Search Results (157)

Diarrhea in young ruminants is a global issue and causes significant economic losses worldwide. In addition to common pathogens like rotavirus, coronavirus, and astrovirus, new viruses can be identified through unbiased next-generation sequencing (NGS) techniques. Here, we report the initial identification of a hunnivirus from a one-month-old goat with diarrhea using shotgun metagenomic NGS. A complete hunnivirus genome was recovered. Phylogenetic tree analysis revealed that this goat hunnivirus was more closely related to cattle hunnivirus than to small ruminant hunnivirus strains, suggesting a prior cross-species transmission event. The genome was used to design primers/probes for the conserved 3D^pol RdRP gene for real-time RT-PCR to screen banked ruminant fecal samples. Screening of 144 ruminant fecal samples showed that 9 of 38 goat, 22 of 96 cattle, and 0 of 8 sheep samples were positive for hunnivirus. Sequencing of the 3D^po region was performed on selected positive samples and revealed two lineages of hunnivirus circulating in North America. Our study highlights the importance of further investigation and monitoring of fecal samples using unbiased metagenomic tools to identify potential pathogens or co-infections in ruminants. Full article

Canine Kobuvirus (CaKoV) has been identified as an agent involved in gastrointestinal diseases among dogs worldwide, with a particular impact on young individuals. This study reports the first molecular detection of CaKoV in Ecuadorian dogs with gastroenteritis, using a sensitive SYBR Green-based RT-qPCR assay. The assay demonstrated high sensitivity, with detection limits approaching a single copy of genetic material (1 copy/μL), with a standard efficiency curve of 100.6% and a correlation coefficient of 0.997, facilitating accurate CaKoV detection even at a minimal number of gene copies; it was also highly specific for CaKoV genome amplification, as no amplification was shown for other canine enteric viruses [Canine Parvovirus (CPV-2), Canine Astrovirus (CaAstV), Canine Coronavirus (CCoV), and Canine Distemper Virus (CDV)], and demonstrated strong reproducibility across different runs. A total of 250 fecal samples were used to validate the assay and detect the presence of CaKoV, with 91 samples testing positive for CaKoV, confirming the virus’ presence across multiple provinces in Ecuador, with Pichincha reporting the highest number of positive samples. Phylogenetic analysis of the partial 3D gene sequence exhibited a nucleotide identity ≥ 90% with sequences of CaKoV strains from different countries around the world. Co-infections with other enteric viruses such as CPV-2, CCoV, and CaAstV were observed in 61.3% of CaKoV-positive samples from dogs with gastroenteritis, with triple co-infections (CPV-2, CaAstV, and CaKoV) being the most frequently detected combination in the study. The present study showed that CaKoV is circulating in domestic dogs affected with gastroenteric disease and in apparently healthy dogs. This work establishes CaKoV as a possible contributor to canine gastroenteritis in Ecuador, in addition to the typical viruses such as CPV-2 and CCoV; moreover, this study illustrates a molecular assay that is both rapid and reliable for the diagnosis of CaKoV. Full article

Bats host a wide range of viruses, including several high-profile pathogens of humans and other animals. The COVID-19 pandemic raised the level of concern regarding the risk of spillover of bat-borne viruses to humans and, conversely, human-borne viruses to bats. From August 2020 to July 2021, we conducted viral surveillance on 254 bats from 10 species across urban, periurban, and rural environments in New Mexico, USA. We used a pan-coronavirus RT-PCR to assay rectal swabs and performed metagenomic sequencing on a representative subset of 14 rectal swabs and colon samples. No coronaviruses were detected by either RT-PCR or metagenomic sequencing. However, four novel viruses were identified: an adenovirus (proposed name lacepfus virus, LCPV), an adeno-associated virus (AAV), an astrovirus (AstV), and a genomovirus (GV). LCPV, detected in a big brown bat (Eptesicus fuscus), is more closely related to canine adenoviruses than to other bat adenoviruses, suggesting historical transmission between bats and dogs. All virus-positive bats were either juvenile or adult individuals captured in urban environments; none exhibited obvious clinical signs of disease. Our findings suggest limited or no circulation of enzootic coronaviruses or SARS-CoV-2 in southwestern U.S. bat populations during the study period. The discovery of a genetically distinct adenovirus related to canine adenoviruses highlights the potential for cross-species viral transmission and underscores the value of continued virome surveillance in animals living with and near humans. Full article

