Viral suppression and HIV-1 drug resistance 1 year after pragmatic transitioning to dolutegravir first-line therapy in Malawi: a prospective cohort study.

BACKGROUND Many countries are now replacing non-nucleoside reverse transcriptase inhibitor (NNRTI)-based first-line antiretroviral therapy (ART) with a regimen containing tenofovir disoproxil fumarate, lamivudine, and dolutegravir (TLD). Recognising laboratory limitations, Malawi opted to transition those on NNRTI-based first-line ART to TLD without viral load testing. We aimed to assess viral load and HIV drug resistance during 1 year following transition to TLD without previous viral load testing. METHODS In this prospective cohort study, we monitored 1892 adults transitioning from NNRTI-based first-line ART to the TLD regimen in the Médecins Sans Frontières-supported decentralised HIV programme in Chiradzulu District, Malawi. Eligible adults were enrolled between Jan 17 and May 11, 2019, at Ndunde and Milepa health centres, and between March 8 and May 11, 2019, at the Boma clinic. Viral load at the start of the TLD regimen was assessed retrospectively and measured at month 3, 6, and 12, and additionally at month 18 for those ever viraemic (viral load ≥50 copies per mL). Dolutegravir minimal plasma concentrations (Cmin) were determined for individuals with viraemia. Drug-resistance testing was done at the start of TLD regimen and at viral failure (viral load ≥50 copies per mL, followed by viral load ≥500 copies per mL; resistance defined as Stanford score ≥15). FINDINGS Of 1892 participants who transitioned to the TLD regimen, 101 (5·3%) were viraemic at TLD start. 89 of 101 had drug-resistance testing with 31 participants (34·8%) with Lys65Arg mutation, 48 (53·9%) with Met184Val/Ile, and 42 (40·4%) with lamivudine and tenofovir disoproxil fumerate dual resistance. At month 12 (in the per-protocol population), 1725 (97·9% [95% CI 97·1-98·5]) of 1762 had viral loads of less than 50 copies per mL, including 83 (88·3% [80·0-94·0]) of 94 of those who were viraemic at baseline. At month 18, 35 (97·2% [85·5-99·9]) of 36 who were viraemic at TLD start with lamivudine and tenofovir disoproxil fumarate resistance and 27 (81·8% [64·5-93·0]) of 33 of those viraemic at baseline without resistance had viral load suppression. 14 of 1838 with at least two viral load tests upon transitioning had viral failure (all with at least one dolutegravir Cmin value <640 ng/mL; active threshold), suggesting suboptimal adherence. High baseline viral load was associated with viral failure (adjusted odds ratio [aOR] 14·1 [2·3-87·4] for 1000 to <10 000 copies per mL; aOR 64·4 [19·3-215·4] for ≥10 000 copies per mL). Two people with viral failure had dolutegravir resistance at 6 months (Arg263Lys or Gly118Arg mutation), both were viraemic with lamivudine and tenofovir disoproxil fumarate resistance at baseline. INTERPRETATION High viral load suppression 1 year after introduction of the TLD regimen supports the unconditional transition strategy in Malawi. However, high pre-transition viral load, ongoing adherence challenges, and possibly existing nucleoside reverse transcriptase inhibitor resistance can lead to rapid development of dolutegravir resistance in a few individuals. This finding highlights the importance of viral load monitoring and dolutegravir-resistance surveillance after mass transitioning to the TLD regimen. FUNDING Médecins Sans Frontières. TRANSLATIONS For the French and Portuguese translations of the abstract see Supplementary Materials section

Etude de la diversité génétique du réservoir au cours de l’infection par le VIH-1

