INTRODUCTION:HIV reservoir is the main barrier to HIV cure but its size dynamics on antiretroviral therapy (ART) in various clinical settings is poorly characterized. METHODS:Responders to a dolutegravir-based regimen (DBR) enrolled in the DRONE study were analyzed for longitudinal total HIV DNA and immune activation biomarkers (sCD14, sCD163, IL-6, IP-10). RESULTS:Overall, 169 participants were allocated to various groups: ART-naive acute infections (AI, n = 20) or chronic infections (CI, n = 21), and ART-treated individuals in virological success (VS, n = 116) or failure (VF, n = 12). HIV DNA significantly decreased at W48 of successful DBR in the AI (median: -1.3log10copies/million PBMCs), CI (-0.6), and VF (-0.5) groups, but not in the VS group. Activation biomarkers decreased on DBR only for individuals with ongoing HIV replication at baseline. CONCLUSION:Successful DBR was associated with rapid HIV DNA decline in ART-naive and ART-failing individuals but not in the context of ART switch.

HIV-2 establishes a persistent viral reservoir despite its lower replication capacity and attenuated clinical course compared with HIV-1. Some studies suggest that the HIV-2 cellular reservoir is substantially smaller, with total HIV-2 DNA levels in peripheral blood mononuclear cells typically 1-2log10 lower than those observed in HIV-1, even in individuals on long-term suppressive antiretroviral therapy. Importantly, HIV-2 proviral DNA remains detectable for many years, indicating durable persistence despite low-level replication. Detailed analyses of reservoir composition suggest that HIV-2 proviruses are preferentially localized within transitional memory CD4+ T-cells, whereas central memory T-cells appear relatively spared. This skewed distribution was suggested to be linked with higher expression of restriction factors and differential expression of coreceptors, highlighting the role of host determinants in shaping the reservoir. Genomic analyses reveal that the majority of HIV-1 proviruses are defective and that clonal expansion of infected cells can occur, but whether this is also applicable to HIV-2 remains unknown. Besides, the inducibility and replication competence of these intact HIV-2 proviruses remain largely undefined due to the lack of validated functional assays on HIV-2. Data on tissue reservoirs are limited, but available evidence suggests that lymphoid tissues and mucosal sites may serve as potential HIV-2 reservoirs. The contribution of myeloid cells to HIV-2 persistence remains unclear, despite efficient infection of macrophages ex vivo. Overall, current data support the existence of a smaller, more restricted, and potentially less inducible HIV-2 reservoir, but major knowledge gaps remain in terms of dynamics, tissue distribution, and cure studies.

ABSTRACT There is limited data on lenacapavir (LEN) use, the newest capsid inhibitor, in observational settings. We describe population characteristics and pharmaco-virological outcomes of people with HIV-1 (PWH) who initiated LEN-based treatment. We conducted a national retrospective observational study of PWH initiating LEN-based treatment in France after its approval (December 2022). Virological failure (VF) was defined as two consecutive viral loads (VLs) ≥50 c/mL, and a non-virological response as a VL decrease of <1 log 10 c/mL or still >50 c/mL at W24. Ninety-six PWH were included; 49 were virologically suppressed at initiation. Median follow-up on LEN was 12 months (IQR = 8–17). Genotypic susceptibility score was <1 in 59 cases (61%). Twelve participants (12.5%) discontinued LEN-based treatment. Among the virologically suppressed and viremic PWH at initiation, 94% and 64% had VL <50 c/mL at the last follow-up visit, respectively. VF occurred in 8 PWH (3 in virological success and 5 viremic at baseline), and a non-virological response was observed in 12 PWH. Capsid sequence at VF was available for eight subjects, showing the emergence of N74D mutation in one. LEN plasma concentrations were available for 13 of the 20 PWH presenting with VF or non-response with adequate concentrations in 90% of cases. Twenty-four participants received cabotegravir + LEN, 18 having VL <50 c/mL at the last follow-up visit. Our observational findings confirm that LEN-based regimens are effective among heavily treatment-experienced individuals with advanced resistance. In this population, LEN-based treatments were associated with high rates of sustained virological suppression and a low incidence of capsid emergent resistance.

