Incidence of HIV‐1 Dual Infection and Its Association with Increased Viral Load Set Point in a Cohort of HIV‐1 Subtype C–Infected Female Sex Workers

Abstract

This longitudinal study aimed to determine the incidence and pathogenic implications of dual human immunodeficiency virus type 1 (HIV-1) infection in a cohort of female sex workers. Blood samples from 31 recently infected women were screened by use of a heteroduplex mobility assay and sequencing. The median viral load set point was 5404 copies/mL (n=22), which was measured by use of the bDNA assay. Within 3 months of infection, 19% (6/31) of the women were dually infected with 2 distinct HIV-1 subtype C viruses. No evidence of superinfection was detected over the course of 24 months of follow-up, indicating that the risk of dual infection is highest around the time of the initial infection. There was a significant association between dual infection and elevated viral load set point.

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection

“…Previous studies characterized HIV-1 env sequences in acute and early infection by using methods that did not involve SGA and direct sequencing, and, as a result, they did not allow for the precise identification or enumeration of transmitted or early founder envs, their pathways of diversification as genetic units, or their corresponding phenotypes (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14). The extent to which differences in experimental approach can impact the interpretation of virus complexity was recently highlighted in a study of acute and early HIV-1 clade C infection (17) and was seen again in the present study in 10 subjects who had been analyzed previously by the HTA method (10).…”

“…Previous reports examined the molecular basis of HIV-1 transmission by analyzing the genetic composition of viruses sampled between 1 and 6 months after infection (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14). A common methodological approach in these studies was to derive viral sequences from the plasma or peripheral blood mononuclear cells of patients by bulk or near-limiting dilution PCR amplification of viral nucleic acid [proviral DNA or viral (v)RNA], followed by cloning, sequencing, and phylogenetic analysis (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12).…”

“…A common methodological approach in these studies was to derive viral sequences from the plasma or peripheral blood mononuclear cells of patients by bulk or near-limiting dilution PCR amplification of viral nucleic acid [proviral DNA or viral (v)RNA], followed by cloning, sequencing, and phylogenetic analysis (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12). Alternatively, bulk amplified viral nucleic acids were analyzed by heteroduplex tracking assay (HTA) where only a small fraction of the gene of interest is interrogated by selective annealing of a short oligonucleotide probe followed by differential migration of the heteroduplex (5-7, 10).…”

“…Bulk or near-endpoint PCR, followed by cloning and sequencing, is compromised by the introduction of Taq polymerase errors (15)(16)(17), Taq polymerasemediated template switching (recombination) (17)(18)(19), and nonproportional representation of target sequences attributable to template resampling or unequal template amplification and cloning (15)(16)(17)20). Based largely on these approaches, previous studies generally have described the virus quasispecies in acute and early infection either as ''homogeneous,'' reflecting transmission of one or few viruses, or ''heterogeneous,'' reflecting a higher multiplicity of infection (2)(3)(4)(5)(6)(7)(8)(9)(10)(11). It even has been suggested that HIV-1 infection commonly results from transmission and early replication of multiple virus variants that subsequently undergo a process of homogenization or purifying selection, giving rise to the appearance of a more homogeneous infection (7).…”

Recombination-mediated escape from primary CD8+ T cells in acute HIV-1 infection

“…Infection with multiple T/F viruses is linked to factors that are known to increase overall transmission rates, such as higher risk sex acts and other concurrent sexually transmitted infections [12,[15][16][17][18][19]. Several studies have associated infection with multiple HIV-1 T/F viruses, multiple subtypes, and/or a diverse virus population, with higher pVL setpoint, faster CD4+ T cell decline, earlier need for anti-retroviral therapy and a worse prognosis for the infected individual [14,[20][21][22][23][24].…”