Astrovirus Biology and Pathogenesis

Cellular vimentin interacts with VP70 protein of goose astrovirus genotype 2 and acts as a structural organizer to facilitate viral replication

The fatal gouty disease caused by goose astrovirus genotype 2 (GAstV-2) still seriously endangers the goose industry in China, causing great economic losses. However, research on its infection mechanism has progressed relatively slowly. VP70 is the structural protein of GAstV-2 and is closely related to virus invasion and replication. To better understand the role of VP70 during GAstV-2 infection, we used immunoprecipitation and mass spectrometry to identify host proteins that interact with VP70. Here, we report that cellular vimentin (VIM) is a host binding partner of VP70. Site-directed mutagenesis showed that amino acid residues 399 to 413 of VP70 interacted with VIM. Using reverse genetics, we found that VP70 mutation disrupts the interaction of VP70 with VIM, which is essential for viral replication. Overexpression of VIM significantly promoted GAstV-2 replication, while knockdown of VIM significantly inhibited GAstV-2 replication. Laser confocal microscopy showed that VP70 protein expression induced the rearrangement of VIM, gradually aggregating from the original uniform grid to the side of the nucleus, and aggregated the originally dispersed GAstV-2 RNA in VIM. This rearrangement was associated with increased VIM phosphorylation caused by GAstV-2. Meanwhile, blocking VIM rearrangement with acrylamide substantially inhibited viral replication. These results indicate that VIM interacts with VP70 and positively regulates GAstV-2 replication, and VIM-VP70 interaction and an intact VIM network are needed for GAstV-2 replication. This study provides a theoretical basis and novel perspective for the further characterization of the pathogenic mechanism of GAstV-2-induced gouty disease in goslings.

Isolation, identification, and epidemiological characteristics of goose astrovirus causing acute gout in Guangdong province, China

Goose astrovirus (GAstV) has been widespread in China since 2016, causing significant growth inhibition and gout symptoms in goslings and leading to substantial economic losses in the goose industry. To better understand the epidemiological characteristics of GAstV in Guangdong Province, 682 samples were collected from geese with suspected GAstV infection across different regions of Guangdong Province from January 2022 to January 2024. Virus isolation, identification, and genetic evolution analysis were performed. The results showed that all samples were GAstV positive, with 52.64% co-infected with GAstV-1 and GAstV-2, and 42.38% positive for GAstV-2 alone, indicating that GAstV-2 remains the most prevalent subtype. Additionally, three GAstV isolates were identified using molecular detection, immunofluorescence, and transmission electron microscopy on LMH cells or goose embryos. Compared with GDYJ2304 and other reported GAstV-2 strains, the ORF2 region of the GDYJ2210 isolates lacked 3 bases, and the replication ability of GDYJ2210 was significantly higher than that of GDYJ2304. Whole genome sequence alignment and genetic evolution analysis revealed that the GDFS2209 isolate was located in the GAstV-1 branch, with a sequence similarity of 89.70 to 99.00% to GAstV-1 reference strains. The GDYJ2210 and GDYJ2304 isolates were located in the GAstV-2 branch, showing a sequence similarity of 96.80 to 98.90% to GAstV-2 reference strains. These results demonstrated that the GAstV isolates were highly similar to each other despite being prevalent in 5 different regions of Guangdong Province. These findings enhance the understanding of the genetic diversity and evolution of GAstV and may facilitate the development of effective preventive strategies.

Seasonality of respiratory, enteric, and urinary viruses revealed by wastewater genomic surveillance

Wastewater surveillance can reveal population-level infectious disease burden and emergent public health threats can be reliably assessed through wastewater surveillance. While molecular methods for wastewater monitoring of microorganisms have traditionally relied on PCR-based approaches, next-generation sequencing (NGS) can provide deeper insights via genomic analyses of multiple diverse pathogens. We conducted a year-long sequencing surveillance of 1,408 composite wastewater samples collected from 12 neighborhood-level access points in the greater Tempe area, Arizona, USA, and show that variation in wastewater viruses is driven by seasonal time and location. The temporal dynamics of viruses in wastewater were influenced cyclically, with the most dissimilarity between samples 23 weeks apart (i.e., winter vs summer, spring vs fall). We identified diverse urinary and enteric viruses including polyomaviruses, astroviruses, and noroviruses, and showed that their genotypes/subtypes shifted across seasons. We show that while wastewater data of certain respiratory viruses like severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strongly correlate with clinical case rates, laboratory-reported case incidences were discordant with surges of high viral load in wastewater for other viruses like human coronavirus 229E. These results demonstrate the utility of wastewater sequencing for informing decision-making in public health.IMPORTANCEWastewater surveillance can provide insights into the spread of pathogens in communities. Advances in next-generation sequencing (NGS) methodologies allow for more precise detection of viruses in wastewater. Long-term wastewater surveillance of viruses is an important tool for public health preparedness. This system can act as a public health observatory that gives real-time early warning for infectious disease outbreaks and improved response times.

Epidemiological Investigation of Goose Astrovirus in Hebei Province, China, 2019-2021

The goose astrovirus (GAstV), a key pathogen causing visceral gout and high mortality in geese, has spread widely in China, with frequent outbreaks in recent years. Outbreaks and transmissions of this virus have been reported across China, causing considerable economic losses to the goose industry worldwide, with losses exceeding tens of billions in China alone. However, there is still no effective prevention strategy against this virus. Therefore, continuous monitoring of the genetic diversity of dominant GAstV strains is crucial for developing targeted vaccines and appropriate therapeutics. As a crucial region for goose breeding in China, Hebei Province has previously lacked reports on the epidemiology of GAstV. Hence, investigating the epidemiology of GAstV in Hebei Province is highly important. From January 2019 to December 2021, 474 samples suspected of having a GAstV infection were collected in Hebei Province in this study. Through detailed histological observations, pathological examinations, virus isolation and identification, and genetic diversity analysis, we found that GAstV-2 has become the predominant circulating genotype. However, the presence of GAstV-1 and mixed infections cannot be ignored and should receive increased attention. The findings of this study not only deepened our understanding of GAstV in waterfowl in China but also provided scientific evidence for developing effective prevention and control measures, thereby promoting the healthy development of the goose industry in China.

Virome survey of the bat, Rhinolophus affinis, in Hainan Province, China

Bats are important mammal reservoirs of zoonotic pathogens. However, due to research limitations involving species, locations, pathogens, or sample types, the full diversity of viruses in bats remains to be discovered. We used next-generation sequencing technology to characterize the mammalian virome and analyze the phylogenetic evolution and diversity of mammalian viruses carried by bats from Haikou City and Tunchang County in Hainan Province, China. We collected 200 pharyngeal swab and anal swab samples from Rhinolophus affinis, combining them into nine pools based on the sample type and collection location. We subjected the samples to next-generation sequencing and conducted bioinformatics analysis. All samples were screened via specific PCR and phylogenetic analysis. The diverse viral reads, closely related to mammals, were assigned into 17 viral families. We discovered many novel bat viruses and identified some closely related to known human/animal pathogens. In the current study, 6 complete genomes and 2 partial genomic sequences of 6 viral families and 8 viral genera have been amplified, among which 5 strains are suggested to be new virus species. These included coronavirus, pestivirus, bastrovirus, bocavirus, papillomavirus, parvovirus, and paramyxovirus. The primary finding is that a SADS-related CoV and a HoBi-like pestivirus identified in R. affinis in Hainan Province could be pathogenic to livestock. This study expands our understanding of bats as a virus reservoir, providing a basis for further research on the transmission of viruses from bats to humans.

Effects of Goose Astrovirus Type 2 Infection on Peripheral Blood Lymphocyte and Macrophage Activity In Vitro

Goose astrovirus type 2 (GAstV-2) is a novel pathogen causing visceral gout in goslings; it not only causes necrosis of renal epithelial cells but also causes spleen damage, indicating that GAstV-2 induces immunosuppression in goslings. However, to date, the interaction between GAstV-2 and immune cells remains unclear. In this study, peripheral blood lymphocytes and macrophages were isolated from goslings without GAstV-2 infection and then inoculated in vitro with GAstV-2, and the virus localization in the lymphocytes and macrophages, proliferation and apoptosis of lymphocytes, and phagocytic activity, reactive oxygen species (ROS) and nitric oxide (NO) production, and cell polarity in macrophages were determined. The results showed that GAstV-2 was observed in the cytoplasm of CD4 and CD8 T cells and macrophages, indicating that GAstV-2 can infect both lymphocytes and macrophages. GAstV-2 infection reduced the lymphocyte proliferation induced by Concanavalin A and lipopolysaccharide stimulation and increased the lymphocyte apoptosis rate and mRNA expression of Fas, demonstrating that GAstV-2 causes damage to lymphocytes. Moreover, GAstV-2 infection enhanced phagocytic activity and production of ROS and NO and induced a proinflammatory phenotype in macrophages (M1 macrophages), indicating that macrophages play an antiviral role during GAstV-2 infection. In conclusion, these results demonstrate that GAstV-2 infection causes damages to lymphocytes, and host macrophages inhibit GAstV-2 invasion during infection.

