19 research outputs found
Genome analyses of species A rotavirus isolated from various mammalian hosts in Northern Ireland during 2013−2016
Publication history: Accepted - 27 June 2023; Published - 4 July 2023.Rotavirus group A (RVA) is the most important cause of acute diarrhoea and severe dehydration in young mammals. Infection in livestock is associated with significant mortality and economic losses and, together with wildlife reservoirs, acts as a potential source of zoonotic transmission. Therefore, molecular surveillance of circulating RVA strains in animal species is necessary to assess the risks posed to humans and their livestock. An RVA molecular epidemiological surveillance study on clinically diseased livestock species revealed high prevalence in cattle and pigs (31 per cent and 18 per cent, respectively) with significant phylogenetic diversity including a novel and divergent ovine artiodactyl DS-1-like constellation G10-P[15]-I2-R2-C2-M2-A11-N2-T6-E2-H3. An RVA gene reassortment occurred in an RVA asymptomatic pig and identified as a G5-P[13] strain, and a non-structural protein (NSP)2 gene had intergenomically reassorted with a human RVA strain (reverse zoonosis) and possessed a novel NSP4 enterotoxin E9 which may relate to the asymptomatic RVA infection. Analysis of a novel sheep G10-P[15] strain viral protein 4 gene imparts a putative homologous intergenic and interspecies recombination event, subsequently creating the new P[15] divergent lineage. While surveillance across a wider range of wildlife and exotic species identified generally negative or low prevalence, a novel RVA interspecies transmission in a non-indigenous pudu deer (zoo origin) with the constellation of G6-P[11]12-R2-C2-M2-A3-N2-T6-E2-H3 was detected at a viral load of 11.1 log10 copies/gram. The detection of novel emerging strains, interspecies reassortment, interspecies infection, and recombination of RVA circulating in animal livestock and wildlife reservoirs is of paramount importance to the RVA epidemiology and evolution for the One Health approach and post-human vaccine introduction era where highly virulent animal RVA genotypes have the potential to be zoonotically transmitted
The First Whole Genome Sequence and Characterisation of Avian Nephritis Virus Genotype 3
Publication history: Accepted - 27 January 2021; Published - 3 February 2021.Avian nephritis virus (ANV) is classified in the Avastroviridae family with disease associations
with nephritis, uneven flock growth and runting stunting syndrome (RSS) in chicken and turkey
flocks, and other avian species. The whole genome of ANV genotype 3 (ANV-3) of 6959 nucleotides
including the untranslated 5’ and 3’ regions and polyadenylated tail was detected in a metagenomic
virome investigation of RSS-affected chicken broiler flocks. This report characterises the ANV-3
genome, identifying partially overlapping open reading frames (ORFs), ORF1a and ORF1b, and an
opposing secondary pseudoknot prior to a ribosomal frameshift stemloop structure, with a separate
ORF2, whilst observing conserved astrovirus motifs. Phylogenetic analysis of the Avastroviridae
whole genome and ORF2 capsid polyprotein classified the first complete whole genome of ANV-3
within Avastroviridae genogroup 2.This research was partially funded by the Department of Agriculture, Environment &
Rural Affairs—Code PG 13/02, and the Agri-Food and Biosciences Institute (AFBI)—Code 44955
Co-infection status of novel parvovirus’s (PPV2 to 4) with porcine circovirus 2 in porcine respiratory disease complex and porcine circovirus-associated disease from 1997 to 2012
Publication history: Accepted - 12 September 2020; Published online - 18 October 2020.As global pig health diseases, porcine respiratory disease complex (PRDC) and porcine
circovirus-associated disease (PCVAD) generate substantial economic losses despite
pigs been vaccinated against the primary causative virus, highlighting the importance
of understanding virome interactions and specifically co-factor infections. Established
primary endemic pathogens for PRDC include porcine circovirus 2 (PCV2), porcine
reproductive and respiratory syndrome virus (PRRSv) and swine influenza virus (SIV),
and PCV2 aetiology in interaction with other co-infecting viruses can result in PCVAD.
