Switch to Rilpivirine/Emtricitabine/Tenofovir Single-Tablet Regimen of Human Immunodeficiency Virus-1 RNA-Suppressed Patients, Agence Nationale de Recherches sur le SIDA et les Hépatites Virales CO3 Aquitaine Cohort, 2012-2014

We evaluated the efficacy and tolerability of a single-tablet regimen strategy in 304 HIV-1 virologically suppressed patients switching to RPV/FTC/TDF for adverse events or treatment simplification. This strategy maintained virologic suppression and was associated with improved tolerability after 12 months follow-up.

Background. The purpose of this study was to assess the efficacy and tolerability of combined antiretroviral therapy (cART) in human immunodeficiency virus (HIV)-1 virologically suppressed patients who switched to rilpivirine (RPV)/tenofovir disoproxil fumarate (TDF)/emtricitabine (FTC) as a single-tablet regimen (STR).

Methods. A retrospective multicenter cohort study was performed between September 2012 and February 2014 in Bordeaux University Hospital-affiliated clinics. Patients with a plasma HIV viral load (VL) lower than 50 copies/mL and switching to STR were evaluated at baseline, 3, 6, 9, and 12 months from switch time (M3, M6, M9, M12) for VL and other biological parameters. Change from baseline in CD4 cell counts was evaluated at M6 and M12. Virological failure (VF) was defined as 2 consecutive VL >50 copies/mL.

Results. Three hundred four patients were included in the analysis. Single-tablet regimen switch was proposed to 116 patients with adverse events, mostly efavirenz (EFV)-based (n = 59), and to 224 patients for cART simplification. Thirty of 196 patients with available genotype resistance test results displayed virus with ≥1 drug resistance mutation on reverse-transcriptase gene. After 12 months of follow-up, 93.4% (95.5% confidence interval, 89.9–96.2) of patients remained virologically suppressed. There was no significant change in CD4 cell count. During the study period, 5 patients experienced VF, one of them harboring RPV resistance mutation. Clinical cART tolerability improved in 79 patients overall (29.9%) at M6, especially neurological symptoms related to EFV. Fasting serum lipid profiles improved, but a significant estimated glomerular function rate decrease (−11 mL/min/1.73 m²; P < 10⁻⁴) was observed.

Conclusions. Overall, virologic suppression was maintained in patients after switching to RPV/TDF/ FTC. This STR strategy was associated with improved tolerability.

Kinetics of HIV-1 CTL epitopes recognized by HLA I alleles in HIV-infected individuals at times near primary infection: the Provir/Latitude45 study

In patients responding successfully to ART, the next therapeutic step is viral cure. An interesting strategy is antiviral vaccination, particularly involving CD8 T cell epitopes. However, attempts at vaccination are dependent on the immunogenetic background of individuals. The Provir/Latitude 45 project aims to investigate which CTL epitopes in proviral HIV-1 will be recognized by the immune system when HLA alleles are taken into consideration. A prior study (Papuchon et al, PLoS ONE 2013) showed that chronically-infected patients under successful ART exhibited variations of proviral CTL epitopes compared to a reference viral strain (HXB2) and that a generic vaccine may not be efficient. Here, we investigated viral and/or proviral CTL epitopes at different time points in recently infected individuals of the Canadian primary HIV infection cohort and assessed the affinity of these epitopes for HLA alleles during the study period. An analysis of the results confirms that it is not possible to fully predict which epitopes will be recognized by the HLA alleles of the patients if the reference sequences and epitopes are taken as the basis of simulation. Epitopes may be seen to vary in circulating RNA and proviral DNA. Despite this confirmation, the overall variability of the epitopes was low in these patients who are temporally close to primary infection.

[Viral epidemiology and clinical severity during the peak of the influenza A(H1N1) variant epidemic in febrile respiratory diseases of children]

En mars 2009, un nouveau virus a fait émergence, le virus Influenzae A(H1N1) variant. Nous avons voulu en étudier la répercussion médicale.

