Functional and structural defects in HIV type 1 nef genes derived from pediatric long-term survivors

DNA sequences and three distinct in vitro functions of Nef were evaluated i n a group of seven perinatally infected children. nef gene sequences obtain ed before and after virus culture showed that one of the five non-/slow pro gressors harbored a virus with large deletions. nef genes from the remainin g four children were full length but contained discrete changes at a higher frequency than the rapid progressors. In functional studies, 40 of 44 Nef proteins derived from the whole study group were capable of binding the cel lular serine kinase p62, indicating that this function is well conserved am ong naturally occurring viruses. In contrast, representative Nef proteins d erived from the long-term non-/slow progressors were found to be defective or far less capable of enhancing viral replication and/or viral infectivity in herpesvirus saimiri-transformed human T cells and peripheral blood mono nuclear cells. On reversion of highly prevalent point mutations in the defe ctive proteins, viral replication could be restored to wild-type levels. Ou r results suggest that nef genes derived from pediatric long-term nonprogre ssors have gross deletions in isolated cases but a higher prevalence of dis crete changes that may impair Nef function in primary T cell assays, but no t all functions reported for Nef.