Sequence comparison of three infectious molecular clones of RD-114 virus

Abstract

RD-114 virus is a replication-competent feline endogenous retrovirus. RD-114 virus contaminates several feline and canine live attenuated vaccines and the issue of contamination of RD-114 virus in vaccines should be solved. To date, three infectious molecular clones (pSc3c, pCRT1, and pRD-UCL) have been reported. In this study, we sequenced the entire nucleotide sequence of pRD-UCL and compared the nucleotide sequences of the three infectious molecular clones. As a result, these three infectious clones were nearly identical with each other in gag-pol and env coding regions. These data support the notion that the active locus of infectious RD-114 virus is single in the feline genome. The length of long terminal repeat (LTR) of pCRT1 was 47 bp shorter than those of pSc3c and pRD-UCL. The 47-bp sequence named direct repeat A (DR-A) was duplicated in the U3 region in pSc3c and pRD-UCL. Although several potential enhancer binding sites are present in the DR-A, there was no significant difference in promoter activities between the LTRs of pRD-UCL and pCRT1 in two human cell lines. We also analyzed the splicing pattern of the RD-114 virus by reverse transcription-polymerase chain reaction and confirmed that RD-114 virus is a simple retrovirus. The data presented here will provide basic information about RD-114 virus to solve the contamination issue in live attenuated vaccines.