Porcine parvovirus (PPV) 1 is a well-characterized virus with an available vaccine preventing
reproductive failure in sows. However, whilst novel PPV 2 to 7 viruses have been
identified since 2001, their viral pathogenic potential in clinical and subclinical disease
remains to be determined. Therefore, this study has sought to develop a better understanding
of their potential role as associated co-infections in PRDC and PCVAD by examining
archival samples for the presence of PCV2 and the novel parvoviruses PPV2-4
from clinically diseased pigs across production age stages. Epidemiologically, the novel
PPV2 was found to be the most prevalent within the fattener age group with PPV2-4
statistically associated with pig respiratory disease and enteric ulcers. Additionally, statistical
modelling by latent class analysis (LCA) on veterinary pathology scored pigs found
a clustering co-factor association between PPV2 and PCV2, suggesting the novel PPV
may be involved in PRDC and PCVAD. Phylogenetic analysis of novel PPVs revealed the
PPV2 capsid evolution to be diverged from the original strains with a low nucleotide homology
of 88%–96% between two distinct clades. These findings determine that novel
PPV 2–4 viruses are statistically associated as co-infectors in a diseased pig population,
and significantly detected PPV2 clustering co-infection frequency with PCV2 in PRDC
and PCVAD diseased pigs through LCA analysis
Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1
Publication history: Accepted - 20 August 2022; Published - 24 August 2022.Bovine respiratory disease (BRD), which is the leading cause of morbidity and mortality in
cattle, is caused by numerous known and unknown viruses and is responsible for the widespread use
of broad-spectrum antibiotics despite the use of polymicrobial BRD vaccines. Viral metagenomics
sequencing on the portable, inexpensive Oxford Nanopore Technologies MinION sequencer and
sequence analysis with its associated user-friendly point-and-click Epi2ME cloud-based pathogen
identification software has the potential for point-of-care/same-day/sample-to-result metagenomic
sequence diagnostics of known and unknown BRD pathogens to inform a rapid response and vaccine
design. We assessed this potential using in vitro viral cell cultures and nasal swabs taken from calves
that were experimentally challenged with a single known BRD-associated DNA virus, namely, bovine
herpes virus 1. Extensive optimisation of the standard Oxford Nanopore library preparation protocols,
particularly a reduction in the PCR bias of library amplification, was required before BoHV-1 could be
identified as the main virus in the in vitro cell cultures and nasal swab samples within approximately
7 h from sample to result. In addition, we observed incorrect assignment of the bovine sequence to
bacterial and viral taxa due to the presence of poor-quality bacterial and viral genome assemblies in
the RefSeq database used by the EpiME Fastq WIMP pathogen identification software
Detection of a novel gammaherpesvirus (genus Rhadinovirus) in wild muntjac deer in Northern Ireland
This study represents the initial part of an investigation into the potential for non-native, wild, free-living muntjac deer (Muntiacus reevesi) to carry viruses that could be a threat to livestock. A degenerate PCR assay was used to screen a range of tissues from muntjac deer culled in Northern Ireland for the presence of herpesviral nucleic acids. This was followed by sequencing of PCR amplicons and phylogenetic analysis. We report the detection of a novel gammaherpesvirus most closely related to a type 2 ruminant rhadinovirus from mule deer. It remains to be determined if this new virus is pathogenic to deer or presents a risk to food security through the susceptibility of domestic livestock
Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1
Bovine respiratory disease (BRD), which is the leading cause of morbidity and mortality in cattle, is caused by numerous known and unknown viruses and is responsible for the widespread use of broad-spectrum antibiotics despite the use of polymicrobial BRD vaccines. Viral metagenomics sequencing on the portable, inexpensive Oxford Nanopore Technologies MinION sequencer and sequence analysis with its associated user-friendly point-and-click Epi2ME cloud-based pathogen identification software has the potential for point-of-care/same-day/sample-to-result metagenomic sequence diagnostics of known and unknown BRD pathogens to inform a rapid response and vaccine design. We assessed this potential using in vitro viral cell cultures and nasal swabs taken from calves that were experimentally challenged with a single known BRD-associated DNA virus, namely, bovine herpes virus 1. Extensive optimisation of the standard Oxford Nanopore library preparation protocols, particularly a reduction in the PCR bias of library amplification, was required before BoHV-1 could be identified as the main virus in the in vitro cell cultures and nasal swab samples within approximately 7 h from sample to result. In addition, we observed incorrect assignment of the bovine sequence to bacterial and viral taxa due to the presence of poor-quality bacterial and viral genome assemblies in the RefSeq database used by the EpiME Fastq WIMP pathogen identification software