In vitro replicative potential of an HIV-1/MO intergroup recombinant virus compared to HIV-1/M and HIV-1/O parental viruses.

Genetic recombination is one of the major evolution processes of HIV-1. Despite their great genetic divergence, HIV-1 groups M and O can generate HIV-1/MO intergroup recombinants. The current description of 20 HIV-1/MO unique recombinant forms suggests a possible benefit of the recombination. The aim of this work was to study in vitro the replicative potential of HIV-1/MO recombinant forms. This analysis was based on a simple recombination pattern, [Ogag/pol-Menv], harboring a breakpoint in Vpr. A chimeric infectious molecular clone, pOM-TB-2016 was synthesized from HIV-1/M subtype B and HIV-1/O subgroup T and recombinant viruses were obtained by transfection/co-culture. To compare the replicative potential of these viruses, two markers were monitored in culture supernatants: Reverse Transcriptase (RT) activity and P24 antigen concentration. The results showed a superiority of the group M parental virus compared to group O for both markers. In contrast, for the recombinant virus, RT activity data did not overlap with the concentration of P24 antigen, suggesting a hybrid behavior of the recombinant, in terms of enzyme activity and P24 production. These results highlighted many hypotheses about the impact of recombination on replicative potential and demonstrated again the significant plasticity of HIV genomes and their infinite possibility of evolution.

Invasive meningoencephalitis as the first manifestation of hepatitis A.

Since mid-2016, Europe has been facing a major hepatitis A epidemic, with more than 25 000 cases reported to the European CDC, in 2018. We describe herein a rare case of invasive HAV meningoencephalitis as a prodrome of the classic hepatitis, which largely explains a delay in diagnosis.

Resistance to integrase inhibitors: a national study in HIV-1-infected treatment-naive and -experienced patients.

OBJECTIVES: To describe integrase strand transfer inhibitor (INSTI) resistance profiles and factors associated with resistance in antiretroviral-naive and -experienced patients failing an INSTI-based regimen in clinical practice. METHODS: Data were collected from patients failing an INSTI-containing regimen in a multicentre French study between 2014 and 2017. Failure was defined as two consecutive plasma viral loads (VL) >50 copies/mL. Reverse transcriptase, protease and integrase coding regions were sequenced at baseline and failure. INSTI resistance-associated mutations (RAMs) included in the Agence Nationale de Recherches sur le SIDA genotypic algorithm were investigated. RESULTS: Among the 674 patients, 359 were failing on raltegravir, 154 on elvitegravir and 161 on dolutegravir therapy. Overall, 90% were experienced patients and 389 (58%) patients showed no INSTI RAMs at failure. The strongest factors associated with emergence of at least one INSTI mutation were high VL at failure (OR = 1.2 per 1 log10 copies/mL increase) and low genotypic sensitivity score (GSS) (OR = 0.08 for GSS ≥3 versus GSS = 0-0.5). Patients failing dolutegravir also had significantly fewer INSTI RAMs at failure than patients failing raltegravir (OR = 0.57, P = 0.02) or elvitegravir (OR = 0.45, P = 0.005). Among the 68 patients failing a first-line regimen, 11/41 (27%) patients on raltegravir, 7/18 (39%) on elvitegravir and 0/9 on dolutegravir had viruses with emergent INSTI RAMs at failure. CONCLUSIONS: These results confirmed the robustness of dolutegravir regarding resistance selection in integrase in the case of virological failure in routine clinical care.

HIV rapid screening tests and self-tests: Be aware of differences in performance and cautious of vendors.