Developing effective vaccines is necessary in combating new virus pandemics. For human immunodeficiency virus (HIV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the induction of neutralizing antibodies (NAb) is important for vaccine protection; however, the exact mechanisms underlying protection require further study. Recent data emphasize that even Abs that do not exhibit neutralizing activity may contribute to immune defense by Ab Fc-mediated inhibition. Abs exhibiting this function may counter virus mutations, which are acquired to escape from NAbs, and therefore broaden the protective Ab response induced by vaccination. The steps leading to inhibition are complex. How can these functions be measured in vitro? What inhibitory assay is physiologically relevant at mimicking effective in vivo protection? This review provides a comprehensive update on the current knowledge gaps on the Ab Fc-mediated functions involved in HIV and SARS-CoV-2 protection. Understanding the inhibitory effects of these Abs is vital for designing the next generation of protective HIV and SARS-CoV-2 vaccines.

ABSTRACT Lymph node T follicular helper (Tfh) cells and germinal center (GC) B cells are critical to generate potent antibodies but are rarely possible to study in humans. To understand how Tfh/GC B-cell interactions during acute HIV-1 infection (AHI) impact the generation of HIV-specific antibodies, we performed a unique cross-sectional analysis of inguinal lymph node biopsies taken prior to antiretroviral therapy (ART) initiation in AHI. Although total Tfh and GC B cell frequencies did not change during AHI, increased frequencies of proliferating Th1-like CXCR3 + Tfh, CXCR3 + non-GC B cells, and total CXCR3 + GC B cells correlated with gp120-specific IgG antibody levels in AHI. Frequencies of proliferating CXCR3 + Tfh in AHI also correlated with gp120-specific IgG antibody levels after 48 weeks of ART, antibody-dependent cellular cytotoxicity, antibody-dependent cellular phagocytosis, and increased antibody binding to infected cells after ART. Importantly, while beneficial for antibody development, CXCR3 + Tfh cells were also infected by HIV-1 at higher frequencies than their CXCR3 − counterparts and may contribute to the initial dissemination of HIV-1 in follicles. Together, these data suggest that activation of CXCR3 + Tfh cells is associated with induction of the germinal center response and subsequent antibody development, making these cells an important target for future therapeutic interventions. IMPORTANCE Early initiation of antiretroviral therapy (ART) is important to limit the seeding of the long-lasting HIV-1 reservoir; however, it also precludes the development of HIV-specific antibodies that can help control the virus if ART is stopped. Antibody development occurs within germinal centers in the lymph node and requires activation of both antigen-specific B cells and T follicular helper cells (Tfh), a specialized CD4 + cell that provides B cell help. To understand how early ART initiation may prohibit antibody development, we analyzed the frequencies and activation status of Tfh and B cells in lymph node biopsies collected in the different stages of acute HIV-1 infection. Our data suggest that decreased antibody development after early ART initiation may be due to limited germinal center development at the time of treatment and that new interventions that target activation of CXCR3 + Tfh may be beneficial to increase long-term HIV-specific antibody levels.