Goose astrovirus (GAstV) infection has emerged as a prevalent cause of urate deposition and viral gout in major goose farming across China, leading to high mortality and substantial economic losses. However, the molecular mechanisms linking GAstV to gout pathogenesis remain elusive. Here, a total of 10 five-day-old Jiangnan white goslings were selected, and tissue damage and kidney gene expression profiles were investigated. The results showed multi-organ damage in GAstV-infected gosling, including kidney, liver, spleen, and lung. Also, 342 differentially expressed genes were identified in infected kidney tissues after 10 days post-infection using transcriptomic sequencing, including 185 upregulated and 157 downregulated genes. In addition, gene set enrichment analysis revealed significant positive correlations between GAstV infection and bile acid metabolism and fatty acid metabolism pathways. Notably, bile acid metabolism was implicated in uric acid regulation and gout progression. Protein–protein interaction network analysis identified AGXT as a central hub gene within the bile acid metabolic pathway, with key upregulated interactors including PIPOX, ALDH1A1, and CAT. AGXT, a critical enzyme in glyoxylate detoxification, directly modulates uric acid biosynthesis. Our findings propose that GAstV-induced activation of bile acid metabolism, particularly AGXT upregulation, drives hyperuricemia and subsequent gout pathology. This study elucidates a novel mechanism of GAstV-associated metabolic dysregulation and provides actionable genetic targets for antiviral breeding strategies in waterfowl. Full article

Duck viral enteritis (DVE) is an acute and highly contagious disease that affects waterfowl such as ducks, geese and swans. Duck enteritis virus (DEV) is the pathogen, causing huge economic losses to waterfowl farming in recent years. Establishing a rapid, simple, and visual detection should facilitate the early identification of DEV. After the amplification primers and reaction conditions were optimized, three multienzyme isothermal rapid amplification (MIRA) methods—basic MIRA, MIRA–quantitative PCR (MIRA–qPCR) and MIRA–lateral flow dipstick (MIRA–LFD)—were established to detect DEV. Specificity analyses showed that the three MIRA methods specifically detected DEV, with no cross-reaction with fowl adenovirus serotype 4, novel goose astrovirus, Muscovy duck reovirus, avian influenza virus subtype H9, or duck circovirus. The basic MIRA reaction was completed in 30 min at 35 °C, requiring only a pair of primers. Detection with MIRA–qPCR or MIRA–LFD was completed within 20 min, and the limits of detection were 1 × 10¹ copies/μL for both. MIRA–LFD required no specialized instruments, and the results could be viewed directly with the naked eye. Compared with the traditional PCR, MIRA assays are simple, rapid, and effective and therefore more suitable for the field detection of DEV. Full article

Pathogenic enteric viruses are a leading cause of gastroenteritis-related mortality worldwide. However, the architecture of this research field remains poorly quantified. This bibliometric analysis provides a comprehensive overview of 35 years of global scientific output on major enteric viruses, such as rotavirus, norovirus, astrovirus, sapovirus, and non-polio enteroviruses, to map trends, methodological developments, and geographic disparities. We conducted a systematic search of PubMed and Scopus (1990–2024), identifying 10,017 records. After deduplication and eligibility screening, a final corpus of 8320 publications was analyzed using Bibliometrix (Biblioshiny 5.0) in R (version 4.3.0) and VOSviewer (Version 1.6.20). We found that scientific production grew steadily (CAGR = 5.84%), reaching its peak in 2021. The field is characterized by profound thematic and geographic disparity: rotavirus dominated the literature (56.3% of publications), followed by norovirus (30.8%), while other viruses were severely underrepresented (<9% each). Geographically, output was highly concentrated, with the top five countries (the USA, China, Japan, India, and Brazil) producing 92.4% of the publications. In contrast, high-burden regions, such as sub-Saharan Africa and Latin America, contributed only 7.6%. Genomic sequencing gained prominence, being cited in over 26.2% of publications from 2020 to 2024, reflecting a methodological shift accelerated by the application of wastewater-based epidemiology during the COVID-19 pandemic. In conclusion, while genomic tools and environmental monitoring are transforming enteric virus research, its progress is hampered by deep and persistent inequalities. These include a narrow focus on rotavirus and a significant disparity between regions with high disease burdens and those with high research outputs. Closing this gap requires targeted investments in equitable collaboration, local genomic capacity, and integrated public health interventions combining vaccination, WASH, and One Health strategies. Full article