Objectifs

Définir la prévalence virale dans les atteintes respiratoires fébriles hospitalisées de l’enfant en période d’épidémie grippale A(H1N1) variant et déterminer les caractéristiques cliniques, paracliniques et évolutives liées aux virus identifiés.

Méthodes

Il s’est agi d’une étude épidémiologique, prospective, monocentrique menée à l’hôpital des Enfants du centre hospitalier universitaire de Bordeaux (Aquitaine, France) pendant l’épidémie grippale du 23 novembre au 20 décembre 2009 inclus. Tous les enfants hospitalisés pour atteinte respiratoire fébrile ont été inclus.

Résultats

Soixante-treize enfants ont été inclus. Une identification virale a été possible dans 52 % des cas, incluant 23 % de A(H1N1) variant [A(H1N1)v] et 29 % d’autres identifications dont 22 % de virus respiratoires syncitiaux. Une seule co-infection a été observée entre le virus [A(H1N1)v] et un pool viral (adénovirus ou virus para-influenzae ou bocavirus). Il n’existait pas de différence significative concernant l’âge, le sexe ou les facteurs de risque de gravité en fonction des virus identifiés. Concernant le virus [A(H1N1)v], les symptômes les plus fréquents étaient l’altération de l’état général, la toux, les atteintes oto-rhino-laryngologiques et les anomalies de la fréquence respiratoire, avec significativement moins de signes de lutte et d’anomalie auscultatoire mais plus de convulsions. Sur le plan paraclinique, il n’y avait pas de différence significative entre les groupes. Évolution et prise en charge ont été comparables.

Conclusion

Une faible prédominance du virus [A(H1N1)v] a été notée pendant l’épidémie grippale en Aquitaine dans les atteintes respiratoires fébriles justifiant une hospitalisation. Les caractéristiques cliniques, paracliniques et évolutives étaient peu spécifiques. L’ensemble de ces éléments n’a pas révélé de gravité particulière liée au virus [A(H1N1)v].

Detection of low-frequency HIV type 1 reverse transcriptase drug resistance mutations by ultradeep sequencing in naive HIV type 1-infected individuals

Genotypic resistance testing is recommended to evaluate the susceptibility of HIV to antiretroviral drugs. These tests are based on bulk population sequencing and thus consider only variants representing more than 20% of the viral population, whereas next generation sequencing methods allow detection below this threshold. We aimed to evaluate the potential use of ultradeep pyrosequencing (UDPS) for genotypic resistance testing in clinical routine at the University Hospital of Bordeaux, France. We performed UDPS on reverse transcriptase (RT) from 47 HIV-1 individuals, naive of antiretroviral treatment and for whom genotypic resistance testing was requested for clinical management in 2011-2012. In 8.5% of the patients, only low-frequency variants harboring RT drug resistance mutations were detected raising the question of their clinical significance. Rilpivirine-associated resistance mutations were detected in 19.1% of our population study. To conclude, UDPS could become a routine tool for the evaluation of HIV-infected patients in hospital laboratories.

Resistance mutations and CTL epitopes in archived HIV-1 DNA of patients on antiviral treatment: toward a new concept of vaccine

Eleven patients responding successfully to first-line antiretroviral therapy (ART) were investigated for proviral drug resistance mutations (DRMs) in RT by ultra-deep pyrosequencing (UDPS). After molecular typing of the class I alleles A and B, the CTL epitopes in the Gag, Nef and Pol regions of the provirus were sequenced and compared to the reference HXB2 HIV-1 epitopes. They were then matched with the HLA alleles with determination of theoretical affinity (TA). For 3 patients, the results could be compared with an RNA sample of the circulating virus at initiation of therapy. Five out of 11 patients exhibited DRMs by UDPS. The issue is whether a therapeutic switch is relevant in these patients by taking into account the identity of the archived resistance mutations. When the archived CTL epitopes were determined on the basis of the HLA alleles, different patterns were observed. Some epitopes were identical to those reported for the reference with the same TA, while others were mutated with a decrease in TA. In 2 cases, an epitope was observed as a combination of subpopulations at entry and was retrieved as a single population with lower TA at success. With regard to immunological stimulation and given the variability of the archived CTL epitopes, we propose a new concept of curative vaccine based on identification of HIV-1 CTL epitopes after prior sequencing of proviral DNA and matching with HLA class I alleles.

