Dextran sulfate from Leuconostoc mesenteroides B512F exerts potent antiviral activity against SARS-CoV-2 in vitro and in vivo

SARS–CoV–2; Dextran sulfate; NebulizationSARS–CoV–2; Sulfato de dextrano; NebulizaciónSARS–CoV–2; Sulfat de dextrano; NebulitzacióThe emergent human coronavirus SARS-CoV-2 and its resistance to current drugs makes the need for new potent treatments for COVID-19 patients strongly necessary. Dextran sulfate (DS) polysaccharides have long demonstrated antiviral activity against different enveloped viruses in vitro. However, their poor bioavailability has led to their abandonment as antiviral candidates. Here, we report for the first time the broad-spectrum antiviral activity of a DS-based extrapolymeric substance produced by the lactic acid bacterium Leuconostoc mesenteroides B512F. Time of addition assays with SARS-CoV-2 pseudoviruses in in vitro models confirm the inhibitory activity of DSs in the early stages of viral infection (viral entry). In addition, this exopolysaccharide substance also reports broad-spectrum antiviral activity against several enveloped viruses such as SARS-CoV-2, HCoV229E, HSV-1, in in vitro models and in human lung tissue. The toxicity and antiviral capacity of DS from L. mesenteroides was tested in vivo in mouse models which are susceptible to SARS-CoV-2 infection. The described DS, administered by inhalation, a new route of administration for these types of polymers, shows strong inhibition of SARS-CoV-2 infection in vivo, significantly reducing animal mortality and morbidity at non-toxic doses. Therefore, we suggest that it may be considered as a potential candidate for antiviral therapy against SARS-CoV-2.Financial support for the study was provided by the REACT-EU 2021 grant from Comunidad de Madrid to the Project COVTRAVI-19-CM, Plataformas y modelos preclínicos para el abordaje multidisciplinar en COVID-19 y en respuesta a futuras pandemias

Mitochondrial dysfunction, lipids metabolism, and amino acid biosynthesis are key pathways for COVID-19 recovery

Biological sciences; Human metabolismCiències biològiques; Metabolisme humàCiencias biológicas; Metabolismo humanoThe metabolic alterations caused by SARS-CoV-2 infection reflect disease progression. To analyze molecules involved in these metabolic changes, a multiomics study was performed using plasma from 103 patients with different degrees of COVID-19 severity during the evolution of the infection. With the increased severity of COVID-19, changes in circulating proteomic, metabolomic, and lipidomic profiles increased. Notably, the group of severe and critical patients with high HRG and ChoE (20:3) and low alpha-ketoglutaric acid levels had a high chance of unfavorable disease evolution (AUC = 0.925). Consequently, patients with the worst prognosis presented alterations in the TCA cycle (mitochondrial dysfunction), lipid metabolism, amino acid biosynthesis, and coagulation. Our findings increase knowledge regarding how SARS-CoV-2 infection affects different metabolic pathways and help in understanding the future consequences of COVID-19 to identify potential therapeutic targets.This work has been developed in the framework of the COVIDOMICS’ project supported by Direcció General de Recerca i Innovació en Salut (DGRIS), Departament de Salut, Generalitat de Catalunya (PoC-6-17 and PoC1-5). The research was also supported by the Programa de Suport als Grups de Recerca AGAUR (2021SGR01404), the SPANISH AIDS Research Network [RD16/0025/0006]-ISCIII-FEDER (Spain) and the CIBER -Consorcio Centro de Investigación Biomédica en Red- (CB21/13/00020 and CB07/08/0012), Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación and Unión Europea – NextGenerationEU. FV is supported by grants from the Programa de Intensificación de Investigadores (INT20/00031)-ISCIII and by “Premi a la Trajectòria Investigadora dels Hospitals de l’ICS 2018”. AR is supported by a grant from IISPV through the project “2019/IISPV/05” (Boosting Young Talent), by GeSIDA through the “III Premio para Jóvenes Investigadores 2019” and by the Instituto de Salud Carlos III (ISCIII) under grant agreement “CP19/00146” through the Miguel Servet Program. Finally, this study would not have been possible without the generous collaboration of all the patients and their families and medical and nursing staff who have taken part in the project. We particularly acknowledge the collaboration of the Departments of Preventive Medicine and Epidemiology, Internal Medicine, Critical Care, Emergency, Occupational Health, Laboratory Medicine and Molecular Biology, and BioBank-IISPV (B.0000853 + B.0000854) integrated into the Spanish National Biobanks Platform (PT20/00197), CERCA Program (Generalitat de Catalunya) and IISPV, for their collaboration

Schlafen 12 restricts HIV-1 latency reversal by a codon-usage dependent post-transcriptional block in CD4+ T cells

