Sequence Analysis For The Complete Proviral Genome Of Avian Leukosis Virus (Subgroup J) Strain SD07LK1 Isolated From Layers

Avian Leukosis Virus Subgroup J (ALV-J) is a new kind of retrovirus that was firstly reported and isolated from meat-type chickens in England in 1991, which mostly induced avian myelcytomatosis (ML) in broilers. It was discriminated from classic ALVs by the neutralization, interference assays and genomic sequences. It was in 1999 that ALV-J was firstly isolated and identified from two broiler flocks by Prof. Cui Zhizhong's labortatory in China.To study the source and trend in evolution of ALV-J strains from layers in China, the genomic DNA extracted from chicken embryo fibroblasts (CEF) infected by ALV-J strain SD07LK1 isolated from layers was used as template to amplify the ALV-J proviral DNA by PCR. Nine continuous and overlapping fragments were amplified with nine pairs of primers according to published sequences, then cloned into the T vector and sequenced. The complete sequence of the whole genome of ALV-J Chinese strain SD07LK1 was first established, which provides direct information about the genomic structure and its possible relationships to the biological functions, and aids in the development of new ALV-J vaccines. Comparisons of SD07LK1 sequence with that of the other Avian leukosis viruse strains, by using DNAstar software, demonstrated that the genes gag and pol of ALV-J were relatively conservative, the nucleotide identity of all the strains was over 95.0%. However, the gene env identity was only in the ranges of 88.6-94.0%. Sequence analysis showed that the entire genome of cDNA of SD07LK1 strain consisted of 7734 nucleotides (nt). The nucleotide sequences of SD07LK1 strain were compared with those of other ALV-J strains: HPRS103, ADOL7501 and NX0101. The results revealed that:The homology of nucleotide sequences of the 5'LTR; the 5'LTR-U3; the 5'LTR-R; the 5'LTR-U5; the 5'UTR among the four strains(SD07LK1 and HPRS103,SD07LK1 and ADOL7501,SD07LK1 and NX0101) was 95.4%,92.6%,94.2%; 95.5%,91.1%,93.8%; 100%,100%,100%; 93.6%,94.9%,93.6%; 95.5%,95.0%,96.3%.The homology of amino acid of the gag,the p19,the p2,the p10,the p27,the p12 and the p15 among the four strains(SD07LK1 and HPRS103,SD07LK1 and ADOL7501,SD07LK1 and NX0101) was 98.0%,96.6%,96.6%; 96.8%,94.8%,98.1%; 100%,100%,100%; 98.4%,100.0%,98.4%; 100.0%,97.1%,94.1%; 95.5%,96.6%,94.4%; 96.8%,95.2%,99.2%.The homology of amino acid of the pol,the RT p68,the IN p32 among the four strains(SD07LK1 and HPRS103,SD07LK1 and ADOL7501,SD07LK1 and NX0101) was 98.9%,99.1%,98.1%; 99.0%,99.7%,97.9%; 99.3%,97.9%,98.3%.The homology of amino acid of the env,the gp85,the gp37 among the four strains(SD07LK1 and HPRS103,SD07LK1 and ADOL7501,SD07LK1 and NX0101) was 91.6%,87.3%,91.7%; 89.0%,81.8%,89.3%; 93.9%,93.4%,93.9%.The homology of nucleotide sequences of the 3'UTR; 3'LTR; 3'LTR-U3; 3'LTR-R: 3'LTR-U5 among the four strains(SD07LK1 and HPRS103,SD07LK1 and ADOL7501,SD07LK1 and NX0101) was 86.0%,87.9%,67.2%; 95.4%,92.0%,93.5%; 95.6%,91.2%,92.5%; 100%,100%,100%; 93.6%,92.3%,94.9%.