Comparison of primer pairs: Greater degeneracy improves small ruminant lentivirus (SRLVs) detection by seminested PCR

• A comparison between degenerate primer pairs to detect small ruminant lentiviruses is showed.
• The higher degree of degeneracy is designed based on twenty gag gene sequences.
• The seminested PCR gave better results with the more degenerate primers.
• The method described is proposed as a supplementary diagnostic tool.

The identification of small ruminant lentivirus (SRLV) infected animals is crucial to obtain success through eradication, control and monitoring programs worldwide. Several authors have demonstrated that serology alone is not sufficient to detect SRLV infection. Polymerase chain reaction (PCR) is suggested as the choice test to identify seronegative infected animals. The aim of this study was to evaluate and compare degenerate primer pairs in order to detect a great number of virus variants by a seminested PCR. Based on already described primers and the alignment of gag nucleotide sequences from databases, degenerate primers were designed. Increasing the degree of degeneracy has improved the detection of the provirus in ovine and caprine genomic DNA samples. The number of positive PCR samples was twice higher when using the more degenerate primers in the established experimental conditions. Thus, we propose the use of this seminested PCR as a diagnostic tool, in combination with serology, especially in the situations where the circulating virus variants are unknown.