The hallmark of HIV-1 infection is the vast genetic diversity and rapid progression, which influence its pathogenesis and its clinical management. The genetic diversity of HIV-1 is due to the lack of a proofreading mechanism in the reverse transcriptase, the viral recombination, the genetic evolution of viral populations over time, viral compartmentalization and host APOBEC-mediated hypermutation. Considering all of these factors is essential in order to better characterize viral reservoirs, to design and optimize new eradication strategies. We have analyzed longitudinal blood samples from patients diagnosed and treated quickly during PHI and with strict effective long-term antiretroviral therapy. We have shown significant decay of HIV DNA over time and the absence of genetic divergence and diversity during the follow up period. Our results reinforce the importance of the rapid initiation of antiretroviral therapy in order to limit the size of the reservoir and to block its evolution over time. To study compartmentalization in viraemic patients, we compared drug resistance mutations to integrase strand transfer inhibitors between the blood and the central nervous system. We have shown for the first time the absence of a significant difference in drug resistance mutations between these two compartments. Finally, in order to better understand factors linked to APOBEC3 activities, we analyzed the clinical and immuno-virological parameters that may be associated with drug resistance mutations resulting from (G) to (A) transitions in a large number of well-controlled HIV-1 patients. We have shown for the first time an independent association between the presence of G-to-A mutations and stop codons with HIV-1 subtype non-B and low proviral DNA.L’infection par le VIH-1 est caractérisée par sa vaste diversité génétique et son évolution rapide qui influencent sa pathogenèse et sa gestion clinique. La diversité génétique du VIH-1 est due en grande partie aux erreurs de la transcriptase inverse, au phénomène de recombinaison, à l’évolution génétique des populations virales au cours du temps, à la compartimentation virale et aux hypermutations médiées par les enzymes cellulaires APOBEC3. La compréhension de tous ces facteurs dont l’interaction définit l’étendu de la diversité génétique, est primordiale afin de mieux caractériser les réservoirs viraux aidant à développer et à optimiser des nouvelles stratégies thérapeutiques d’éradication du virus ou de rémission fonctionnelle. Nous avons étudié de façon qualitative et quantitative l’évolution longitudinale du réservoir au niveau périphérique chez des patients diagnostiqués et traités rapidement durant la PHI pendant au moins cinq ans sans aucun rebond virologique. Nous avons mis en évidence une diminution rapide et continue des niveaux d’ADN VIH chez ces patients jusqu’à l’atteinte des niveaux très bas. Nous avons démontré l’absence d’arguments en faveur de l’évolution et de la diversité virale chez ces patients. Nos résultats renforcent l’importance de l’initiation rapide de la thérapie antirétrovirale afin de limiter la taille du réservoir et bloquer son évolution au cours du temps. Afin d’étudier la compartimentation chez des patients virémiques, nous avons comparé les mutations de résistance aux inhibiteurs de l’intégrase entre le sang et le système nerveux central. Nous avons montré pour la première fois, l’absence de différence significative des mutations de résistance entre ces deux compartiments, confirmant l’absence de compartimentation chez certains patients virémiques. Finalement, afin de mieux comprendre les facteurs liés à l’activité des apolipoprotéines APOBEC3, nous avons analysé les paramètres cliniques et immuno-virologiques pouvant être associés à des mutations de résistances résultant des transitions (G) vers (A) chez un grand nombre de patients VIH-1 bien contrôlés virologiquement. Nous avons montré pour la première fois la corrélation indépendante entre l’activité des protéines APOBEC3 avec une petite taille du réservoir viral et avec le sous-type non B

