Biology subjects

Ross, C. S.

Publications and source records attributed to Ross, C. S..

3 recordsLinked to original sources

bioRxiv2026

Revolutionising notifiable avian disease diagnostics: validation of direct swab testing for Avian Influenza and Newcastle disease using the CENOS platform

Existing molecular diagnostic approaches for notifiable avian diseases (NADs) involve a suite of PCR assays that enable both generic detection, and where positive, subtyping of both avian influenza virus (AIV) and Newcastle disease virus (NDV). Novel rapid and direct diagnostic assays for the detection of AIV and NDV were developed and evaluated using unprocessed cloacal (C) and oropharyngeal (OP) poultry swab material. Both assays employ a closed tube direct real-time reverse transcription polymerase chain reaction (RRT-PCR) approach in which viral lysis is achieved by heat treatment and a dedicated PCR compatible buffer, followed by detection using a RRT-PCR approach. Primer and probe sets were designed using globally circulating AIV and NDV sequences collected over the preceding five years, rather than region-specific sequence datasets, so that the assays detect all circulating genotypes. Analytical performance assessment demonstrated that both assays were highly sensitive and specific, successfully detecting all unextracted target antigens without cross reactivity to a panel of other common poultry pathogens. For each assay, viral lysis and amplification were achieved directly from samples at single digit genome copy numbers. Furthermore, low levels of viral RNA could be reliably detected in the presence of C and OP matrix material, providing proof-of-concept for direct detection of these economically significant avian pathogens in a field setting. Additional use case scenarios, including pooled sample screening and combined C/OP testing from individual birds, were also explored. These findings establish a foundation for ongoing studies incorporating paired-sample testing against validated laboratory reference assays.

molecular biology↗

bioRxiv2025

Phylogenetic analysis of pigeon paramyxovirus type 1 (PPMV-1) detected in the British Isles between 1983 - 2023.

Newcastle Disease (ND), caused by virulent strains of avian paramyxovirus type-1 (APMV-1), is one of the most important poultry diseases globally due to its economic impact and endemicity in lower- and middle-income countries. A variant of APMV-1 is endemic in Columbiformes (pigeons and doves) worldwide and is commonly termed pigeon paramyxovirus-1 (PPMV-1). Since its initial detection in the 1980s, PPMV-1 has caused numerous ND outbreaks in poultry, including in high income countries, and was the causative agent for the last ND outbreak in the British Isles in 2006. Here, we have undertaken sequencing of PPMV-1 isolates between 1983 and 2023 and define three distinct genotypes of PPMV-1 being present in the British Isles. Analysis of the contemporary VI.2.1.1.2.2 genotype, demonstrated likely incursion from mainland Europe, whilst this genotype has subsequently spread across China, with detection also occurring in Australia. The presence of a virulent fusion-gene cleavage site in sequences highlights the continued risk to poultry from PPMV-1 genotypes which were detected in pigeons and doves across the British Isles.

evolutionary biology↗

bioRxiv2022

Investigating the genetic diversity of H5 avian influenza in the UK 2020-2022

Since 2020, the UK and Europe, have experienced annual epizootics of high pathogenicity avian influenza virus (HPAIV). The first during autumn/winter 2020/21 involved the detected with six H5Nx subtypes although H5N8 HPAIV dominated in the UK. Whilst genetic assessment of the H5N8 HPAIVs within the UK demonstrated relative homogeneity, there was a background of other genotypes circulating at a lower degree with different neuraminidase and internal genes. Following a small number of summer detections of H5N1 in wild birds over the summer of 2021, autumn/winter 2021/22 saw another European H5 HPAIV epizootic, that has dwarfed the prior epizootic. This second epizootic was dominated almost exclusively by H5N1 HPAIV, although six distinct genotypes were defined. We have used genetic analysis to evaluate the emergence of different genotypes and proposed reassortment events that have been observed. The existing data suggests that the H5N1 circulating in Europe during late 2020, continued to circulate in wild birds throughout 2021, with minimal adaptation, but has then gone on to reassort with AIVs in the wild bird population. We have undertaken an in-depth genetic assessment of H5 HPAIVs detected in the UK, over the last two winter seasons and demonstrate the utility of in-depth genetic analyses in defining the diversity of H5 HPAIVs circulating in avian species, the potential for zoonotic risk and whether incidents of lateral spread can be defined over independent incursion of infection from wild birds. Key supporting data for mitigation activities. ImportanceHigh pathogenicity avian influenza virus (HPAIV) outbreaks devastate avian species across all sectors having both economic and ecological impacts through mortalities in poultry and wild birds, respectively. These viruses can also represent a significant zoonotic risk. Since 2020, the UK has experienced two successive outbreaks of H5 HPAIV. Whilst H5N8 HPAIV was predominant during the 2020/21 outbreak, other H5 subtypes were also detected. The following year there was a shift in subtype dominance to H5N1 HPAIV, but multiple H5N1 genotypes were detected. Through thorough utilisation of whole-genome sequencing, it was possible to track and characterise the genetic evolution of these H5 HPAIVs in UK poultry and wild birds. This has enabled us to assess the risk posed by these viruses at the poultry:wild bird and the avian:human interface and to investigate potential lateral spread between infected premises, a key factor in understanding threat to the commercial sector.

molecular biology↗