Activated sludge and UV-C254 for Sapovirus, Aichivirus, Astrovirus, and Adenovirus processing

In this study, the detection rates of four enteric viruses, Human Astrovirus (HAstVs), Aichivirus (AiVs), Human Adenovirus (HAdVs), and Sapovirus (SaVs) are carried out to assess the virological quality of the treated wastewater. A total of 140 samples was collected from wastewater treatment plant WWTP of Tunis-City. Real-time RT-PCR and conventional RT-PCR results showed high frequencies of detection of the four enteric viruses investigated at the entry and exit of the biological activated sludge procedure and a significant reduction in viral titers after tertiary treatment with UV-C254 irradiation. These results revealed the ineffectiveness of the biological activated sludge treatment in removing viruses and the poor quality of the treated wastewater intended for recycling, agricultural reuse, and safe discharge into the natural environment. The UV-C254 irradiation, selected while considering the non-release of known disinfection by-products because of eventual reactions with the large organic and mineral load commonly present in the wastewater.

Epidemiological investigation and pathogenicity analysis of waterfowl astroviruses in some areas of China

Waterfowl astroviruses are mainly duck astroviruses and goose astroviruses, of which duck astroviruses (DAstV-3, -4), goose astroviruses (GoAstV-1, -2) are the four new waterfowl 21 astroviruses in recent years, which can lead to enteritis, viral hepatitis, gout and reduce the growth performance of waterfowl, affecting the healthy development of the waterfowl farming industry. Since no targeted drugs or vaccines on the market, studies on the epidemiology of the virus are necessary for vaccine development. In this study, we collected 1546 waterfowl samples from 13 provinces in China for epidemiological investigation. The results showed that 260 samples (16.8%) were positive. Four species of astrovirus were detected in 13 provinces except Fujian province. Among the four sites tested, the highest positive rates were found in farms and slaughterhouses. Cross-host and mixed infection were observed in four species of waterfowl astroviruses. The whole genome of 17 isolates was sequenced and compared with published sequences. Genetic evolution and homology analysis showed that the isolated strains had high similarity to their reference sequences. To assess the pathogenicity of GoAstV, 7-day-old goslings were inoculated with GoAstV-1 and GoAstV-2 by the intramuscular route, and infected geese showed similar clinical signs, such as anorexia, depression, and weight loss. Organ damage was seen after infection, with histopathological changes in the heart, liver, spleen, kidney, and intestine, and higher viral loads in throat and anal swabs. These findings increase our understanding of the pathogenicity of GoAstV-1 and GoAstV-2 in goslings and provide more references for future research.

Metagenomic survey of viral diversity obtained from feces of piglets with diarrhea

Pigs are natural host to various zoonotic pathogens including viruses. In this study, we analyzed the viral communities in the feces of 89 piglets with diarrhea under one month old which were collected from six farms in Jiangsu Province of the Eastern China, using the unbiased virus metagenomic method. A total of 89 libraries were constructed, and 46937894 unique sequence reads were generated by Illumina sequencing. Overall, the family Picornaviridae accounted for the majority of the total reads of putative mammalian viruses. Ten novel virus genomes from different family members were discovered, including Parvoviridae (n = 2), Picobirnaviridae (n = 4) and CRESS DNA viruses (n = 4). A large number of phages were identified, which mainly belonged to the order Caudovirales and the family Microviridae. Moreover, some identified viruses were closely related to viruses found in non-porcine hosts, highlighting the potential for cross-species virus dissemination. This study increased our understanding of the fecal virus communities of diarrhea piglets and provided valuable information for virus monitoring and preventing.

In Vitro Models for Investigating Intestinal Host-Pathogen Interactions

Infectious diseases are increasingly recognized as a major threat worldwide due to the rise of antimicrobial resistance and the emergence of novel pathogens. In vitro models that can adequately mimic in vivo gastrointestinal physiology are in high demand to elucidate mechanisms behind pathogen infectivity, and to aid the design of effective preventive and therapeutic interventions. There exists a trade-off between simple and high throughput models and those that are more complex and physiologically relevant. The complexity of the model used shall be guided by the biological question to be addressed. This review provides an overview of the structure and function of the intestine and the models that are developed to emulate this. Conventional models are discussed in addition to emerging models which employ engineering principles to equip them with necessary advanced monitoring capabilities for intestinal host-pathogen interrogation. Limitations of current models and future perspectives on the field are presented.

Leveraging machine learning for taxonomic classification of emerging astroviruses

Astroviruses are a family of genetically diverse viruses associated with disease in humans and birds with significant health effects and economic burdens. Astrovirus taxonomic classification includes two genera, Avastrovirus and Mamastrovirus. However, with next-generation sequencing, broader interspecies transmission has been observed necessitating a reexamination of the current host-based taxonomic classification approach. In this study, a novel taxonomic classification method is presented for emergent and as yet unclassified astroviruses, based on whole genome sequence k-mer composition in addition to host information. An optional component responsible for identifying recombinant sequences was added to the method's pipeline, to counteract the impact of genetic recombination on viral classification. The proposed three-pronged classification method consists of a supervised machine learning method, an unsupervised machine learning method, and the consideration of host species. Using this three-pronged approach, we propose genus labels for 191 as yet unclassified astrovirus genomes. Genus labels are also suggested for an additional eight as yet unclassified astrovirus genomes for which incompatibility was observed with the host species, suggesting cross-species infection. Lastly, our machine learning-based approach augmented by a principal component analysis (PCA) analysis provides evidence supporting the hypothesis of the existence of human astrovirus (HAstV) subgenus of the genus Mamastrovirus, and a goose astrovirus (GoAstV) subgenus of the genus Avastrovirus. Overall, this multipronged machine learning approach provides a fast, reliable, and scalable prediction method of taxonomic labels, able to keep pace with emerging viruses and the exponential increase in the output of modern genome sequencing technologies.

Identification of Astrovirus in the virome of the upper and lower respiratory tracts of calves with acute signs of bronchopneumonia

IMPORTANCE

Astroviruses (AstV) are known suspects of enteric disease in humans and livestock. Recently, AstV have been linked to encephalitis in immunocompromised patients and other animals, such as cattle, minks, and swine. In our study, we also identified AstV in the respiratory samples of calves with signs of bronchopneumonia, suggesting that their tropism could be even broader. We obtained one bovine AstV (BAstV) complete genome sequence by next-generation sequencing and showed that respiratory and enteric AstV from different species formed a divergent genetic cluster with AstV isolated from encephalitis cases, indicating that tropism might be strain-specific. These data provide further insight into understanding the biology of these understudied pathogens and suggest BAstV as a potential new candidate for bovine respiratory disease.

Molecular characterization of chicken astrovirus and pathogenicity of a novel isolate in China

As an enteric virus, chicken astrovirus has been related to various kinds of diseases in chickens, including white chick syndrome, runting-stunting syndrome, severe kidney disease, urate deposits and visceral gout, generating economic losses in the poultry industry globally. The complete ORF2 gene of 31 CAstV isolates in six provinces of China during 2020-2022 was characterized and analyzed with the purpose of better understanding the molecular epidemiology and genetic diversity of CAstV field isolates. Phylogenetic analysis which was based on the complete ORF2 (capsid) amino acid sequence of 31 CAstV isolates and 57 reference strains indicated that 2 isolates belonged to subgroup Ai, 10 isolates belonged to subgroup Bi, 3 isolates belonged to subgroup Bii, 5 isolates belonged to subgroup Biii, 7 isolates belonged to subgroup Biv, 3 isolates belonged to subgroup Bv, and one isolate (JS202103) belonged to a new B subgroup. In addition, the novel CAstV strain JS202103 was successfully isolated in vitro, and its whole genome shared 76.9-94.3% identity with the 29 CAstV reference strains. JS202103 caused hatchability reduction, dead embryos, kidney disease and visceral gout in chicken embryos. Moreover, this is the also the initial study focusing on diverse CAstV strains including subgroups Biii, Biv, and Bv circulate in China. The current work contributes to improving our understanding of CAstV isolates in China, and it will also provide references for developing efficient measures to control this virus.

