Molecular cloning and analysis of functional envelope genes from human immunodeficiency virus type 1 sequence subtypes A through G. The WHO and NIAID Networks for HIV Isolation and Characterization

Abstract

Present knowledge of human immunodeficiency virus type 1 (HIV-1) envelope immunobiology has been derived almost exclusively from analyses of subtype B viruses, yet such viruses represent only a minority of strains currently spreading worldwide. To generate a more representative panel of genetically diverse envelope genes, we PCR amplified, cloned, and sequenced complete gp160 coding regions of 35 primary (peripheral blood mononuclear cell-propagated) HIV-1 isolates collected at major epicenters of the current AIDS pandemic. Analysis of their deduced amino acid sequences revealed several important differences from prototypic subtype B strains, including changes in the number and distribution of cysteine residues, substantial length differences in hypervariable regions, and premature truncations in the gp41 domain. Moreover, transiently expressed glycoprotein precursor molecules varied considerably in both size and carbohydrate content. Phylogenetic analyses of full-length env sequences indicated that the panel included members of all major sequence subtypes of HIV-1 group M (clades A to G), as well as an intersubtype recombinant (F/B) from an infected individual in Brazil. In addition, all subtype E and three subtype G viruses initially classified on the basis of partial env sequences were found to cluster in subtype A in the 3 half of their gp41 coding region, suggesting that they are also recombinant. The biological activity of PCR-derived env genes was examined in a singleround virus infectivity assay. This analysis identified 20 clones, including 1 from each subtype (or recombinant), which expressed fully functional envelope glycoproteins. One of these, derived from a patient with rapid CD4 cell decline, contained an amino acid substitution in a highly conserved endocytosis signal (Y721C), as well as a premature truncation of its gp41 domain, which lacked 17 amino acids. Several other env constructs mediated virus entry with very poor efficiency, although they did not contain sequence changes predicted to alter protein function. These results indicate that the env genes of primary HIV-1 isolates collected worldwide can vary considerably in their genetic, phylogenetic, and biological properties. The panel of env constructs described here should prove valuable for future structure-function studies of naturally occurring envelope glycoproteins as well as AIDS vaccine development efforts targeted against a broader spectrum of viruses.

Human Immunodeficiency Virus Type 1 Subtype C Exhibits Higher Transactivation Activity of Tat than Subtypes B and E

“…The Ser 57 and Glu 63 were highly conserved among subtype C isolates reported previously (Fig. 5) (14,32,33,38,49,55).…”

Macrophage-tropic HIV-1 variants from brain demonstrate alterations in the way gp120 engages both CD4 and CCR5

“…JR-CSF and YU2 Envs were included as controls. All of the Envs are cloned into the pSVIII-Env mammalian expression vector [70] and have been described previously [25,26].…”

DNA vaccines: an historical perspective and view to the future

“…This mutation is the reason that the traditional influenza vaccine (where the protective response is antibody-mediated) needs to be remade each year to target that year's strain (1). Likewise, human immunodeficiency virus (HIV) envelope protein (Env) is not only quite variable but also changes rapidly to escape antibodies that arise in an infected individual (2). The rationale for targeting proteins that are less likely to mutate due to their functional restrictions is critical for making vaccines and immunotherapies that can be broadly protective or effective against varied strains of virus or bacteria or against tumors arising in different individuals (3).…”