Impact of Mutations Outside the V3 Region on Coreceptor Tropism Phenotypically Assessed in Patients Infected with HIV-1 Subtype B ▿

HIV coreceptor tropism (CTR) testing is a prerequisite for prescribing a coreceptor antagonist. CTR is increasingly deduced by analyzing the V3 loop sequence of gp120. We investigated the impact of mutations outside V3 on CTR as determined by the enhanced-sensitivity Trofile assay (ESTA). Paired ESTA and gp120 sequencing (population sequencing; from codon 32 of the conserved C1 to the variable V5 domains) were obtained from 60 antiretroviral treatment (ART)-naïve patients (15 with AIDS) infected with subtype B HIV-1. For gp120 sequence analysis, nucleotide mixtures were considered when the second highest electropherogram peak was >25%; sequences were translated into all possible permutations and classified as X4, dual/mixed (DM), and R5 based on coincident ESTA results. ESTA identified R5 and DM viruses in 72 and 28% of patients, respectively; no pure X4 was labeled. Forty percent of AIDS patients had R5 strains. Thirty-two positions, mostly outside V3, were significantly (P < 0.05) different between R5 and DM sequences. According to multivariate analysis, amino acid changes at 9 and 7 positions within the C1 to C4 and V1 to V5 regions, respectively, maintained a statistical significance, as did the net charge of V3 and C4. When analyzing only R5 sequences, 6 positions in the variable regions were found which, along with the V4 net charge, were significantly different for sequences from early- and end-stage disease patients. This study identifies specific amino acid changes outside V3 which contribute to CTR. Extending the analysis to include pure X4 and increasing the sample size would be desirable to define gp120 variables/changes which should be included in predictive algorithms

HIV-1 coreceptor tropism: A syllogistic connection with the veterans aging cohort study index and the CD4/CD8 ratio

Background The association between X4 virus and an increased risk of non-AIDS-events has been reported. Morbidity/mortality due to non-AIDS events, which are properly predicted by the CD4/CD8 ratio and VACS index, have become particularly remarkable in HIV-infected patients receiving effective combined antiretroviral therapy (cART). Methods We verified the validity of the syllogism: As HIV-tropism (CRT) contributes to the onset of non-AIDS events which are successfully predicted by the CD4/CD8 ratio and VACS index, then CRT correlates with these two variables. The CD4/CD8 ratio and VACS index at baseline and overtime were analyzed according to CRT tested before the first successful cART regimen in newly-diagnosed patients. Results Patients with R5 variants had a significantly lower baseline VACS percentage risk [mean (95%CI):18.2%(16.1-20.3) vs 24.3%(18.2-22.5), p = 0.002] and higher baseline CD4/CD8 ratio [mean (95%CI):0.43 (0.38-0.47) vs 0.28 (0.19-0.36), p = 0.002] than non-R5 patients. After an initial drop, VACS increased again in R5 and non-R5 patients and the two trend curves almost overlapped. The CD4/CD8 ratio had an increasing trend in both R5 and non- R5 patients; however, even though non-R5 patients had a greater gain of CD4+, they maintained a lower CD4/CD8 ratio at any time point. Conclusion Our study confirms an association between pre-therapy CRT, CD4/CD8 ratio and VACS. A successful cART regimen positively affects the CD4/CD8 ratio; however, the disadvantage conferred by a non-R5 CRT is maintained overtime. The restoration of VACS in all patients could be directly due to variables included in the VACS calculation and to factors that adversely influence these variables

Identification of a new HIV-1 BC circulating recombinant form (CRF60_BC) in Italian young men having sex with men

