Integrated immunovirological profiling validates plasma SARS-CoV-2 RNA as an early predictor of COVID-19 mortality.

peer reviewedDespite advances in COVID-19 management, identifying patients evolving toward death remains challenging. To identify early predictors of mortality within 60 days of symptom onset (DSO), we performed immunovirological assessments on plasma from 279 individuals. On samples collected at DSO11 in a discovery cohort, high severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA (vRNA), low receptor binding domain–specific immunoglobulin G and antibody-dependent cellular cytotoxicity, and elevated cytokines and tissue injury markers were strongly associated with mortality, including in patients on mechanical ventilation. A three-variable model of vRNA, with predefined adjustment by age and sex, robustly identified patients with fatal outcome (adjusted hazard ratio for log-transformed vRNA = 3.5). This model remained robust in independent validation and confirmation cohorts. Since plasma vRNA’s predictive accuracy was maintained at earlier time points, its quantitation can help us understand disease heterogeneity and identify patients who may benefit from new therapies

Persistance du VIH-1 et reconstitution des lymphocytes T CD4+ dans la muqueuse intestinale sous traitement antirétroviral

Chez les individus infectés par le VIH-1, le traitement antirétroviral a pour but de supprimer durablement la réplication virale, et de préserver et/ou restaurer les fonctions immunitaires. Néanmoins, le virus persiste sous forme de provirus intégrés latents dans le génome de cellules réservoirs à longue durée de vie qui sont un obstacle majeur à l'éradication et donc à la guérison du VIH-1. La persistance d'une réplication virale résiduelle pourrait également contribuer à ré-ensemencer le réservoir viral et contribuer à sa stabilité. L'intestin est le compartiment clé dans la physiopathologie de l'infection VIH-1 car il contient de nombreux lymphocytes T CD4+ mémoires effecteurs particulièrement permissifs à la réplication virale. Les travaux présentés dans ce manuscrit ont porté sur l'analyse comparée des compartiments intestinaux et sanguins d'individus infectés par le VIH-1 sous traitement antirétroviral prolongé. Nos résultats démontrent: (i) une compartimentation entre le sang et l'intestin de la quasiespèce virale, avec un enrichissement en virus utilisant le corécepteur d'entrée CCR5 dans l'intestin; (ii) une production virale résiduelle dans le compartiment intestinal qui ré-ensemence ce réservoir; (iii) une stimulation antigénique chronique par la production virale résiduelle et contrôle immunitaire du réservoir. La persistance du VIH-1 dans la muqueuse intestinale semble également impliquée dans le défaut de reconstitution immunitaire de ce compartiment sous traitement antirétroviral. La réponse T effectrice induite par la persistance virale est en effet associée à une diminution d'expression par les entérocytes de CCL25, chimiokine nécessaire au recrutement des lymphocytes T CD4+CCR9+ dans la muqueuse intestinale. Parmi les sous-populations de lymphocytes T CD4+ intestinaux, la fréquence des Th17 reste diminuée sous traitement antirétroviral, alors que celle des Th22 est normale. Les Th17 dépendent de l'axe CCR6-CCL20 pour migrer dans l'intestin; axe déficitaire du fait d'une diminution de l'expression de la chimiokine CCL20 par les entérocytes. Nous avons mis en évidence que les lymphocytes Th22 peuvent utiliser alternativement les axes CCR10-CCL28 ou CCR6-CCL20, selon le ratio CCL28/CCL20 présent dans le micro-environnement intestinal. L'IL-22 produite par les Th22 participe au défaut de production de CCL20 par les entérocytes, par un mécanisme indirect faisant intervenir l'IL-18, alors que la production de CCL28 est maintenue, permettant donc le recrutement préférentiel des Th22 dans la muqueuse intestinale par cet axe.Current antiretroviral therapies control HIV-1 replication allowing subsequent reconstitution of the immune system. However, the persistence of integrated proviruses in long-lived reservoir cells precludes virus eradication. Residual virus replication could also replenish the reservoir and contributes to its stability. The gut is a key compartment during HIV-1 infection as it contains numerous effector memory CD4+ T cells that are highly permissive to HIV-1 replication. Here we characterized the blood and intestine compartments of HIV-1-infected individuals on prolonged antiretroviral therapy and showed: (i) a compartmentation of viral quasispecies between the blood and gut compartments, with an enrichment of CCR5-using virus in the gut; (ii) the persistence of a residual production in gut which replenishes the viral reservoir; (iii)a chronic antigenic stimulation exerted by residual virus production; (iv) a dynamic equilibrium between the residual production and immune control of the reservoir. HIV-1 persistence in the intestine mucosa under antiretroviral therapy also contributes to the default of immune reconstitution in this compartment. The HIV-1-specific immune response is associated with the reduction of CCL25 expression by enterocytes, a chemokine required for CD4+CCR9+ T cell migration in the intestine. Among gut CD4+ T cell subsets, th17 cells remain depleted contrasting with a normal frequency of Th22 cells. Th17 cells migration to the gut remains impaired because of the reduced production of CCL20 by enterocytes. Th22 cells could alternatively use the CCR10-CCL28 and CCR6-CCL20 chemotactic axes, depending on the CCL28/CCL20 ratio in the intestinal microenvironment. Th22 cells produce IL-22 that reduces CCL20 production by an IL-18-dependant mechanism, thus blunting Th17 cells recruitment to the gut mucosa. By contrast, CCL28 production is maintained and allows Th22 cells to be recruited along this axis

