The biological and clinical significance of emerging SARS-CoV-2 variants.

The past several months have witnessed the emergence of SARS-CoV-2 variants with novel spike protein mutations that are influencing the epidemiological and clinical aspects of the COVID-19 pandemic. These variants can increase rates of virus transmission and/or increase the risk of reinfection and reduce the protection afforded by neutralizing monoclonal antibodies and vaccination. These variants can therefore enable SARS-CoV-2 to continue its spread in the face of rising population immunity while maintaining or increasing its replication fitness. The identification of four rapidly expanding virus lineages since December 2020, designated variants of concern, has ushered in a new stage of the pandemic. The four variants of concern, the Alpha variant (originally identified in the UK), the Beta variant (originally identified in South Africa), the Gamma variant (originally identified in Brazil) and the Delta variant (originally identified in India), share several mutations with one another as well as with an increasing number of other recently identified SARS-CoV-2 variants. Collectively, these SARS-CoV-2 variants complicate the COVID-19 research agenda and necessitate additional avenues of laboratory, epidemiological and clinical research

Setting of Methods for Analysis of Mucosal Antibodies in Seminal and Vaginal Fluids of HIV Seropositive Subjects from Cambodian and Italian Cohorts

International audienceBACKGROUND: Genital mucosae play a key role in protection from STD and HIV infection, due to their involvement in both horizontal and vertical disease transmission. High variability of published observations concerning IgA isolation and quantification underlies the strong requirement of specific methods able to maximize investigation on HIV-specific IgA. METHODOLOGY: Genital fluids from 109 subjects, including male and female cohorts from Italy and Cambodia, were collected, aliquoted and processed with different techniques, to assess optimal conditions maximizing mucosal antibody recovery. Three sampling techniques, up to sixteen preservation conditions, six ELISA methods and four purifications protocols were compared. PRINCIPAL FINDINGS: The optimal method here described took advantage of Weck-Cel sampling of female mucosal fluids. Immediate processing of genital fluids, with the addition of antibiotics and EDTA, improved recovery of vaginal IgA, while the triple addition of EDTA, antibiotics and protease inhibitors provided the highest amount of seminal IgA. Due to low amount of IgA in mucosal fluids, a high sensitive sandwich ELISA assay was set; sensitivity was enhanced by milk-based overcoating buffer and by a two-step biotin-streptavidin signal amplification. Indeed, commercial antisera to detect human immunoglobulins showed weak cross-reactivity to different antibody types. Three-step affinity purification provided reproducible immunoglobulin recovery from genital specimens, while conventional immuno-affinity IgA purification was found poorly manageable. Affinity columns were suitable to isolate mucosal IgA, which are ten-fold less concentrated than IgG in genital specimens, and provided effective separation of IgA monomers, dimers, and J-chains. Jacalin-bound resin successfully separated IgA1 from IgA2 subfraction. CONCLUSIONS/SIGNIFICANCE: Specific, effective and reliable methods to study local immunity are key items in understanding host mucosal response. The sequence of methods here described is effective and reliable in analysing humoral local responses, and may provide a solid advance to identify and measure the effective mucosal responses to HIV

High efficacy of lopinavir/r-based second-line antiretroviral treatment after 24 months of follow up at ESTHER/Calmette Hospital in Phnom Penh, Cambodia

<p>Abstract</p> <p>Background</p> <p>The number of patients on second-line highly active antiretroviral therapy (HAART) regimens is increasing in resource-limited settings. We describe the outcomes after 24 months for patients on LPV/r-based second-line regimens followed up by the ESTHER programme in Phnom Penh, Cambodia.</p> <p>Methods</p> <p>Seventy patients who initiated second-line HAART regimens more than 24 months earlier were included, and immuno-virological data analyzed. HIV RNA viral load was determined by real-time RT-PCR. HIV-1 drug resistance was interpreted according to the ANRS algorithm.</p> <p>Results</p> <p>Of the 70 patients, two were lost to follow up, three died and 65 (92.8%) remained on second-line treatment after 24 months of follow up (median duration of treatment: 27.4 months). At switch to second-line, the median CD4 T cell count was 106 cells/mm³and the median viral load was 4.7 Log₁₀. Second-line regimens prescribed were ddI/3TC/LPV_/r(65.7%), ddI/TDF/LPV_/r(10.0%), ddI/AZT/LPV_/r(8.6%) and TDF/3TC/LPV_/r(7.1%). The median CD4 T cell gain was +258 cells/mm³at 24 months (n = 63). After 24 months of follow up, 92.3% (60/65) of the patients presented undetectable viral loads, giving an overall treatment success rate of 85.7% (CI: 75.6- 92.0) in intent-to-treat analysis.</p> <p>Conclusions</p> <p>These data suggest that a LPV_/r-based second-line regimen is associated with a high rate of virological suppression and immune reconstitution after 24 months of follow up in Cambodia.</p

Rôles de l'immunité innée cellulaire et marqueurs inflammatoires dans le syndrome de reconstitution immunitaire observé au cours de la co-infection avec la tuberculose chez les patients infectés par le VIH au Cambodge

