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Structure (London, England : 1993) Dec 2022Despite their worldwide prevalence and association with human disease, the molecular bases of human astrovirus (HAstV) infection and evolution remain poorly...
Despite their worldwide prevalence and association with human disease, the molecular bases of human astrovirus (HAstV) infection and evolution remain poorly characterized. Here, we report the structure of the capsid protein spike of the divergent HAstV MLB clade (HAstV MLB). While the structure shares a similar folding topology with that of classical-clade HAstV spikes, it is otherwise strikingly different. We find no evidence of a conserved receptor-binding site between the MLB and classical HAstV spikes, suggesting that MLB and classical HAstVs utilize different receptors for host-cell attachment. We provide evidence for this hypothesis using a novel HAstV infection competition assay. Comparisons of the HAstV MLB spike structure with structures predicted from its sequence reveal poor matches, but template-based predictions were surprisingly accurate relative to machine-learning-based predictions. Our data provide a foundation for understanding the mechanisms of infection by diverse HAstVs and can support structure determination in similarly unstudied systems.
Topics: Humans; Capsid; Mamastrovirus; Capsid Proteins; Binding Sites; Machine Learning
PubMed: 36417907
DOI: 10.1016/j.str.2022.10.010 -
Brazilian Journal of Microbiology :... Mar 2023Astroviruses are considered the cause of gastroenteritis in humans and animals. Studies in recent years show avian astroviruses are also associated with duckling...
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.
Topics: Humans; Animals; Geese; Astroviridae Infections; Phylogeny; Genome, Viral; Poultry Diseases; Avastrovirus; China
PubMed: 36327040
DOI: 10.1007/s42770-022-00854-7 -
Viruses Oct 2022Astroviruses (AstVs) are single-stranded RNA viruses, including two main genera: Mamastroviruses (MAstVs) and Avastroviruses (AAstVs). AstVs have been detected in more...
Astroviruses (AstVs) are single-stranded RNA viruses, including two main genera: Mamastroviruses (MAstVs) and Avastroviruses (AAstVs). AstVs have been detected in more than 80 different mammals and birds, with the characteristics of multiple cross-species transmission and gene recombination. All these have accelerated the process of virus mutation and posed a potential threat to human beings and animal husbandry. Yunnan province is a global hotspot with rich biodiversity and abundant animal resources and an important area with significance for public health and security because it neighbors a few Southeast Asian countries. This study collected 860 samples from 13 species of animals in Yunnan province for AstVs detection. The results showed that the positive rate of AstVs was 6.05%, and its extremely high genetic diversity was observed in different animal species. Potential cross-species transmission events were also detected from rodents to birds. Therefore, AstVs, which are widely distributed with highly diverse genes and the risk of cross-species transmission to people, deserve more attention in this region.
Topics: Animals; Humans; Astroviridae Infections; Phylogeny; China; Avastrovirus; Mamastrovirus; Mammals; Birds; Rodentia; Genetic Variation
PubMed: 36298789
DOI: 10.3390/v14102234 -
Microorganisms Sep 2022This article characterises viral fraction metatranscriptomes (smaller than 0.2 µm) from the pelagic zone of oligotrophic Lake Baikal (Russia). The study revealed the...
This article characterises viral fraction metatranscriptomes (smaller than 0.2 µm) from the pelagic zone of oligotrophic Lake Baikal (Russia). The study revealed the dominance of transcripts of DNA viruses: bacteriophages and algal viruses. We identified transcripts similar to , a nucleocytoplasmic large DNA virus (NCLDV) isolated from the permafrost region of Eastern Siberia. Among the families detected were RNA viruses assigned to Retroviridae, Metaviridae, Potyviridae, Astroviridae, and Closteroviridae. Using the PHROG, SEED subsystems databases, and the VOGDB, we indicated that the bulk of transcripts belong to the functional replication of viruses. In a comparative unweighted pair group method with arithmetic mean (UPGMA) analysis, the transcripts from Lake Baikal formed a separate cluster included in the clade with transcripts from other freshwater lakes, as well as marine and oceanic waters, while there was no separation based on the trophic state of the water bodies, the size of the plankton fraction, or salinity.
PubMed: 36296212
DOI: 10.3390/microorganisms10101937 -
Poultry Science Dec 2022Fatal gout in geese caused by goose astrovirus (GAstV) has been spreading rapidly in China since 2018, causing serious economic losses in the goose breeding industry. To...