Activation of GCN2 upon HIV-1 infection and inhibition of translation

Higher eukaryotic organisms have a variety of specific and nonspecific defense mechanisms against viral invaders. In animal cells, viral replication may be limited through the decrease in translation. Some viruses, however, have evolved mechanisms that counteract the response of the host. We report that infection by HIV-1 triggers acute decrease in translation. The human protein kinase GCN2 (eIF2AK4) is activated by phosphorylation upon HIV-1 infection in the hours following infection. Thus, infection by HIV-1 constitutes a stress that leads to the activation of GCN2 with a resulting decrease in protein synthesis. We have shown that GCN2 interacts with HIV-1 integrase (IN). Transfection of IN in amino acid-starved cells, where GCN2 is activated, increases the protein synthesis level. These results point to an as yet unknown role of GCN2 as an early mediator in the cellular response to HIV-1 infection, and suggest that the virus is able to overcome the involvement of GCN2 in the cellular response by eliciting methods to maintain protein synthesis.

Dried cervical spots for human papillomaviruses identification

Financial and operational constraints limit low-resource countries in the screening of high-risk genital human papillomaviruses (HR-HPV), the etiological agents of cervical cancer. With its simple storage, conservation and shipping, dried cervical sample (DCS) could represent an efficient tool. The aim of the study was to evaluate the reliability of HPV genotyping from DCS. Cervical samples were obtained from 50 women infected with HIV-1 in Côte d'Ivoire. After DNA extraction from both DCS and matched liquid cervical samples (LCS), HPV genotyping was performed and the concordance of genotyping results was evaluated. HPV prevalence was 88% in LCS and 78% in DCS. Kappa statistic was 0.51 for the presence of any genotype (95% confidence interval, 0.25-0.77) and 0.73 for HR-HPV (0.45-0.99). Out of 50 samples, 45 were HPV-positive for DCS and/or LCS, and HR-HPV were detected in 37 samples (74%) with 36 HR-HPV multiple infections. Any genotype and HR genotype identification was concordant/compatible in 86% (43/50) and 88% (44/50) of samples, respectively. In most instances, kappa statistics for detection of type-specific HPV was over 0.6 (including HPV-16, -18, -31, -33). An excellent agreement (kappa statistic ≥ 0.81) was found for eight genotypes (HPV-6, -31, -35, -40, -56, -58, -66, and -82). In spite of interfering factors (multiple infections, different HPV loads, amplification competition, different inputs), DCS and LCS led to concordant/compatible results in most cases. DCS could represent an efficient tool for epidemiological field studies in resource-limited settings, and more importantly for improving the screening coverage and care management in women infected with HPV.

Molecular characterization of HIV type 1 in Brazzaville, Republic of Congo, and first data on resistance to antiretroviral drugs

One hundred patients have been enrolled in the CTA (ambulatory treatment center) of Brazzaville, Republic of Congo, from February to April 2011: 41 naive individuals and 59 patients at failure of first line regimen [two nucleoside reverse transcriptase inhibitors (NRTIs) plus one nonnucleoside reverse transcriptase inhibitor (NNRTI)]. Phylogenetic analysis of HIV-1 isolates allowed identification of subtypes and circulating recombinant forms (CRFs). The drug resistance mutations (DRMs) in reverse transcriptase and protease were analyzed in both subpopulations. Globally, 92 viruses were characterized, exhibiting a high diversity of HIV-1 with a majority of undetermined recombinant forms (URF) followed by CRF02_AG, CRF37_cpx, G, A1, B, D, H, and several other subtypes and CRF: F1, A2, C, CRF13_cpx, CRF11_cpx, CRF20_BG, CRF21_A2D, CRF33_01B G, CRF02_AG, CRF37_cpx, and A1. In naive patients, DRMs were observed with percentages ranging from 4% to 9% depending on drug classes. In treated patients at failure, numerous DRMs could be noted that induce actual or potential resistance to major NRTIs and NNRTIs.

