Wide Variation in the Multiplicity of HIV-1 Infection among Injection Drug Users

Abstract

Recent studies indicate that sexual transmission of human immunodeficiency virus type 1 (HIV-1) generally results from productive infection by only one virus, a finding attributable to the mucosal barrier. Surprisingly, a recent study of injection drug users (IDUs) from St. Petersburg, Russia, also found most subjects to be acutely infected by a single virus. Here, we show by single-genome amplification and sequencing in a different IDU cohort that 60% of IDU subjects were infected by more than one virus, including one subject who was acutely infected by at least 16 viruses. Multivariant transmission was more common in IDUs than in heterosexuals (60% versus 19%; odds ratio, 6.14; 95% confidence interval [CI], 1.37 to 31.27; P ‫؍‬ 0.008). These findings highlight the diversity in HIV-1 infection risks among different IDU cohorts and the challenges faced by vaccines in protecting against this mode of infection.Elucidation of virus-host interactions during and immediately following the transmission event is one of the great challenges and opportunities in human immunodeficiency virus (HIV)/AIDS prevention research (14-16, 31, 34, 45). Recent innovations involving single-genome amplification (SGA), direct amplicon sequencing, and phylogenetic inference based on a model of random virus evolution (18)(19)(20)43) have allowed for the identification of transmitted/founder viruses that actually cross from donor to recipient, leading to productive HIV type 1 (HIV-1) infection. Our laboratory and others have made the surprising finding that HIV-1 transmission results from productive infection by a single transmitted/founder virus (or virally infected cell) in ϳ80% of HIV-infected heterosexuals and in ϳ60% of HIV-infected men who have sex with men (MSM) (1,13,18,24). These studies thus provided a precise quantitative estimate for the long-recognized genetic bottleneck in HIV-1 transmission (6, 11-13, 17, 25, 28, 30, 35, 38, 42, 47-49) and a plausible explanation for the low acquisition rate per coital act and for graded infection risks associated with different exposure routes and behaviors (15,36).In contrast to sexual transmission of HIV-1, virus transmission resulting from injection drug use has received relatively little attention (2, 3, 29, 42) despite the fact that injection drug use-associated transmission accounts for as many as 10% of new infections globally (26, 46). We hypothesized that SGA strategies developed for identifying transmitted/founder viruses following mucosal acquisition are applicable to deciphering transmission events following intravenous inoculation and that, due to the absence of a mucosal barrier, injection drug users (IDUs) exhibit a higher frequency of multiple-variant transmission and a wider range in numbers of transmitted viruses than do acutely infected heterosexual subjects. We obtained evidence in support of these hypotheses from the simian immunodeficiency virus (SIV)-Indian rhesus macaque infection model, where we showed that discrete low-diversity viral lineages emanating from singl...

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

“…Here, our more detailed sampling clearly shows that primary HIV-1 specific T cell responses can select recombination between distinct T/F viruses even more rapidly, within weeks of infection when pVL is stabilizing prior to the establishment of setpoint. These observations provide empirical evidence of a mechanism beyond stochastic events to explain the emergence of recombination reported in acute infection [12,14,15,17]. A striking feature of the results presented here are the five independent recombinations observed in a very short time period and the fact that two separate T cell responses, neither immunodominant, combined to select the recombinations.…”

“…The proportion of multiple T/F viruses initiating infection increases in other groups, such as men who have sex with men and intravenous drug users. 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].…”

“…HIV-1 is highly recombinogenic [26] and HIV-1 recombination has been observed in patients infected with multiple viruses within weeks-months of infection [12,14,15,17]. Although none of these acute-phase studies have experimentally linked the emergence of recombinants to immune responses, several mathematical models have suggested that recombination may impact escape from CD8+ T cell responses [27,28].…”

Resistance to type 1 interferons is a major determinant of HIV-1 transmission fitness

“…However, by sequencing plasma virion RNA (vRNA) in the first few weeks following transmission, it is possible to enumerate and infer the genome(s) of the virus(es) that established the infection (9,(12)(13)(14). In the absence of adaptive immune pressures, HIV-1 diversifies in a random fashion, with viral sequences exhibiting a Poisson distribution of mutations and a star-like phylogeny that coalesces to an inferred consensus sequence.…”

“…This consensus sequence represents the genome of the virus that initiated the infection, termed the transmitted founder (TF) virus (9). Single genome amplification (SGA) of plasma vRNA, which precludes PCR artifacts such as Taq polymerase-mediated recombination (15)(16)(17)(18), revealed that in the great majority (∼80%) of sexual transmission cases, a single TF virus establishes the new infection (9,12,13,(19)(20)(21).…”