IntroductionMolecular surveillance is an important tool for detecting chains of transmission and controlling the HIV epidemic. This can also improve our knowledge of molecular and epidemiological factors for the optimization of prevention. Our objective was to illustrate this by studying the molecular and epidemiological evolution of the cluster including the new circulating recombinant form (CRF) 94_cpx of HIV-1, detected in 2017 and targeted by preventive actions in 2018.MethodsIn June 2022, 32 HIV-1 sequence databases from French laboratories were screened to identify all individuals who had acquired CRF94_cpx or a similar strain, whatever the date of diagnosis. Phylogenetic analyses were performed with the sequences identified, and biological parameters were collected at the time of diagnosis and after the start of treatment to analyse the evolution of the cluster. Full genomes were sequenced to characterize the new strains.ResultsWe analysed 98 HIV-1 isolates: 63 were CRF94, three were unclassifiable, and the other 32 formed a new cluster containing a new recombinant, CRF132_94B, derived from CRF94 and a subtype B strain. At least 95% of the individuals in both the CRF94 and CRF132 clusters were men who have sex with men (MSM), most of whom had acquired HIV less than 12 months before diagnosis. The number of CRF94 diagnoses declined drastically after 2018, but CRF132 strains spread widely between 2020 and 2022, into a different area of Ile-de-France region and within a younger population nevertheless aware of pre-exposure prophylaxis. Higher viraemia, lower CD4 cell counts and delayed treatment efficacy suggested that CRF94 was more virulent than CRF132, possibly due to the F subtype fragment of the vif gene.ConclusionsThese findings highlight the role of the MSM transmission cluster in spreading HIV and new variants. They show also the benefits of cluster surveillance for improving the targeting of preventive interventions, detecting the emergence of new strains and enriching our knowledge on virulence mechanisms. However, these investigations require support with sufficient resources dedicated to a regional or national programme to be responsive and effective.

BackgroundHepatitis Delta virus (HDV) infection is a major cause of liver-related morbidity and mortality in patients infected with HBV, with a global HDV prevalence uncertain. In France, 2 to 5 % of HBs antigen (HBsAg) carriers present anti-HDV antibodies (anti-HDV). The EASL recommends testing for anti-HDV in all HBsAg-positive patients. Since January 2022, we have systematically carried out anti-HDV serology when a positive HBsAg is discovered (new HBsAg carriers).ObjectivesWe evaluated the benefit of anti-HDV reflex testing after one year of practice by comparing anti-HDV and HBsAg serology data over the last six years, among the new HBsAg carriers and all the HBsAg carriers.Study designHBsAg and anti-HDV were screened using the Abbott Architect HBsAg quanti kit and the DIA.PRO HDVAb kit. Serological, demographic, virological, and clinical data were analyzed.ResultsImplementing anti-HDV reflex testing leads to more than a 2-fold increase in diagnoses of HDV infection among all HBsAg carriers. If the anti-HDV positive rate remains stable among the new HBsAg carriers, a significant increase in the anti-HDV positive rate from 6.8 % to 10.3 % was observed considering all HBsAg carriers. Interestingly, the discovery of anti-HDV carriage increased from 3.9 % to 6.5 % in 2022, allowing earlier identification of HBV-HDV-infected patients and a fast referral to hepatologists for adequate clinical management and, in some cases, the introduction of bulevirtide-based therapy.ConclusionsOur preliminary results at one year seem promising and evaluating the cost-effectiveness of reflex tests in real life with feedback would be helpful.

Journal Article Corrected proof Insights in Dolutegravir-Resistance Pathways Get access Thibault Mesplede, Thibault Mesplede Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Pierre Gantner Pierre Gantner Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, FranceINSERM UMR_S1109, Strasbourg University, Strasbourg, France Correspondence: P. Gantner, Institut de Virologie, 3 rue Koeberlé, F67000 Strasbourg, France (pierre.gantner@chru-strasbourg.fr). https://orcid.org/0000-0002-3984-883X Search for other works by this author on: Oxford Academic PubMed Google Scholar Clinical Infectious Diseases, ciae127, https://doi.org/10.1093/cid/ciae127 Published: 11 March 2024 Article history Published: 11 March 2024 Corrected and typeset: 30 March 2024

Background: Vector-borne diseases such as malaria and arboviruses are common etiologies of post-travel fever. Methods: After excluding malaria, we retrospectively analyzed the diagnosis of dengue virus (DENV), chikungunya virus (CHIKV), and zika virus (ZIKV) infections following recent travel by patients treated at the Strasbourg University Hospital between 2014 and 2023. Available serums (n = 35) sampled in 2023 were retrospectively tested for DENV, CHIKV, and ZIKV infections. Results: Our results showed that 78% of the 915 malaria-negative patients without changes over the course of ten years had not undergone arbovirus infection testing. Retrospective testing revealed missing arbovirus infections: two DENV infections and one CHIKV infection, representing 8.6% (3/35) of patients for whom no mandatory declaration or vector control could be undertaken. Conclusion: Our results highlight the need for early case detection, particularly in the context of the upcoming 2024 Olympic Games.