Drug resistance mutations in HIV type 1 isolates from patients failing antiretroviral therapy in Morocco

The emergence of viral-resistant strains is a major problem for the medical management of HIV-infected individuals. The aim of this study was to characterize viral subtypes and drug-resistance mutations (DRMs) in HIV-1 isolates from patients failing antiretroviral therapy (ART). A total of 45 HIV-1-infected patients failing ART were enrolled. The viral RT and Prot genes were amplified and sequenced to determine subtypes and potential DRMs. The subtype distribution was 74% subtype B, 11% subtype A, 9% CRF02-AG, 4% subtype G, and 2% subtype C. Virus samples from 34% of the patients had no DRM while 53%, 27%, and 2% of samples carried at least one DRM conferring resistance to drugs of one, two, or three classes, respectively. DRMs were observed in 50% of the patients infected with non-B strains. The prevalence of nucleoside transcriptase inhibitor (NRTI) mutations was 48%, M184V being largely predominant. The prevalence of nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations was 13%, with K103N present in 57% of samples from NNRTIs-exposed patients. The prevalence of protease inhibitor (PI) mutations was 22%, with major mutations V82A and M46I seen in 16% and 11% of viruses from PI-exposed individuals, respectively. Our study shows the emergence of DRMs in HIV-1 isolates from Moroccan patients failing ART. Although not surprising, the data plead for longitudinal surveys of the dynamics of emergence of DRMs (with a focus on multidrug resistance) in treated patients and circulation of resistant HIV-1 strains in this country.

Cervical human papillomavirus and HIV infection in women of child-bearing age in Abidjan, Côte d'Ivoire, 2010

Background:

We sought to document the association of Human immunodeficiency Virus (HIV) infection and immunodeficiency with oncogenic Human Papillomavirus (HPV) infection in women with no cervical neoplastic lesions identified through a cervical cancer screening programme in Côte d’Ivoire.

Methods:

A consecutive sample of women stratified on their HIV status and attending the national blood donor clinic or the closest HIV clinic was recruited during a cervical cancer screening programme based on the visual inspection. Diagnosis of HPV infection and genotype identification were based on the Linear Array; HPV test.

Results:

A total of 445 (254 HIV-positive and 191 HIV-negative) women were included. The prevalence of oncogenic HPV infection was 53.9% (95% confidence interval (CI) 47.9–59.9) in HIV-positive women and 33.7% (95% CI 27.1–40.3) in HIV-negative women (odds ratio (OR)=2.3 (95% CI 1.5–3.3)). In multivariate analysis, HIV-positive women with a CD4 count <200 cells mm³ or between 200 and 499 cells mm³ were more likely to harbour an oncogenic HPV compared with women with a CD4 count ⩾500 cells mm³ with OR of 2.8 (95% CI 1.1–8.1) and 1.7 (95% CI 1.0–2.9), respectively.

Conclusion:

A high prevalence of oncogenic HPV was found in women with no cervical neoplastic lesions, especially in HIV-positive women. Despite antiretroviral use, immunodeficiency was a main determinant of the presence of oncogenic HPV.