Study of the genetic diversity of the reservoir during HIV-1 infection

L’infection par le VIH-1 est caractérisée par sa vaste diversité génétique et son évolution rapide qui influencent sa pathogenèse et sa gestion clinique. La diversité génétique du VIH-1 est due en grande partie aux erreurs de la transcriptase inverse, au phénomène de recombinaison, à l’évolution génétique des populations virales au cours du temps, à la compartimentation virale et aux hypermutations médiées par les enzymes cellulaires APOBEC3. La compréhension de tous ces facteurs dont l’interaction définit l’étendu de la diversité génétique, est primordiale afin de mieux caractériser les réservoirs viraux aidant à développer et à optimiser des nouvelles stratégies thérapeutiques d’éradication du virus ou de rémission fonctionnelle. Nous avons étudié de façon qualitative et quantitative l’évolution longitudinale du réservoir au niveau périphérique chez des patients diagnostiqués et traités rapidement durant la PHI pendant au moins cinq ans sans aucun rebond virologique. Nous avons mis en évidence une diminution rapide et continue des niveaux d’ADN VIH chez ces patients jusqu’à l’atteinte des niveaux très bas. Nous avons démontré l’absence d’arguments en faveur de l’évolution et de la diversité virale chez ces patients. Nos résultats renforcent l’importance de l’initiation rapide de la thérapie antirétrovirale afin de limiter la taille du réservoir et bloquer son évolution au cours du temps. Afin d’étudier la compartimentation chez des patients virémiques, nous avons comparé les mutations de résistance aux inhibiteurs de l’intégrase entre le sang et le système nerveux central. Nous avons montré pour la première fois, l’absence de différence significative des mutations de résistance entre ces deux compartiments, confirmant l’absence de compartimentation chez certains patients virémiques. Finalement, afin de mieux comprendre les facteurs liés à l’activité des apolipoprotéines APOBEC3, nous avons analysé les paramètres cliniques et immuno-virologiques pouvant être associés à des mutations de résistances résultant des transitions (G) vers (A) chez un grand nombre de patients VIH-1 bien contrôlés virologiquement. Nous avons montré pour la première fois la corrélation indépendante entre l’activité des protéines APOBEC3 avec une petite taille du réservoir viral et avec le sous-type non B.The hallmark of HIV-1 infection is the vast genetic diversity and rapid progression, which influence its pathogenesis and its clinical management. The genetic diversity of HIV-1 is due to the lack of a proofreading mechanism in the reverse transcriptase, the viral recombination, the genetic evolution of viral populations over time, viral compartmentalization and host APOBEC-mediated hypermutation. Considering all of these factors is essential in order to better characterize viral reservoirs, to design and optimize new eradication strategies. We have analyzed longitudinal blood samples from patients diagnosed and treated quickly during PHI and with strict effective long-term antiretroviral therapy. We have shown significant decay of HIV DNA over time and the absence of genetic divergence and diversity during the follow up period. Our results reinforce the importance of the rapid initiation of antiretroviral therapy in order to limit the size of the reservoir and to block its evolution over time. To study compartmentalization in viraemic patients, we compared drug resistance mutations to integrase strand transfer inhibitors between the blood and the central nervous system. We have shown for the first time the absence of a significant difference in drug resistance mutations between these two compartments. Finally, in order to better understand factors linked to APOBEC3 activities, we analyzed the clinical and immuno-virological parameters that may be associated with drug resistance mutations resulting from (G) to (A) transitions in a large number of well-controlled HIV-1 patients. We have shown for the first time an independent association between the presence of G-to-A mutations and stop codons with HIV-1 subtype non-B and low proviral DNA

Role of super-spreader phenomenon in a Covid-19 cluster among healthcare workers in a Primary Care Hospital

International audienceRole of super-spreader phenomenon in a Covid-19 cluster among healthcare workers in a Primary Care Hospital We read with great interest the recent publication of Majra et al. 1 focusing on "societal" superspreading events (SSE) as a major risk factor for epidemic spread. We report another situation of SSE with a nosocomial cluster amongst healthcare workers (HCW) in Tenon Hospital, Paris, France, a middle-sized hospital of 525 beds, between February 21 and March 6, following the admission of our first confirmed COVID-19 case. A suspected COVID-19 case was someone exhibiting compatible symptoms who had been in direct or indirect contact with the index case. A confirmed case was a suspected case with laboratory confirmation through real time reverse transcriptase polymerase chain reaction (RT-PCR) performed on a nasopharyngeal swab

Prolonged replication of BA.1 and BA.2 Omicron lineages compared to Delta variant in nasopharyngeal samples from COVID-19 patients

International audienceObjectives: We aimed to characterize and compare the viral loads (VL) of the Omicron BA.1 and BA.2 lineages and the Delta variant in nasopharyngeal samples from newly diagnosed COVID-19 patients and their kinetics over time.Patients and methods: The kinetics of the VL were measured on the CT data from 215 SARS-CoV-2 positive patients who presented at least two positive PCRs a day apart and were screened for SARS-CoV-2 viral lineages.Results: We observed no significant difference in median CT value during the first diagnostic test between the Delta variant and the two Omicron lineages. However, the kinetics of CT decreases for the BA.1 and BA.2 lineage were significantly lengthier in time than the kinetics for the Delta variant. The BA.2 lineage presented lower median CT value (-2 CT) (inversely proportional to the VL) than the BA.1 lineage.Conclusions: BA.2 Omicron lineage presented higher VL than BA.1 Omicron lineage at diagnostic. Omicron BA.1 and BA.2 lineages have more prolonged replication than the Delta variant

More HIV-1 RNA detected and quantified with the Cobas 6800 system in patients on antiretroviral therapy