Facile, ultrasensitive, and highly specific diagnosis of goose astrovirus via reverse transcription-enzymatic recombinase amplification coupled with a CRISPR-Cas12a system detection.
Fatal gout in geese caused by goose astrovirus (GAstV) has been spreading rapidly in China since 2018, causing serious economic losses in the goose breeding industry. To achieve simple, convenient and sensitive detection of GAstV, a novel diagnostic test was developed by combining reverse transcription-enzymatic recombinase amplification (RT-ERA) and CRISPR-Cas12a technologies. RT-ERA primers were designed to pre-amplify the conserved region of the ORF2 gene of GAstV and the predefined target sequence detected using the Cas12a/crRNA complex at 37℃ for 30 min. Specific detection of GAstV was achieved with no cross-reaction with non-GAstV templates and a sensitivity detection limit of 2 copies. The experimental procedure could be completed within 1 h, including RNA extraction (15 min), RT-ERA reaction (20 min), CRISPR-Cas12a/crRNA detection (5 min) and result readout (within 2 min) steps. In conclusion, the combination of RT-ETA and CRISPR-Cas12a provides a rapid and specific method that should be effective for the control and surveillance of GAstV infections in farms from remote locations.
Topics: Animals; Reverse Transcription; Recombinases; Geese; CRISPR-Cas Systems; Chickens; Avastrovirus
PubMed: 36279605
DOI: 10.1016/j.psj.2022.102208 -
ISME Communications Oct 2022Amphibians and non-avian reptiles represent a significant proportion of terrestrial vertebrates, however knowledge of their viruses is not proportional to their...
Amphibians and non-avian reptiles represent a significant proportion of terrestrial vertebrates, however knowledge of their viruses is not proportional to their abundance. Many amphibians and reptiles have strict habitual environments and localised populations and are vulnerable to viral outbreaks and potential elimination as a result. We sought to identify viruses that were hidden in amphibian and reptile metatranscriptomic data by screening 235 RNA-sequencing datasets from a 122 species covering 25 countries. We identified 26 novel viruses and eight previously characterised viruses from fifteen different viral families. Twenty-five viruses had RNA genomes with identity to Arteriviridae, Tobaniviridae, Hantaviridae, Rhabdoviridae, Astroviridae, Arenaviridae, Hepeviridae, Picornaviridae, Orthomyxoviridae, Reoviridae, Flaviviridae and Caliciviridae. In addition to RNA viruses, we also screened datasets for DNA viral transcripts, which are commonly excluded from transcriptomic analysis. We identified ten DNA viruses with identity to Papillomaviridae, Parvoviridae, Circoviridae and Adomaviridae. With the addition of these viruses, we expand the global amphibian and reptile virome and identify new potentially pathogenic viruses that could challenge populations. We speculate that amphibian viruses often have simpler genomes than those in amniotes, as in the case of the Secondpapillomavirinae and Orthomyxoviridae viruses identified in this study. In addition, we find evidence of inter-family recombination in RNA viruses, and we also identify new members of the recombinant Adomaviridae family. Overall, we provide insights into the uncharacterised diversity of amphibian and reptile viruses with the aim of improving population management, treatment and conservation into the future.
PubMed: 37938670
DOI: 10.1038/s43705-022-00180-x -
Scientific Reports Sep 2022Farm animals may harbor viral pathogens, some with zoonotic potential which can possibly cause severe clinical outcomes in animals and humans. Documenting the viral...
Farm animals may harbor viral pathogens, some with zoonotic potential which can possibly cause severe clinical outcomes in animals and humans. Documenting the viral content of dust may provide information on the potential sources and movement of viruses. Here, we describe a dust sequencing strategy that provides detailed viral sequence characterization from farm dust samples and use this method to document the virus communities from chicken farm dust samples and paired feces collected from the same broiler farms in the Netherlands. From the sequencing data, Parvoviridae and Picornaviridae were the most frequently found virus families, detected in 85-100% of all fecal and dust samples with a large genomic diversity identified from the Picornaviridae. Sequences from the Caliciviridae and Astroviridae familes were also obtained. This study provides a unique characterization of virus communities in farmed chickens and paired farm dust samples and our sequencing methodology enabled the recovery of viral genome sequences from farm dust, providing important tracking details for virus movement between livestock animals and their farm environment. This study serves as a proof of concept supporting dust sampling to be used in viral metagenomic surveillance.