HIV infections; Restriction factorsInfecciones por VIH; Factores de restricciónInfeccions pel VIH; Factors de restriccióLatency is a major barrier towards virus elimination in HIV-1-infected individuals. Yet, the mechanisms that contribute to the maintenance of HIV-1 latency are incompletely understood. Here we describe the Schlafen 12 protein (SLFN12) as an HIV-1 restriction factor that establishes a post-transcriptional block in HIV-1-infected cells and thereby inhibits HIV-1 replication and virus reactivation from latently infected cells. The inhibitory activity is dependent on the HIV-1 codon usage and on the SLFN12 RNase active sites. Within HIV-1-infected individuals, SLFN12 expression in PBMCs correlated with HIV-1 plasma viral loads and proviral loads suggesting a link with the general activation of the immune system. Using an RNA FISH-Flow HIV-1 reactivation assay, we demonstrate that SLFN12 expression is enriched in infected cells positive for HIV-1 transcripts but negative for HIV-1 proteins. Thus, codon-usage dependent translation inhibition of HIV-1 proteins participates in HIV-1 latency and can restrict the amount of virus release after latency reversal.This work was supported by following grants: M.K.I., JSPS Oversea Research Fellowship and Takeda Science Foundation; A.E.C., PT17/0009/0019 (ISCIII/MINECO and FEDER); M.J.B., RTI2018-101082-B-I00 and PID2021-123321OB-I00 [MINECO/FEDER]), and the Miguel Servet program by ISCIII (CP17/00179 and CPII22/00005); C.B., M.R.R., C.D.C., European Union’s Horizon 2020 research and innovation program under grant agreement 681137-EAVI2020 and NIH grant P01-AI131568; J.D., the Spanish Ministry of Science and Innovation (PID2019106959RB-I00/AEI/10.13039/501100011033); A.M., the Spanish Ministry of Science and Innovation (PID2019-106323RB-I00 AEI//10.13039/501100011033) and the institutional “María de Maeztu” Programme for Units of Excellence in R&D (CEX2018-000792-M)

Potent Cell-Intrinsic Immune Responses in Dendritic Cells Facilitate HIV-1-Specific T Cell Immunity in HIV-1 Elite Controllers

The majority of HIV-1 elite controllers (EC) restrict HIV-1 replication through highly functional HIV-1-specific T cell responses, but mechanisms supporting the evolution of effective HIV-1-specific T cell immunity in these patients remain undefined. Cytosolic immune recognition of HIV-1 in conventional dendritic cells (cDC) can facilitate priming and expansion of HIV-1-specific T cells; however, HIV-1 seems to be able to avoid intracellular immune recognition in cDCs in most infected individuals. Here, we show that exposure of cDCs from EC to HIV-1 leads to a rapid and sustained production of type I interferons and upregulation of several interferon-stimulated effector genes. Emergence of these cell-intrinsic immune responses was associated with a reduced induction of SAMHD1 and LEDGF/p75, and an accumulation of viral reverse transcripts, but inhibited by pharmacological blockade of viral reverse transcription or siRNA-mediated silencing of the cytosolic DNA sensor cGAS. Importantly, improved cell-intrinsic immune recognition of HIV-1 in cDCs from elite controllers translated into stronger abilities to stimulate and expand HIV-1-specific CD8 T cell responses. These data suggest an important role of cell-intrinsic type I interferon secretion in dendritic cells for the induction of effective HIV-1-specific CD8 T cells, and may be helpful for eliciting functional T cell immunity against HIV-1 for preventative or therapeutic clinical purposes

Impact of very early antiretroviral therapy during acute HIV infection on long-term immunovirological outcomes

