Recovery of Virtually Full-Length HIV-1 Provirus of Diverse Subtypes from Primary Virus Cultures Using the Polymerase Chain Reaction

In the course of the global pandemic, the human immunodeficiency virus type-1 (HIV-1) has established at least eight distinct genotypes in the main (M), or prevalent, group of isolates, a variety of rare outlier forms, and intergenotypic recombinants of group M viruses. This genotypic diversity has been documented, for the most part, by sequencing of subgenomic segments of the provirus. Using DNA from virus cultures on peripheral blood mononuclear cells (PBMC) and recent improvements of the PCR technique, we have amplified virtually full-length HIV-1 genomes from genetic subtypes A through G of group M viruses and molecularly cloned several of them. Resequencing of the complete genome of a prototype strain after long PCR amplification and cloning has established a PCR error rate of 0.14%. We also report the first complete PCR-derived sequence of a U.S. clinical isolate of genotype B expanded only in primary PBMC; this provirus harbors a uniquely truncated V3 loop.