Plasma human immunodeficiency virus 1 RNA and CD4+ T-Cell counts are determinants of virological nonsuppression outcomes with initial integrase inhibitor-based regimens: a prospective RESPOND cohort study

Background: There are conflicting data regarding baseline determinants of virological nonsuppression outcomes in persons with human immunodeficiency virus (HIV) starting antiretroviral treatment (ART). We evaluated the impact of different baseline variables in the RESPOND cohort. Methods:We included treatment-naive participants aged ≥18 who initiated 3-drug ART, in 2014-2020. We assessed the odds of virological suppression (VS) at weeks 48 and 96 using logistic regression. Viral blips, low-level viremia (LLV), residual viremia (RV), and virological failure (VF) rates were assessed using Cox regression. Results: Of 4310 eligible participants, 72% started integrase strand transfer inhibitor (INSTI)-based regimens. At 48 and 96 weeks, 91.0% and 93.3% achieved VS, respectively. At 48 weeks, Kaplan-Meier estimates of rates were 9.6% for viral blips, 2.1% for LLV, 22.2% for RV, and 2.1% for VF. Baseline HIV-1 RNA levels >100 000 copies/mL and CD4+ T-cell counts ≤200/µL were negatively associated with VS at weeks 48 (adjusted odds ratio, 0.51 [95% confidence interval, .39-.68] and .40 [.27-.58], respectively) and 96 and with significantly higher rates of blips, LLV, and RV. CD4+ T-cell counts ≤200/µL were associated with higher risk of VF (adjusted hazard ratio, 3.12 [95% confidence interval, 2.02-4.83]). Results were consistent in those starting INSTIs versus other regimens and those starting dolutegravir versus other INSTIs. Conclusions:Initial high HIV-1 RNA and low CD4+ T-cell counts are associated with lower rates of VS at 48 and 96 weeks and higher rates of viral blips, LLV, and RV. Low baseline CD4+ T-cell counts are associated with higher VF rates. These associations remain with INSTI-based and specifically with dolutegravir-based regimens. These findings suggest that the impact of these baseline determinants is independent of the ART regimen initiated.</p

Novel splice junctions identified in this study.

<p>Consensus sequences at both sides of splice junctions are shown. Splice sites involved in splice junctions are indicated, with HXB2 positions in parentheses. Nearby splice sites used in the corresponding samples are also indicated.</p

Schematic depiction of HIV-1 splicing and locations of PCR primers.

<p>Open reading frames are shown as open boxes and exons as black bars. Exons are named as previously [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158525#pone.0158525.ref001" target="_blank">1</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158525#pone.0158525.ref006" target="_blank">6</a>]. All spliced transcripts incorporate exon 1 and all DS transcripts incorporate exon 7. Optionally, noncoding exons 2 or 3 or both can be incorporated into <i>nef</i>, <i>rev</i>, <i>tat</i>, or <i>env-vpu</i> transcripts, and exon 2 into <i>vpr</i> transcripts. A minority of <i>nef</i> RNAs are generated by splicing from exon 1 to exon 7. Proteins encoded in spliced RNAs are indicated on the right of the middle exon in DS RNAs and of the 3’-terminal exon in SS RNAs. Locations of sequences recognized by primers used for RT-PCR and nested PCR for DS and SS RNA amplification are indicated with arrows, with HXB2 positions of the primers’ 3’ ends in parentheses. 5’RU5-S and 3’nef3 were used for RT-PCR and US22 and TRN-AS for nested PCR for DS RNA amplification; 5’RU5-S and SSD2c were used for RT-PCR, and US22 and SSD1 for nested PCR amplification of SS RNAs.</p

Clinical data and subtypes of samples used in this study.

<p>Clinical data and subtypes of samples used in this study.</p

Phylogenetic tree of DS HIV-1 RNA sequences.

<p>The analysis was done with the fragment comprising exons 5 and 7 (HXB2 positions 5977–6045; 8379–8533), common to all DS transcripts, using 20 randomly chosen sequences per sample. Clades comprising sequences from each sample are compressed in triangles. SH-like node support values for sample clades and for subtype clades are shown.</p

Sequences surrounding newly identified 3’ss used for splicing at the 3’-terminal exon of DS RNAs.

<p>Sequences correspond to consensuses of exon 7 of DS RNAs of the corresponding samples. The HXB2 reference sequence is shown on top and names and positions in the HXB2 proviral genome of 3’ss are indicated above the alignment. AG dinucleotides immediately upstream of these sites are in red and pyrimidine-rich tracts upstream of these AGs are underlined. Nucleotides corresponding to the new 3’ss are boxed. The yUnAy human consensus branch point sequence present upstream of the newly identified sites is shown in blue. AG, pyrimidine-rich tract, and yUnAy motif are also signaled in SPX21, although no usage of new 3’ss was detected in this sample.</p

Distribution of viruses of the subtype F cluster sequenced by us according to city of sample collection.

<p>Distribution of viruses of the subtype F cluster sequenced by us according to city of sample collection.</p

Maximum likelihood tree of near full-length genome sequences of viruses of the subtype F cluster.

<p>F1 subsubtype references are included in the analysis, with country of sample collection indicated with the ISO two-letter country code. The tree is rooted with an F2 subsubtype sequence. Only bootstrap values ≥80% are shown.</p

Maximum clade credibility tree of PR-RT sequences of the subtype F Western European cluster and Galician subcluster.

<p>Nodes supported by PP = 1 and PP = 0.95–0.99 are marked with filled and unfilled circles, respectively. Colors of terminal and internal branches represent sampling locations and most probable locations of the corresponding nodes, respectively, according to the legend on the right. For the nodes corresponding to the Galician subcluster and the Western European cluster, the posterior probabilities for the most probable locations and the tMRCAs are indicated above the subtending branches (95% HPD intervals are in parentheses).</p

Bayesian skyline plot of the population growth of the subtype F cluster.

<p>The black line represents the median estimate of the effective number of infections through time (logarithmic scale) and the shaded area represents the 95% HPD credibility interval. The horizontal axis represents calendar years.</p