Evaluating the zoonotic potential of RNA viromes of rodents provides new insight into rodent-borne zoonotic pathogens in Guangdong, China

Emerging and re-emerging infectious diseases have been on the rise, with a significant proportion being zoonotic. Rodents, as the natural reservoirs of numerous diverse zoonotic viruses, pose a substantial threat to human health. To investigate the diversity of known and unknown viruses harbored by rodents in Guangdong (southern province of China), we conducted a comprehensive analysis of viral genomes through metagenomic sequencing of organs from 194 rodents. Our analysis yielded 2163 viral contigs that were assigned to 25 families known to infect a wide range of hosts, including vertebrates, invertebrates, amoebas, and plants. The viral compositions vary considerably among different organs, but not in rodent species. We also assessed and prioritized zoonotic potential of those detected viruses. Ninety-two viral species that are either known to infect vertebrates and invertebrates or only vertebrates were identified, among which 21 are considered high-risk to humans. The high-risk viruses included members of the Hantavirus, Picobirnaviruses, Astroviruses and Pestivirus. The phylogenetic trees of four zoonotic viruses revealed features of novel viral genomes that seem to fit evolutionarily into a zone of viruses that potentially pose a risk of transmission to humans. Recognizing that zoonotic diseases are a One Health issue, we approached the problem of identifying the zoonotic risk from rodent-transmitted disease in the Guangdong province by performing next-generation sequencing to look for potentially zoonotic viruses in these animals.

Characterisation of human astrovirus in a diarrhoea outbreak using nanopore and Sanger sequencing protocols

Human astroviruses (HAstV) are etiologic agents of acute gastroenteritis that most often afflict young children and elderly adults. Most studies of HAstV have focused on epidemiology. In this study, we collected 10 stool samples from a diarrhea outbreak from a diarrhea sentinel surveillance hospital in Beijing. Samples were evaluated immediately using parallel multiplex RT-qPCR and nanopore sequencing, and were then amplified by designed primers and Sanger sequencing to obtain whole genome sequences. Six isolates were categorized as HAstV-5 and subjected to whole genome analysis to characterize their genetic variation and evolution. Full genome analysis revealed low genetic variation (99.38-100% identity) among isolates. Phylogenetic analysis showed that all isolates were closely related to domestic strains Yu/1-CHN and 2013/Fuzhou/85. The recombination breakpoint of the six isolates was located at 2741 bp in the overlap region of ORF1a and ORF1b, similar to those of Yu/1-CHN and 2013/Fuzhou/85. Overall, our study highlights the combined use of RT-qPCR and sequencing as an important tool in rapid diagnosis and acquisition of whole genome sequences of HAstV.

Diversity of classic and novel human astrovirus in outpatient children with acute gastroenteritis in Shanghai, China

Introduction

Human astrovirus (HAstV) is an important pathogen of acute gastroenteritis (AGE) in children. This study was aimed at investigating the diversity and epidemiology of classic and novel HAstV in outpatient children aged 0-16 years old with AGE in Shanghai.

Methods

From May 2020 to December 2022, a total of 1,482 stool samples were collected from children diagnosed as AGE from the Children's Hospital of Fudan University. HAstV was identified using pan-astrovirus consensus primers by Reverse transcription PCR.

Results

During the study period, 3.3% (49/1,482) of specimens were identified as HAstV, with a detection rate of 2.5% (37/1,482) for classic HAstV and 0.8% (12/1,482) for novel HAstV. Among the 12 novel HAstV strains, 11 (91.7%) belonged to the HAstV-MLB and 1 (8.3%) was HAstV-VA. Genotyping revealed six circulating genotypes. Strain HAstV-1 was predominant in the study population with a detection rate of 1.8% (26/1,482) followed by HAstV-MLB1 (0.7%, 10/1,482) and HAstV-4 (0.6%, 9/1,482). Of note, all the HAstV-4 strains detected in this study were close to one astrovirus strain isolated from Bactrian camels with 99.0-100.0% amino acid sequences identity. In this study, HAstV was detected in all age groups with the highest detection rate of HAstV-positive specimens observed in children older than 73 months (5.7%, 12/209).

Discussion

This study provided useful information and contributed to the molecular epidemiology of both classic and novel HAstV, which were simultaneously characterized and reported for the first time in Shanghai.

Structure and immunogenicity of the murine astrovirus capsid spike

Human astroviruses (HAstVs) are small, non-enveloped icosahedral RNA viruses that are a significant cause of diarrhoea in young children. Despite their worldwide prevalence, HAstV pathogenesis studies and vaccine development remain challenging due to the lack of an animal model for HAstV infection. The recent development of a murine astrovirus (MuAstV) infection model in mice provides the opportunity to test proof-of-concept vaccines based on MuAstV antigens. To help establish a system in which an astrovirus capsid spike-based vaccine could be tested in vivo, we designed and produced a recombinant MuAstV capsid spike protein based on predicted secondary structure homology to HAstV spike proteins. The recombinant MuAstV spike can be expressed with high efficiency in Escherichia coli and retains antigenicity to polyclonal antibodies elicited by MuAstV infection. We determined the crystal structure of the MuAstV spike to 1.75 Å and assessed its structural conservation with HAstV capsid spike. Despite low sequence identity between the MuAstV and HAstV spikes and differences in their overall shapes, they share related structural folds. Additionally, we found that vaccination with MuAstV spike induced anti-MuAstV-spike antibodies, highlighting that the recombinant spike is immunogenic. These studies lay a foundation for future in vivo MuAstV challenge studies to test whether MuAstV spike can be the basis of an effective vaccine.

Near-complete genome sequence of human astrovirus recovered from a child with acute flaccid paralysis in Guinea, 2021

Astroviruses are common causes of gastroenteritis in humans and other animals. Herein, we reported a near-complete human astrovirus (HAstV) sequence detected in a child with acute flaccid paralysis. The sample was collected in Guinea in January 2021. Phylogenetic analyses indicated that this virus belonged to the HAstV-1 genotype.

Immunomodulation by Enteric Viruses

Enteric viruses display intricate adaptations to the host mucosal immune system to successfully reproduce in the gastrointestinal tract and cause maladies ranging from gastroenteritis to life-threatening disease upon extraintestinal dissemination. However, many viral infections are asymptomatic, and their presence in the gut is associated with an altered immune landscape that can be beneficial or adverse in certain contexts. Genetic variation in the host and environmental factors including the bacterial microbiota influence how the immune system responds to infections in a remarkably viral strain-specific manner. This immune response, in turn, determines whether a given virus establishes acute versus chronic infection, which may have long-lasting consequences such as susceptibility to inflammatory disease. In this review, we summarize our current understanding of the mechanisms involved in the interaction between enteric viruses and the immune system that underlie the impact of these ubiquitous infectious agents on our health.

Astrovirus replication is dependent on induction of double-membrane vesicles through a PI3K-dependent, LC3-independent pathway

Human astrovirus is a positive-sense, single-stranded RNA virus. Astrovirus infection causes gastrointestinal symptoms and can lead to encephalitis in immunocompromised patients. Positive-strand RNA viruses typically utilize host intracellular membranes to form replication organelles, which are potential antiviral targets. Many of these replication organelles are double-membrane vesicles (DMVs). Here, we show that astrovirus infection leads to an increase in DMV formation through a replication-dependent mechanism that requires some early components of the autophagy machinery. Results indicate that the upstream class III phosphatidylinositol 3-kinase (PI3K) complex, but not LC3 conjugation machinery, is utilized in DMV formation. Both chemical and genetic inhibition of the PI3K complex lead to significant reduction in DMVs, as well as viral replication. Elucidating the role of autophagy machinery in DMV formation during astrovirus infection reveals a potential target for therapeutic intervention for immunocompromised patients. IMPORTANCE These studies provide critical new evidence that astrovirus replication requires formation of double-membrane vesicles, which utilize class III phosphatidylinositol 3-kinase (PI3K), but not LC3 conjugation autophagy machinery, for biogenesis. These results are consistent with replication mechanisms for other positive-sense RNA viruses suggesting that targeting PI3K could be a promising therapeutic option for not only astrovirus, but other positive-sense RNA virus infections.

Entry and egress of human astroviruses

Astroviruses encapsidate a positive-sense, single-stranded RNA genome into ∼30nm icosahedral particles that infect a wide range of mammalian and avian species, but their biology is not well understood. Human astroviruses (HAstV) are divided into three clades: classical HAstV serotypes 1-8, and novel or non-classical HAstV of the MLB and VA clades. These viruses are part of two genogroups and phylogenetically cluster with other mammalian astroviruses, highlighting their zoonotic potential. HAstV are a highly prevalent cause of nonbacterial gastroenteritis, primarily in children, the elderly and immunocompromised. Additionally, asymptomatic infections and extraintestinal disease (e.g., encephalitis), are also observed, mostly in immunocompetent or immunocompromised individuals, respectively. While these viruses are highly prevalent, no approved vaccines or antivirals are available to prevent or treat infections. This is in large part due to their understudied nature and the limited understanding of even very basic features of their life cycle and pathogenesis at the cellular and organismal level. This review will summarize molecular features of human astrovirus biology, pathogenesis, and tropism, and then focus on two stages of the viral life cycle, namely entry and egress, since these are proven targets for therapeutic interventions. We will further highlight gaps in knowledge in hopes of stimulating future research into these understudied viruses.

Epidemiology of pediatric astrovirus gastroenteritis in a Nicaraguan birth cohort

Background

Astrovirus is a leading cause of acute gastroenteritis in children worldwide. However, few prospective studies have analyzed astrovirus in community-dwelling pediatric populations in low-and-middle-income countries.

