-
Veterinary Sciences Feb 2023Astroviruses are important human enteric pathogens transmissible with contaminated food and water. Astroviruses have also been identified in mammals, birds, lower...
Astroviruses are important human enteric pathogens transmissible with contaminated food and water. Astroviruses have also been identified in mammals, birds, lower vertebrates and invertebrates. The genetic diversity of human and animal astroviruses poses a challenge for diagnostics and taxonomy. As a proof of concept, we used a panastrovirus consensus primer set, able to amplify in a nested RT-PCR protocol a 400-nt-long fragment of the RNA-dependent RNA polymerase of most members of the family, in conjunction with a nanopore sequencing platform, to generate information on the astrovirome in filter-feeding mollusks. Amplicons generated from bivalve samples were used to generate libraries for deep sequencing. In three samples, only one unique RdRp sequence type was obtained. However, in seven samples and in three barcodes with eleven pooled samples, we identified a variety of known and unknown RdRp sequence types, in most cases distantly related to astrovirus sequences available in the databases. In total, 37 different sequence contigs were generated. Avian-origin astrovirus sequences were predominant, likely due to contamination of shellfish harvesting waters by marine birds. Astroviruses of the aquatic eco-system were also identified, whereas human astroviruses were not detected.
PubMed: 36977214
DOI: 10.3390/vetsci10030175 -
Veterinary Research Communications Sep 2023Chicken astroviruses (CAstV) were associated with retarded growth, enteritis, kidney diseases, and white chick syndrome. In the current study, we aimed to evaluate the...
Chicken astroviruses (CAstV) were associated with retarded growth, enteritis, kidney diseases, and white chick syndrome. In the current study, we aimed to evaluate the effect of CAstV infection on growth, performance, and gross and histopathological picture of commercial chicken flocks suffering increased culling rate and decreased performance. Samples were collected for virus isolation, identification, and sequencing on day one, 15 days, and 30 days of age. Body weight, feed conversion rate, and mortality rates were determined. A gross examination was performed, and tissue samples from the liver, intestine, kidneys, heart, and lungs were kept in formalin for histopathological evaluation. Embryos inoculated with CAstV revealed dwarfism, and edema. The cytopathic effect on CAstV inoculated cells included aggregation,, and sloughing. The isolated Egyptian isolates shared the highest nucleotide homology (93%) with the Korean isolate Kr/ADL102655-1/2010 and showed the most distant relation to the Indian isolate Indovax/APF/1319 with 82-83% homology. Body weight exhibited significant reduction with a decrease in feed conversion rate in CAstV infected flocks. Gross examination of CAstV-infected chickens revealed white feathered chicks on day one, and poor body condition in older chickens as well as swollen kidneys. Histopathological examination of CAstV-infected birds showed mild proventriculitis, shortening of intestinal villi, enteritis, focal hepatocellular necrosis, pericarditis, myocarditis, and proliferative response in lung tissue. Kidneys showed interstitial nephritis, urate deposition, and glomerular hypercellularity. CAstV is a chicken pathogen that could be related to decreased performance, and screening of flocks for CAstV might be an essential step for breeders.
Topics: Animals; Chickens; Astroviridae Infections; Enteritis; Kidney; Avastrovirus; Poultry Diseases
PubMed: 36976444
DOI: 10.1007/s11259-023-10109-x -
Journal of Virology Mar 2023Coronaviruses infect a wide variety of host species, resulting in a range of diseases in both humans and animals. The coronavirus genome consists of a large...