Les traitements simultanés des antituberculeux et de thérapie antirétrovirale (ARV) chez les patients co-infectés par le VIH et la tuberculose (TB) peut être compliqué en raison de la survenue du syndrome inflammatoire de reconstitution immunitaire associé à la TB (TB-IRIS) dont le diagnostic est basé sur les manifestations cliniques. La compréhension de l’immunopathologie de TB-IRIS est cruciale pour améliorer le diagnostic et la prise en charge des patients. L'immunité innée semble de plus en plus jouer un rôle dans le TB-IRIS. Dans la présente thèse de doctorat, j'ai étudié le rôle de l'immunité innée cellulaire, notamment des cellules NKT et γδ t, ainsi que l'implication des marqueurs soluble plasmatique : IL-1Ra, sCD14 et sCD163 liés à l’activation des monocytes/macrophages dans la survenue de l’iris chez les patients co-infectés par le VIH et TB au Cambodge.Les résultats ont montré que : 1/. Le TB-IRIS est associé a une forte activation des cellules γδ T et des sous populations γδ2+ avant l’initiation des ARV, 2/. Aucun des marqueurs IL-1Ra, sCD14 et sCD163 n’était prédictif de la survenue de l’iris. L'analyse longitudinale des taux plasmatiques d’ IL-1Ra pourrait être utile pour le diagnostic de l’iris et l’évaluation de la réponse au traitement antituberculeux. En conclusion, nos résultats révèlent l’association entre une activation importante de l’immunité innée et l’émergence de TB-IRIS dans la physiopathologie. De plus, nos données apportent des nouveaux éléments de l'iris et des marqueurs pour évaluer l'efficacité du traitement antituberculeux.Simultaneous anti-tuberculosis and antiretroviral (ARY) therapy in HIV and tuberculosis (TB) co-infected patients can be complicated due to the occurrence of TB-associated immune reconstitution inflammatory syndrome (TB-IRIS). The diagnosis test of TB-IRIS is not yet available and mainly based on clinical data. A better understanding of TB-IRIS immunopathology is crucial to improve diagnostic test and patients’ clinical outcomes. Innate immunity seems increasingly play a role in TB-IRIS. In the present doctoral thesis, is studied the role of cellular innate immunity, including NKT and γδ t cells, and as well as the implication of IL-1Ra, sCD14 and sCD163 plasma soluble markers related to the activation of monocytes/macrophages in the development of iris in HIV and TB co-infected patients in Cambodia. The results have shown that 1/. TB-IRIS is associated with a strong activation of γδ t cells and γδ2+ subset before initiation of ARY, 2/. None of IL-1Ra, sCD14 and sCD163 markers was predictive of the onset of iris. Longitudinal analysis of IL-1Ra plasma level could be useful for the diagnosis of the iris occurrence and for the evaluation of response to TB-IRIS In conclusion, our results reveal the association between important activation of innate immunity and the emergence of TB-IRIS in the physiopathology. In addition, our data provides new element of TB-IRIS and markers for evaluation of TB treatment efficacy

SARS-CoV-2 Antiviral Therapy

The development of effective antiviral therapy for COVID-19 is critical for those awaiting vaccination, as well as for those who do not respond robustly to vaccination. This review summarizes 1 year of progress in the race to develop antiviral therapies for COVID-19, including research spanning preclinical and clinical drug development efforts, with an emphasis on antiviral compounds that are in clinical development or that are high priorities for clinical development.</jats:p

Coronavirus Antiviral Research Database (CoV-RDB): An Online Database Designed to Facilitate Comparisons between Candidate Anti-Coronavirus Compounds

Background: To prioritize the development of antiviral compounds, it is necessary to compare their relative preclinical activity and clinical efficacy. Methods: We reviewed in vitro, animal model, and clinical studies of candidate anti-coronavirus compounds and placed extracted data in an online relational database. Results: As of August 2020, the Coronavirus Antiviral Research Database (CoV-RDB; covdb.stanford.edu) contained over 2800 cell culture, entry assay, and biochemical experiments, 259 animal model studies, and 73 clinical studies from over 400 published papers. SARS-CoV-2, SARS-CoV, and MERS-CoV account for 85% of the data. Approximately 75% of experiments involved compounds with known or likely mechanisms of action, including monoclonal antibodies and receptor binding inhibitors (21%), viral protease inhibitors (17%), miscellaneous host-acting inhibitors (10%), polymerase inhibitors (9%), interferons (7%), fusion inhibitors (5%), and host protease inhibitors (5%). Of 975 compounds with known or likely mechanism, 135 (14%) are licensed in the U.S. for other indications, 197 (20%) are licensed outside the U.S. or are in human trials, and 595 (61%) are pre-clinical investigational compounds. Conclusion: CoV-RDB facilitates comparisons between different candidate antiviral compounds, thereby helping scientists, clinical investigators, public health officials, and funding agencies prioritize the most promising compounds and repurposed drugs for further development.</jats:p

Coronavirus Antiviral Research Database (CoV-RDB): An Online Database Designed to Facilitate Comparisons between Candidate Anti-Coronavirus Compounds

Background: To prioritize the development of antiviral compounds, it is necessary to compare their relative preclinical activity and clinical efficacy. Methods: We reviewed in vitro, animal model, and clinical studies of candidate anti-coronavirus compounds and placed extracted data in an online relational database. Results: As of August 2020, the Coronavirus Antiviral Research Database (CoV-RDB; covdb.stanford.edu) contained over 2800 cell culture, entry assay, and biochemical experiments, 259 animal model studies, and 73 clinical studies from over 400 published papers. SARS-CoV-2, SARS-CoV, and MERS-CoV account for 85% of the data. Approximately 75% of experiments involved compounds with known or likely mechanisms of action, including monoclonal antibodies and receptor binding inhibitors (21%), viral protease inhibitors (17%), miscellaneous host-acting inhibitors (10%), polymerase inhibitors (9%), interferons (7%), fusion inhibitors (5%), and host protease inhibitors (5%). Of 975 compounds with known or likely mechanism, 135 (14%) are licensed in the U.S. for other indications, 197 (20%) are licensed outside the U.S. or are in human trials, and 595 (61%) are pre-clinical investigational compounds. Conclusion: CoV-RDB facilitates comparisons between different candidate antiviral compounds, thereby helping scientists, clinical investigators, public health officials, and funding agencies prioritize the most promising compounds and repurposed drugs for further development