Methods

We assessed the incidence, risk factors, clinical characteristics, genotypes, viral coinfections and seasonality of astrovirus gastroenteritis in 443 healthy Nicaraguan children born in 2017-2018, followed for 36 months. Children were recruited from maternity hospitals and birth records in an economically-diverse neighborhood of León, the second-largest city in Nicaragua. Astrovirus-positive episodes and genotypes were identified from diarrheal specimens with reverse transcription quantitative polymerase chain reaction and Sanger sequencing.

Results

Of 1708 total specimens tested, eighty children (18%) experienced at least 1 astrovirus episode, and 9 experienced repeat episodes, mostly during the rainy season (May-October). The incidence of astrovirus episodes was 7.8/100 child-years (95% CI: 6.2, 9.8). Genotype-specific incidence of astrovirus also exhibited seasonality. Median age of astrovirus episode onset was 16 months (IQR 9, 23). Initial astrovirus episodes were not associated with protection against future episodes during the age span studied. Astrovirus cases were exclusively breastfed for a shorter period than uninfected children, and the human milk oligosaccharide lacto-N-fucopentaose-I was more concentrated in mothers of these children. Home toilets appeared to protect against future astrovirus episodes (HR=0.19, 95% CI 0.04-0.91). Human astrovirus-5 episodes, comprising 15% of all typed episodes, were associated with longer diarrhea and more symptomatic rotavirus co-infections.

Conclusion

Astrovirus was a common cause of gastroenteritis in this cohort, and future studies should clarify the role of astrovirus genotype in clinical infection severity.

Pathogenesis and outcome of VA1 astrovirus infection in the human brain are defined by disruption of neural functions and imbalanced host immune responses

Astroviruses (AstVs) can cause of severe infection of the central nervous system (CNS) in immunocompromised individuals. Here, we identified a human AstV of the VA1 genotype, HAstV-NIH, as the cause of fatal encephalitis in an immunocompromised adult. We investigated the cells targeted by AstV, neurophysiological changes, and host responses by analyzing gene expression, protein expression, and cellular morphology in brain tissue from three cases of AstV neurologic disease (AstV-ND). We demonstrate that neurons are the principal cells targeted by AstV in the brain and that the cerebellum and brainstem have the highest burden of infection. Detection of VA1 AstV in interconnected brain structures such as thalamus, deep cerebellar nuclei, Purkinje cells, and pontine nuclei indicates that AstV may spread between connected neurons transsynaptically. We found transcriptional dysregulation of neural functions and disruption of both excitatory and inhibitory synaptic innervation of infected neurons. Importantly, transcriptional dysregulation of neural functions occurred in fatal cases, but not in a patient that survived AstV-ND. We show that the innate, but not adaptive immune response was transcriptionally driving host defense in the brain of immunocompromised patients with AstV-ND. Both transcriptome and molecular pathology studies showed that most of the cellular changes were associated with CNS-intrinsic cells involved in phagocytosis and injury repair (microglia, perivascular/parenchymal border macrophages, and astrocytes), but not CNS-extrinsic cells (T and B cells), suggesting an imbalance of innate and adaptive immune responses to AstV infection in the brain as a result of the underlying immunodeficiencies. These results show that VA1 AstV infection of the brain in immunocompromised humans is associated with imbalanced host defense responses, disruption of neuronal somatodendritic compartments and synapses and increased phagocytic cellular activity. Improved understanding of the response to viral infections of the human CNS may provide clues for how to manipulate these processes to improve outcomes.

Detection and Genetic Characterization of Astroviruses in Brain Tissues of Wild Raccoon Dogs

Astroviruses (AstVs) have been detected in a wide range of animal species, including mammals and birds. Recently, a novel AstV associated with neurological symptoms has been detected in the brains of some mammals. Raccoon dog AstV has been reported recently in China. However, there have been no reports in South Korea. Therefore, the present study aimed to detect and genetically characterize AstVs in the intestine and brain tissues of 133 wild raccoon dogs collected in Korea between 2017 and 2019. Of the seven raccoon dogs, AstVs were detected in six intestinal tissues and four brain tissues. Analysis of the capsid protein amino acid sequences of raccoon dog AstVs detected in Korea revealed a high similarity to canine AstVs, suggesting possible interspecies transmission between raccoon dogs and dogs. Phylogenetic and capsid protein amino acid sequence analysis of raccoon dog AstVs detected in the brain the 17-148B strain belonging to the HMO clade and exhibiting conserved sequences found in neurotropic AstVs (NT-AstVs), indicating their potential as NT-AstVs. However, the pathogenicity and transmission routes of the raccoon dog AstV detected in Korea have not yet been elucidated, so further research and continued surveillance for AstV in wild raccoon dogs are needed.

Worldwide prevalence and genotype distribution of human astrovirus in gastroenteritis patients: A systematic review and meta-analysis

AIM

Human astrovirus (HAstV) is an important causative agent of gastroenteritis in humans, which mainly infects young children and the elderly. The goal of this study was to conduct a meta-analytic review of the prevalence of HAstV amongst patients with gastroenteritis, and to shed light on the connection between HAstV infection and gastroenteritis.

METHODS

Systematic literature searches were conducted to identify all potentially relevant studies recorded up to April 8th, 2022. For study weighting, the inverse variance method was employed and the random-effects model was applied to evaluate data. For case-control studies, the pooled odds ratio (OR) and 95% confidence interval (CI) were calculated to establish the relationship between HAstV infection and gastroenteritis.

RESULTS

Among 302423 gastroenteritis patients from 69 different countries, the overall pooled prevalence of HAstV infection was 3.48% (95% CI: 3.11%-3.89%). Case-control approach was used in 39 investigations, and the overall prevalence of HAstV infection among the 11342 healthy controls was 2.01% (95% CI: 1.40%-2.89%). Gastroenteritis and HAstV infection were associated with a pooled OR of 2.16 (95% CI: 1.72-2.71; P < 0.0001; I² = 33.7%). The most commonly found HAstV genotypes in gastroenteritis patients were HAstV1 (62.18%), HAstV7 (33.33%), and HAstV-MLB1 (17.43%).

CONCLUSION

The frequency of HAstV infection was the highest in children under the age of five, and in developing countries. The prevalence rate of HAstV was not influenced by gender. Semi-nested and nested RT-PCR were highly sensitive assays for detecting HAstV infections.

Gastrointestinal tract and viral pathogens

Viral gastroenteritis is the most common viral illness that affects the gastrointestinal (GI) tract, causing inflammation and irritation of the lining of the stomach and intestines. Common signs and symptoms associated with this condition include abdominal pain, diarrhea, and dehydration. The infections commonly involved in viral gastroenteritis are rotavirus, norovirus, and adenovirus, which spread through the fecal-oral and contact routes and cause non-bloody diarrhea. These infections can affect both immunocompetent and immunocompromised individuals. Since the pandemic in 2019, coronavirus gastroenteritis has increased in incidence and prevalence. Morbidity and mortality rates from viral gastroenteritis have declined significantly over the years due to early recognition, treatment with oral rehydration salts, and prompt vaccination. Improved sanitation measures have also played a key role in reducing the transmission of infection. In addition to viral hepatitis causing liver disease, herpes virus, and cytomegalovirus are responsible for ulcerative GI disease. They are associated with bloody diarrhea and commonly occur in im-munocompromised individuals. Hepatitis viruses, Epstein-Barr virus, herpesvirus 8, and human papillomavirus have been involved in benign and malignant diseases. This mini review aims to list different viruses affecting the GI tract. It will cover common symptoms aiding in diagnosis and various important aspects of each viral infection that can aid diagnosis and management. This will help primary care physicians and hospitalists diagnose and treat patients more easily.

Outbreak of human astroviruses 1 and Melbourne 2 in acute gastroenteritis pediatric patients in Japan during the COVID-19 pandemic, 2021

BACKGROUND

Human astrovirus (HAstV) infection is one of the leading causes of acute gastroenteritis in young children. The present study reports the outbreak of HAstV in children with acute gastroenteritis in Kyoto, Japan, during the COVID-19 pandemic, 2021.

METHODS

A total of 61 stool samples were collected from children with acute gastroenteritis who visited a pediatric outpatient clinic in Maizuru city, Kyoto, Japan from July to October, 2021. HAstV was screened by RT-PCR, and the genotypes were identified by nucleotide sequence analysis.

RESULTS

Of 61 cases of acute gastroenteritis, 20 were mono-infected with HAstV alone. In addition, mixed infection of HAstV and NoV, and HAstV and RVA were also detected in 15 and 1 cases, respectively. Of 36 HAstV strains detected in this outbreak, 29 and 7 were HAstV1 and MLB2 genotypes, respectively. All HAstV1 strains were closely related to the HAstV1 reported from Thailand and Japan in 2021 and all of them belonged to subgenotype HAstV1a. Among MLB2, they were most closely related to the MLB2 strains reported from China in 2016 and 2018.