Coronaviruses infect a wide variety of host species, resulting in a range of diseases in both humans and animals. The coronavirus genome consists of a large positive-sense single-stranded molecule of RNA containing many RNA structures. One structure, denoted s2m and consisting of 41 nucleotides, is located within the 3' untranslated region (3' UTR) and is shared between some coronavirus species, including infectious bronchitis virus (IBV), severe acute respiratory syndrome coronavirus (SARS-CoV), and SARS-CoV-2, as well as other pathogens, including human astrovirus. Using a reverse genetic system to generate recombinant viruses, we investigated the requirement of the s2m structure in the replication of IBV, a globally distributed economically important that infects poultry causing respiratory disease. Deletion of three nucleotides predicted to destabilize the canonical structure of the s2m or the deletion of the nucleotides corresponding to s2m impacted viral replication . passaging of the recombinant IBV with the s2m sequence deleted resulted in a 36-nucleotide insertion in place of the deletion, which was identified to be composed of a duplication of flanking sequences. A similar result was observed following serial passage of human astrovirus with a deleted s2m sequence. RNA modeling indicated that deletion of the nucleotides corresponding to the s2m impacted other RNA structures present in the IBV 3' UTR. Our results indicated for both IBV and human astrovirus a preference for nucleotide occupation in the genome location corresponding to the s2m, which is independent of the specific s2m sequence. Coronaviruses infect many species, including humans and animals, with substantial effects on livestock, particularly with respect to poultry. The coronavirus RNA genome consists of structural elements involved in viral replication whose roles are poorly understood. We investigated the requirement of the RNA structural element s2m in the replication of the infectious bronchitis virus, an economically important viral pathogen of poultry. Using reverse genetics to generate recombinant IBVs with either a disrupted or deleted s2m, we showed that the s2m is not required for viral replication in cell culture; however, replication is decreased in tracheal tissue, suggesting a role for the s2m in the natural host. Passaging of these viruses as well as human astrovirus lacking the s2m sequence demonstrated a preference for nucleotide occupation, independent of the s2m sequence. RNA modeling suggested deletion of the s2m may negatively impact other essential RNA structures.
Topics: Animals; Humans; 3' Untranslated Regions; Chickens; Infectious bronchitis virus; Mamastrovirus; Mutagenesis, Insertional; Poultry Diseases; RNA, Viral; Virus Replication; RNA Stability; Sequence Deletion
PubMed: 36779761
DOI: 10.1128/jvi.00038-23 -
Viruses Dec 2022In order to acquire information regarding viral agents and epidemiologic features of severe paediatric Viral Acute Gastroenteritis (VAGE) across multiple seasons in the...
In order to acquire information regarding viral agents and epidemiologic features of severe paediatric Viral Acute Gastroenteritis (VAGE) across multiple seasons in the pre-rotavirus-vaccine era, the epidemiologic characteristics of VAGE were investigated among paediatric patients hospitalized in a major Sicilian paediatric hospital from 2003 to 2013. Overall, 4725 children were observed and 2355 (49.8%) were diagnosed with a viral infection: 1448 (30.6%) were found positive to rotavirus, 645 (13.7%) to norovirus, 216 (4.6%) to adenovirus, and 46 (0.97%) to astrovirus. Viral infections showed different patterns of hospitalization in terms of age at risk (younger for rotavirus and adenovirus infections), seasonality (increased risk in winter for rotavirus and norovirus), trend over time (reduced risk in 2011-2013 for norovirus and rotavirus) and major diagnostic categories (digestive diseases more frequent in adenovirus and astrovirus but not in norovirus). This study increases general knowledge of VAGE epidemiology and contributes to suggest some a priori diagnostic criteria that could help clinicians to identify and treat viral agents responsible for gastroenteritis in hospital settings.
Topics: Child; Humans; Infant; Adenoviridae; Adenoviridae Infections; Adenovirus Infections, Human; Astroviridae; Caliciviridae Infections; Child, Hospitalized; Enteritis; Enterovirus Infections; Feces; Gastroenteritis; Rotavirus; Rotavirus Infections; Sicily; Virus Diseases
PubMed: 36680081
DOI: 10.3390/v15010041 -
Archives of Virology Jan 2023Viral pathogens are the primary cause of canine gastroenteritis. However, few structured comprehensive studies on the viral etiology of canine gastroenteritis have been...
Viral pathogens are the primary cause of canine gastroenteritis. However, few structured comprehensive studies on the viral etiology of canine gastroenteritis have been conducted. In this study, 475 rectal swabs collected over three years (2018-2021) from clinical canine gastroenteritis cases were screened for the presence of six major enteric viruses - canine parvovirus 2 (CPV-2), canine distemper virus (CDV), canine adenovirus 2 (CAdV-2), canine coronavirus (CCoV), canine astrovirus (CaAstV), and canine rotavirus (CRV) - by real-time PCR. The most frequently detected virus was CPV-2, which was present in 64.8% of the samples (subtype 2a, 21.1%; 2b, 77.4%; 2c, 1.5%), followed by CDV (8%), CaAstV (7.2%), CCoV (5.9%), and CAdV-2 (4.6%). Two to four of these viruses in different combinations were found in 16.8% of the samples, and CRV was not detected. The complete genome sequences of Indian isolates of CDV, CCoV, and CaAstV were determined for the first time, and phylogenetic analysis was performed. This study highlights the need for routine prophylactic vaccination with the appropriate vaccines. Notably, 70.3% of animals vaccinated with DHPPiL were found to be positive for at least one virus. Hence, regular molecular analysis of the prevalent viruses is crucial for addressing vaccination failures.
