Abstract
HIV-1 coreceptor tropism assays are required to rule out the presence of CXCR4-tropic (non-R5) viruses prior treatment with CCR5 antagonists. Phenotypic (e.g., Trofile™, Monogram Biosciences) and genotypic (e.g., population sequencing linked to bioinformatic algorithms) assays are the most widely used. Although several next-generation sequencing (NGS) platforms are available, to date all published deep sequencing HIV-1 tropism studies have used the 454™ Life Sciences/Roche platform. In this study, HIV-1 co-receptor usage was predicted for twelve patients scheduled to start a maraviroc-based antiretroviral regimen. The V3 region of the HIV-1 env gene was sequenced using four NGS platforms: 454™, PacBio® RS (Pacific Biosciences), Illumina®, and Ion Torrent™ (Life Technologies). Cross-platform variation was evaluated, including number of reads, read length and error rates. HIV-1 tropism was inferred using Geno2Pheno, Web PSSM, and the 11/24/25 rule and compared with Trofile™ and virologic response to antiretroviral therapy. Error rates related to insertions/deletions (indels) and nucleotide substitutions introduced by the four NGS platforms were low compared to the actual HIV-1 sequence variation. Each platform detected all major virus variants within the HIV-1 population with similar frequencies. Identification of non-R5 viruses was comparable among the four platforms, with minor differences attributable to the algorithms used to infer HIV-1 tropism. All NGS platforms showed similar concordance with virologic response to the maraviroc-based regimen (75% to 80% range depending on the algorithm used), compared to Trofile (80%) and population sequencing (70%). In conclusion, all four NGS platforms were able to detect minority non-R5 variants at comparable levels suggesting that any NGS-based method can be used to predict HIV-1 coreceptor usage.
Highlights
The discovery that human immunodeficiency virus type 1 (HIV-1) requires a co-receptor to enter target cells, mainly the chemokine receptors CCR5 or CXCR4 [1,2], was crucial to better understand HIV-1 transmission and pathogenesis but opened the door for the designing of novel antiretroviral drugs targeting host cell entry
The overall low rates of indels and substitutions resulted in a high number of successfully translated V3 sequences from the original V3 spanning reads, suggesting that each one of the next-generation sequencing (NGS) platforms could be used for genotyping of complex HIV-1 populations
The use of CCR5 antagonists to block HIV-1 replication has accelerated the development of HIV-1 coreceptor tropism assays [7,8,9] and stressed the need for novel, sensitive, and more affordable tests to increase treatment with this drug class
Summary
The discovery that human immunodeficiency virus type 1 (HIV-1) requires a co-receptor to enter target cells, mainly the chemokine receptors CCR5 or CXCR4 [1,2], was crucial to better understand HIV-1 transmission and pathogenesis but opened the door for the designing of novel antiretroviral drugs targeting host cell entry. Multiple strategies to block the replication of CCR5- or CXCR4-tropic (R5 or X4, respectively) viruses have been studied [3], leading to the approval for clinical use of the first CCR5-receptor antagonist (maraviroc, Selzentry/Celsentri, Pfizer, NY) in 2007 [4]. Like other co-receptor antagonists in development, maraviroc’s activity is very specific, showing no direct activity against viruses able to use CXCR4 to enter the target cell [5,6]. Several phenotypic and genotypic assays have been developed to assess HIV-1 co-receptor usage or tropism [7]. Most phenotypic assays involve the generation of patient-derived env-recombinant viruses to determine their ability to infect reporter cell lines expressing HIV-1 receptors and co-receptors [10,11,12,13]. Phenotypic assays share a few practical limitations such as high cost and long turnaround time, which restrict their use and consequentially hinder access to future CCR5 antagonists/agonists
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