Enteric diseases represent one of the main causes of morbidity and mortality in poultry production, especially in turkeys (Meleagris gallopavo), significantly affecting the profitability of the sector. Turkey enteric complex (PEC) is a multifactorial syndrome characterized by diarrhea, stunting, poor feed conversion, and increased mortality in young turkeys. Its aetiologia includes multiple avian enteric viruses, including astrovirus, rotavirus, reovirus, parvovirus, adenovirus, and coronavirus, which can act singly or in co-infection, increasing clinical severity. This study performs a systematic review of the literature on these viruses and a meta-analysis of their prevalence in different regions of the world. Phylogenetic analyses were used to assess the genetic diversity of the main viruses and their geographical distribution. The results show a wide regional and genetic variability, which underlines the need for continuous epidemiological surveillance. Health and production implications are discussed, proposing control strategies based on biosecurity, targeted vaccination, and optimized nutrition. These findings highlight the importance of integrated management to mitigate the impact of CSF in poultry. Full article

CrAssphage, a bacteriophage that infects human gut-associated Bacteroides spp., has emerged as a potential anthropogenic fecal pollution indicator in environmental matrices. This study investigated the presence and concentration of crAssphages in bivalve mollusks (oysters and mussels) marketed in three cities in the state of Rio de Janeiro, Brazil, sampled from January to December 2022. CrAssphages were detected during the study period in 66.7% (48/72) of sampled oysters and 54.8% (34/62) of sampled mussels, at median concentrations of 1.9 × 10⁴ and 4.2 × 10⁴ genome copies (GC)/g, respectively. These levels were 1–2 log₁₀ higher than those observed for major human enteric viruses, including norovirus genogroups GI and GII, sapovirus, human mastadenovirus (HAdV), rotavirus A, human astrovirus (HAstV), and hepatitis A virus. CrAssphage specificity and sensitivity were calculated for all viruses. Moderate correlations between crAssphage (log₁₀ GC/g) and norovirus GI and GII, HAdV, SaV, and HAstV (Spearman’s rho = 0.581–0.464, p < 0.001) were observed in mussels. Altogether, the data support the use of crAssphage as a molecular indicator of human viral contamination in shellfish, with potential application in routine environmental and food safety monitoring in production areas. Full article

Diarrhea is a common disease in sika deer. The causes of diarrhea in sika deer are complex and involve a variety of pathogens. Additionally, new virulent pathogens are continuously emerging, which poses a serious threat to deer’s health and particularly affects fawns’ survival rate. In the present study, feces samples were collected from fawns with diarrhea in Jilin Province, in the northeast of China. The viral communities were investigated using the metagenomic method. Viral metagenome data revealed that the viruses in the fecal samples were mainly from 21 families in 14 orders. The major viruses in high abundance were astrovirus, rotavirus, coronavirus, and bovine viral diarrhea virus. In addition, a large number of phages, which mainly belonged to the family Siphoviridae, were identified. Then, the known causative virus species were investigated via RT-qPCR. The results showed that the infection rates of bovine coronavirus, bovine rotavirus, and bovine viral diarrhea virus were 59.44%, 58.89%, and 21.67%, respectively, and mixed infections were commonly seen in the samples. A bovine rotavirus strain was successfully isolated from the positive samples. Whole-genome sequencing revealed that the genotype of the strain was G6-P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3, indicating the recombination of rotavirus. This study revealed the profiles and characteristics of viruses that cause sika deer diarrhea, which will be helpful for understanding diarrhea diseases in sika deer. Full article