HIV-1 recombination, reverse transcriptase (RT) low fidelity and high replication rate are the drivers of variability and evolution on the global scale. Only few of these HIV-1 chimeric forms have been characterized in Europe, despite 20% of infections are due to unique or circulating recombinant forms worldwide. An outbreak of BC recombinants has been recently described in a southern region of Italy, Apulia, in men having sex with men (MSM) seeking sexual partners on-line. We analyzed the full length genome of HIV-1 BC recombinants harbored by three recently infected subjects, two MSM and a heterosexual woman, with no evidence of epidemiological link. The recombination analysis showed a unique recombination pattern of a subtype C genome with 3 subtype B fragments corresponding to HXB2 positions: [1-463] in the 5'LTR , [2804-3037] in RT and [8662-9548] corresponding to the C-terminal segment of gp41, nef and most of 3'LTR. Phylogenetic analysis revealed the South American origin of the C subtype parental strain. A research conducted in an Italian nationwide database provided six additional similar sequences from other Italian regions with identical recombination pattern in pol gene; a further BLAST search retrieved one full length genome isolated in France with the same mosaic pattern, except an additional B subtype short fragment in the integrase region. These recombinant isolates, designated CRF60_BC, led to the identification of the first Italian circulating recombinant form, which gave rise to an epidemic burst mainly involving MSM

HIV tropism and its relationship with transmitted resistance in naive patients

Aim: The objective of the present study was to investigate whether patients with transmitted resistance more frequently harbor X4/DM tropic viral strains. Patients & methods: Patients were included from an Italian nationwide database if they were tested for tropism and resistance at the same time. HIV tropism was assessed by the Geno2pheno coreceptor system (false-positive rate: ≤10%) and enhanced-sensitivity Trofile assay. Overall, 299 naive patients, tested between 2009 and 2011, were included: 252 patients tested by Geno2pheno, 116 by enhanced-sensitivity Trofile assay and 80 by both methods. Results & conclusion: Using Geno2pheno, X4/DM tropic virus was detected in 55 patients (21.8%), with an overall mean false-positive rate of 42.3% (standard deviation: ±33.3). Using the enhanced-sensitivity Trofile assay, 29 patients (25.0%) carried X4/DM tropic virus. Resistance mutations were more frequently detected in patients harboring X4/DM tropic virus (mean: 1.18 ± 3.0 vs 0.41 ± 1.2 per patient; p = 0.001) and with both Geno2pheno (0.82 ± 2.6 vs 0.35 ± 0.9; p = 0.034) and enhanced-sensitivity Trofile assay (1.11 ± 1.9 vs 0.46 ± 1.1; p = 0.039). However, significant differences were found for reverse transcriptase-related mutations, but not for transmitted protease resistance, and this might be explained by the low frequency of transmitted protease resistance. Among single mutations, L33F and L90M with regards to protease and K65R, K70E, K219E and V106A/M with regards to reverse transcriptase were found to be significantly associated with X4/DM tropic virus. X4/DM tropism was also associated with lower CD4+cell count, but not with higher HIV RNA levels. X4/DM tropic HIV strains were related to a higher frequency of transmitted reverse transcriptase resistance mutations in this unselected set of naive patients. As a consequence, if a patient harbors a non-CCR5 tropic virus and bears more reverse transcriptase resistance and less protease resistance, a boosted protease inhibitor-based first-line regimen should be preferred. © 2013 Future Medicine Ltd

Virological and immunological response to antiretroviral regimens containing maraviroc in HIV type 1-infected patients in clinical practice: role of different tropism testing results and of concomitant treatments

We assessed the immunovirological response to antiretroviral regimens containing maraviroc in HIV-infected viremic patients with viral tropism predicted by different assays. We selected antiretroviral treatment-experienced HIV-1-infected patients initiating regimens containing maraviroc after different phenotypic or genotypic viral tropism assays, with at least one HIV-1 RNA determination during follow-up. Survival analysis was employed to assess the virological response as time to HIV-1 RNA <50 copies/ml and immunological response as time to a CD4 cell count increase of 65 100/\u3bcl from baseline. Predictors of these outcomes were analyzed by multivariate Cox regression models. In 191 treatments with maraviroc, virological response was achieved in 65.4% and the response was modestly influenced by the baseline viral load and concomitant drug activity but not influenced by the type of tropism assay employed. Immunological response was achieved in 58.1%; independent predictors were baseline HIV-1 RNA (per log10 higher: HR 1.29, 95% CI 1.05-1.60) and concomitant therapy with enfuvirtide (HR 2.05, 0.96-4.39) but not tropism assay results. Of 17 patients with baseline R5-tropic virus and available tropism results while viremic during follow-up on maraviroc, seven (41%) showed a tropism switch to non-R5 virus. A significant proportion of experienced patients treated with regimens containing maraviroc achieved virological response. The tropism test type used was not associated with immunovirological response and concomitant treatment with enfuvirtide increased the chance of immunological response. More than half of virological failures with maraviroc were not accompanied by tropism switch