International audienceAbstract Background Target-detected (TD) results or low-level viraemia (LLV) can be observed in HIV-1 patients on ART, which regularly raises questions. Objectives We describe here the impact on HIV-1 RNA quantification of switching from the COBAS AmpliPrep/COBAS TaqMan (CAP/CTM) to the Cobas 6800 system (C6800), based on analyses of viraemia close to the lower limit of quantification (LLoQ). Patients and methods We retrospectively selected two groups of patients: 200 individuals whose viral loads (VLs) were consistently &lt;50 copies/mL with CAP/CTM for at least 3 years before switching to C6800 (group 1), and 35 other patients with confirmed LLV when C6800 was in use (group 2). In both groups, we compared several consecutive VL results performed before and after the change of quantification assay. Analyses were performed with McNemar’s paired tests or Fisher’s exact tests. Results In group 1, the frequency of TD results (below or above the LLoQ) increased significantly after the switch to C6800 for patients with &lt;25% of results being TD for VLs performed with CAP/CTM (P &lt; 0.0001). Significantly more patients had at least one VL ≥20 or ≥50 copies/mL with C6800, in both group 1 (37.0% versus 18.5%; P &lt; 0.0001 and 6.5% versus 0%; P = 0.0009, respectively) and group 2 (100% versus 66%; P = 0.0015 and 97% versus 40%; P &lt; 0.0001, respectively). Conclusions C6800 revealed residual or low-level HIV-1 RNA that was not detected with CAP/CTM, resulting in twice as many patients being found to have a VL ≥20 copies/mL. Physicians and patients should be aware of possible differences in results between assays, and it is crucial to specify the quantitative assay used in studies

Medical features of COVID-19 and influenza infection: A comparative study in Paris, France

International audienc

Medical features of COVID-19 and influenza infection: A comparative study in Paris, France

International audienceNo abstract availabl

No difference in HIV-1 integrase resistance between CSF and blood compartments Short title: HIV-1 integrase resistance in compartments

International audienceBackground: Little is known about the HIV-1 integrase resistance in CNS. This study aimed to evaluate integrase resistance in CSF, as a marker of CNS, and compare it to the HIV resistance in plasma. Methods: The HIV integrase was sequenced both in plasma and CSF for 59 HIV-1 patients. The clinical and biological data were collected from clinical routine care. Results: Among the 59 HIV-1 patients, 32 (54.2%) were under antiretroviral (ARV) treatment. The median (IQR) HIV-1 RNA in viremic patients was 5.32 (3.85-5.80) and 3.59 (2.16-4.50) versus 4.79 (3.56-5.25) and 3.80 (2.68-4.33) in CSF log10 copies/mL for ARV naïve and treated patients, respectively. The patients were mainly infected with non-B subtypes (72.2%) with the most prevalent recombinant form CRF02_AG (42.4%). The HIV-1 integrase sequences presented resistance mutations for 9/27 (33.3%) and 8/32 (25.0%) in CSF for ARV naïve (L74I n=3, L74I/M n=1, T97A n=1, E157Q n=4) and treated (L74I n=6, L74M n=1, 1 T97A n=1, 1 N155H n=1) patients, respectively. Integrase resistance mutations in CSF were similar to that in plasma, except for 1/59 patients. Conclusions: This work shows similar integrase resistance profiles in CNS and plasma in a population of HIV-1 viremic patients

Evolution of viral quasispecies during SARS-CoV-2 infection

International audienceObjectives: Studies are needed to better understand the genomic evolution of the recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study aimed to describe genomic diversity of SARS-CoV-2 by next-generation sequencing (NGS) in a patient with longitudinal follow-up for SARS-CoV-2 infection.Methods: Sequential samples collected between January 29th and February 4th, 2020, from a patient infected by SARS-CoV-2 were used to perform amplification of two genome fragments-including genes encoding spike, envelope, membrane and nucleocapsid proteins-and NGS was carried out with Illumina® technology. Phylogenetic analysis was performed with PhyML and viral variant identification with VarScan.Results: Majority consensus sequences were identical in most of the samples (5/7) and differed in one synonymous mutation from the Wuhan reference sequence. We identified 233 variants; each sample harboured in median 38 different minority variants, and only four were shared by different samples. The frequency of mutation was similar between genes and correlated with the length of the gene (r = 0.93, p = 0.0002). Most of mutations were substitution variations (n = 217, 93.1%) and about 50% had moderate or high impact on gene expression. Viral variants also differed between lower and upper respiratory tract samples collected on the same day, suggesting independent sites of replication of SARS-CoV-2.Conclusions: We report for the first time minority viral populations representing up to 1% during the course of SARS-CoV-2 infection. Quasispecies were different from one day to the next, as well as between anatomical sites, suggesting that in vivo this new coronavirus appears as a complex and dynamic distributions of variants