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Pathogens (Basel, Switzerland) Dec 2023Plant-infecting RNA viruses from 30 families and floating genera, as well as a great number of uncultured as yet-unclassified plant-associated viruses have been...
Plant-infecting RNA viruses from 30 families and floating genera, as well as a great number of uncultured as yet-unclassified plant-associated viruses have been described. Even so, the plant RNA virosphere is still underexplored. RNA extracted from enriched virus particles of 50 L water samples from the Teltow Canal and the Havel River in Berlin, Germany, was sequenced using Illumina next-generation sequencing. Sequences were searched for plant viruses with BLAST and DIAMOND. Phylogenetic analyses were conducted with IQ-TREE 2. Altogether, 647 virus sequences greater than 1 kb were detected and further analyzed. These data revealed the presence of accepted and novel viruses related to , , , , , , , , and . The vast majority of the sequences were novel and could not be taxonomically assigned. Several tombus- and endorna-like viruses make use of alternative translation tables that suggest unicellular green algae, ciliates, or diplomonades as their hosts. The identification of 27 albeto-like satellite viruses increases available sequence data five-fold. Sixteen new poty-like viruses align with other poty-like viruses in a link that combines the and families. Further, the identification of viruses with peptidase A6-like and peptidase A21-like capsid proteins suggests horizontal gene transfer in the evolution of these viruses.
PubMed: 38133341
DOI: 10.3390/pathogens12121458 -
Scientific Reports Aug 2023Bats are described as the natural reservoir host for a wide range of viruses. Although an increasing number of bat-associated, potentially human pathogenic viruses were...
Bats are described as the natural reservoir host for a wide range of viruses. Although an increasing number of bat-associated, potentially human pathogenic viruses were discovered in the past, the full picture of the bat viromes is not explored yet. In this study, the virome composition of Miniopterus phillipsi bats (formerly known as Miniopterus fuliginosus bats in Sri Lanka) inhabiting the Wavul Galge cave, Sri Lanka, was analyzed. To assess different possible excretion routes, oral swabs, feces and urine were collected and analyzed individually by using metagenomic NGS. The data obtained was further evaluated by using phylogenetic reconstructions, whereby a special focus was set on RNA viruses that are typically associated with bats. Two different alphacoronavirus strains were detected in feces and urine samples. Furthermore, a paramyxovirus was detected in urine samples. Sequences related to Picornaviridae, Iflaviridae, unclassified Riboviria and Astroviridae were identified in feces samples and further sequences related to Astroviridae in urine samples. No viruses were detected in oral swab samples. The comparative virome analysis in this study revealed a diversity in the virome composition between the collected sample types which also represent different potential shedding routes for the detected viruses. At the same time, several novel viruses represent first reports of these pathogens from bats in Sri Lanka. The detection of two different coronaviruses in the samples indicates the potential general persistence of this virus species in M. phillipsi bats. Based on phylogenetics, the identified viruses are closely related to bat-associated viruses with comparably low estimation of human pathogenic potential. In further studies, the seasonal variation of the virome will be analyzed to identify possible shedding patterns for particular viruses.
Topics: Animals; Humans; Chiroptera; Phylogeny; Virome; Sri Lanka; Coronavirus
PubMed: 37553373
DOI: 10.1038/s41598-023-39534-3 -
Poultry Science Jul 2023The epidemic of goose astrovirus (GoAstV) caused huge losses to the poultry industry. Epidemiological studies in China revealed 2 circulating genotypes of GoAstV, but...
The epidemic of goose astrovirus (GoAstV) caused huge losses to the poultry industry. Epidemiological studies in China revealed 2 circulating genotypes of GoAstV, but there is a lack of differential diagnosis tools. By analyzing all published genomes of GoAstV, this study designed specific PCR primers and Taqman probes to recognize different genotypes of GoAstV. After optimization and verification, this study developed a Taqman-based real-time quantitative PCR method that is capable of differential diagnosis. The established qPCR exhibited detection limitations of 100 copies/μL or 10 copies/μL, respectively, for GoAstV genotype 1 and genotype 2, and showed no false positive for other common avian viruses. This method was then used to analyze 72 samples collected from different regions in Jiangxi, and the results were verified by genome sequencing and phylogenetic analysis. These results revealed a complex coinfection of GoAstV different genotypes in China, highlighting the importance of long-term focus on the prevalence and genome evolution of GoAstV.
Topics: Animals; Geese; Phylogeny; Chickens; Avastrovirus; Real-Time Polymerase Chain Reaction; Genotype; Sensitivity and Specificity
PubMed: 37167886
DOI: 10.1016/j.psj.2023.102730 -
Emerging Microbes & Infections Dec 2023Characterized by high genetic diversity, broad host range, and resistance to adverse conditions, coupled with recent reports of neurotropic astroviruses circulating in...