CONCLUSIONS

After the kindergartens and schools were re-opened at the middle of 2021 in Japan, an outbreak of HAstV was reported. Control measures against the COVID-19 pandemics might affect the spread of diarrheal virus infection. Here we report the outbreak of HAstV1 and MLB2 in Kyoto, Japan, during COVID-19 pandemic in 2021.

Genome Sequences and Characterization of Chicken Astrovirus and Avian Nephritis Virus from Tanzanian Live Bird Markets

The enteric chicken astrovirus (CAstV) and avian nephritis virus (ANV) are the type species of the genus Avastrovirus (AAstV; Astroviridae family), capable of causing considerable production losses in poultry. Using next-generation sequencing of a cloacal swab from a backyard chicken in Tanzania, we assembled genome sequences of ANV and CAstV (6918 nt and 7318 nt in length, respectively, excluding poly(A) tails, which have a typical AAstV genome architecture (5'-UTR-ORF1a-ORF1b-ORF2-'3-UTR). They are most similar to strains ck/ANV/BR/RS/6R/15 (82.72%) and ck/CAstV/PL/G059/14 (82.23%), respectively. Phylogenetic and sequence analyses of the genomes and the three open reading frames (ORFs) grouped the Tanzanian ANV and CAstV strains with Eurasian ANV-5 and CAstV-Aii viruses, respectively. Compared to other AAstVs, the Tanzanian strains have numerous amino acid variations (substitutions, insertions and deletions) in the spike region of the capsid protein. Furthermore, CAstV-A has a 4018 nt recombinant fragment in the ORF1a/1b genomic region, predicted to be from Eurasian CAstV-Bi and Bvi parental strains. These data should inform future epidemiological studies and options for AAstV diagnostics and vaccines.

Astrovirus replication is dependent on induction of double membrane vesicles through a PI3K-dependent, LC3-independent pathway

Human astrovirus is a positive sense, single stranded RNA virus. Astrovirus infection causes gastrointestinal symptoms and can lead to encephalitis in immunocompromised patients. Positive strand RNA viruses typically utilize host intracellular membranes to form replication organelles, which are potential antiviral targets. Many of these replication organelles are double membrane vesicles (DMVs). Here we show that astrovirus infection leads to an increase in DMV formation, and this process is replication-dependent. Our data suggest that astrovirus infection induces rearrangement of endoplasmic reticulum fragments, which may become the origin for DMV formation. Transcriptional data suggested that formation of DMVs during astrovirus infection requires some early components of the autophagy machinery. Results indicate that the upstream class III phosphatidylinositol 3-kinase (PI3K) complex, but not LC3 conjugation machinery, is utilized in DMV formation. Inhibition of the PI3K complex leads to significant reduction in viral replication and release from cells. Elucidating the role of autophagy machinery in DMV formation during astrovirus infection reveals a potential target for therapeutic intervention for immunocompromised patients.

Importance

These studies provide critical new evidence that astrovirus replication requires formation of double membrane vesicles, which utilize class III PI3K, but not LC3 conjugation autophagy machinery for biogenesis. These results are consistent with replication mechanisms for other positive sense RNA viruses. This suggests that targeting PI3K could be a promising therapeutic option for not only astrovirus, but other positive sense RNA virus infections.

Identification and characterization of a novel avian nephritis virus variant in chickens with enteritis in Hunan province, China

Avian nephritis virus (ANV) infection is associated with diarrhea, uricosis, stunting, tubulonephrosis, interstitial nephritis, and mortality of chicken flocks, leading to economic losses in the poultry industry. In this study, an ANV strain designated as HNU-ANV-ML-2020 was identified in tissue samples collected from chickens with severe enteritis on a poultry farm in Hunan province, China, and analyzed. The genome of HNU-ANV-ML-2020 is 6943 nucleotides in length. It showed the highest sequence identity (88.1%) to ANV strain CHN/GXJL815/2017 (MN732559) from Guangxi province, China, while it showed less than 86% identity to other astrovirus (AstV) genome sequences available in the GenBank database. The capsid protein of this virus showed the highest sequence identity to ANV strains HQ330482 and HQ330498 from the UK (81.2% and 81.06%, respectively), while it showed only 73.9% identity to MN732559 and less than 80% identity to the capsid proteins of other AstVs available in GenBank. Further phylogenetic analysis demonstrated that HNU-ANV-ML-2020 belongs to group 4, together with ANV strains identified in Australia, Brazil, the UK, and the Netherlands. Furthermore, ANV strains identified in chickens in China were found to be separated into four distinct groups/genotypes, indicating substantial genetic divergence and a complex circulation pattern in China. The virus characterized in the present study is a novel ANV variant identified for the first time in Hunan province, China.

Discovery of novel Mamastroviruses in Bactrian camels and dromedaries reveals complex recombination history

Virus emergence may occur through interspecies transmission and recombination of viruses coinfecting a host, with potential to pair novel and adaptive gene combinations. Camels are known to harbor diverse ribonucleic acid viruses with zoonotic and epizootic potential. Among them, astroviruses are of particular interest due to their cross-species transmission potential and endemicity in diverse host species, including humans. We conducted a molecular epidemiological survey of astroviruses in dromedaries from Saudi Arabia and Bactrian camels from Inner Mongolia, China. Herein, we deployed a hybrid sequencing approach coupling deep sequencing with rapid amplification of complementary deoxyribonucleic acid ends to characterize two novel Bactrian and eight dromedary camel astroviruses, including both partial and complete genomes. Our reported sequences expand the known diversity of dromedary camel astroviruses, highlighting potential recombination events among the astroviruses of camelids and other host species. In Bactrian camels, we detected partially conserved gene regions bearing resemblance to human astrovirus types 1, 4, and 8 although we were unable to recover complete reading frames from these samples. Continued surveillance of astroviruses in camelids, particularly Bactrian species and associated livestock, is highly recommended to identify patterns of cross-species transmission and to determine any epizootic threats and zoonotic risks posed to humans. Phylogenomic approaches are needed to investigate complex patterns of recombination among the astroviruses and to infer their evolutionary history across diverse host species.

Isolation, identification, and pathogenicity analysis of newly emerging gosling astrovirus in South China

Goose astroviruses (GoAstV) cause fatal gout and decrease product performance in the waterfowl industry across the world. Since no effective vaccines are available, studies on the epidemiology of the virus are necessary for vaccine development. In this study, we collected 94 gout samples from goose farms in the Guangdong Province of South China. Among them, 87 samples (92.6%) tested positive for GoAstV, out of which five GoAstV strains were isolated after four generations of blind transmission through healthy 13-day-old goose embryos. The whole genome of the isolates was sequenced and further analyzed by comparing the sequences with published sequences from China and other parts of the world. The results of the alignment analysis showed that nucleotide sequence similarities among the five GoAstV isolates were around 97.4-98.8%, 98.6-100%, 98.1-99.8%, and 96.7-100% for the whole genome, ORF1a, ORF1b, and ORF2, respectively. These results showed that the GoAstV isolates were highly similar to each other, although they were prevalent in five different regions of the Guangdong Province. The results of the phylogenetic analysis showed that the whole genome, along with the ORF1a, ORF1b, and ORF2 genes of the isolates, were clustered on a single branch, along with the recently published GoAstV-2, and were very distinct from the DNA sequences of the GoAstV-1 virus. In this study, we also reproduced the clinical symptoms of natural infection using the GoAstV-GD2101 isolates, confirming that the gout-causing pathogen in goslings was the goose astrovirus. These findings provided new insights into the pathogenicity and genetic evolution of GoAstV and laid the foundation for effectively controlling the disease.

Novel RNA Viruses Discovered in Weeds in Rice Fields

Weeds often grow alongside crop plants. In addition to competing with crops for nutrients, water and space, weeds host insect vectors or act as reservoirs for viral diversity. However, little is known about viruses infecting rice weeds. In this work, we used metatranscriptomic deep sequencing to identify RNA viruses from 29 weed samples representing 23 weed species. A total of 224 RNA viruses were identified: 39 newly identified viruses are sufficiently divergent to comprise new families and genera. The newly identified RNA viruses clustered within 18 viral families. Of the identified viruses, 196 are positive-sense single-stranded RNA viruses, 24 are negative-sense single-stranded RNA viruses and 4 are double-stranded RNA viruses. We found that some novel RNA viruses clustered within the families or genera of several plant virus species and have the potential to infect plants. Collectively, these results expand our understanding of viral diversity in rice weeds. Our work will contribute to developing effective strategies with which to manage the spread and epidemiology of plant viruses.