Topics: Animals; Dogs; Phylogeny; Dog Diseases; Gastroenteritis; Real-Time Polymerase Chain Reaction; Rotavirus; Coronavirus, Canine; Mamastrovirus; Parvovirus, Canine; Distemper Virus, Canine; Parvoviridae Infections; Distemper
PubMed: 36609588
DOI: 10.1007/s00705-022-05674-6 -
Multiplex gel-based PCR assay for the simultaneous detection of 5 genotypes of porcine astroviruses.Journal of Veterinary Diagnostic... Mar 2023Porcine astrovirus (PAstV) has been associated experimentally with diarrhea in piglets, but much more knowledge is needed about this virus. PAstV has high genetic...
Porcine astrovirus (PAstV) has been associated experimentally with diarrhea in piglets, but much more knowledge is needed about this virus. PAstV has high genetic variability, and 5 genotypes have been identified, namely PAstV1-5. To obtain information on the epidemiology of PAstV, we established a multiplex PAstV PCR assay to detect and differentiate the 5 PAstV genotypes simultaneously. The assay utilized specific primers for each genotype, producing fragments of 307, 353, 205, 253, and 467 bp, representing PAstV1-5, respectively. Our multiplex PCR assay amplified all 5 DNA fragments from single or mixed viral genomes without cross-reactions with other PAstV genotypes or other viruses in pigs. The limit of detection of the multiplex PCR assay was 5 × 10 copies/μL for PAstV1 and PAstV4, and 5 × 10 copies/μL for PAstV2, PAstV3, and PAstV5. We examined 76 pig fecal specimens with our multiplex PCR assay. PAstV was detected in 36 of 76 (47.4%) samples; ≥2 PAstVs were found in 20 of 76 (26.3%) samples. The multiplex PCR assay results were essentially the same as the results using a monoplex PAstV PCR assay, with a coincidence rate of >96%. Our multiplex PCR method provides a simple, sensitive, and specific detection tool for PAstV detection and epidemiologic surveys.
Topics: Animals; Swine; Astroviridae Infections; Multiplex Polymerase Chain Reaction; Swine Diseases; Genotype; Sensitivity and Specificity
PubMed: 36573660
DOI: 10.1177/10406387221145329 -
Frontiers in Cellular and Infection... 2022Bats are critical to maintaining healthy ecosystems and many species are threatened primarily due to global habitat loss. Bats are also important hosts of a range of...
INTRODUCTION
Bats are critical to maintaining healthy ecosystems and many species are threatened primarily due to global habitat loss. Bats are also important hosts of a range of viruses, several of which have had significant impacts on global public health. The emergence of these viruses has been associated with land-use change and decreased host species richness. Yet, few studies have assessed how bat communities and the viruses they host alter with land-use change, particularly in highly biodiverse sites.
METHODS
In this study, we investigate the effects of deforestation on bat host species richness and diversity, and viral prevalence and richness across five forested sites and three nearby deforested sites in the interior Atlantic Forest of southern Brazil. Nested-PCR and qPCR were used to amplify and detect viral genetic sequence from six viral families (corona-, adeno-, herpes-, hanta-, paramyxo-, and astro-viridae) in 944 blood, saliva and rectal samples collected from 335 bats.
RESULTS
We found that deforested sites had a less diverse bat community than forested sites, but higher viral prevalence and richness after controlling for confounding factors. Viral detection was more likely in juvenile males located in deforested sites. Interestingly, we also found a significant effect of host bat species on viral prevalence indicating that viral taxa were detected more frequently in some species than others. In particular, viruses from the family were detected more frequently in generalist species compared to specialist species.
DISCUSSION
Our findings suggest that deforestation may drive changes in the ecosystem which reduce bat host diversity while increasing the abundance of generalist species which host a wider range of viruses.
Topics: Humans; Animals; Male; Ecosystem; Chiroptera; Brazil; Prevalence; Forests; Viruses
PubMed: 36569210
DOI: 10.3389/fcimb.2022.921950 -
Viruses Dec 2022To investigate virus diversity in hot zones of probable pathogen spillover, 54 oral-fecal swabs were processed from five bat species collected from three cave systems in...
BACKGROUND AND METHODS
To investigate virus diversity in hot zones of probable pathogen spillover, 54 oral-fecal swabs were processed from five bat species collected from three cave systems in Kenya, using metagenome sequencing.
