Impact of extensive HIV-1 variability on molecular diagnosis in the Congo Basin

BACKGROUND: Previous studies have shown a high HIV-1 genetic variability in the Republic of Congo. This can greatly influence the performance of molecular assays for HIV-1 diagnosis. OBJECTIVES: To define a reliable test for detection of HIV-1 DNA in this area. STUDY DESIGN: We compared a commercial nested PCR (C-PCR) assay and an in house nested PCR (H-PCR) assay for the detection of HIV-1 DNA in the first 30 seropositive pregnant women enrolled into the ongoing "Kento-Mwana" project, for the prevention of HIV mother-to-child transmission in the city of Pointe Noire, Republic of Congo, Africa. Sequencing and phylogenetic analysis of partial HIV-1 pol sequences were also performed. RESULTS: C-PCR detected HIV-1 DNA in only 15/30 samples from seropositive women (50.0%), as opposed to 29/30 (96.6%) by H-PCR (P<0.0001). Phylogenetic analysis and bootscanning showed that only 10 sequences could be assigned to known clades (seven pure subtypes and three circulating recombinant forms), whereas the other 20 sequences were unique recombinant forms. CONCLUSIONS: The great genetic variability of HIV-1 in this area strongly advises to for using molecular methods only after local validation to avoid false negative results.