BACKGROUND: Rapid tests for HIV testing are essential tools to achieve the 90-90-90 target of the World Health Organization. Many tests are available, some directly from websites. Evaluation of the performance of rapid tests, under close to real-life usage, is therefore needed to ensure accurate diagnosis in the context of the recommendation for their more widespread use. METHOD: Nine third- (3G) or fourth-generation (4G) rapid screening tests or self-tests (two bought on websites), were evaluated on an extensive panel of 200 HIV-negative and 312 HIV-positive samples, representative of a wide variety of clinical situations and HIV genetic diversity. A whole blood reconstitution protocol was designed to simulate real-life usage of these tests in community-based and private settings. FINDINGS: The specificity was high (98.5-100%) and sensitivity excellent (100%) for samples from patients chronically infected with the pandemic strains. The performance for infrequent situations with a major epidemiological and clinical impact, such as infection with divergent viruses or primary infection, was highly variable, depending on the test. One of the two 4G tests allowed detection of additional positive samples from early stages of infection, whereas the second (sold as a 4G test on a website) corresponded in reality to a 3G test. INTERPRETATION: Our study showed that not all tests are equal for the detection of major HIV variants or early stages of HIV infection; adding the detection of specific p24Ag improved the latter point. This study also showed, for the first time, that buying through web-based vendors can be risky, due to the varying performance of the tests and questionable sales practices. Our results are of particular importance in the context of the increasing use of rapid tests in an "outside laboratory" settings. FUND: Santé Publique France, COREVIH - Normandie, and Rouen University Hospital.

Impact of natural polymorphisms of HIV-1 non-group M on genotypic susceptibility to the attachment inhibitor fostemsavir.

Background: Fostemsavir belongs to the new class of attachment inhibitors (AIs); it inhibits the entry of HIV into CD4+ T-lymphocytes by blocking conformational changes in gp120. This is a promising AI, but previous phenotypic data showed that genetically divergent HIV-1 group O could present natural resistance to this drug. These data were obtained from only two strains, which are not representative of the high intra-group genetic diversity. Moreover, no data are available concerning the other divergent HIV-1 groups (N and P). Objectives: To further investigate the natural genotypic susceptibility of HIV-1 groups O, N and P (HIV-1 non-M) to fostemsavir, using a large set of sequences. Methods: The frequency of eight substitutions associated with decreased susceptibility to fostemsavir (L116P, A204D, S375M/H, M426L, M434I, M475I and V506M), was investigated in 111 gp120 sequences from groups O (n = 100), N (n = 9) and P (n = 2). Results: All HIV-1 group N sequences harboured the three substitutions S375M, M426L and M434I, whereas only 1% and 10% of HIV-1 group O sequences harboured the S375H + M426L and S375H + M434I patterns, respectively. The main genetic profile of HIV-1 groups P and O combined S375H with two atypical substitutions (M426S and M434L). Five group O sequences did not display any of the eight substitutions, but had atypical residues with unknown impact. Conclusions: The genetic polymorphisms in the gp120 of HIV-1 non-M viruses support the hypothesis that these viruses could largely be resistant to inhibition by fostemsavir. Only 5% of group O strains could display full genetic susceptibility. Extensive phenotypic studies are now required.

Detection of numerous HIV-1/MO recombinants in France.

BACKGROUND: The broad genetic divergence of HIV-1/O relative to HIV-1/M has important implications for diagnosis, monitoring and treatment. Despite this divergence, some HIV-1/M+O dual infections and HIV-1/MO recombinant forms have been reported, mostly in Cameroon, where both groups are prevalent. Here, we describe the characteristics of such infections detected in France in 10 new patients, and discuss their implications for biological and clinical practice, owing to the presence of group O species. METHODS: The French National Reference Centre for HIV received samples within the framework of mandatory notification of HIV infections, and for expert analysis. A strategy combining serotyping, viral quantification, group-specific molecular amplification and whole-genome sequencing was used for strain characterization and complementary investigations. RESULTS: We identified one patient with M+O infection, three patients with M+O infection associated with an MO recombinant, and six patients with only an MO recombinant. These atypical infections were detected upon strain characterization (n = 4) or because of anomalies during patient monitoring (n = 6). We identified eight new URF_MO, all but one originating from Cameroon. Interestingly, two distinct recombinant strains were found in two unrelated patients, representing possible precursors of a CRF_MO. CONCLUSION: Our work highlights the fact that the continuous evolution of HIV can hinder diagnosis and complicate clinical practice. We stress that unexpected results during diagnosis or monitoring necessitate further serological and molecular exploration, these atypical infections influence biological and therapeutic management and necessitate appropriate tools, and specific surveillance is necessary, especially as the frequency of such infections may be underestimated.