Acute HIV infection; Antiretroviral treatment; Immune recoveryInfección aguda por VIH; Tratamiento antirretroviral; Recuperación inmunitariaInfecció aguda per VIH; Tractament antiretroviral; Recuperació immunitàriaObjectives We aimed to determine if starting antiretroviral therapy (ART) in the first 30 days after acquiring HIV infection has an impact on immunovirological response. Methods Observational, ambispective study including 147 patients with confirmed acute HIV infection (January/1995-August/2022). ART was defined as very early (≤30 days after the estimated date of infection), early (31-180 days), and late (>180 days). We compared time to viral suppression (viral load [VL] <50 copies/ml) and immune recovery (IR) (CD4+/CD8+ ratio ≥1) according to the timing and type of ART using survival analysis. Results ART was started in 140 (95.2%) patients. ART was very early in 24 (17.1%), early in 77 (55.0%), and late in 39 (27.9%) cases. Integrase strand transfer inhibitor (INSTI)-based regimens were the most used in both the overall population (65%) and the very early ART group (23/24, 95.8%). Median HIV VL and CD4+/CD8+ ratio pre-ART were higher in the very early ART group (P <0.05). Patients in the very early and early ART groups and treated with INSTI-based regimens achieved IR earlier (P <0.05). Factors associated with faster IR were the CD4+/CD8+ ratio pre-ART (hazard ratio: 9.3, 95% CI: 3.1-27.8, P <0.001) and INSTI-based regimens (hazard ratio: 2.4, 95% CI: 1.3-4.2, P = 0.003). Conclusions The strongest predictors of IR in patients who start ART during AHI are the CD4+/CD8+ ratio pre-ART and INSTI-based ART regimens.This work was founded by Instituto de Salud Carlos III (Acción Estratégica en Salud) and Fondo Europeo de Desarrollo Regional (FEDER) through grant PI20/00823. The study was also supported by the Spanish Network for AIDS Research (RIS) through the Instituto de Salud Carlos III – Red Temática de Investigación Cooperativa en Sida (RD06/006, RD12/0017/0018 and RD16/0002/0006) as part of the Plan Nacional R+D+I and by ISCIII Subdirección General de Evaluación and Fondo Europeo de Desarrollo Regional (FEDER). For this project, PS has received a grant from the Catalan Society of Infectious Diseases and Clinical Microbiology (SCMIMC) funded by ViiV Healthcare. MJB is supported by the Miguel Servet program funded by the Spanish Health Institute Carlos III (CPII22/00005). The funders had no role in the study design, data collection, and interpretation, or the decision to submit the work for publication

KLRG1 expression on natural killer cells is associated with HIV persistence, and its targeting promotes the reduction of the viral reservoir

HIV infection; HIV reservoir; ImmunotherapyInfección por VIH; Reservorio de VIH; InmunoterapiaInfecció per VIH; Reservori de VIH; ImmunoteràpiaHuman immunodeficiency virus (HIV) infection induces immunological dysfunction, which limits the elimination of HIV-infected cells during treated infection. Identifying and targeting dysfunctional immune cells might help accelerate the purging of the persistent viral reservoir. Here, we show that chronic HIV infection increases natural killer (NK) cell populations expressing the negative immune regulator KLRG1, both in peripheral blood and lymph nodes. Antiretroviral treatment (ART) does not reestablish these functionally impaired NK populations, and the expression of KLRG1 correlates with active HIV transcription. Targeting KLRG1 with specific antibodies significantly restores the capacity of NK cells to kill HIV-infected cells, reactivates latent HIV present in CD4+ T cells co-expressing KLRG1, and reduces the intact HIV genomes in samples from ART-treated individuals. Our data support the potential use of immunotherapy against the KLRG1 receptor to impact the viral reservoir during HIV persistence.The project leading to these results has received funding from “la Caixa” Banking Foundation under the project code LCF/PR/HR20-00218. This study was also supported by the Agencia Estatal de Investigación project PID2021-123321OB-I00 funded by MCIN/AEI/10.13039/501100011033/FEDER, UE; The Spanish “Ministerio de Economia y Competitividad, Instituto de Salud Carlos III” (ISCIII, PI20/00160); and the Gilead fellowships GLD19/00084, GLD18/00008, GLD21-00049, and GLD22/00152. Part of the methodology was developed with the support of the grant 202104-30-31 from Fundació la Marató de TV3. M.B. is supported by the Miguel Servet program funded by the Spanish Health Institute Carlos III (CPII22/00005). A.A.-G. was supported by the Spanish Secretariat of Science and Innovation Ph.D. fellowship (BES-2016-076382). D.P. was supported by the VHIR Ph.D programme 2020. Spanish Secretariat of Science and Innovation Ph.D. fellowship. E.M.G. was supported by the Ramón y Cajal Program (RYC2018-024374-I) funded by the Spanish Secretariat of Science and Innovation, by the Comunidad de Madrid Talento Program (2017-T1/BMD-5396), and by the project PID2021-127899OB-I00 funded by MCIN /AEI /10.13039/501100011033/ FEDER, UE. We thank Dr. Joan Puñet from the flow cytometry core at the Vall d’Hebron Research Institute for his technical and scientific expertise. The funders had no role in study design, data collection, and analysis, the decision to publish, or preparation of the manuscript

