieved from GenBank database. Their genotypes were assigned using MEGA X software based on the partial ORF1b (RdRp) and ORF2 (capsid) regions, and the recombination breakpoints of recombinant strains were determined by SimPlot and RDP4 analyses.

Results: Five inter-genotype recombinant strains with three recombination patterns of ORF1b/ORF2 of classic HAstV, HAstV8/HAstV1, HAstV8/HAstV3, and HAstV3/HAstV2, were detected. The recombination breakpoints of all strains were located at the 3′-end region of ORF1b close to the ORF1b/ORF2 junction.

Conclusion: Several novel inter-genotype recombinant strains of classic HAstV genotypes were detected in pediatric patients with acute gastroenteritis in Chiang Mai, Thailand, during the period of 10 years from 2011 to 2020.

Development and application of a TaqMan-based real-time PCR assay for specifically detecting feline astrovirus

Feline astrovirus (FeAstV), an enteric RNA virus of recent concern that is associated with diarrheal illness in cats, has been described in several countries throughout the world. However, no scientific and sensitive diagnostic method against FeAstV was reported up to now. Here, we developed a specific, sensitive and repeatable TaqMan fluorescence quantitative PCR (qPCR) assay to investigate the prevalence of FeAstV in domestic cats from China, especially low copy numbers in clinical sample. Specific assay showed that no cross-reactivity was observed with other non-FeAstV cat-derivied pathogens, suggesting this method was highly specific for FeAstV. The lowest detection limit of this assay was 3.52 copies/μl, and 1000-times more sensitive than conventional PCR. Intra- and inter-assay variability was less than 1.72%, means a high degree of repeatability. A total of 578 clinical fecal samples were collected from northeast China, and were tested for FeAstV using our developed qPCR assay. 105 samples were positive for FeAstV with an overall prevalence of 18.17%. Moreover, a higher positive rate was found in cats with diarrhea (32.26%, 80/248) than that in asymptomatic cats (7.58%, 25/330), further demonstrating that FeAstV infection was associated with diarrhea in cats. In brief, our developed assay showed high specificity, sensitivity, reproducibility for detecting FeAstV, and can be used for clinical diagnosis and epidemiological investigation of FeAstV.

Astrovirus Outbreak in an Animal Shelter Associated With Feline Vomiting

An outbreak of cat vomiting was observed in an animal shelter. Testing for known enteric feline pathogens did not identify a causative agent. Viral metagenomics on four mini pools of feces from cases and controls housed in the same area revealed the presence of feline astrovirus in all pools. Also found with fewer reads in one pool each were rotavirus I, carnivore bocaparvovirus 3, norovirus (NoV) GVI, and a novel dependovirus. The genome of the highly prevalent astrovirus was sequenced and classified into mamastrovirus species two, also known as feline astrovirus. Real-time RT-PCR on longitudinally acquired fecal samples from 11 sick cases showed 10 (91%) to be shedding astrovirus for as long as 19 days. Affected cats were sick for an average of 9.8 days, with a median of 2.5 days (range = 1–31 days). Unaffected control cats housed in the same areas during the outbreak showed five out of nine (56%) to also be shedding astrovirus. Feline fecal samples collected from the same animal shelter ~1 year before (n = 8) and after (n = 10) showed none to be shedding astrovirus, indicating that this virus was temporarily associated with the vomiting outbreak and is not part of the commensal virome for cats in this shelter. Together with the absence of highly prevalent known pathogens, our results support a role for feline astrovirus infection, as well as significant asymptomatic shedding, in an outbreak of contagious feline vomiting.

Development of SYBR Green I-based real-time reverse transcription polymerase chain reaction for the detection of feline astrovirus

In this study, a SYBR Green I-based real-time reverse transcription-polymerase chain reaction (RT-PCR) was developed for the clinical diagnosis of feline astroviruses (FeAstVs). Specific primers were designed based on the conserved region of the FeAstV ORF1b gene. Experiments for specificity, sensitivity, and repeatability of the assay were carried out. In addition, the assay was evaluated using clinical samples. Specificity analysis indicated that the assay showed negative results with samples of Feline Parvovirus, Feline Herpesvirus, Feline Calicivirus, Feline Bocavirus, and Feline Coronavirus, indicating good specificity of the assay. Sensitivity analysis showed that the SYBR Green I-based real-time RT-PCR method could detect as low as 3.72 × 10¹ copies/μL of template, which is 100-fold more sensitive compared to the conventional RT-PCR. Both intra-assay and inter-assay variability were lower than 1 %, indicating good reproducibility. Furthermore, an analysis of 150 fecal samples showed that the positive detection rate of SYBR Green I-based real-time RT-PCR was higher than that of the conventional RT-PCR, indicating the high reliability of the method. The assay is cheap and effective. Therefore, it could provide support for the detection of FeAstV in large-scale clinical testing and epidemiological investigation.