Low Frequency of CXCR4-Using Viruses in Patients at the Time of Primary Non-Subtype-B HIV-1 Infection

Abstract

We used genotypic and phenotypic assays to estimate the frequency of X4/DM viruses in 131 patients infected with non-subtype-B viruses at the time of primary HIV-1 infection (PHI). All patients were enrolled in the French PRIMO Cohort from 1996 to 2007. Most strains belonged to CRF02_AG (51.1%) and subtype A (14.5%). Sixteen viruses (12.2%) were classified as CXCR4 tropic ("X4 strains") by the combined criteria of amino acids 11 and 25 of the V3 loop (11/25) and net charge rules and/or the SVMgeno2pheno 10% algorithm: 6 strains by the combined genotypic rule, 7 by the SVMgeno2pheno 10% algorithm, and 3, clustering in subtype D, by both algorithms. However, only one strain (0.8%), belonging to subtype A, was defined as a dual-tropic (DM) virus by the phenotypic assay. The 67 CRF02_AG strains included 2 classified as X4 strains by the combined genotypic rule (3%) and 2 others classified as X4 strains by SVMgeno2pheno 10% (3%), but none of these 4 strains was an X4 or DM strain according to the phenotypic assay. These results suggest that the cellular virus reservoir was established with X4 strains in very few non-subtype-B-infected patients at the time of PHI. Genotypic predictions can overestimate the proportion of non-subtype-B X4 viruses at PHI.

Determination of the High Prevalence of Dual/Mixed- or X4-Tropism Among HIV Type 1 CRF01_AE in Hong Kong by Genotyping and Phenotyping Methods

“…However, the prevalence of X4 or D/M in CRF01_AE is about 39.1% in Hong Kong, which is slightly lower than other studies at around 50%. 21,23,24 Indeed, the prevalence of X4 or D/M in CRF01_AE viruses is nearly 2-fold higher than subtype B. In our study, over 50% of CRF01_AE samples with D/M reported by ESTA had discordant genotypic predictions by G2P and WebPSSM.…”

“…19 Several genotypic studies focused on non-B subtypes suggested that subtype CRF01_AE, the major circulating strains among Southeast Asian countries, 20 had a higher proportion of X4-tropic (X4) or Dual/Mixed-tropic (D/M) than other subtypes. [21][22][23][24] However, the small sample size and unknown treatment background led to many uncertainties in these studies. In addition, no phenotypic data on CRF01_AE tropism were available to validate any of the above-mentioned genotypic algorithms.…”

Sexually-Transmitted/Founder HIV-1 Cannot Be Directly Predicted from Plasma or PBMC-Derived Viral Quasispecies in the Transmitting Partner

“…In cases of misamplification, different primers were used (334-bp fragment): first round: sense primer Env31 (5'-CAGTACAATGTACACATGG-3'), antisense primer Env8 (5'-ATGGGAGGGGCATACATTG-3'); second round: sense primer Env7 (5'-AATGGCAGTCTAGCAGAAG-3'; nucleotide position relative to HXB2 genome start: 7008->7026), antisense primer ED33 (5'-TTACAGTAGAAAAATTCCCCTC-3'; nucleotide position relative to HXB2 genome start: 7381->7360). PCR were performed in a reaction volume of 50 µl with cycling parameters as previously published [22]. The amplified products were purified using a QIAquick PCR Purification Kit® (Qiagen SA, Courtaboeuf, France).…”

Sensitive Cell-Based Assay for Determination of Human Immunodeficiency Virus Type 1 Coreceptor Tropism

“…HIV-1 was then classified, according to its coreceptor usage or tropism, as a CCR5-or CXCR4-tropic virus (R5 or X4, respectively), while HIV-1 strains able to use both coreceptors were termed dual tropic (R5/ X4) (6). Since then, HIV-1 coreceptor tropism has been associated with virus transmission and disease progression, i.e., R5 variants are commonly associated with the establishment of infection (7)(8)(9), while X4 variants seem to emerge in later disease stages and have been linked to a more rapid CD4 ϩ T-cell depletion and progression to AIDS (10)(11)(12).…”