Species-specific oligonucleotide probes for the identification of human filarial parasites

Species-specific oligonucleotide probes have been constructed for the filarial parasites Brugia malayi and Brugia pahangi. Both parasites contain a 322 base pair repeated DNA sequence that is cleaved once by the restriction endonuclease HhaI. A consensus repeat sequence was determined from the DNA sequence of 15 cloned isolates of each species. Although the two repeats have an average homology of 89%, half the differences are clustered in a region of 66 nucleotides that has a homology of only 72%. Within this region, two probes, a 29-mer that is B. malayi specific and a 21-mer that is B. pahangi specific, were constructed. The sequence of both probes was chosen to obtain the maximum difference between the consensus sequences of the two species. The probes were also selected to be GC rich to increase their stability as a DNA hybrid. In a filter hybridization assay, the B. malayi probe has a 500-fold preference for B. malayi DNA versus B. pahangi DNA and a sensitivity of 200 pg. The B. pahangi probe has similar specificity and sensitivity for B. pahangi DNA. A rapid lysis procedure allows the probes to detect 1-2 third stage larvae of either B. malayi or B. pahangi in a filter hybridization assay.