RESULTS
Viruses belonging to the , , , , and were detected, with unclassified viruses. Retroviral sequences were prevalent; 74.1% of all samples were positive, with distinct correlations between virus, site and host bat species. Detected retroviruses comprised , , and Galidia endogenous retroviruses, murine leukemia virus-related virus and retrovirus (RFRV). A near-complete genome of a local RFRV strain with identical genome organization and 2.8% nucleotide divergence from the prototype isolate was characterized. Bat coronavirus sequences were detected with a prevalence of 24.1%, where analyses on the ORF1ab region revealed a novel alphacoronavirus lineage. Astrovirus sequences were detected in 25.9%of all samples, with considerable diversity. In 9.2% of the samples, other viruses including Actinidia yellowing virus 2, bat betaherpesvirus, Bole tick virus 4, Cyclovirus and Rhopalosiphum padi virus were identified.
CONCLUSIONS
Further monitoring of bats across Kenya is essential to facilitate early recognition of possibly emergent zoonotic viruses.
Topics: Animals; Alphacoronavirus; Astroviridae; Chiroptera; COVID-19; Herpesviridae; Kenya; Phylogeny; Retroviridae; RNA Viruses; SARS-CoV-2
PubMed: 36560824
DOI: 10.3390/v14122820 -
Viruses Dec 2022Goose astrovirus (GAstV) is an important pathogen causing visceral gout and high mortality in goslings, which has broken out and spread across China. In 2021, a disease...
Goose astrovirus (GAstV) is an important pathogen causing visceral gout and high mortality in goslings, which has broken out and spread across China. In 2021, a disease characterized by urate deposition on the visceral surface and 30% mortality occurred in commercial adult Landaise geese in Zhejiang Province, China. A systematic study identified an infecting astrovirus, designated ZJCX, that was efficiently isolated from a diseased goose with a chicken hepatocellular carcinoma cell line (LMH). In contrast to other GAstVs originating from goslings, ZJCX caused cytopathogenic effects in LMH cells, and the crystalline arrangement of viral particles was observed through transmission electron microscopy. Indeed, phylogenetic analysis and nucleotide homology comparison revealed that ZJCX isolate belongs to the genotype II cluster of GAstVs and displays 97.8-98.4% identity with other GAstV II strains. However, several specific mutations occurred in the polyprotein and capsid protein regions. Moreover, a pathogenicity assessment of ZJCX with a gosling model was conducted, and typical visceral gout was reproduced and led to 18% mortality. The viral loads of ZJCX in the blood, kidney, and liver were detected with specific primers after inoculation, which demonstrated that the kidney and liver presented viral loads peaking at seven days post-inoculation (dpi). Biochemical parameter examination showed that AST, ALT, γ-GT, UA, and BUN levels were significantly increased by GAstV, whereas body weight was reduced. Overall, this study indicated that the GAstV isolate could infect adult geese, and the results regarding the viral loads and biochemical parameters induced by ZJCX provide insight into GAstV pathogenicity.
Topics: Animals; Geese; Astroviridae Infections; Phylogeny; Virulence; Poultry Diseases; Avastrovirus; Gout; China
PubMed: 36560810
DOI: 10.3390/v14122806 -
Virology Journal Dec 2022Aim of this study was to investigate the molecular diversity of human astroviruses (HAstV) in Germany. A follow-up study was performed with human stool samples collected...
Aim of this study was to investigate the molecular diversity of human astroviruses (HAstV) in Germany. A follow-up study was performed with human stool samples collected in 2018-2019, which were genotyped retrospectively. A total of 2645 stool samples, collected between January 2018 and December 2019 from sporadic cases and outbreaks of acute gastroenteritis were analyzed. An algorithm of PCR systems was used to characterize human astrovirus. Human astroviruses were found in 40 samples (positive rate: 1.6%). During the study period, children aged 1-2 years (48%) were most affected by HAstV. Genotyping revealed a number of nine circulating genotypes representing four human Mamastrovirus species. Strain MLB1 was predominant in the study population with a detection rate of 25% followed by HAstV1 with a positive rate of 20%. The diversity of astrovirus genotypes seems to be rather stable in Germany in the last years. A clustering of regionally and/or temporally linked human astroviruses in Germany was not detectable.
Topics: Child; Humans; Mamastrovirus; Retrospective Studies; Follow-Up Studies; Astroviridae Infections; Feces; Phylogeny; Genotype
PubMed: 36544187
DOI: 10.1186/s12985-022-01955-3