K65R in subtype C HIV-1 isolates from patients failing on a first-line regimen including d4T or AZT: comparison of Sanger and UDP sequencing data

Background

We and others have shown that subtype C HIV-1 isolates from patients failing on a regimen containing stavudine (d4T) or zidovudine (AZT) exhibit thymidine-associated mutations (TAMs) and K65R which can impair the efficacy of Tenofovir (TDF) at second line. Depending on the various studies, the prevalence of K65R substitution as determined by the Sanger method ranges from 4 to 30%. Our aim was to determine whether ultra-deep pyrosequencing (UDPS) could provide more information than the Sanger method about selection of K65R in this population of patients.

Methods

27 subtype C HIV-1 isolates from treated patients failing on a regimen with d4T or AZT plus lamivudine (3TC) plus nevirapine (NVP) or efavirenz (EFV) and who had been sequenced by Sanger were investigated by UDPS at codon 65 of the reverse transcriptase (RT). 18 isolates from naïve patients and dilutions of a control K65R plasmid were analysed by Sanger plus UDPS.

Results

Analysis of Sanger sequences of subtype C HIV-1 isolates from naïve patients exhibited expected polymorphic substitutions compared to subtype B but no drug resistance mutations (DRMs). Quantitation of K65R variants by UDPS ranged from <0.4% to 3.08%. Sanger sequences of viral isolates from patients at failure of d4T or AZT plus 3TC plus NVP or EFV showed numerous DRMs to nucleoside reverse transcriptase inhibitors (NRTIs) including M184V, thymidine-associated mutations (TAMs) plus DRMs to non- nucleoside reverse transcriptase inhibitors (NNRTIs). Two K65R were observed by Sanger in this series of 27 samples with UDPS percentages of 27 and 87%. Other samples without K65R by Sanger exhibited quantities of K65R variants ranging from <0.4% to 0.80%, which were below the values observed in isolates from naïve patients.

Conclusions

While Sanger sequencing of subtype C isolates from treated patients at failure of d4T or AZT plus 3TC plus NVP or EFV exhibited numerous mutations including TAMs and 8% K65R, UDPS quantitation of K65R variants in the same series did not provide any more information than Sanger.

Necrotic ulcerated lesion in a young boy caused by cowpox virus infection

The case presented here points towards the fact that skin lesion observed with a cowpox virus is a rare event but should be considered more as the number of cases has increased in the last years. Cowpox virus (CPXV) belongs to the Poxviridae family. The transmission of CPXV to humans is caused by wild rodents or mostly by domestic animals and pet rats. In humans, CPXV is responsible for localized skin lesions regularly accompanied by lymphadenopathy. The lesions remain localized but self-inoculation from the primary lesions could occur. Then physicians have to be vigilant concerning bandages. In this case report, a necrotic and ulcerated lesion of a CPXV infection in a young boy is reported. The CPXV was possibly transmitted by wild rodents. The importance of performing the diagnosis is also pointed out. Virus information was obtained from phylogenetic analyses showing that the CPXV isolate was distinct from outbreaks of human cowpox which occurred in 2009 in France and Germany but was close to the CPXV Brighton Red strain. For several years, cases of viral zoonosis caused by CPXV have increased and physicians should be made aware that people could be infected without history of direct contact with animals.

Presence of drug resistance mutations among drug-naive patients in Morocco

The aim of the present study was to determine viral subtypes and resistance mutations to antiretroviral treatment (ART) in HIV-1-infected treatment-naive patients from Rabat, Morocco during the period 2005-2009. The protease and reverse transcriptase (RT) genes were sequenced, the phylogenetic trees were inferred, and the resistance-associated mutations to NRTIs, NNRTIs, and PIs were recorded according to the international list of surveillance drug resistance mutations (SDRMs). The viral subtypes were subtype B (74%), CRF02_AG (15%), A1 (6%), C (2%), F1 (1%), CRF09 (1%), and CRF25_cpx (1%). The presence of DRMs was found in four (5.06%) of 91 patients; resistance mutations to NRTIs were M184V and T215I/S revertant mutations; resistance to NNRTIs was associated with K103N and resistance to PIs with V82A. These findings have relevant implications for the local molecular mapping of HIV-1 and future ART surveillance studies in the region.