Background: Throughout HIV infection, productively infected cells generate billions of viral particles and are thus responsible for body-wide HIV dissemination, but their phenotype during AIDS is unknown. As AIDS is associated with immunological changes, analyzing the phenotype of productively infected cells can help understand HIV production during this terminal stage. Methods: Blood samples from 15 untreated viremic participants (recent infection, n=5; long-term infection, n=5; active opportunistic AIDS-defining disease, n=5) and 5 participants virologically controlled on antiretroviral therapy (ART) enrolled in the Analysis of the Persistence, Reservoir and HIV Latency (APRIL) study (NCT05752318) were analyzed. Cells expressing the capsid protein p24 (p24+ cells) after 18 hours of resting or 24 hours of stimulation (HIV-Flow) revealed productively infected cells from viremic participants or translation-competent reservoir cells from treated participants, respectively. Results: The frequency of productively infected cells tended to be higher during AIDS in comparison with recent and long-term infections (median, 340, 72, and 32/million CD4+ T cells, respectively) and correlated with the plasma viral load at all stages of infection. Altogether, these cells were more frequently CD4low, HLA-ABClow, CD45RA-, Ki67+, PD-1+, with a non-negligible contribution from pTfh (CXCR5+PD-1+) cells, and were not significantly enriched in HIV coreceptors CCR5 nor CXCR4 expression. The comparison markers expression between stages showed that productively infected cells during AIDS were enriched in memory and exhausted cells. In contrast, the frequencies of infected pTfh were lower during AIDS compared to non-AIDS stages. A UMAP analysis revealed that total CD4+ T cells were grouped in 7 clusters and that productive p24+ cells were skewed to given clusters throughout the course of infection. Overall, the preferential targets of HIV during the latest stages seemed to be more frequently highly differentiated (memory, TTD-like) and exhausted cells and less frequently pTfh-like cells. In contrast, translation-competent reservoir cells were less frequent (5/million CD4+ T cells) and expressed more frequently HLA-ABC and less frequently PD-1. Conclusions: In long-term infection and AIDS, productively infected cells were differentiated and exhausted. This could indicate that cells with these given features are responsible for HIV production and dissemination in an immune dysfunction environment occurring during the last stages of infection.

Dolutegravir/lamivudine (DTG/3TC) has a high genetic barrier against the development of human immunodeficiency virus drug resistance. We report 2 cases of R263K + M184V mutations during DTG/3TC failure followed by viral suppression after adherence intervention without treatment change that we attribute to residual drug activity, reduced viral fitness, and robust immune competence.

Tick-borne encephalitis (TBE) is a vector-borne disease caused by the TBE virus (TBEV). Although TBEV infection in children seems to lead to a milder clinical presentation, data in pediatrics are scarce. We aimed to determine the incidence of TBE among pediatric patients presenting with neurological symptoms from January 2020 to December 2022 at the University Hospital of Strasbourg (HUS), France. 462 Patients for whom cerebrospinal fluid (CSF) samples were available were included and categorized by age group: 0–4 years, 5–9 years, and 10–15 years. Serological tests and RT-PCR were carried out on the CSF samples, and the positive results were confirmed by seroneutralization test (SNT). A CSF IL-6 assay was performed for confirmed cases. We retrospectively detected four TBE-confirmed cases. We found an incidence of 1.51 cases per 100,000 inhabitants in the pediatric population over 2020–2022. The four cases were girls, with a median age of 10.4 years. The symptoms appeared in two cases in October 2022, outside the seasonal peak. Signs of encephalitis were present in two patients, and persistent sequelae were reported in three patients and two more than a year after hospitalization. None of the confirmed cases were vaccinated against TBEV despite frequent exposure to ticks. Intrathecal concentrations of IL-6 were increased for two patients; for one patient, the concentration was significantly higher than the values found in control cases. Our data highlight the need for early diagnosis and long-term follow-up of affected children and raise questions about the evolution of vaccination recommendations.

