Molecular characterization of transmitted/founder HIV-1 envelope Glycoproteins of Subtypes D and AD Recombinant viruses

Abstract

Infection by HIV-1 among heterosexuals most often results from successful transmission and propagation of a single virus variant, called Transmitted/Founder virus (TFV). This indicates that TFV have particular traits over other quasispecies that make them fit to overcome stringent mucosal bottlenecks during the early stages of infection. Understanding these traits could have important implications for HIV-1 vaccine design and other prevention strategies. There is limited data of T/F characteristics for HIV-1 subtypes A, D and recombinants circulating in Uganda. In this study we identified TFV genomes from 14 acutely infected plasma samples using Single genome amplification(SGA), assessed for recombination breakpoints, generated T/F HIV-1 Envelope clones for phenotypic and genotypic coreceptor usage. Single T/F virus transmission were found in 10 (71%) subjects whereas 4(29%) subjects had evidence of multivariant infections. A high transmission rate of unique intersubtype recombinants was seen in 71%(10/14) with recombination breakpoints highly enriched within the gp120, vpu, nef, LTR regions and variable loops (V1-V2) while 29%(4/14) subjects were infected with subtype D. Coreceptor prediction analysis of the ten(10) T/F envelope glycoproteins revealed that 70%(7/10) of subjects were infected with CCR5(R5) strains whereas tropism switch from CCR5 to CXCR4-using strains was identified in 30% (3/10 ) of the subjects suggesting rapid disease progression in some individuals. In contrast, phenotypic coreceptor analysis showed all Transmitted/Founder psuedoviruses with the ability to infect CCR5, CXCR4, CXCR4/CCR5 and CXCR6 coreceptors at varying infectivity. The ability to infect both CCR5 and CXCR4 indicates transmission of dual-trophic viruses or an early coreceptor switch leading to rapid disease progression. In addition, the use of other co-receptors like CXCR6 might suggest an expanded range of co-receptor usage The high transmission rate of unique intersubtype recombinants is striking and emphasizes the need to re-subtype HIV-1 using near-full length sequences. This research brings out the challenges for vaccine design in particular for the highly variable and recombinogenic envelope gene and also highlights the complexities in vaccine design, subtyping methods and other therapeutic treatment interventions targeting coreceptors for subtypes A and AD circulating in Uganda. Key words; HIV-1, Transmitted/Founder viruses(TFV), Single genome amplification (SGA), Envelope glycoproteins, Cloning and Coreceptor usage(CCR5 and CXCR4, X4R5 and CXCR6)