Characterized by high genetic diversity, broad host range, and resistance to adverse conditions, coupled with recent reports of neurotropic astroviruses circulating in humans, mamastroviruses pose a threat to public health. The current astrovirus classification system based on host source prevents determining whether strains with distinct tropism or virulence are emerging. By using integrated phylogeny, we propose a standardized demarcation of species and genotypes, with reproducible cut-off values that reconcile the pairwise sequence distribution, genetic distances between lineages, and the topological reconstruction of the genus. We further define the various links established by co-evolution and resolve the dynamics of transmission chains to identify host-jump events and the sources from which different mamastrovirus species circulating in humans have emerged. We observed that recombination is relatively infrequent and restricted to within genotypes. The well-known "human" astrovirus, defined here as mamastrovirus species 7, has co-speciated with humans, while there have been two additional host-jumps into humans from distinct hosts. Newly defined species 6 genotype 2, linked to severe gastroenteritis in children, resulted from a marmot to human jump taking place ∼200 years ago while species 6 genotype 7 (MastV-Sp6Gt7), linked to neurological disease in immunocompromised patients, jumped from bovines only ∼50 years ago. Through demographic reconstruction, we determined that the latter reached coalescent viral population growth only 20 years ago and is evolving at a much higher evolutionary rate than other genotypes infecting humans. This study constitutes mounting evidence of MastV-Sp6Gt7 active circulation and highlights the need for diagnostics capable of detecting it.
Topics: Child; Humans; Animals; Cattle; Mamastrovirus; Astroviridae Infections; Astroviridae; Phylogeny; Gastroenteritis; Feces
PubMed: 37222427
DOI: 10.1080/22221751.2023.2217942 -
Virology Journal Nov 2023Human astroviruses (HAstV) are etiologic agents of acute gastroenteritis that most often afflict young children and elderly adults. Most studies of HAstV have focused on...
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.
Topics: Child; Adult; Humans; Child, Preschool; Aged; Mamastrovirus; Phylogeny; Nanopores; Astroviridae Infections; Genotype; Feces; Diarrhea; Disease Outbreaks
PubMed: 37964283
DOI: 10.1186/s12985-023-02224-7 -
BMC Veterinary Research Sep 2023Goose astrovirus 2 (GAstV-2) causes visceral gout in goslings and has resulted in significant economic losses in the goose industry of China since its outbreak in 2017....
Goose astrovirus 2 (GAstV-2) causes visceral gout in goslings and has resulted in significant economic losses in the goose industry of China since its outbreak in 2017. To further investigate the distribution and localization of GAstV-2 in different tissues at different times, a monoclonal antibody (mAb)-based immunohistochemical (IHC) assay was developed to detect GAstV-2. A total of 80 1-day-old healthy goslings were inoculated with GAstV-2 via the oral (n = 40) and intramuscular routes (n = 40). GAstV-2 in the tissues of interest was detected using the established IHC assay. The results showed that positive signals were detected in most tissues at 1 day post-infection (dpi). Viral antigens were mainly distributed in the cytoplasm, and the staining intensity was higher in the renal tubular epithelial cells than in other cells. Taken together, our data demonstrated that GAstV-2 has a broad tissue tropism and primarily targets the kidneys. These results are likely to provide a scientific basis for further elucidation of the pathogenesis of GAstV-2.
Topics: Animals; Geese; Antigens, Viral; Antibodies, Monoclonal; Avastrovirus; Biological Assay
PubMed: 37741982
DOI: 10.1186/s12917-023-03688-z -
Frontiers in Molecular Biosciences 2023Astroviruses are a family of genetically diverse viruses associated with disease in humans and birds with significant health effects and economic burdens. Astrovirus...
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, and 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 -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 () subgenus of the genus , and a goose astrovirus () subgenus of the genus . 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.
PubMed: 38274100
DOI: 10.3389/fmolb.2023.1305506 -
Frontiers in Cellular and Infection... 2023RNA viruses are a major group contributing to emerging infectious diseases and neonatal diarrhoea, causing morbidity and mortality in humans and animals. Hence, the...
