Whole-genome analysis of an emerging recombinant avian leukosis virus in yellow chickens, south China.

Avian leukosis virus (ALV) is the cause of a variety of tumour diseases in poultry, causing huge economic losses all over the world. As a retrovirus, its genome is highly variable and easily recombined between different subgroups. Previous studies found several recombinant events among subgroup A, B and E, but few data show that in subgroup J, which is the most prevalent and pathogenic in chickens. This study identified and sequenced an emerging recombinant ALV from yellow chicken, and analysis showed that the homology between the env gene of the new isolate and the representative strain (BR119) of subgroup J is as high as 98.7%, while its long terminal repeat (LTR) was highly consistent with some representative strains of subgroup E (94.9%-98.4%). This study also found that such LTR has appeared in some published strains of subgroup B and subgroup K, indicating that it can combine with the coding region of many different subgroups of ALV, thus forming natural recombinant strains. At the same time, a pair of polymerase chain reaction primers were selected according to the sequence, which can specifically detect the recombinant strains in wild, facilitating the future ALV eradication program. Overall, this study reminds us to pay more attention to tracking the genome variation of ALV in the future.