Integrated and Total HIV-1 DNA Predict Ex Vivo Viral Outgrowth

The persistence of a reservoir of latently infected CD4 T cells remains one of the major obstacles to cure HIV. Numerous strategies are being explored to eliminate this reservoir. To translate these efforts into clinical trials, there is a strong need for validated biomarkers that can monitor the reservoir over time in vivo. A comprehensive study was designed to evaluate and compare potential HIV-1 reservoir biomarkers. A cohort of 25 patients, treated with suppressive antiretroviral therapy was sampled at three time points, with median of 2.5 years (IQR: 2.4–2.6) between time point 1 and 2; and median of 31 days (IQR: 28–36) between time point 2 and 3. Patients were median of 6 years (IQR: 3–12) on ART, and plasma viral load (<50 copies/ml) was suppressed for median of 4 years (IQR: 2–8). Total HIV-1 DNA, unspliced (us) and multiply spliced HIV-1 RNA, and 2LTR circles were quantified by digital PCR in peripheral blood, at 3 time points. At the second time point, a viral outgrowth assay (VOA) was performed, and integrated HIV-1 DNA and relative mRNA expression levels of HIV-1 restriction factors were quantified. No significant change was found for long- and short-term dynamics of all HIV-1 markers tested in peripheral blood. Integrated HIV-1 DNA was associated with total HIV-1 DNA (p<0.001, R² = 0.85), us HIV-1 RNA (p = 0.029, R² = 0.40), and VOA (p = 0.041, R2 = 0.44). Replication-competent virus was detected in 80% of patients by the VOA and it correlated with total HIV-1 DNA (p = 0.039, R² = 0.54). The mean quantification difference between Alu-PCR and VOA was 2.88 log10, and 2.23 log10 between total HIV-1 DNA and VOA. The levels of usHIV-1 RNA were inversely correlated with mRNA levels of several HIV-1 restriction factors (TRIM5α, SAMHD1, MX2, SLFN11, pSIP1). Our study reveals important correlations between the viral outgrowth and total and integrated HIV-1 DNA measures, suggesting that the total pool of HIV-1 DNA may predict the size of the replication-competent virus in ART suppressed patients

Comprehensive longitudinal characterization of HIV-1 reservoir markers in patients on stable antiretroviral treatment

Background: There is an increasing interest in characterisation of the viral reservoir in patients on long-term antiretroviral therapy in the context of HIV cure studies. The main question remains which assay is most relevant to accurately predict the size of the replication competent viral reservoir. Although both PCR and viral outgrowth assays have been proposed, mainly PCR based assays have been validated in clinical trials. Conflicting data exists about the correlation of viral outgrowth assays and PCR based assays. In addition, within individual patients, the long term variability of PCR reservoir markers of total HIV DNA, 2LTR circles and full length cell-associated (CA) RNA is poorly addressed. Materials and Methods: We set-up a study with a well-defined patient cohort (N=25) to characterize the longitudinal kinetics of the viral reservoir by PCR based methods and to assess the correlation of the viral reservoir markers with the viral outgrowth assay. Blood samples were drawn at three time points with median (IQR) of 2.5 years (IQR 2.4-2.6) between time point 1 and 2; and median of 31 days (28-36) between time point 2 and 3. Total HIV-1 DNA, unspliced (us-) and multiply spliced (ms-) HIV-1 RNA, and 2LTR circles were quantified in peripheral blood mononuclear cells (PBMCs) using droplet digital PCR. Parameters of HIV-1 persistence were quantified at 3 time points. Alu-PCR was used to quantify integrated HIV-1 DNA. Viral outgrowth assay and integrated HIV-1 DNA were performed at one time point (2nd time point). Results: No significant change was found for long- and short-term dynamics of all markers (total HIV-1 DNA, unspliced and multiply spliced HIV-1 RNA, and 2LTR circles) of HIV-1 persistence in peripheral blood. Integrated HIV-1 DNA was detected in all patients with median (IQR) of 3.04 (2.65-3.37) log10 copies/10⁶ PBMCs; and it correlated well with total HIV-1 DNA (p=0.002, R²=0.54); unspliced HIV-1 RNA (p=0.001, R²=0.40); and viral outgrowth assay (p=0.014, R²=0.20). Replication competent virus was detected in 80% (20/25) of patients and it correlated well with total HIV-1 DNA (p=0.017, R²=0.54). The mean difference (bias) between the HIV copy numbers generated with Alu-PCR and viral outgrowth assay, assessed with Bland-Altman test, was 2.38 ± 0.83 log10 (95% Limits of Agreement). And a corresponding bias between total HIV-1 DNA and VOA was 0.8 ± 0.72 log10 (95% Limits of Agreement). Conclusion: This study supports the finding that viral reservoir size and long- and short-term dynamics remain stable over time in patients receiving stable cART. Our study shows the presence of a very stable reservoir in terms of viral dynamics (2LTR circles and CA RNA) in patient under ART. Interestingly, we found a correlation between integrated HIV DNA and the viral outgrowth assay, indicating that a stable fraction of integrated HIV is replication competent