Antiretroviral genotypic resistance in plasma RNA and whole blood DNA in HIV-1 infected patients failing HAART

The extent to which HIV-1 proviral DNA mutations cause clinically relevant antiretroviral resistance is still controversial. Paired plasma HIV-1 RNA and whole blood DNA were compared in patients failing HAART to investigate if the additional knowledge of archived mutations could improve the selection of potentially active drugs. Seventy-three HIV-1-infected patients with first/second HAART failure were studied before starting a new regimen based on RNA genotyping. Follow-up data after a 12-week therapy were available. DNA genotyping was retrospectively performed on stored whole blood samples and mutational profiles were compared to those from RNA. The mean number of IAS pol mutations was significantly higher in RNA (4.45 ± 2.76) than in DNA (2.88 ± 2.47) (P < 0.001). DNA genotyping provided a 6% increase in detection of resistance-associated mutations. Among 64/73 patients showing discordant DNA/RNA profiles, 54 (84%) also differed for predicted active drugs. 16/73 (22%) patients had ≥1 mutation revealed by DNA genotyping alone, probably affecting therapy success in 2/16. However, neither RNA/DNA discordance nor detection of isolated DNA mutations were statistically associated with outcome. In conclusion, plasma RNA remains the elective choice for HIV genotyping in patients with therapy failure, even if the detection of proviral resistance-associated mutations, not simultaneously found in RNA, is a frequent event. Therefore, in some cases DNA plus RNA genotyping might assist in choosing more accurately subsequent antiretroviral regimens. © 2008 Wiley-Liss, Inc

Prognostic Value of Transaminases and Bilirubin Levels at Admission to Hospital on Disease Progression and Mortality in Patients with COVID-19&mdash;An Observational Retrospective Study

Introduction: Given the impact of COVID-19 on the world healthcare system, and the efforts of the healthcare community to find prognostic factors for hospitalization, disease progression, and mortality, the aim of the present study was to investigate the prognostic impact of transaminases and bilirubin levels at admission to hospital on disease progression and mortality in COVID-19 patients. Methods: Using the CoviCamp database, we performed a multicenter, observational, retrospective study involving 17 COVID-19 Units in southern Italy. We included all adult patients hospitalized for SARS-CoV-2 infection with at least one determination at hospital admission of aminotransaminases and/or total bilirubin. Results: Of the 2054 patients included in the CoviCamp database, 1641 were included in our study; 789 patients (48%) were considered to have mild COVID-19, 347 (21%) moderate COVID-19, 354 (22%) severe COVID-19, and 151 patients (9%) died during hospitalization. Older age (odds ratio (OR): 1.02; 95% confidence interval (CI) 1.01&ndash;1.03), higher Charlson comorbidity index (CCI) (OR 1.088; 95%CI 1.005&ndash;1.18), presence of dementia (OR: 2.20; 95% CI: 1.30&ndash;3.73), higher serum AST (OR: 1.002; 95% CI: 1.0001&ndash;1.004), and total bilirubin (OR: 1.09; 95% CI: 1.002&ndash;1.19) values were associated with a more severe clinical outcome. Instead, the 151 patients who died during hospitalization showed a higher serum bilirubin value at admission (OR 1.1165; 95% CI: 1.017&ndash;1.335); the same did not apply for AST. Discussion: Patients with COVID-19 with higher levels of AST and bilirubin had an increased risk of disease progression