RNA viruses are a major group contributing to emerging infectious diseases and neonatal diarrhoea, causing morbidity and mortality in humans and animals. Hence, the present study investigated the metatranscriptomic-derived faecal RNA virome in rotavirus group A (RVA)-infected diarrheic piglets and calves from India. The viral genomes retrieved belonged to in both species, while were found only in piglets. The nearly complete genomes of porcine RVA (2), astrovirus (AstV) (6), enterovirus G (EVG) (2), porcine sapelovirus (PSV) (2), Aichivirus C (1), and porcine teschovirus (PTV) (1) were identified and characterised. In the piglet, AstVs of PAstV2 (MAstV-26) and PAstV4 (MAstV-31) lineages were predominant, followed by porcine RVA, EVG, PSV, Aichivirus C, teschovirus (PTV-17) in decreasing order of sequence reads. In contrast, AstV accounted for the majority of reads in bovines and belonged to MAstV-28 and a proposed MAstV-35. Both RVA G4P[6] strains exhibited prototype Gottfried strains like a genotypic constellation of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. Ten out of eleven genes were of porcine origin, while the VP7 gene clustered with G4-lineage-1, consisting of human strains, suggesting a natural porcine-human reassortant. In the recombination analysis, multiple recombination events were detected in the PAstV4 and PAstV2 genomes, pointing out that these viruses were potential recombinants. Finally, the study finds diverse RNA virome in Indian piglets and calves for the first time, which may have contributed to diarrhoea. In the future, the investigation of RNA virome in animals will help in revealing pathogen diversity in multifactorial diseases, disease outbreaks, monitoring circulating viruses, viral discovery, and evaluation of their zoonotic potential.
Topics: Animals; Cattle; Humans; Infant, Newborn; Swine; Rotavirus; Rotavirus Infections; Diarrhea; Genome, Viral; Genotype; Feces; RNA; Phylogeny; Swine Diseases
PubMed: 37965252
DOI: 10.3389/fcimb.2023.1258660 -
Poultry Science Aug 2023The emergence of Goose astrovirus (GoAstV) has led to the gout in geese. This study aimed to isolate and identify the GoAstV from diseased goslings in Sichuan Province,...
The emergence of Goose astrovirus (GoAstV) has led to the gout in geese. This study aimed to isolate and identify the GoAstV from diseased goslings in Sichuan Province, China, followed by performing whole genome phylogenetic analysis of the isolate. The GoAstV was successfully isolated by inoculating the diseased gosling liver and kidney homogenate into the 11-day-old goose embryo allantoic cavity for 3 passages, and the isolate was named as GoAstV-C2 strain. The virus particles were spherical, without capsule, and the size was about 28 nm under transmission electronic microscope. The complete genome length of GoAstV-C2 was 7.035 nt, and the whole genome sequence phylogenetic analysis revealed that it belongs to the GoAstV genotype II (GoAstV-II) subgenotype IIc. The isolated GoAstV-C2 strain was able to be stably passaged in the goose embryo and uric acid sedimentation was observed. The complete genome bioinformation of GoAstV-C2 determined the evolutionary characteristics of the GoAstV isolated from Sichuan, China. This finding lays a foundation for the development of preventive measures, effective vaccines, and therapeutic drugs.
Topics: Animals; Geese; Astroviridae Infections; Phylogeny; Poultry Diseases; Chickens; Avastrovirus; Genotype; China
PubMed: 37300911
DOI: 10.1016/j.psj.2023.102800 -
Archives of Virology Sep 2023In this study, 306 rectal swabs from diarrheal pigs of various ages (0-3 weeks, 3-6 weeks, and >6 weeks) were collected from 54 piggery units in different climatic zones...
In this study, 306 rectal swabs from diarrheal pigs of various ages (0-3 weeks, 3-6 weeks, and >6 weeks) were collected from 54 piggery units in different climatic zones in Haryana state, India. These samples were tested for the presence of porcine astrovirus (PAstV), porcine rotavirus group A (PRV-A), and classical swine fever virus (CSFV) by reverse transcription polymerase chain reaction (RT-PCR), and porcine circovirus 2 (PCV-2) by polymerase chain reaction (PCR). Out of the 306 samples tested, 153 (50%), 108 (35.3%), 32 (10.6%), and three (0.9%) tested positive for PAstV, PCV-2, PRV-A, and CSFV, respectively. A single infection was detected in 135 samples, while mixed infections were found in 77 samples: 70 with two viruses and seven samples with more than two. PAstV was detected most frequently (55.31%) in pigs aged 3-6 weeks. PCV-2 was more predominant in pigs aged 0-3 weeks (36.53%), whereas PRV-A was more common in pigs aged 3-6 weeks (11.3%). CSFV was observed in the age group of 0-3 weeks (1.92%). Phylogenetic analysis revealed the circulation of lineages 2 and 4 of PAstV in this region. Thus, it can be concluded that one or more than one virus is circulating in piggery units in Haryana, India.
Topics: Swine; Animals; Coinfection; Phylogeny; Mamastrovirus; Rotavirus; India; Circovirus; Classical Swine Fever Virus
PubMed: 37676345
DOI: 10.1007/s00705-023-05865-9