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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 -
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 -
BioRxiv : the Preprint Server For... Nov 2023Bats (order: ) are known to host a diverse range of viruses, some of which present a public health risk. Thorough viral surveillance is therefore essential to predict...
Bats (order: ) are known to host a diverse range of viruses, some of which present a public health risk. Thorough viral surveillance is therefore essential to predict and potentially mitigate zoonotic spillover. Astroviruses (family: ) are an understudied group of viruses with a growing amount of indirect evidence for zoonotic transfer. Astroviruses have been detected in bats with significant prevalence and diversity, suggesting that bats may act as important astrovirus hosts. Most astrovirus surveillance in wild bat hosts has, to date, been restricted to single-gene PCR detection and concomitant Sanger sequencing; additionally, many bat species and many geographic regions have not yet been surveyed for astroviruses at all. Here, we use metagenomic Next Generation Sequencing (mNGS) to detect astroviruses in three species of Madagascar fruit bats, and . We detect numerous partial sequences from all three species and one near-full length astrovirus sequence from , which we use to characterize the evolutionary history of astroviruses both within bats and the broader mammalian clade, . Taken together, applications of mNGS implicate bats as important astrovirus hosts and demonstrate novel patterns of bat astrovirus evolutionary history, particularly in the Southwest Indian Ocean region.
PubMed: 37961349
DOI: 10.1101/2023.10.27.564436 -
Frontiers in Veterinary Science 2023Oropharyngeal (OP) and cloacal (CL) swabs from 2049 adult backyard chickens collected at 12 live bird markets, two each in Arusha, Dar es Salaam, Iringa, Mbeya, Morogoro...
Virulent Newcastle disease virus genotypes V.3, VII.2, and XIII.1.1 and their coinfections with infectious bronchitis viruses and other avian pathogens in backyard chickens in Tanzania.
Oropharyngeal (OP) and cloacal (CL) swabs from 2049 adult backyard chickens collected at 12 live bird markets, two each in Arusha, Dar es Salaam, Iringa, Mbeya, Morogoro and Tanga regions of Tanzania were screened for Newcastle disease virus (NDV) using reverse transcription real-time PCR (rRT-PCR). The virus was confirmed in 25.23% of the birds ( = 517; rRT-PCR ≤ 30), with the highest positivity rates observed in birds from Dar es Salaam region with higher prevalence during the dry season (September-November 2018) compared to the rainy season (January and April-May 2019). Next-generation sequencing of OP/CL samples of 20 out of 32 birds that had high amounts of viral RNAs ( ≤ 25) resulted in the assembly of 18 complete and two partial genome sequences (15,192 bp and 15,045-15,190 bp in length, respectively) of NDV sub-genotypes V.3, VII.2 and XIII.1.1 ( = 1, 13 and 4 strains, respectively). Two birds had mixed NDV infections (V.3/VII.2 and VII.2/XIII.1.1), and nine were coinfected with viruses of families , , , , , and . Of the coinfecting viruses, complete genome sequences of two avastroviruses (a recombinant chicken astrovirus antigenic group-Aii and avian nephritis virus genogroup-5) and two infectious bronchitis viruses (a turkey coronavirus-like recombinant and a GI-19 virus) were determined. The fusion (F) protein F/F cleavage sites of the Tanzanian NDVs have the consensus motifs RRRKR↓F (VII.2 strains) and RRQKR↓F (V.3 and XIII.1.1 strains) consistent with virulent virus; virulence was confirmed by intracerebral pathogenicity index scores of 1.66-1.88 in 1-day-old chicks using nine of the 20 isolates. Phylogenetically, the complete F-gene and full genome sequences regionally cluster the Tanzanian NDVs with, but distinctly from, other strains previously reported in eastern and southern African countries. These data contribute to the understanding of NDV epidemiology in Tanzania and the region.
PubMed: 37929287
DOI: 10.3389/fvets.2023.1272402 -
The Journal of General Virology Nov 2023Human astroviruses (HAstVs) are small, non-enveloped icosahedral RNA viruses that are a significant cause of diarrhoea in young children. Despite their worldwide...
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 , 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 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 MuAstV challenge studies to test whether MuAstV spike can be the basis of an effective vaccine.