Misidentification of recombinant hepatitis C virus leading to treatment failure with direct acting antivirals.

The use of new Direct Acting Antivirals, specific of HCV, has greatly improved the HCV treatment. Most of the DAA are specific of HCV genotypes. Genotyping methods may target different regions of the HCV genome, though only the whole genome sequencing could confirm the correct genotype. The present study describes the virological investigation of a treatment failure due to the false identification of an unusual 2k/1b recombinant HCV form. It describes the sequencing methods, and the similarity analysis of the sequences to different genotype query sequences, to identify the recombination breakpoint.

Mumps virus: a comprehensive review.

Once very common in children, mumps virus infection is now much rarer thanks to vaccination, recommended in the majority of countries in the world. This virus of the family Paramyxoviridae has a marked tropism for glandular tissues which explains the great diversity of pathologies related to this virus, including parotitis, orchitis or meningitis. Due to the lower circulation of the virus, the proportion of infected adults increases. A surveillance system for mumps virus infections at the national and international levels is organized, particularly at the molecular level. In France, it is provided by the national reference center for Measles, Mumps and Rubella. Although it has led to a significant reduction in the number of cases, the long-term effectiveness of mumps vaccination is questionable. The nature of the vaccine strains and the lack of regular stimulation of populations by circulating wild viruses may explain, in part, the decrease in immunity over time. Thus, the vaccination recommandations could evolve in the future to reach eradication in a medium or long term.

[Mumps virus: a comprehensive review]. / Le virus des oreillons.

Once very common in children, mumps virus infection is now much rarer thanks to vaccination, recommended in the majority of countries in the world. This virus of the family Paramyxoviridae has a marked tropism for glandular tissues which explains the great diversity of pathologies related to this virus, including parotitis, orchitis or meningitis. Due to the lower circulation of the virus, the proportion of infected adults increases. A surveillance system for mumps virus infections at the national and international levels is organized, particularly at the molecular level. In France, it is provided by the national reference center for Measles, Mumps and Rubella. Although it has led to a significant reduction in the number of cases, the long-term effectiveness of mumps vaccination is questionable. The nature of the vaccine strains and the lack of regular stimulation of populations by circulating wild viruses may explain, in part, the decrease in immunity over time. Thus, the vaccination recommandations could evolve in the future to reach eradication in a medium or long term.

Impact of Human Immunodeficiency Virus Type 1 Minority Variants on the Virus Response to a Rilpivirine-Based First-line Regimen.

Background: Minority resistant variants of human immunodeficiency virus type 1 (HIV-1) could influence the virological response to treatment based on nonnucleoside reverse transcriptase inhibitors (NNRTIs). Data on minority rilpivirine-resistant variants are scarce. This study used next-generation sequencing (NGS) to identify patients harboring minority resistant variants to nucleos(t)ide reverse transcriptase inhibitors and NNRTIs and to assess their influence on the virological response (VR). Methods: All the subjects, 541 HIV-1-infected patients started a first-line regimen containing rilpivirine. VR was defined as a HIV-1 RNA load <50 copies/mL at month 6 with continued suppression at month 12. NGS was performed at baseline (retrospectively) on the 454 GS-FLX platform (Roche). Results: NGS revealed resistance-associated mutations accounting for 1% to <5% of variants in 17.2% of samples, for 5%-20% in 5.7% of samples, and for >20% in 29% of samples. We identified 43 (8.8%) and 36 (7.4%) patients who harbored rilpivirine-resistant variants with a 1% sensitivity threshold according to the French National Agency for Research on AIDS and Viral Hepatitis and Stanford algorithms, respectively. The VR was 96.9% at month 12. Detection of minority rilpivirine resistant variants was not associated with virological failure (VF). Multivariate analysis indicated that VF at month 12 was associated with a CD4 count <250 cells/µL at baseline, a slower decrease in viral load at month 3, and rilpivirine resistance at baseline using the Stanford algorithm with a 20% threshold. Conclusions: Minority resistant variants had no impact on the VR of treatment-naive patients to a rilpivirine-based regimen.

A Simple and Reliable Strategy for BK Virus Subtyping and Subgrouping.