Gastroenteritis is commonly caused by viral etiologies. The inclusion of astrovirus on multiplex, syndromic gastrointestinal PCR panels allows for the detection and characterization of infected patients. This retrospective, observational, clinical study examines the epidemiology and clinical characteristics of astrovirus infections in adults from our institution in Washington D.C. (USA) over a seven-year period. Chart abstraction was performed to collect patient demographics, laboratory results, clinical presentation, and management. The overall positivity rate of astrovirus was 0.6%. Peak seasons were late winter to spring (February–April). The mean age was 32 years old (range: 18–52 years). All patients presented with gastroenteritis symptoms and were immunocompetent except one. Symptoms varied among diarrhea, abdominal pain, vomiting, and fever, but patients in age group 30–39 years experienced less vomiting (p = 0.01). Infected patients had an increase in monocytes and neutrophils and a decrease in lymphocytes (p < 0.001). Gastrointestinal co-infections were seen in 24% of our patients. In all patients, clinicians acknowledged the detection of astrovirus and discharged patients without further treatment. The median length of stay was 6 h, and no patients were admitted into the intensive care unit. We show that astrovirus infections in immunocompetent adults were associated with mild disease associated with specific cell counts and different symptoms correlated with age. Full article

Since 2017, an infectious disease characterized by gosling gout and caused by goose astrovirus (GAstV) has affected geese in most major goose-producing regions of China. In this study, a total of 385 geese displaying gout symptoms were sampled from 12 cities in Guangdong Province, China, between 2019 and 2021. RT-PCR analysis revealed that all samples were positive for GAstV (385/385), with GAstV-II being the predominant subtype, accounting for 90.4% (348/385) of the cases. Co-infection with GAstV-I and GAstV-II was detected in 50.4% (194/385) of the samples. Additionally, different GAstV subtypes were successfully isolated using goose embryos, namely GDYJ-21-01 (GAstV-I) and GDZJ-21-01 (GAstV-II). Analysis of viral copy numbers in major pathological tissues following infection of goslings and goose embryos revealed that GDZJ strain exhibited broader tissue tropism than GDYJ strain. Compared to other tissues, GDYJ strain displayed tissue tropism exclusively in the cecal tonsils of goslings and the allantoic fluid of embryos. Structural prediction and alignment using AlphaFold 2.0 identified an α-helix in the S223-A226 region of the GDZJ VP34 protein, while a loop structure was observed in the Q235-Q237 region of the corresponding GDYJ VP34 protein. Furthermore, although the VP27 protein regions of both subtypes contained five β-sheet structures, the overall sequence similarity was relatively low, at 37.1%. This study broadens our understanding of the prevalence differences among GAstV subtypes and provides valuable insights into the development of reagents for preventing these viral infections. Full article

Quantitative Polymerase Chain Reaction (qPCR) is a molecular technique that has become a gold standard in various disciplines, including environmental microbiology, due to its high sensitivity and specificity. In recent years, it has been extensively used in wastewater-based epidemiology to monitor the prevalence of different viruses in the population. In this study, we evaluated whether the no inclusion of a standard curve in each single experiment to reduce time and costs could have an impact on the accuracy of the results. Thirty independent RT-qPCR standard curve experiments using quantitative synthetic RNA material were conducted for seven different viruses, which include two targets of the novel SARS-CoV-2, hepatitis A and E, noroviruses genogroups I and II, human astrovirus, and rotavirus. Results showed that although all the viruses presented adequate efficiency rates (>90%), variability was also observed between them, independently of the viral concentration tested. NoVGII was the virus that presented the higher inter-assay variability in terms of efficiency while showing better sensitivity. In terms of heterogeneity in results, the two targets of SARS-CoV-2 showed the highest rates, being N2 the gene that presented the largest variability (CV 4.38–4.99%) and the lowest efficiency (90.97%). These findings indicate that including a standard curve in every experiment is recommended to obtain reliable results. Full article

