Frequency of coreceptor tropism in PBMC samples from HIV-1 recently infected blood donors by massively parallel sequencing: the REDS II study

Abstract

BackgroundThe interaction of HIV-1 and target cells involves sequential binding of the viral gp120 Env protein to the CD4 receptor and a chemokine co-receptor (either CCR5 or CXCR4). CCR5 antagonists have proved to be an effective salvage therapy in patients with CCR5 using variants (R5) but not with variants capable of using CXCR4 (×4) phenotype. Thus, it is critically important to determine cellular tropism of a country’s circulating HIV strains to guide a management decision to improve treatment outcome. In this study, we report the prevalence of R5 and ×4 HIV strains in 45 proviral DNA massively parallel sequencing “MPS” data from recently infected Brazilian blood donors.MethodsThe MPS data encompassing the tropism-related V3 loop region of the HIV‐1 env gene was extracted from our recently published HIV-1 genomes sequenced by a paired-end protocol (Illumina). HIV‐1 tropism was inferred using Geno2pheno[coreceptor] algorithm (3.5 % false-positive rate). V3 net charge and 11/25 rules were also used for coreceptor prediction.ResultsAmong the 45 samples for which tropism were determined, 39 were exclusively R5 variants, 5 ×4 variants, and one dual-tropic or mixed (D/M) populations of R5 and ×4 viruses, corresponding to 86.7, 11.1 and 2.2 %, respectively. Thus, the proportion of all blood donors that harbor CXCR4-using virus was 13.3 % including individuals with D/M-tropic viruses.ConclusionsThe presence of CCR5-tropic variants in more than 85 % of our cohort of antiretroviral-naïve blood donors with recent HIV-1 infection indicates a potential benefit of CCR5 antagonists as a therapeutic option in Brazil. Therefore, determination of viral co-receptor tropism is an important diagnostic prerequisite.

Frequent detection of CXCR4-using viruses among Brazilian blood donors with HIV-1 long-standing infection and unknown clinical stage: Analysis of massive parallel sequencing data

“…Also, a higher rate (14.3%) of CXCR4-using viruses was observed among the LS group in this study. These results were comparable to our previous study [9] , which reported a relatively high frequency (13.3%) of CXCR4-using viruses in 45 HIV-1 recently infected donors, despite the fact that they were based on different FPR algorithms (>3.5% and >2.5%). Our results can also be compared with those reported in drug-naive chronically HIV-infected individuals [27] and in suppressed patients with a shorter history of viremia suppression [24] .…”

“…Recently we reported our initial findings of the prevalence of coreceptor tropism of the archived strains at the time of primary infection using a total of 45 MPS data from HIV-1 recently infected Brazilian first-time blood donors [9] . In the present study, we expanded our previous work by determining the prevalence of CXCR4-using viruses in MPS data from a total of 84 Brazilian first-time blood donors consisting of 63 subjects with LS infection and 21 with unknown stage information.…”

“…Some studies have reported the presence of X4 strains in recent HIV-1 seroconverter Spanish, Brazilian and French subjects [16] , [22] and in drug-naive chronically HIV-infected individuals [23] , in immunosuppressed patients with a shorter history of viremia suppression [24] , in patients failing antiretroviral therapy [25] , and in patients with detectable HIV-1 subtype B RNA receiving highly active antiretroviral therapy [26] . However, to our knowledge, only one relevant study to date has explored the coreceptor use in MPS data but from recently infected and therapy naive first-time Brazilian blood donors [9] .…”

“…Our group has recently reported the prevalence of co-receptor tropism of the archived viral strains at the time of primary infection using MPS data from 45 recently infected Brazilian first-time blood donors [9] . In continuation with our previous study, here, we assessed the prevalence of virus co-receptor use in MPS data from 84 Brazilian first-time blood donors with long-standing infection (LS, n =63) and others lacking the stage information ( n =21).…”

“…Although plasma HIV-1 RNA has been widely used to determine the viral tropism the proviral PBMC DNA sequence can contain a variety of multiple archived genomes that are not present in plasma. This, combined with the stability of DNA compared with RNA, and the fact that HIV DNA recovered from the proviral compartment can reliably be used as an alternative to RNA tropism testing [9] , [10] , [11] , [12] , [13] influenced our decision to use proviral DNA in this study. No data, to the best of our knowledge, have been published so far for genotypic tropism analysis in such a specific patient group.…”