BK virus (BKV)-associated diseases in transplant recipients are an emerging issue. However, identification of the various BK virus subtypes/subgroups is a long and delicate process on the basis of currently available data. Therefore, we wanted to define a simple and effective one-step strategy for characterizing all BK virus strains from the VP1 gene sequence. Based on the analysis of 199 available complete DNA VP1 sequences, phylogenetic trees, alignments, and isolated polymorphisms were used to define an effective strategy for distinguishing the 12 different BK virus subtypes/subgroups. Based on the 12 subtypes identified from the 199 complete BKV VP1 sequences (1,089 bp), 60 mutations that can be used to differentiate these various subtypes/subgroups were identified. Some genomic areas were more variable and comprised mutational hot spots. From a subregion of only 100 bp in the VP1 region (1977 through 2076), we therefore constructed an algorithm that enabled rapid determination of all BKV subtypes/subgroups with 99% agreement (197/199) relative to the complete VP1 sequence. We called this domain of the BK viral genome the BK typing and grouping region (BKTGR). Finally, we validated our viral subtype identification process in a population of 100 transplant recipients with 100% efficiency. The new simpler method of BKV subtyping/subgrouping reported here constitutes a useful tool for future studies that will help us to more clearly understand the impact of BKV subtypes/subgroups on diagnosis, infection, and BK virus-associated diseases.

Multiple HIV-1/M + HIV-1/O dual infections and new HIV-1/MO inter-group recombinant forms detected in Cameroon.

BACKGROUND: Due to the prevalence of HIV-1 group M and the endemicity of HIV-1 group O infections in Cameroon, patients may be infected with both viruses and/or with HIV-1/MO recombinant forms. Such atypical infections may be deleterious in terms of diagnosis and therapeutic management due to the high divergence of HIV-1/O. The aim of this study was to identify prospectively such atypical infections in Cameroon. RESULTS: Based on serological screening by env-V3 serotyping and a molecular strategy using group-specific (RT)-PCRs, we identified 10 Cameroonian patients harboring three different profiles of infection: (1) 4 HIV-1/M + O dual infections without evidence of recombinant; (2) 5 recombinants associated with one or both parental strains; and (3) 1 new recombinant form without parental strains. CONCLUSIONS: This work highlights the dynamic co-evolution of these two HIV groups in Cameroon that could lead to the emergence of a circulating recombinant form MO, and the need for accurate identification of such atypical infections for precise diagnosis, virological monitoring and therapeutic management with adapted tools.

Performance Evaluation of the New HIV-1 Quantification Assay, Xpert HIV-1 Viral Load, on a Wide Panel of HIV-1 Variants.

OBJECTIVE: To evaluate the quantification performance of the new Cepheid GeneXpert HIV-1 viral load assay, on a wide panel of HIV-1 variants. METHODS: Clinical performance was evaluated relative to the Abbott RealTime HIV-1 assay on 285 HIV-1 seropositive samples selected to cover the assays quantification range (40 copies/mL-10,000,000 copies/mL), and included RNA undetectable or detected seropositive samples. The panel comprised 120 subtype B, 150 non-B, and 15 nontypable clinical samples; serial dilutions of 18 viral supernatants representative of the divergent viruses of HIV-1 groups N, O, and P were also tested. RESULTS: Based on samples selected according to the Abbott assay viral loads (VL), the Cepheid assay detected or quantified 222/285 (78%) samples and the Abbott assay 240/285 (84%). Xpert yielded VLs for 162 (76%) of the 213 quantifiable samples with Abbott. This difference corresponded to 51 samples with VL >40 copies/mL by the Abbott assay (all below 200 copies/mL) but detected (n = 40) or undetectable (n = 11) by the Cepheid assay. VL of samples quantifiable by both assays (n = 162) showed very strong correlation, with a Spearman correlation coefficient of 0.985 and a Bland-Altman's mean of differences of -0.01. Performance for quantification of the non-M samples showed very good correlation, with significantly higher values with Cepheid for the group N and 2 group O samples. CONCLUSIONS: Our study showed that the Xpert HIV-1 VL assay offered very good performance for detection and quantification of the current HIV-1 genetic diversity; differences reported at the threshold could be an issue and requires further evaluations. The practicability of this new assay makes it suitable for low-income countries, where it could facilitate and improve follow-up of patients, as well as for high-income regions.

