Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken

David Wragg, Andrew S. Mason, Le Yu, Richard Kuo, Raman A. Lawal, Takele Taye Desta, Joram M. Mwacharo, Chang Yeon Cho, Steve Kemp, David W. Burt, Olivier Hanotte

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)


Background: EAV-HP is an ancient retrovirus pre-dating Gallus speciation, which continues to circulate in modern chicken populations, and led to the emergence of avian leukosis virus subgroup J causing significant economic losses to the poultry industry. We mapped EAV-HP integration sites in Ethiopian village chickens, a Silkie, Taiwan Country chicken, red junglefowl Gallus gallus and several inbred experimental lines using whole-genome sequence data. Results: An average of 75.22±9.52 integration sites per bird were identified, which collectively group into 279 intervals of which 5% are common to 90% of the genomes analysed and are suggestive of pre-domestication integration events. More than a third of intervals are specific to individual genomes, supporting active circulation of EAV-HP in modern chickens. Interval density is correlated with chromosome length (P<2.31-6), and 27% of intervals are located within 5kb of a transcript. Functional annotation clustering of genes reveals enrichment for immune-related functions (P<0.05). Conclusions: Our results illustrate a non-random distribution of EAV-HP in the genome, emphasising the importance it may have played in the adaptation of the species, and provide a platform from which to extend investigations on the co-evolutionary significance of endogenous retroviral genera with their hosts.

Original languageEnglish
Article number784
JournalBMC Genomics
Issue number1
Early online date14 Oct 2015
Publication statusFirst published - 14 Oct 2015
Externally publishedYes


  • Adaptation
  • Gallus
  • Genetics
  • Immunogenetics
  • NGS
  • Retrovirus
  • Symbiosis


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