Metatranscriptomics has recently revealed greater species richness and host range of the Avastrovirus genus, quadrupling the number of avian orders known to host them in less than a decade. Despite this growing awareness of astrovirus presence in wild birds, limited attention has been paid to these viruses in the context of disease in Australian avifauna. Here we used unbiased RNA sequencing of intestinal samples from a galah (Eolophus roseicapilla) and an Australian king parrot (Alisterus scapularis) with a chronic diarrhoeal and wasting disease to detect the entire genomes of two novel astrovirus species. We propose naming these viruses Avastrovirus eolorosei (PQ893528) and Avastrovirus aliscap (PQ893527). The phylogenetic positions of these viruses highlight the importance of current and future metatranscriptomic virus screening in investigations of avian host landscapes beyond Galloanserae. This is also the first documentation of avastrovirus infections in Psittaciformes and the first to report their potential role as disease agents in them. Full article

Pigs serve as critical reservoirs and amplifiers for numerous zoonotic viral diseases, presenting substantial public health challenges in India. This study highlights the epidemiology and emerging trends of key zoonotic viruses associated with pigs, emphasizing their role in endemic and emerging disease dynamics. Japanese encephalitis virus (JEV) persists as a major concern, with pigs acting as amplifying host, while hepatitis E virus (HEV) remains a prominent cause of viral hepatitis, transmitted via contaminated water and pork products. Emerging high-fatality viral zoonoses caused by Nipah virus (NiV) and recurrent threats from swine influenza virus (SIV) demonstrate that the zoonotic landscape is evolving. Furthermore, zoonotic viruses like rotavirus, pseudorabies (ADV or SuHV-1), porcine astrovirus (PAstV), and Torque teno sus virus (TTSuV) reflect the expanding diversity of pig-associated pathogens in India. Emerging evidence also implicates viruses such as Chandipura virus (CHPV) in localized outbreaks, indicating broader zoonotic potential. Novel risks such as swine acute diarrhea syndrome coronavirus (SADS-CoV) and SARS-CoV-2 emphasize the role of pigs as potential intermediaries for pandemic-prone viruses. This comprehensive study evaluates the prevalence, outbreak dynamics, and public health implications of zoonotic viral diseases of pigs in India, providing valuable direction for developing effective control measures. Full article

Porcine viral diarrhea has always been one of the main obstacles to the healthy development of the pig industry in China with its variety of pathogens and complexity of co-infections. Analysis of the dominant mixed-infection model is a fundamental step in boosting the prevention and control of porcine diarrhea. In this study, 3256 porcine fecal samples were collected from 17 pig herds in Shanghai, China, from 2015 to 2023 to identify novel pathogenic infection patterns. The results confirmed that porcine astrovirus (PAstV), porcine sapelovirus (PSV), and porcine epidemic diarrhea virus (PEDV) were the top three agents with positive rates of 28.47%, 20.71%, and 20.23%, respectively. Porcine rotavirus (PoRV) and transmissible gastroenteritis virus (TGEV) accounted for only 8.12% and 1.12%, respectively. Importantly, mixed infection rates were high and complicated. The double infection rate was higher than that of a single infection. Next, the mixed-infection model of PEDV and emerging diarrheal pathogens was explored. The predominant dual-infection models were PEDV/PKoV (porcine kobuvirus) (14.18%), PEDV/PAstV (10.02%), and PEDV/PSV (9.29%). The predominant triple infection models were PEDV/PKoV/PAstV (18.93%), PEDV/PSV/PAstV (10.65%), and PEDV/PKoV/PSV (7.10%). The dominant quadruple-infection model was PEDV/PAstV/PSV/PKoV (46.82%). In conclusion, PEDV is mainly mix-infected with PAstV, PSV, and PKoV in clinical settings. Furthermore, multiple-factor logistic regression analysis confirmed that PAstV, PKoV, bovine viral diarrhea virus (BVDV), and PEDV were closely related to porcine diarrhea. PEDV/PKoV, PEDV/porcine sapovirus (PoSaV), PKoV/BVDV, PoSaV/BVDV, and porcine deltacoronavirus (PDCoV)/PoSaV had great co-infection dominance, which will be helpful for porcine co-infection research. Full article