Browsing by Author "Knox MA"
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- ItemAbundant dsRNA picobirnaviruses show little geographic or host association in terrestrial systems.(Elsevier, 2023-08) Knox MA; Wierenga J; Biggs PJ; Gedye K; Almeida V; Hall R; Kalema-Zikusoka G; Rubanga S; Ngabirano A; Valdivia-Granda W; Hayman DTSPicobirnaviruses are double-stranded RNA viruses known from a wide range of host species and locations but with unknown pathogenicity and host relationships. Here, we examined the diversity of picobirnaviruses from cattle and gorillas within and around Bwindi Impenetrable Forest National Park (BIFNP), Uganda, where wild and domesticated animals and humans live in relatively close contact. We use metagenomic sequencing with bioinformatic analyses to examine genetic diversity. We compared our findings to global Picobirnavirus diversity using clustering-based analyses. Picobirnavirus diversity at Bwindi was high, with 14 near-complete RdRp and 15 capsid protein sequences, and 497 new partial viral sequences recovered from 44 gorilla samples and 664 from 16 cattle samples. Sequences were distributed throughout a phylogenetic tree of globally derived picobirnaviruses. The relationship with Picobirnavirus diversity and host taxonomy follows a similar pattern to the global dataset, generally lacking pattern with either host or geography.
- ItemDevelopment of a non-infectious control for viral hemorrhagic fever PCR assays.(PLOS, 2024-04-22) Knox MA; Bromhead C; Hayman DTS; Viennet EAssay validation is an essential component of disease surveillance testing, but can be problematic in settings where access to positive control material is limited and a safety risk for handlers. Here we describe a single non-infectious synthetic control that can help develop and validate the PCR based detection of the viral causes of Crimean-Congo hemorrhagic fever, Ebola virus disease, Lassa fever, Marburg virus disease and Rift Valley fever. We designed non-infectious synthetic DNA oligonucleotide sequences incorporating primer binding sites suitable for five assays, and a T7 promotor site which was used to transcribe the sequence. Transcribed RNA was used as template in a dilution series, extracted and amplified with RT-PCR and RT-qPCR to demonstrate successful recovery and determine limits of detection in a range of laboratory settings. Our results show this approach is adaptable to any diagnostic assay requiring validation of nucleic acid extraction and/or amplification, particularly where sourcing reliable, safe material for positive controls is infeasible.
- ItemGenomic Characterization of Canis Familiaris Papillomavirus Type 25, a Novel Papillomavirus Associated with a Viral Plaque from the Pinna of a Dog(MDPI (Basel, Switzerland), 2023-06-02) Munday JS; Gedye K; Knox MA; Robinson L; Lin XA 14-year-old West Highland White terrier dog developed multiple raised plaques that were confined to the concave surface of the right pinna. Histology allowed a diagnosis of viral plaque, although the lesions contained some unusual microscopic features. A papillomaviral (PV) DNA sequence was amplified from the plaque using consensus PCR primers. The amplified sequence was used as a template to design 'outward facing' PCR primers, which allowed amplification of the complete PV DNA sequence. The sequence was 7778 bp and was predicted to code for five early genes and two late genes. The ORF L1 showed the highest (83.9%) similarity to CPV15, and phylogenetic analysis revealed the novel PV clustered with the species 3 ChiPVs. The novel PV was designated as canine papillomavirus (CPV) type 25. As CPV25 was not previously detected in a canine viral plaque, this PV type may be a rare cause of skin disease in dogs. However, as plaques that remain confined to the pinna were not previously reported in dogs, it is possible that CPV25 could be more common in plaques from this area of skin. The findings from this case expand the number of PV types that cause disease in dogs. Evidence from this case suggests that, compared to the other canine ChiPV types, infection by CPV25 results in viral plaques in atypical locations with unusual histological features.