Detection and differentiation of re-emerging fowlpox virus (FWPV) strains carrying integrated reticuloendotheliosis virus (FWPV-REV) by real-time PCR.

Current strains of fowlpox virus (FWPV) carrying circulating reticuloendotheliosis virus (FWPV-REV) sequence are becoming more pathogenic to poultry. This is evidenced by the fact that vaccination with current available FWPV vaccines provides limited protection against them. To characterize REV insertions in a collection of both older and more recent field isolates, we developed three different types of adjacent oligoprobes and primer sets from specific genomic locations of FWPV and REV: REV-ENV (accession no. K02537, 1382-2260), FWPV-REV integration site (accession no. AF006064, 86-1328), FWPV (accession no. AF198100, 232461-232670), and REV-LTR (accession no. V01204, 305-496). The data indicated that the primers from the REV-ENV region and the TaqMan probes specifically targeted REV-ENV sequences of FWPV-REV strains. Furthermore, the strains were differentiated based on quantitative melting temperature (T(m)) of their amplified products using FRET-based probes. The amplified products were further characterized by sequencing and multiple sequence alignment analysis. The results suggest that integrated REV-ENV sequences are both common and mostly conserved in field isolates. However, the minor variations found within the short-targeted ENV sequence from FWPV-REV strains suggest that these strains could have either undergone periodic point mutational changes or integration with different REV-ENV subtypes.