First evidence of transmission of an HIV-1 M/O intergroup recombinant virus.

OBJECTIVE: Despite the genetic divergence between HIV-1 groups M and O, HIV-1  M/O intergroup recombinants were reported. Actually, there is no data on the transmissibility of such recombinant forms. During a surveillance of HIV genetic diversity in Cameroon, we investigated the possible direct transmission of an HIV-1  M/O recombinant virus in an HIV-infected couple. METHODS: Consecutive samples obtained from the couple were analysed for detection of dual HIV-1 groups M and O infections, and HIV-1  M/O recombinant forms. Analyses were performed using a serological and molecular algorithm based on HIV serotyping and group-specific PCRs targeting the polymerase and envelope genes. Pattern characterization of the strains found in both patients was based on complete genome sequencing. Phylogenetic and similarity profile analyses were performed to investigate the genetic relationship between viruses from both spouses and the previously described recombinant forms. RESULTS: The sero-molecular algorithm data showed a group O serotype confirmed by molecular analysis in the envelope regions, whereas molecular tests identified HIV-1 group M in the polymerase. Phylogenetic analyses and similarity profiles of the full-length genome sequences showed that both spouses were infected with a unique recombinant virus having two recombination breakpoints in the vpr gene and LTR region. No phylogenetic link was found with the previous M/O recombinants. CONCLUSION: We provide, for the first time, molecular evidence of direct transmission of an HIV-1  M/O recombinant, highlighting the potential spread of these divergent viruses. The importance of HIV-1 recombination on genetic evolution and public health when implying divergent strains as group O has to be carefully considered.

Comparison of the bioMérieux NucliSENS EasyQ HIV-1 v2.0-HIV-1 RNA quantification assay versus Abbott RealTime HIV-1 and Roche Cobas TaqMan HIV-1 v2.0 on current epidemic HIV-1 variants.

BACKGROUND: An improved version of the bioMérieux NucliSENS(®) EasyQ(®) HIV-1 v2.0 has been introduced to overcome the underquantification observed with previous versions, especially with non-B HIV-1 subtypes. OBJECTIVES: Comparing bioMérieux NucliSENS(®) EasyQ(®) HIV-1 v2.0 versus Roche Cobas CA/CTM v2.0 and Abbott RealTime HIV-1 assays for HIV-1 group M and non-M (N, O, P) viral load measurement. STUDY DESIGN: The three assays were tested in parallel on 103HIV-1 group M plasma samples, and on non-group M HIV-1 culture supernatants. RESULTS: Values obtained for the 103HIV-1 group M plasma samples tested with bioMérieux assay showed good overall correlation compared to the 2 others. The Roche Cobas assay gave higher values than the bioMérieux assay, while Abbott and bioMérieux both displayed similar results. However, analysis showed a wider dispersion in results when comparing the bioMérieux NucliSENS(®) EasyQ(®) HIV-1 v2.0 and the other 2 techniques. All data taken into account, we observed frequent discrepancies in quantification, of the plasma samples and major differences above 1log in 10/72 (13.8%). The quantification of non-M HIV groups in culture supernatant has shown variable results, with better quantification of HIV-O and of HIV-N respectively with the Abbott assay and the bioMérieux assay. CONCLUSIONS: The bioMérieux NucliSENS(®) EasyQ(®) HIV-1 v2.0 showed improved sensitivity to non-B HIV-M subtypes compared to previous versions. Notwithstanding, we observed frequent discrepancies and a wide dispersion in results when comparing bioMérieux NucliSENS(®) EasyQ(®) HIV-1 v2.0 and the other 2 techniques.

Naturally Occurring Resistance-Associated Variants of Hepatitis C Virus Protease Inhibitors in Poor Responders to Pegylated Interferon-Ribavirin.

