Discovery and Characterisation of Novel Avian Leukosis Virus Subgroup-E (ALVE) Insertions in Commercial Chickens Using Next Generation Sequencing Data

Endogenous retroviruses (ERVs) elicit prolonged genomic and immunological stress on their host organism. In chickens, the most prevalent group of ERVs are Avian Leukosis Virus subgroup-E (ALVE) insertions. The impacts of ALVEs are wide ranging, from influencing feather colour to negatively effecting productivity traits such as total egg count and muscle growth rate. Furthermore, ALVEs are known to modulate immune response to exogenous ALV, contrastingly through both cell-entry-receptor interference and the induction of persistent viremia. Traditional ALVE identification methods are laborious, but the availability of next generation sequencing (NGS) data enables improved characterisation of ALVE abundance and diversity.

Here we present an ALVE identification pipeline which makes use of existing NGS datasets (rather than requiring additional targeted sequencing experiments), and common NGS analysis software. Eight commercial layer lines were analysed with this pipeline, resulting in identification of twenty-one ALVEs, five of which were novel. White Leghorn lines had the fewest ALVEs (2-4), whereas the brown egg layer breeds had 5-10 insertions, including all novel ALVEs. KASP (Kompetitive Allele-Specific PCR) assays were developed for each identified ALVE and used for genotyping of multiple generations of the commercial elite layer lines. Each ALVE insertion identified was sequenced and the retrotransposition, recombination and viral expression potential was assessed. In addition, a phenotypic revertant at the ALVE21-associated slow feathering (K) locus was identified, enabling further characterisation of this commercially important locus.

This work was part of a BBSRC CASE studentship in association with Hy-Line International.