Avian Endogenous Retrovirus EAV-HP Shares Regions of Identity with Avian Leukosis Virus Subgroup J and the Avian Retrotransposon ART-CH

Abstract

To resolve the genome structure of these retroviral elements, we have determined the complete sequence of two proviral clones of EAV-HP from a line N chicken genomic DNA yeast artificial chromosome library and from a meat-type chicken line 21 lambda library. The EAV-HP sequences from the two lines were 98% identical and had a typical provirus structure. The two EAV-HP clones showed identical large deletions spanning part of the gag, the entire pol, and part of the env genes. The env region of the EAV-HP clones was 97% identical to the env sequence of HPRS-103, the prototype subgroup J ALV. The 5 region of EAV-HP comprising the R and U5 regions of the long terminal repeat (LTR), the untranslated leader, and the 5 end of the putative gag region were 97% identical to the avian retrotransposon sequence, ART-CH. The remaining gag sequence shared less than 60% identity with other ALV sequences. The U3 region of the LTR was distinct from those of other retroviruses but contained some of the conserved motifs required for functioning as a promoter. To examine the ability of this endogenous retroviral LTR to function as a transcriptional promoter, the EAV-HP and HPRS-103 LTR U3 regions were compared in a luciferase reporter gene assay. The low luciferase activity detected with the EAV-HP LTR U3 constructs, at levels close to those observed for a control vector lacking the promoter or enhancer elements, suggested that these elements function as a weak promoter, possibly accounting for their low expression levels in chicken embryos.Endogenous retrovirus (ERV) sequences inherited as Mendelian genes have been recognized in most of the vertebrate genomes. In the chicken genome, four different families of ERVs have been identified. The CR1 (chicken repeat 1) element, a short interspersed repetitive DNA element belonging to the non-long terminal repeat (LTR) class of retrotransposons, forms one of these families (15). The majority of these elements, existing as approximately 7,000 to 20,000 repeats per haploid genome, have a common 3Ј end but show variable 5Ј truncations, with a few elements containing open reading frames encoding reverse transcriptase (13). CR1 elements have been identified in several avian and reptilian species, demonstrating that they are ancient sequences that arose before the divergence of birds and reptiles (40).The second family of chicken retrovirus-like elements, with the best-characterized ev loci, are the avian leukosis virus (ALV) subgroup E (ALV-E) ERVs. There are over 22 ev loci documented in layer-type birds and probably more in meattype breeds (17), with an average of 5 loci in each bird (33). Although the majority of the ev loci are defective, some of them encode infectious ERVs closely related to the ALVs (reviewed in reference 18). The ev2 locus, for example, encodes Rous-associated virus-0, the prototype of ALV-E (27). The ev loci are considered to represent recent germ line integrations because of their (i) low copy numbers, (ii) segregation in the population, and (iii) distribution restrict...

Intact EAV-HP Endogenous Retrovirus in Sonnerat's Jungle Fowl

“…The genus Gallus is composed of four species: the Sonnerat's or grey jungle fowl (SJF; G. sonneratii), the green jungle fowl (GJF; G. varius), the Ceylonese jungle fowl (CJF; G. lafayettei), and the red jungle fowl (RJF; G. gallus), of which domesticated chickens are a subspecies (G. gallus domesticus) (4). EAV-HP proviruses have also been detected in both RJF and SJF by hybridization of env and LTR sequences and PCR amplification of the env region (10,12). In this study, we have used a PCR approach to examine whether (i) the EAV-HP proviruses in RJF and SJF have the same pol region deletions as in chickens, (ii) the EAV-HP1 and EAV-HP2 loci, present in chickens, could be detected in the jungle fowls, and (iii) the genomic deletion and integration events occurred before or after the separation of Gallus species.…”

“…A single clone, designated ev/J clone 4-1, forms the fourth type of proviral structure, comprising a cDNA of the env subgenomic transcript bounded by long terminal repeats (LTRs) (9). The EAV-HP proviruses are more than 97% identical to the newly emerged subgroup J avian leukosis virus (ALV-J) env gene and demonstrate Ͼ96% sequence identity to other EAV family members in the R and U5 regions, the 5Ј untranslated region, and portions of the gag gene (6,9,10).…”

“…Three of these 4-kbplong provirus structures, designated types I, II, and III, show large deletions spanning the entire pol gene and parts of the gag and env regions. Each structure has a different gag-env deletion junction, with the type II and III provirus deletions extending an additional 57 and 86 bp, respectively, than the smallest (type I) provirus deletion size (9,10). These proviruses are found at multiple loci, with the type I provirus appearing to be the most abundant, based on its frequency in clones randomly screened from separate chicken genomic DNA libraries (9,10).…”

“…Each structure has a different gag-env deletion junction, with the type II and III provirus deletions extending an additional 57 and 86 bp, respectively, than the smallest (type I) provirus deletion size (9,10). These proviruses are found at multiple loci, with the type I provirus appearing to be the most abundant, based on its frequency in clones randomly screened from separate chicken genomic DNA libraries (9,10). A single clone, designated ev/J clone 4-1, forms the fourth type of proviral structure, comprising a cDNA of the env subgenomic transcript bounded by long terminal repeats (LTRs) (9).…”

Development and application of genome sequencing in studies on poultry production traits and health

“…Avian Endogenous Retrovirus-HP (EAV-HP) is a retrovirus, which integrated with the chicken genome before the domestication event and until today is an integral part of its genome. EAV-HP is able to mutate and give rise to the Avian Leukosis Virus (ALV), which confers epidemiological problems in the poultry industry (29). Retroviruses are able to integrate into the host genome, using the molecular mechanisms present in the host cell.…”