Objectives. Identifying biomarkers causing differential SARS-CoV-2 infection kinetics associated with severe COVID-19 is fundamental for effective diagnostics and therapeutic planning. Methods. In this work, we applied mathematical modelling to investigate the relationships between patient characteristics, plasma SARS-CoV-2 RNA dynamics and COVID-19 severity. Using a straightforward mathematical model of within-host viral kinetics, we estimated key model parameters from serial plasma viral RNA (vRNA) samples from 256 hospitalised COVID-19(+) patients. Results. Our model predicted that clearance rates distinguish key differences in plasma vRNA kinetics and severe COVID-19. Moreover, our analyses revealed a strong correlation between plasma vRNA kinetics and plasma receptor for advanced glycation end products (RAGE) concentrations (a plasma biomarker of lung damage), collected in parallel to plasma vRNA from patients in our cohort, suggesting that RAGE can substitute for viral plasma shedding dynamics to prospectively classify seriously ill patients. Conclusion. Overall, our study identifies factors of COVID-19 severity, supports interventions to accelerate viral clearance and underlines the importance of mathematical modelling to better understand COVID-19.

Antigen-experienced memory CD4+ T cells are the major target of HIV infection and support both productive and latent infections, thus playing a key role in HIV dissemination and persistence, respectively. Here, we reviewed studies that have shown direct association between HIV infection and antigen specificity. During untreated infection, some HIV-specific cells host productive infection, while other pathogen-specific cells such as cytomegalovirus (CMV) and Mycobacterium tuberculosis also contribute to viral persistence on antiretroviral therapy (ART). These patterns could be explained by phenotypic features differing between these pathogen-specific cells. Mechanisms involved in these preferential infection and selection processes include HIV entry and restriction, cell exhaustion, survival, self-renewal and immune escape. For instance, MIP-1β expressing cells such as CMV-specific memory cells were shown to resist infection by HIV CCR5 coreceptor downregulation/inhibition. Conversely, HIV-infected CMV-specific cells undergo clonal expansion during ART. We have identified several research areas that need further focus such as the role of other pathogens, viral genome intactness, inducibility and phenotypic features. However, given the sheer diversity of both the CD4+ T cell repertoire and antigenic history of each individual, studying HIV-infected, antigen-experienced cells still imposes numerous challenges.

Objective: HIV DNA sequencing is now routinely used for HIV-infected individuals on antiretroviral therapy (ART) with or without partial genotypic history. Successful amplification of HIV pol gene has yet to be correlated with HIV DNA levels. Here, we assessed the relationship between HIV DNA load and sequencing results. Methods: We analyzed three different qPCR measurements of total (LTR and LTR-gag) and integrated (Alu-LTR) HIV DNA in blood samples collected from viremic as well as virally suppressed HIV-infected individuals on ART. HIV DNA levels were compared to HIV DNA Sanger sequencing and clinical and therapeutic parameters. Results: Among the 135 individuals analyzed for HIV DNA measurements and sequencing, all three HIV DNA measurements were associated with HIV DNA Sanger sequencing results. A threshold of around 2 and 1.5 log copies/million leukocytes of total HIV DNA was identified for LTR and LTR-gag qPCRs, respectively. Integrated HIV DNA positivity was also associated with successful sequencing. We further compared HIV DNA measurement techniques in an extended cohort of 312 individuals and showed that all measurements correlated between the different techniques, regardless of the HIV-1 subtypes analyzed. However, higher detection rates were observed with LTR (96%) compared to LTR-gag (86%) and Alu-LTR (59%) qPCRs. Duration of virological control on ART and CD4 nadir were the main determinants of HIV reservoir size. Conclusions: HIV DNA measurement is associated with Sanger sequencing success, regardless of the technique used. In a clinical setting, Application of HIV DNA quantification before sequencing should be further evaluated.