Complete genome sequence and phylogenetic analysis of a goose astrovirus isolate in China

Astroviruses are considered the cause of gastroenteritis in humans and animals. Studies in recent years show avian astroviruses are also associated with duckling hepatitis, gosling gout, and chicken nephritis. In this study, a GAstV strain, designated as JS2019/China, was detected in dead goslings from a commercial goose farm in Jiangsu province of China. Viral strain was proliferated in goose embryos and sequence analysis showed the isolated strain had a classical structure arrangement and a series of conserved regions compared with other GAstVs. Sequence comparison and phylogenetic analysis of whole genome and ORF2 revealed that JS2019/China belongs to the GAstV-1 group, which consists of most of the GAstV strains. Amino acid analysis indicated that some mutants might have an impact on viral protease capacity, such as V505I and K736E of ORF1a and T107I, F342S, and S606P of ORF2. Taken together, a novel GAstV strain was isolated and genomic analysis and protein polymorphism analysis indicated that some amino acid mutants might affect the viral virulence.

Prevalence and genetic diversity of coronaviruses, astroviruses and paramyxoviruses in wild birds in southeastern Kazakhstan

Wild birds are natural reservoirs of many emerging viruses, including some zoonoses. Considering that the territory of Kazakhstan is crossed by several bird migration routes, it is important to know pathogenic viruses circulating in migratory birds in this region. Therefore, the aim of this study was to identify the host range, diversity and spatial distribution of avian paramyxoviruses, coronaviruses, and astroviruses in free-ranging wild birds in the southeastern region of Kazakhstan. For this purpose, we collected tracheal and cloacal swabs from 242 wild birds belonging to 51 species and screened them using conventional PCR assays. Overall, 4.1% (10/242) and 2.9% (7/242) of all examined birds tested positive for coronaviruses and astroviruses, respectively. Coronaviruses were found in the orders Pelecaniformes (30%; 3/10), Charadriiformes (30%; 3/10), Columbiformes (20%; 2/10), Anseriformes (10%; 1/10), and Passeriformes (10%; 1/10). All detected strains belonged to the genus Gammacoronavirus. Astroviruses were detected in birds representing the orders Passeriformes (57%; 4/7), Coraciiformes (14%; 1/7), Charadriiformes (14%; 1/7), and Columbiformes (14%; 1/7). Paramyxoviruses were observed in only two birds (0.8%; 2/242). Both strains were closely related to the species APMV-22, which had not been previously detected in Kazakhstan. Phylogenetic analysis of the partial RdRp gene sequences of the virus strains revealed three different clades of astroviruses, two clades of coronaviruses, and one clade of paramyxoviruses. The results of this study provide valuable information on the diversity and spatial distribution of paramyxoviruses, coronaviruses, and astroviruses in wild birds in southeastern Kazakhstan and highlight the importance of further thorough monitoring of wild birds in this region.

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First study on CoVs and AstroVs in wild birds in Kazakhstan.

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APMVs, CoVs and AstroVs are confirmed by RT-PCR and partial RdRp gene sequencing.

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The CoVs prevalence is higher in aquatic birds as compared to terrestrial species.

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The obtained CoV strains belong to the genus Gammacoronavirus

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Strains closely related to APMV-22 not previously detected in Kazakhstan are shown.

Highly diverse ribonucleic acid viruses in the viromes of eukaryotic host species in Yunnan province, China

Background

The diversity in currently documented viruses and their morphological characteristics indicates the need for understanding the evolutionary characteristics of viruses. Notably, further studies are needed to obtain a comprehensive landscape of virome, the virome of host species in Yunnan province, China.

Materials and methods

We implemented the metagenomic next-generation sequencing strategy to investigate the viral diversity, which involved in 465 specimens collected from bats, pangolins, monkeys, and other species. The diverse RNA viruses were analyzed, especially focusing on the genome organization, genetic divergence and phylogenetic relationships.

Results

In this study, we investigated the viral composition of eight libraries from bats, pangolins, monkeys, and other species, and found several diverse RNA viruses, including the Alphacoronavirus from bat specimens. By characterizing the genome organization, genetic divergence, and phylogenetic relationships, we identified five Alphacoronavirus strains, which shared phylogenetic association with Bat-CoV-HKU8-related strains. The pestivirus-like virus related to recently identified Dongyang pangolin virus (DYPV) strains from dead pangolin specimens, suggesting that these viruses are evolving. Some genomes showed higher divergence from known species (e.g., calicivirus CS9-Cali-YN-CHN-2020), and many showed evidence of recombination events with unknown or known strains (e.g., mamastroviruses BF2-astro-YN-CHN-2020 and EV-A122 AKM5-YN-CHN-2020). The newly identified viruses showed extensive changes and could be assigned as new species, or even genus (e.g., calicivirus CS9-Cali-YN-CHN-2020 and iflavirus Ifla-YN-CHN-2020). Moreover, we identified several highly divergent RNA viruses and estimated their evolutionary characteristics among different hosts, providing data for further examination of their evolutionary dynamics.

Conclusion

Overall, our study emphasizes the close association between emerging viruses and infectious diseases, and the need for more comprehensive surveys.

A Review of the Emerging Poultry Visceral Gout Disease Linked to Avian Astrovirus Infection

Avian astroviruses, including chicken astrovirus (CAstV), avian nephritisvirus (ANV), and goose astrovirus (GoAstV), are ubiquitous enteric RNA viruses associated with enteric disorders in avian species. Recent research has found that infection of these astroviruses usually cause visceral gout in chicken, duckling and gosling. However, the underlying mechanism remains unknown. In the current article, we review recent discoveries of genetic diversity and variation of these astroviruses, as well as pathogenesis after astrovirus infection. In addition, we discuss the relation between avian astrovirus infection and visceral gout in poultry. Our aim is to review recent discoveries about the prevention and control of the consequential visceral gout diseases in poultry, along with the attempt to reveal the possible producing process of visceral gout diseases in poultry.

Diversity of Astrovirus in Goats in Southwest China and Identification of Two Novel Caprine Astroviruses

A total of 232 goat fecal samples (124 diarrheic and 108 nondiarrheic) collected from 12 farms in Southwest China were tested for astrovirus using RT-PCR. A total of 16.9% (21/124) of diarrheic and 20.4% (22/108) of nondiarrheic samples were astrovirus-positive, and no statistical difference was found in the detection rate between healthy and sick goats. Furthermore, 28 obtained complete ORF2 sequences could be classified into six genotypes according to the species classification criteria of the International Committee on Taxonomy of Viruses (ICTV). It is worth noting that, in addition to four known caprine astrovirus genotypes (MAstV-33, MAstV-34, Caprine Astrovirus G5.1, and Caprine Astrovirus G3.1), MAstV-13 and MAstV-24 genotypes were identified in goats. Interestingly, five of 19 ORF2 sequences in the Caprine Astrovirus G3.1 genotype showed possible intragenotypic recombination events. Furthermore, nearly complete caprine astrovirus genomes of MAstV-13 and MAstV-24 genotypes were obtained. The genome of the SWUN/ECJK3/2021 strain shared the highest similarity (62.0% to 73.9%) with astrovirus in MAstV-13, and clustered in the so-called human-mink-ovine (HMO) clade, which contained the majority of the neurotropic astrovirus strains. Moreover, the SWUN/LJK2-2/2020 strain showed the highest similarity (69.7% to 78.6%) and the closest genetic relationship to the known porcine and bovine astroviruses in MAstV-24. In conclusion, this study confirmed six genotypes of astrovirus circulating among goats in Southwest China, including MAstV-13 and MAstV-24 genotypes. These findings enhance our knowledge of the prevalence and diversity of astroviruses. IMPORTANCE Caprine astrovirus is a newly emerging virus, and information regarding its prevalence and molecular characteristics remains limited. In this study, six genotypes of astrovirus, including MAstV-13 and MAstV-24, were identified in goats, adding two novel caprine astrovirus genotypes to the four previously known genotypes, thereby enriching the diversity of the caprine astrovirus. Moreover, genomes of MAstV-13 SWUN/ECJK3/2021 and MAstV-24 SWUN/LJK2-2/2020 strains were obtained from goats, which aids in the understanding of the infection spectrum and host range of the two genotypes. This study is the first to demonstrate the presence of neurotropic-like astrovirus (MAstV-13) in goats, which has significant implications for the diagnosis of neurological diseases in goats.

Metagenomic analysis of viral diversity and a novel astroviruse of forest rodent

Background

Rodents are important virus reservoirs and natural hosts for multiple viruses. They are one of the wild animals that are extremely threatening to the spread of human viruses. Therefore, research on rodents carrying viruses and identifying new viruses that rodents carry is of great significance for preventing and controlling viral diseases.

Methods

In this study, fecal samples from six species of forest rodents in Northeast China were sequenced using metagenomics, and an abundance of virome information was acquired. Selection of important zoonotic in individual rodents for further sequence and evolutionary analysis.