Topics: Animals; Chickens; Dust; Farms; Humans; Metagenome; Metagenomics
PubMed: 36175536
DOI: 10.1038/s41598-022-20701-x -
Viruses Sep 2022The swine industry plays an essential role in agricultural production in China. Diseases, especially viral diseases, affect the development of the pig industry and...
The swine industry plays an essential role in agricultural production in China. Diseases, especially viral diseases, affect the development of the pig industry and threaten human health. However, at present, the tissue virome of diseased pigs has rarely been studied. Using the unbiased viral metagenomic approach, we investigated the tissue virome in sick pigs (respiratory symptoms, reproductive disorders, high fever, diarrhea, weight loss, acute death and neurological symptoms) collected from farms of Anhui, Jiangsu and Sichuan Province, China. The eukaryotic viruses identified belonged to the families , , , , and ; prokaryotic virus families including , and occupied a large proportion in some samples. This study provides valuable information for understanding the tissue virome in sick pigs and for the monitoring, preventing, and treating of viral diseases in pigs.
Topics: Anelloviridae; Animals; Metagenome; Metagenomics; Phylogeny; Swine; Virus Diseases; Viruses
PubMed: 36146854
DOI: 10.3390/v14092048 -
International Journal of Molecular... Sep 2022Avian astroviruses, including chicken astrovirus (CAstV), avian nephritisvirus (ANV), and goose astrovirus (GoAstV), are ubiquitous enteric RNA viruses associated with... (Review)
Review
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.
Topics: Animals; Astroviridae Infections; Avastrovirus; Geese; Gout; Phylogeny; Poultry; Poultry Diseases
PubMed: 36142340
DOI: 10.3390/ijms231810429 -
Veterinary Research Communications Dec 2022In this study, the aetiological background of an outbreak of severe haemorrhagic gastroenteritis (HGE) in a colony of purebred Jack Russell Terriers vaccinated against...
Unusual "Asian-origin" 2c to 2b point mutant canine parvovirus (Parvoviridae) and canine astrovirus (Astroviridae) co-infection detected in vaccinated dogs with an outbreak of severe haemorrhagic gastroenteritis with high mortality rate in Hungary.
In this study, the aetiological background of an outbreak of severe haemorrhagic gastroenteritis (HGE) in a colony of purebred Jack Russell Terriers vaccinated against CPV-2 in Hungary was investigated. Canine parvovirus 2 (CPV-2, Parvoviridae) and canine astrovirus (CaAstV, Astroviridae) co-infection was identified by viral metagenomics and next-generation sequencing (VM-NGS) methods from a rectal swab of an affected 7-week-old puppy. The complete coding sequence of CPV-2 strain FR1/CPV2-2021-HUN (ON733252) and the complete genome of CaAstV strain FR1/CaAstV-2021-HUN (ON733251) were determined by VM-NGS and PCR methods. Results of sequence and phylogenetic analyses showed that CPV-2 strain FR1/CPV2-2021-HUN was different from the applied vaccine strains and previously identified strains from Hungary but showed high sequence identity (> 99.8%) and close phylogenetic relationship to recently described "Asian-origin" CPV-2c strains from Italy. But, based on the single amino acid difference on position 426 of VP2 (Glu/Asp) between the study strain and the closest relatives, FR1/CPV2-2021-HUN belonged to the 2b antigenic type rather than 2c. The CaAstV strain FR1/CaAstV-2021-HUN showed close relationship with a CaAstV strain identified previously from a diarrhoeic dog in Hungary. Both viruses were continuously detectable by PCR in additional enteric samples, and the CPV-2 could also be detected in several (n = 32) tissue samples from 9 affected deceased puppies. Further comparative studies are necessary to confirm the role of the point mutation causing the change in the antigenic type of this "Asian-origin" CPV-2 and/or the role of CaAstV co-infection in the development and/or severity of (haemorrhagic) gastroenteritis among dogs vaccinated against CPV-2.
Topics: Dogs; Animals; Parvovirus, Canine; Astroviridae; Parvoviridae; Phylogeny; Coinfection; Hungary; Parvoviridae Infections; Dog Diseases; Gastroenteritis; Disease Outbreaks
PubMed: 36129562
DOI: 10.1007/s11259-022-09997-2