Upon infection, HIV disseminates throughout the human body within 1-2 weeks. However, its early cellular targets remain poorly characterized. We analyzed productively and latently infected cells in blood and lymphoid tissue from individuals in acute infection. The phenotype of productively infected cells rapidly evolved with time and differed between blood and lymph nodes. The TCR repertoire of productively infected cells was heavily biased, with preferential infection of previously expanded/disseminated cells, but composed almost exclusively of unique clonotypes, indicating that they were the product of independent infection events. Latent genetically intact proviruses were already archived early in infection. Hence, productive infection is initially established in a pool of phenotypically and clonotypically distinct T cells in blood and lymph nodes and latently infected cells are generated simultaneously. One-Sentence Summary HIV initially infects phenotypically and clonotypically distinct T cells and establishes a latent reservoir concomitantly.

Background:SARS-CoV-2 breakthrough infections after complete vaccination are increasing whereas their determinants remain uncharacterized.Methods:We analyzed two cases of post-vaccination SARS-CoV-2 infections by α and β variants, respectively. For each participant both humoral (binding and neutralizing antibodies) and cellular (activation markers and cytokine expression) immune responses were characterized longitudinally.Results:The first participant (P1) was infected by an α variant and displayed an extended and short period of viral excretion and symptom. Analysis of cellular and humoral response 72 h post-symptom onset revealed that P1 failed at developing neutralizing antibodies and a potent CD4 memory response (lack of SARS-CoV-2 specific CD4+IL-2+ cells) and CD8 effector response (CD8+IFNγ+ cells). The second participant (P2) developed post-vaccination SARS-CoV-2 infection by a β variant, associated with a short period of viral excretion and symptoms. Despite displaying initially high levels and polyfunctional T cell responses, P2 lacked initial β-directed neutralizing antibodies. Both participants developed and/or increased their neutralization activity and cellular responses against all variants, namely, β and δ variants that lasts up to 3 months after breakthrough infection.Conclusions:An analysis of cellular and humoral response suggests two possible mechanisms of breakthrough infection: a poor immune response to vaccine and viral evasion to neutralizing antibodies.

Assessment of the kinetics of SARS-CoV-2 antibodies is essential in predicting protection against reinfection and durability of vaccine protection. Here, we longitudinally measured Spike (S) and Nucleocapsid (N)-specific antibodies in 1,309 healthcare workers (HCWs), including 916 COVID-19 negative HCWs and 393 convalescent COVID-19 for up to 422 days post-symptom. From month (M)1 to M7-9 post-infection, SARS-CoV-2 antibodies decreased moderately in convalescent HCWs in a biphasic model, with men showing a slower decay of anti-N (p=0.02), and a faster decay of anti-S (p=0.0008) than women. At M11-13, anti-N dramatically decreased (half-life: 283 days) while anti-S stabilized (half-life: 725 days) at a median of 2.39 log Arbitrary Units (AU)/mL (Interquartile Range (IQR): 2.10 -2.75). Overall, 69 SARS-CoV-2 infections developed in the COVID-19 negative group (incidence of 12.22 per 100 person-years) versus one in the COVID-19 positive group (incidence of 0.40 per 100 person-years), indicating a relative reduction in the incidence of SARS-CoV-2 reinfection of 96.7% (p<0.0001). Correlation with live-virus neutralization assay revealed that variants D614G and B.1.1.7, but not B.1.351, were sensitive to anti-S antibodies at 2.3 log AU/mL, while IgG ≥ 3 log AU/mL neutralized all three variants. After SARS-CoV-2 vaccination, anti-S levels reached at least 3 logs regardless of pre-vaccination IgG levels, type of vaccine, and number of doses. Our study demonstrates a long-term persistence of anti-S IgG antibodies that may protect against reinfection. By significantly increasing cross-neutralizing antibody titers, a single-dose vaccination strengthens protection against escape mutants.