Results

Among the top 10 most abundant viral families, RNA virus include Orthomyxoviridae, Picornaviridae, Bunyaviridae and Arenaviridae, DNA virus include Herpesviridae, Insect virus include Nodaviridae and Baculoviridae, Plant virus Tombusviridae and Phage (Myoriviridae). Except for Myoviridae, there was no significant difference in the abundance of virus families in the feces of each rodent species. In addition, a new strain of astrovirus was discovered, with an ORF and genome arrangement comparable to other rodent astroviruses.The newly identified astrovirus had the highest similarity with the rodent astrovirus isolate, CHN/100.

Conclusions

The data obtained in this study provided an overview of the viral community present in these rodent fecal samples, revealing some rodent-associated viruses closely related to known human or animal pathogens. Strengthening our understanding of unclassified viruses harbored by rodents present in the natural environment could provide scientific guidance for preventing and controlling new viral outbreaks that can spread via rodents.

Global public health implications of human exposure to viral contaminated water

Enteric viruses are common waterborne pathogens found in environmental water bodies contaminated with either raw or partially treated sewage discharge. Examples of these viruses include adenovirus, rotavirus, noroviruses, and other caliciviruses and enteroviruses like coxsackievirus and polioviruses. They have been linked with gastroenteritis, while some enteric viruses have also been implicated in more severe infections such as encephalitis, meningitis, hepatitis (hepatitis A and E viruses), cancer (polyomavirus), and myocarditis (enteroviruses). Therefore, this review presents information on the occurrence of enteric viruses of public health importance, diseases associated with human exposure to enteric viruses, assessment of their presence in contaminated water, and their removal in water and wastewater sources. In order to prevent illnesses associated with human exposure to viral contaminated water, we suggest the regular viral monitoring of treated wastewater before discharging it into the environment. Furthermore, we highlight the need for more research to focus on the development of more holistic disinfection methods that will inactivate waterborne viruses in municipal wastewater discharges, as this is highly needed to curtail the public health effects of human exposure to contaminated water. Moreover, such a method must be devoid of disinfection by-products that have mutagenic and carcinogenic potential.

Eugenol alleviates transmissible gastroenteritis virus-induced intestinal epithelial injury by regulating NF-κB signaling pathway

Increasing evidence supports the ability of eugenol to maintain intestinal barrier integrity and anti-inflammatory in vitro and in vivo; however, whether eugenol alleviates virus-mediated intestinal barrier damage and inflammation remains a mystery. Transmissible gastroenteritis virus (TGEV), a coronavirus, is one of the main causative agents of diarrhea in piglets and significantly impacts the global swine industry. Here, we found that eugenol could alleviate TGEV-induced intestinal functional impairment and inflammatory responses in piglets. Our results indicated that eugenol improved feed efficiency in TGEV-infected piglets. Eugenol not only increased serum immunoglobulin concentration (IgG) but also significantly decreased serum inflammatory cytokine concentration (TNF-α) in TGEV-infected piglets. In addition, eugenol also significantly decreased the expression of NF-κB mRNA and the phosphorylation level of NF-κB P65 protein in the jejunum mucosa of TGEV-infected piglets. Eugenol increased villus height and the ratio of villus height to crypt depth in the jejunum and ileum, and decreased serum D-lactic acid levels. Importantly, eugenol increased tight junction protein (ZO-1) and mRNA expression levels of nutrient transporter-related genes (GluT-2 and CaT-1) in the jejunum mucosa of TGEV-infected piglets. Meanwhile, compared with TGEV-infected IPEC-J2 cells, treatment with eugenol reduced the cell cytopathic effect, attenuated the inflammatory response. Interestingly, eugenol did not increase the expression of ZO-1 and Occludin in IPEC-J2 cells. However, western blot and immunofluorescence results showed that eugenol restored TGEV-induced down-regulation of ZO-1 and Occludin, while BAY11-7082 (The NF-κB specific inhibitor) enhanced the regulatory ability of eugenol. Our findings demonstrated that eugenol attenuated TGEV-induced intestinal injury by increasing the expression of ZO-1 and Occludin, which may be related to the inhibition of NF-κB signaling pathway. Eugenol may offer some therapeutic opportunities for coronavirus-related diseases.

Advances in understanding interferon-mediated immune responses to enteric viruses in intestinal organoids

Interferons (IFN) are antiviral cytokines with critical roles in regulating pathogens at epithelial barriers, but their capacity to restrict human enteric viruses has been incompletely characterized in part due to challenges in cultivating some viruses in vitro, particularly human norovirus. Accordingly, advancements in the development of antiviral therapies and vaccine strategies for enteric viral infections have been similarly constrained. Currently emerging is the use of human intestinal enteroids (HIEs) to investigate mechanisms of human enteric viral pathogenesis. HIEs provide a unique opportunity to investigate host-virus interactions using an in vitro system that recapitulates the cellular complexity of the in vivo gastrointestinal epithelium. This approach permits the exploration of intestinal epithelial cell interactions with enteric viruses as well as the innate immune responses mediated by IFNs and IFN-stimulated genes. Here, we describe recent findings related to the production, signaling, and function of IFNs in the response to enteric viral infections, which will ultimately help to reveal important aspects of pathogenesis and facilitate the future development of therapeutics and vaccines.

Insight into the Epidemiology and Evolutionary History of Novel Goose Astrovirus-Associated Gout in Goslings in Southern China

A novel gout disease, characterized by visceral urate deposition with high-mortality, with outbreaks in goslings in China since 2016 was caused by a novel goose astrovirus (GoAstV) and resulted in serious economic loss. However, the epidemiology and variation of the GoAstV in goslings in southern China and its evolutionary history as well as the classification of the GoAstV are unclear. In the present study, systematic molecular epidemiology, and phylogenetic analyses of the GoAstV were conducted to address these issues. Our results showed that the GoAstV is widespread in goslings in southern China, and the genomes of six GoAstV strains were obtained. Two amino acid mutations (Y36H and E456D) were identified in capsid proteins in this study, which is the dominant antigen for the GoAstV. In addition, the GoAstV could be divided into two distinct clades, GoAstV-1 and GoAstV-2, and GoAstV-2 is responsible for gout outbreaks in goslings and could be classified into Avastrovirus 3 (AAstV-3), while GoAstV-1 belongs to Avastrovirus 1 (AAstV-1). Moreover, the emergence of GoAstV-2 in geese was estimated to have occurred in January 2010, approximately 12 years ago, while GoAstV-1 emerged earlier than GoAstV-2 and was estimated to have emerged in April 1985 based on Bayesian analysis. The mean evolutionary rate for the GoAstV was also calculated to be approximately 1.42 × 10⁻³ nucleotide substitutions per site per year. In conclusion, this study provides insight into the epidemiology of the GoAstV in goslings in southern China and is helpful for understanding the origin and evolutionary history as well as the classification of the GoAstV in geese.

Potential zoonotic swine enteric viruses: The risk ignored for public health

Swine could serve as a natural reservoir for a large variety of viruses, including potential zoonotic enteric viruses. The presence of viruses with high genetic similarity between porcine and human strains may result in the emergence of zoonotic or xenozoonotic infections. Furthermore, the globalization and intensification of swine industries exacerbate the transmission and evolution of zoonotic viruses among swine herds and individuals working in swine-related occupations. To effectively prevent the public health risks posed by zoonotic swine enteric viruses, designing, and implementing a comprehensive measure for early diagnosis, prevention, and mitigation, requires interdisciplinary a collaborative ''One Health" approach from veterinarians, environmental and public health professionals, and the swine industry. In this paper, we reviewed the current knowledge of selected potential zoonotic swine enteric viruses and explored swine intensive production and its associated public health risks.

An Insight into the Molecular Characteristics and Associated Pathology of Chicken Astroviruses

The chicken astrovirus (CAstV) is a ubiquitous enteric RNA virus that has been associated mainly with conditions, such as the runting-stunting syndrome, severe kidney disease, visceral gout, and white chick syndrome, in broiler-type chickens worldwide. Sequence analysis of the capsid genes’ amino acids of the strains involved in these conditions reveals a genetic relationship and diversity between and within the CAstV genogroups and subgroups based on phylogenetic analysis, genetic distance (p-dist), and pathogenicity. While the two genogroups (A and B) are demarcated phylogenetically, their pairwise amino acid sequence identity is 39% to 42% at a p-dist of 0.59 to 0.62. Group-A consists of three subgroups (Ai, Aii, and Aiii) with an inter- and intra-subgroup amino acid identity of 78% to 82% and 92% to 100%, respectively, and a p-dist of 0.18 to 0.22. On the other hand, the six subgroups (Bi, Bii, Biii, Biv, Bv, and Bvi) in Group-B, with a p-dist of 0.07 to 0.18, have an inter- and intra-subgroup amino acid identity of 82% to 93% and 93% to 100%, respectively. However, these groupings have little to no effect on determining the type of CAstV-associated pathology in chickens.

Molecular epidemiological characteristics of the virus in 96 children with acute diarrhea in Changdu of Tibet, China

OBJECTIVES

To study the molecular epidemiological characteristics of the virus in children with acute viral diarrhea in Changdu of Tibet, China.