The pretherapeutic presence of protease inhibitor (PI) resistance-associated variants (RAVs) has not been shown to be predictive of triple-therapy outcomes in treatment-naive patients. However, they may influence the outcome in patients with less effective pegylated interferon (pegIFN)-ribavirin (RBV) backbones. Using hepatitis C virus (HCV) population sequence analysis, we retrospectively investigated the prevalence of baseline nonstructural 3 (NS3) RAVs in a multicenter cohort of poor IFN-RBV responders (i.e., prior null responders or patients with a viral load decrease of <1 log IU/ml during the pegIFN-RBV lead-in phase). The impact of the presence of these RAVs on the outcome of triple therapy was studied. Among 282 patients, the prevalances (95% confidence intervals) of baseline RAVs ranged from 5.7% (3.3% to 9.0%) to 22.0% (17.3% to 27.3%), depending to the algorithm used. Among mutations conferring a >3-fold shift in 50% inhibitory concentration (IC50) for telaprevir or boceprevir, T54S was the most frequently detected mutation (3.9%), followed by A156T, R155K (0.7%), V36M, and V55A (0.35%). Mutations were more frequently found in patients infected with genotype 1a (7.5 to 23.6%) than 1b (3.3 to 19.8%) (P = 0.03). No other sociodemographic or viroclinical characteristic was significantly associated with a higher prevalence of RAVs. No obvious effect of baseline RAVs on viral load was observed. In this cohort of poor responders to IFN-RBV, no link was found with a sustained virological response to triple therapy, regardless of the algorithm used for the detection of mutations. Based on a cross-study comparison, baseline RAVs are not more frequent in poor IFN-RBV responders than in treatment-naive patients and, even in these difficult-to-treat patients, this study demonstrates no impact on treatment outcome, arguing against resistance analysis prior to treatment.

Association of dolutegravir and rilpivirine, enhanced by foscarnet induction, in effective salvage antiretroviral therapy.

We report the case of a multi-experienced patient, infected with an HIV-1 strain, with selected multiple resistance mutations. We designed a novel well-tolerated and effective rescue treatment including dolutegravir, rilpivirine, and foscarnet, allowing a 60-week sustained virological response for the first time in 23 years of HIV infection.

In-vitro phenotypic susceptibility of HIV-1 'non-B' integrase inhibitors naive clinical isolates to dolutegravir and raltegravir.

In this study, we assessed phenotypic susceptibility to dolutegravir and raltegravir in a large variety of HIV-1 'non-B' subtypes (n = 72) issued from integrase inhibitor-naive clinical isolates. All samples were susceptible to both dolutegravir and raltegravir with median IC50 values of 1.22 nmol/l and 1.53 nmol/l, respectively; similar to that observed for the B subtype. Thus, despite the high prevalence of polymorphic substitutions in integrase in 'non-B' clinical isolates, phenotypic susceptibility to dolutegravir remained unchanged.

Non-M variants of human immunodeficiency virus type 1.

The AIDS pandemic that started in the early 1980s is due to human immunodeficiency virus type 1 (HIV-1) group M (HIV-M), but apart from this major group, many divergent variants have been described (HIV-1 groups N, O, and P and HIV-2). The four HIV-1 groups arose from independent cross-species transmission of the simian immunodeficiency viruses (SIVs) SIVcpz, infecting chimpanzees, and SIVgor, infecting gorillas. This, together with human adaptation, accounts for their genomic, phylogenetic, and virological specificities. Nevertheless, the natural course of non-M HIV infection seems similar to that of HIV-M. The virological monitoring of infected patients is now possible with commercial kits, but their therapeutic management remains complex. All non-M variants were principally described for patients linked to Cameroon, where HIV-O accounts for 1% of all HIV infections; only 15 cases of HIV-N infection and 2 HIV-P infections have been reported. Despite improvements in our knowledge, many fascinating questions remain concerning the origin, genetic evolution, and slow spread of these variants. Other variants may already exist or may arise in the future, calling for close surveillance. This review provides a comprehensive, up-to-date summary of the current knowledge on these pathogens, including the historical background of their discovery; the latest advances in the comprehension of their origin and spread; and clinical, therapeutic, and laboratory aspects that may be useful for the management and the treatment of patients infected with these divergent viruses.