Genomic organization of the human endogenous retrovirus HERV-K(HML-2.HOM) (ERVK6) on chromosome 7

Recently, we reported an almost intact human endogenous retrovirus (HERV-K(HML-2.HOM); HGMW-approved symbol ERVK6) located on human chromosome 7, with open reading frames for all retroviral genes and a mutation only within the reverse transcriptase. We further characterized the genomic organization of this endogenous retrovirus by subcloning and sequencing of the proviral insert contained within a chromosome 7-specific cosmid clone and found HERV-K(HML-2.HOM) to be organized as a tandem repeat. Examination of various human DNA samples for this specific proviral repeat suggests a relatively ubiquitous distribution of the HERV-K(HML-2.HOM) tandem structure. However, we identified two human samples having only a single provirus at this locus. In addition, we investigated the presence of HERV-K(HML-2.HOM) alleles having an intact YXDD motif within the reverse transcriptase domain by sequencing the corresponding polymerase gene from various human DNA samples. We identified a HERV-K(HML-2.HOM) polymerase with an intact YXDD motif in two samples, thus potentially coding for an active reverse transcriptase. Our results show for the first time an endogenous retrovirus tandem repeat in human populations and suggest the existence of alleles harboring an intact human endogenous retrovirus including an intact polymerase gene.