Topics: Child; Humans; Animals; Mice; Child, Preschool; Capsid; Capsid Proteins; Astroviridae; Astroviridae Infections; Vaccines
PubMed: 37910165
DOI: 10.1099/jgv.0.001913 -
International Journal of Molecular... Oct 2023miRNAs represent ubiquitous regulators of gene expression and play an important and pivotal regulatory role in viral disease pathogenesis and virus-host interactions....
miRNAs represent ubiquitous regulators of gene expression and play an important and pivotal regulatory role in viral disease pathogenesis and virus-host interactions. Although previous studies have provided basic data for understanding the role of miRNAs in the molecular mechanisms of viral infection in birds, the role of miRNAs in the regulation of host responses to chicken astrovirus (CAstV) infection in chickens is not yet understood. In our study, we applied next-generation sequencing to profile miRNA expression in CAstV-infected chickens and to decipher miRNA-targeted specific signaling pathways engaged in potentially vital virus-infection biological processes. Among the 1354 detected miRNAs, we identified 58 mature miRNAs that were significantly differentially expressed in infected birds. Target prediction resulted in 4741 target genes. GO and KEGG pathway enrichment analyses showed that the target genes were mainly involved in the regulation of cellular processes and immune responses.
Topics: Animals; MicroRNAs; Chickens; Avastrovirus; High-Throughput Nucleotide Sequencing; Host Microbial Interactions
PubMed: 37894809
DOI: 10.3390/ijms242015128 -
Brazilian Journal of Veterinary Medicine 2023The canine circovirus (CanCV) is a single-stranded DNA virus that has become an important emerging virus associated with gastroenteritis in dogs worldwide. In the...
The canine circovirus (CanCV) is a single-stranded DNA virus that has become an important emerging virus associated with gastroenteritis in dogs worldwide. In the present study, the CanCV was detected by PCR in 15% (22/147) of dogs from animal shelters in Belém, between 2019 and 2020. We observed an association between the CanCV infection and the presence of diarrhea in animals younger than one year of age (p > 0.01). The Brazilian strains were grouped in Chinese genotypes, with 99.54 to 100% nucleotilde homology. The GMRF Bayesian Skyride used the molecular clock model, which was the best suited technique to plot the dataset. The most recent common ancestor (TMRCA) was estimated in 2017, with the evolution rate of 1.6 x 10 s/s/y. The viral family diversity was also investigated, with emphasis on the families of the enteric pathogenic viruses Parvoviridae, Picornaviridae and Astroviridae, which were detected in the CanCV positive pooled samples. This study highlights the importance of the CanCV as an emergent virus that causes diarrhea in Brazilian dogs. The results found herein contribute to the understanding of the role of CanCV in enteric diseases and in the evolutionary molecular characterization of the circulating genotypes. Furthermore, we increased the understanding of the fecal virome in dogs with diarrhea, providing data for the monitoring and prevention viral gastroenteric diseases in domestic animals.
PubMed: 37859867
DOI: 10.29374/2527-2179.bjvm000723 -
Advances in Virus Research 2023Astroviruses encapsidate a positive-sense, single-stranded RNA genome into ∼30nm icosahedral particles that infect a wide range of mammalian and avian species, but... (Review)
Review
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.
Topics: Animals; Child; Humans; Aged; Mamastrovirus; Gastroenteritis; Genotype; Phylogeny; Mammals
PubMed: 37832992
DOI: 10.1016/bs.aivir.2023.08.001 -
Microbiology Spectrum Dec 2023Compared with other domestic animals, the virome and viral diversity of small ruminants especially in caprine are less studied even of its zoonotic potential. In this...
The genomic and epidemiological investigations of enteric viruses of domestic caprine () revealed the presence of multiple novel viruses related to known strains of humans and ruminant livestock species.
Compared with other domestic animals, the virome and viral diversity of small ruminants especially in caprine are less studied even of its zoonotic potential. In this study, the enteric virome of caprine was investigated in detail using next-generation sequencing and reverse transcription PCR techniques. The complete or nearly complete genomes of seven novel viruses were determined which show a close phylogenetic relationship to known human and ruminant viruses. The high similarity between the identified caprine tusavirus (family ) and an unassigned CRESS DNA virus with closely related human strains could indicate the (reverse) zoonotic potential of these viruses. Others, like astroviruses (family ), enteroviruses, or novel caripiviruses (named after the term ne corna) of family found mostly in multiple co-infections in caprine and ovine, could indicate the cross-species transmission capabilities of these viruses between small ruminants.
Topics: Humans; Animals; Sheep; Goats; Livestock; Phylogeny; Viruses; Enterovirus; Ruminants; Enterovirus Infections; Genomics
PubMed: 37823638
DOI: 10.1128/spectrum.02533-23 -
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