Detection of phylogenetically diverse human immunodeficiency virus type 1 groups M and O from plasma by using highly sensitive and specific generic primers

The high degree of genetic diversity within human immunodeficiency virus ty pe 1 (HIV-1), which includes two major groups, M (major) and O (outlier), a nd various env subtypes within group M (subtypes A to J), has made designin g assays that will detect all known HIV-1 strains difficult. We have develo ped a generic primer set based on the conserved immunodominant region of tr ansmembrane protein gp41 that can reliably amplify as few as 10 copies/PCR of viral DNA from near-full-length clones representing group M subtypes A t o H (subtypes I and J were not available). The assay is highly sensitive in detecting plasma viral RNA from HIV-1 strains of diverse geographic origin s representing different subtypes of HIV I group M as well as HIV-1 group O , Of the 253 group M plasma specimens (subtypes A, 68 specimens; B, 71; C, 19; D, 27; E, 23; F, 33; and G, 12), 250 (98.8%) were amplified by using th e gp41 M/O primer set. More importantly, all 32 (100%) group O plasma sampl es were also amplified with these primers. In vitro spiking experiments fur ther revealed that the assay could reliably detect as few as 25 copies/ml o f viral RNA and gave positive signals in HIV-1-seropositive specimens with plasma copy numbers below the limits of detection by all commercially avail able viral load assays. In addition, analysis of five seroconversion panels indicated that the assay is highly sensitive for early detection of plasma viremia during the "window period." Thus, the highly sensitive assay will be useful for early detection of HIV-1 in clinical specimens from all known HIV-1 infections, regardless of their genotypes and geographic origins.