METHODS

Fecal specimens were collected from 96 children with acute diarrhea who visited the People's Hospital of Changdu, Tibet, from November 2018 to November 2020 and were tested for adenovirus, norovirus, astrovirus, sapovirus, and rotavirus. Gene sequencing was performed for the genotypes of these viruses.

RESULTS

The overall positive rate of the five viruses was 39% (37/96), among which astrovirus had the highest positive rate of 17%, followed by norovirus (9%), rotavirus (8%), adenovirus (7%), and sapovirus (5%). There was no significant difference in the positive rate of the five viruses among different age groups (P>0.05). Only the positive rate of astrovirus was significantly different among the four seasons (P<0.05). For adenovirus, 6 children had F41 type and 1 had C2 type; for norovirus, 6 had GⅠ.3 type, 1 had GⅠ.7 type, 1 had GⅡ.3 type, and 2 had GⅡ.4 Sydney_2012 type; HAstrV-1 type was observed in all children with astrovirus infection; for sapovirus, 1 child each had sporadic GⅠ.2, GⅠ.6, and GⅡ.1 sapovirus and 2 children had unknown type; 6 children had rotavirus G9[P8].

CONCLUSIONS

Astrovirus and norovirus are important pathogens in children with acute diarrhea in Changdu, Tibet. The positive rate of adenovirus, norovirus, astrovirus, sapovirus, and rotavirus is not associated with age, and only the positive rate of astrovirus has obvious seasonality. F41 type is the dominant genotype of adenovirus; GⅠ.3 is the dominant genotype of norovirus; HAstrV-1 is the dominant genotype of astrovirus; sporadic GⅠ.2, GⅠ.6, and GⅡ.1 are the dominant genotypes of sapovirus; G9[P8] is the dominant genotype of rotavirus.

Core antigenic advantage domain-based ELISA to detect antibody against novel goose astrovirus in breeding geese

Goose astrovirus (GAstV), the major causative agent of visceral and joint gout in goslings, is a novel pathogen greatly threatening waterfowl industry. Importantly, the horizontal and vertical transmissibility of GAstV posed a great challenge for disease prevention and control. Given the absence of commercial vaccine, restricting vertical transmission and protecting susceptible goslings must be a priority. Although many detection methods have been established, there is no serological method to detect GAstV-specific antibody, greatly limiting inspection and elimination of infected breeding bird. In this study, the B-cell epitopes of GAstV capsid protein were predicted, and its core antigenic advantage domain (shCAP) was expressed and purified. After authenticating the antigenicity, the recombinant shCAP protein was taken as the coating antigen, and an easily accessible indirect enzyme-linked immunosorbent assay (ELISA) was established to detect GAstV-specific antibody. The working conditions, including antigen concentration, serum dilution and incubation time, blocking buffer concentration, and color developing time, were gradually optimized by checkerboard titration. The cut-off OD₄₅₀ value of the indirect ELISA for positive sample was 0.379, and the analytical sensitivity was 1:800. There was no cross-reaction with sera against goose parvovirus (GPV), Tembusu virus (TUMV), H5 and H7 subtype avian influenza virus (AIV H5 + H7), and Newcastle disease virus (NDV). The assay was further applied to examine 73 breeding goose serum samples and shared excellent agreement of 93.5% (68/73) with western blot, which also suggested that GAstV is circulating in the goose population in China. In conclusion, the developed indirect ELISA is simple, specific, and sensitive, which will be greatly useful to screen GAstV infection and block vertical transmission. KEY POINTS: • B-cell epitopes of GAstV capsid protein were predicted and expressed as immunogen • A core antigenic advantage domain-based ELISA was established to detect GAstV-specific antibody • The established ELISA will contribute to inspection and elimination of infected breeding geese and provide a useful tool for large scale serological testing of GAstV in geese.

Development and Large-Scale Testing of a Novel One-Step Triplex RT-qPCR Assay for Simultaneous Detection of “Neurotropic” Porcine Sapeloviruses, Teschoviruses (Picornaviridae) and Type 3 Porcine Astroviruses (Astroviridae) in Various Samples including Nasal Swabs

Porcine sapeloviruses, teschoviruses of family Picornaviridae and type 3 porcine astroviruses of family Astroviridae are (re-)emerging enteric pathogens that could be associated with severe, disseminated infections in swine, affecting multiple organs including the central nervous system (CNS). Furthermore, small-scale pioneer studies indicate the presence of these viruses in porcine nasal samples to various extents. The laboratory diagnostics are predominantly based on the detection of the viral RNA from faecal and tissue samples using different nucleic-acid-based techniques such as RT-qPCR. In this study, a novel highly sensitive one-step triplex RT-qPCR assay was introduced which can detect all known types of neurotropic sapelo-, tescho- and type 3 astroviruses in multiple types of samples of swine. The assay was evaluated using in vitro synthesized RNA standards and a total of 142 archived RNA samples including known sapelo-, tescho- and type 3 astrovirus positive and negative CNS, enteric and nasal specimens. The results of a large-scale epidemiological investigation of these viruses on n = 473 nasal swab samples from n = 28 industrial-type swine farms in Hungary indicate that all three neurotropic viruses, especially type 3 astroviruses, are widespread and endemically present on most of the investigated farms.

Isolation, Identification, and Genomic Characterization of Chicken Astrovirus Isolates From China

Chicken astrovirus (CAstV) infection can cause diarrhea, nephritis, stunted growth, and “white chickens” condition, resulting in economic losses to the poultry industry. Currently, a few CAstVs were isolated and a few full-length genome sequences of CAstV have been deposited in the GenBank. In the present study, two CAstV isolates (AAstV/Chicken/CHN/2017/NJ01 and AAstV/Chicken/CHN/2018/CZ01) were successfully isolated by using LMH cells, and we molecularly characterized these two CAstV isolates and observed the effect of these two isolates on hatchability using chicken embryo infection experiment. The genetic analysis demonstrated that these two strains had the typical characteristics of avian astroviruses, which were composed of three open reading frames, 5′UTR, and 3′UTR. The full-length genome sequence showed a high-degree identity at nucleotide level of 97.5–98.7% among Chinese isolates suggesting their common ancestors and limited sequence divergence. Sequence analysis of ORF2, which encodes the capsid protein associated with classification of avian astrovirus, revealed our two isolates belonging to CAstV Bi subtype. At the amino acid level, the complete capsid region of Chinese strains shared genetic distances of 0.03–0.04 with FP3 strains isolated from the UK, suggesting their common origin. Meanwhile, hatchability reduction was observed. These results provided novel insights into the molecular epidemiology and hatchability effect of CAstV.

Molecular Epidemiology of Human Adenovirus, Astrovirus, and Sapovirus Among Outpatient Children With Acute Diarrhea in Chongqing, China, 2017-2019

OBJECTIVE

To investigate the epidemiology of human adenovirus (HAdV), human astrovirus (HAstV), and sapovirus (SaV), children with acute diarrhea in Chongqing, China from 2017 to 2019 were enrolled. Improved surveillance could provide better guidance for diarrhea prevention.

METHODS

Between 2017 and 2019, fecal specimens were collected from children <14 years of age presenting with acute diarrhea for treatment at the outpatient department of the Children's Hospital, Chongqing Medical University. Human HAdV in the fecal specimens was detected by PCR, while RT-PCR was adopted for the detection of HAstV and SaV.

RESULTS

A total of 1,352 fecal specimens were screened in this study. The detection rate of HAdV was 4.44% (60/1352), HAstV was 2.81% (38/1352), and SaV was 1.04% (14/1352). The prevalence of enteric viruses in males was not significantly different to females (p > 0.05). We found 96.67% (58/60) of the HAdV-positive cases, 92.11% (35/38) of the HAstV-positive cases, and 100% (14/14) of the SaV-positive cases among the children under 4 years old. HAdV cases were identified throughout the year, while the infection of HAstV peaked from March to May every year. By contrast, SaV was detected in May, July, and from September to December. In total, 41 strains of HAdV-F were identified, including F41 (39/60) and F40 (2/60). Furthermore, A31, B3, B7, C1, C2, C5, and C6 were also detected in the study. In addition, we detected two genotypes of HAstV, HAstV-1 (34/38) and HAstV-5 (4/38), and two genotypes of SaV, GI0.1 (13/14), GI0.2 (1/14).

CONCLUSION

The enteric viruses HAdV, HAstV, and SaV contribute to the overall burden of diarrhea in Chongqing, especially in children <4 years of age. Two genotypes were identified for HAstV (HAstV-1 and HAstV-5) and SaV (GI.1 and GI.2) with an additional nine genotypes detected in HAdV cases. While the F41 HAdV strain was predominant, HAdV-A31 was also detected in 10% of cases. The study results along with continuous surveillance of enteric viruses will aid in the design and implementation of future enteric vaccines and diarrhea mitigation strategies.