In-Depth Analysis of a Heterosexually Acquired Human Immunodeficiency Virus Type 1 Superinfection: Evolution, Temporal Fluctuation, and Intercompartment Dynamics from the Seronegative Window Period through 30 Months Postinfection

Abstract

Human immunodeficiency virus type 1 (HIV-1) superinfection refers to the acquisition of another strain by an already infected individual. Here we report a comprehensive genetic analysis of an HIV-1 superinfection acquired heterosexually. The infected individual was in a high-risk cohort in Tanzania, was exposed to multiple subtypes, and was systematically evaluated every 3 months with a fluorescent multiregion genotyping assay. The subject was identified in the window period and was first infected with a complex ACD recombinant strain, became superinfected 6 to 9 months later with an AC recombinant, and was monitored for >2.5 years. The plasma viral load exceeded 400,000 copies/ml during the first 9 months of infection but resolved to the set point of 67,000 copies/ml by 3 months after superinfection; the CD4 cell count was 377 cells/l at 30 months. Viral diversity was evaluated with techniques designed to fully sample the quasispecies, permitting direct observation of the evolution, temporal fluctuation, and intercompartment dynamics of the initial and superinfecting strains and recombinants derived from them. Within 3 months of superinfection, seven different molecular forms were detected in gag and six were detected in env. The proportions of forms fluctuated widely over time in plasma and peripheral blood mononuclear cells, illustrating how challenging the detection of dually infected individuals can be. Strain-specific nested PCR confirmed that the superinfecting strain was not present until the 9 month follow-up. This study further defines the parameters and dynamics of superinfection and will foster appropriate studies and approaches to gain a more complete understanding of risk factors for superinfection and its impact on clinical progression, epidemiology, and vaccine design.

Longitudinal Quasispecies Analysis of Viral Variants in HIV Type 1 Dually Infected Individuals Highlights the Importance of Sequence Identity in Viral Recombination

“…In addition to the ACD and AC parental URF strains, three intersubtype recombinants were detected in gag and four were detected in gp41=nef over the course of the study, although often as only one or two clones at a single time point. 9 Similarly, the second study included an in-depth analysis of the quasispecies infecting a subject exhibiting symptoms of late-stage disease in gag, vpu=gp120, and gp41=nef over 12 months. This subject was triply infected by two strains of subtype A and a subtype C virus.…”

“…Furthermore, the genomic regions analyzed for recombination in the studies included the gp41=nef, gag, or the whole gp120, which are not entirely identical to those analyzed in the present study. 9,11 This could, in part, contribute to some discrepancies in the recombinants identified among these various studies.…”

“…Thus, this relatively high rate of intrasubtype recombination is not surprising; however, even infection by subtype-concordant viruses in these cases did not yield the huge arrays of recombinants predicted by in vitro analyses. 9,11,29,30 The present in-depth analysis of five dually HIV-1-infected subjects employed frequent longitudinal sampling and analysis of genomic loci predicted to be common areas for recombination by in vitro studies. This analysis is the first of its kind to focus on dually infected members of the general HIV þ population in Africa, and has demonstrated that although recombination between subtype-discordant strains was uncommon, recombinants of relatively similar strains were easily detected.…”

“…[1][2][3][4][5][6][7][8][9] Among such studies includes one published by Baird et al, which examined the C1C4 region of env for recombination between two discordant HIV-1 subtypes, A and D, in cell culture demonstrating an abundance of recombinants and revealing recombination breakpoints occurring more frequently in the constant than in the variable regions of the viral envelope. 8 Subsequent in vitro studies with these discordant strains also revealed that factors such as replicative fitness contribute to the frequency at which two viral strains recombine.…”

HIV-1 Diversity in Tanzania and its Implication toward Development of Effective Vaccines: A Review Article

“…It is one of the countries in SSA that has been severely affected by the HIV epidemic. Molecular epidemiological studies have reported that HIV-1 subtypes A1, A2, C, D, G, CRF10_CD and other inter-subtype recombinant viruses are circulating in Tanzania [13,23,33]. HIV-1 subtypes A1, A2, C, D, CRF10_CD and other inter-subtype recombinant viruses were reported among bar and hotel workers in Moshi town at Kilimanjaro region [24].…”