HIV type 1 envelope quasispecies in the thymus and lymph nodes of AIDS patients

To test for the presence of HIV syncytium-inducing (SI) strains in the thymus in vivo we sequenced HIV envelope V3 variants from thymic and peripheral lymph node tissues of three subjects who died of AIDS. Phylogenetic analysis of proviral sequences derived by direct sequencing of multiple independent PCRs showed that the HIV-1 quasispecies did not segregate into distinct clusters in the thymus versus lymph nodes. Examination of env sequences for V3 loop amino acids associated with the SI phenotype did not show its preferential localization in either thymus or lymph node. One subject harbored only putative SI variants, another only putative NSI variants, and the third subject carried a mixture of genotypes in both tissues. The thymus and lymph nodes of terminal AIDS patients therefore appeared to harbor closely related proviral envelope quasispecies.