Genetic Characterization of the nef Gene from Human Immunodeficiency Virus Type 1 Group M Strains Representing Genetic Subtypes A, B, C, E, F, G, and H

Abstract

Most efforts to characterize sequence variation of HIV isolates has been directed toward the structural envelope gene. Few studies have evaluated the sequence variability of auxiliary genes such as nef. In this study 41 new HIV-1 strains, representing the majority of the described envelope subtypes of HIV-1 (A to H), were genetically characterized in the nef region. Phylogenetic analysis showed that 34 strains could be classified in the same subtype in nef and env, and 7 (19%) of the 41 new viruses were recombinants. For two of the seven strains, recombination occurred upstream of the nef gene, whereas for five of the seven strains recombination occurred within the nef gene with a crossover close to the 5' end of the LTR (long terminal repeat). The low intersubtype distance between subtype B and D in the nef gene confirms previous observations in the pol, env, and gag genes, which suggest a common ancestor for these subtypes. The majority of all the previously described functional domains in the nef gene were relatively conserved among the different subtypes, with only minor differences being observed. The myristoylation signal among the different subtypes, with only minor differences being observed. The myristoylation signal was less conserved for subtype C, with one or more amino acid changes being observed at positions 3, 4, and 5. The highly conserved acidic region (positions 62 to 65), critical for the enhancement of viral synthesis with an increased virus growth rate, was less conserved among the subtype G strains from our study. At least three epitopic regions of the nef gene have been defined and each can be recognized by CTLs under a variety of HLA restrictions; all were also relatively well conserved between the different genetic subtypes. Despite the relatively important genetic variation in nef sequences obtained among the different genetic subtypes, functional domains and CTL epitopes were relatively well conserved. In vitro and/or in vivo studies are necessary to study the relevance of the observed differences.

Cyclin K Inhibits HIV-1 Gene Expression and Replication by Interfering with Cyclin-dependent Kinase 9 (CDK9)-Cyclin T1 Interaction in Nef-dependent Manner

“…This interaction is not subtype-specific as both subtypes B and C Nef bind to CycK. Our data seem to corroborate previous reports (48), suggesting that despite significant sequence differences in the Nef gene from various subtypes functional properties remain relatively well conserved.…”

Polymorphism of the Human Immunodeficiency Virus Type 1 in Brazil: Genetic Characterization of the nef Gene and Implications for Vaccine Design

“…Although the amplified fragment does not cover all the extension of the overlapping CTL epitopes mapped in the 3' portion of the nef region (DPEREVLEWRFDSRLA FHHVAREL in the HXB2 reference sample), it is possible to verify the highly polymorphism of this region among the Brazilian HIV-1 samples, independent of the subtype, as can be depicted in the Figure, confirming previous works (Jubier-Maurin et al 1999, Korber et al 2000. Conserved E 3 →H, E 8 →Q and R 14 →K were observed among the three subtype C samples included in the present study.…”

“…Once again, typical substitution from histidine (H) to asparagine (N) in the WIYHTQGYFDPWQNY CTL epitope was observed among the Brazilian subtype C samples. The presence of this H→N substitution, although rare among the subtype B samples, can be frequently observed among other non-B subtypes (Jubier-Maurin et al 1999, Korber et al 2000.…”

“…Multiple HLA-restricted CTL epitopes have been identified in the nef gene (Korber et al 2000), which are described as quite conserved among the HIV-1 subtypes (Artenstein et al 1996, Jubier-Maurin et al 1999. Moreover, CTL response against nef epitopes have been postulated to be associated with protection from infection in HIV-1 exposed individuals (Langlade-Demoyen et al 1994).…”

“…The nef CTL epitopes have been described as conserved among the HIV-1 subtypes (Jubier-Maurin et al 1999). Such restricted variability observed among these CTL epitopes probably occur due to their overlapping with crucial regions for the maintenance of some nef biological functions.…”