HIV-1 persistence and CD4 T lymphocytes reconstitution in intestine mucosa on antiretroviral therapy

Chez les individus infectés par le VIH-1, le traitement antirétroviral a pour but de supprimer durablement la réplication virale, et de préserver et/ou restaurer les fonctions immunitaires. Néanmoins, le virus persiste sous forme de provirus intégrés latents dans le génome de cellules réservoirs à longue durée de vie qui sont un obstacle majeur à l'éradication et donc à la guérison du VIH-1. La persistance d'une réplication virale résiduelle pourrait également contribuer à ré-ensemencer le réservoir viral et contribuer à sa stabilité. L'intestin est le compartiment clé dans la physiopathologie de l'infection VIH-1 car il contient de nombreux lymphocytes T CD4+ mémoires effecteurs particulièrement permissifs à la réplication virale. Les travaux présentés dans ce manuscrit ont porté sur l'analyse comparée des compartiments intestinaux et sanguins d'individus infectés par le VIH-1 sous traitement antirétroviral prolongé. Nos résultats démontrent: (i) une compartimentation entre le sang et l'intestin de la quasiespèce virale, avec un enrichissement en virus utilisant le corécepteur d'entrée CCR5 dans l'intestin; (ii) une production virale résiduelle dans le compartiment intestinal qui ré-ensemence ce réservoir; (iii) une stimulation antigénique chronique par la production virale résiduelle et contrôle immunitaire du réservoir. La persistance du VIH-1 dans la muqueuse intestinale semble également impliquée dans le défaut de reconstitution immunitaire de ce compartiment sous traitement antirétroviral. La réponse T effectrice induite par la persistance virale est en effet associée à une diminution d'expression par les entérocytes de CCL25, chimiokine nécessaire au recrutement des lymphocytes T CD4+CCR9+ dans la muqueuse intestinale. Parmi les sous-populations de lymphocytes T CD4+ intestinaux, la fréquence des Th17 reste diminuée sous traitement antirétroviral, alors que celle des Th22 est normale. Les Th17 dépendent de l'axe CCR6-CCL20 pour migrer dans l'intestin; axe déficitaire du fait d'une diminution de l'expression de la chimiokine CCL20 par les entérocytes. Nous avons mis en évidence que les lymphocytes Th22 peuvent utiliser alternativement les axes CCR10-CCL28 ou CCR6-CCL20, selon le ratio CCL28/CCL20 présent dans le micro-environnement intestinal. L'IL-22 produite par les Th22 participe au défaut de production de CCL20 par les entérocytes, par un mécanisme indirect faisant intervenir l'IL-18, alors que la production de CCL28 est maintenue, permettant donc le recrutement préférentiel des Th22 dans la muqueuse intestinale par cet axe.Current antiretroviral therapies control HIV-1 replication allowing subsequent reconstitution of the immune system. However, the persistence of integrated proviruses in long-lived reservoir cells precludes virus eradication. Residual virus replication could also replenish the reservoir and contributes to its stability. The gut is a key compartment during HIV-1 infection as it contains numerous effector memory CD4+ T cells that are highly permissive to HIV-1 replication. Here we characterized the blood and intestine compartments of HIV-1-infected individuals on prolonged antiretroviral therapy and showed: (i) a compartmentation of viral quasispecies between the blood and gut compartments, with an enrichment of CCR5-using virus in the gut; (ii) the persistence of a residual production in gut which replenishes the viral reservoir; (iii)a chronic antigenic stimulation exerted by residual virus production; (iv) a dynamic equilibrium between the residual production and immune control of the reservoir. HIV-1 persistence in the intestine mucosa under antiretroviral therapy also contributes to the default of immune reconstitution in this compartment. The HIV-1-specific immune response is associated with the reduction of CCL25 expression by enterocytes, a chemokine required for CD4+CCR9+ T cell migration in the intestine. Among gut CD4+ T cell subsets, th17 cells remain depleted contrasting with a normal frequency of Th22 cells. Th17 cells migration to the gut remains impaired because of the reduced production of CCL20 by enterocytes. Th22 cells could alternatively use the CCR10-CCL28 and CCR6-CCL20 chemotactic axes, depending on the CCL28/CCL20 ratio in the intestinal microenvironment. Th22 cells produce IL-22 that reduces CCL20 production by an IL-18-dependant mechanism, thus blunting Th17 cells recruitment to the gut mucosa. By contrast, CCL28 production is maintained and allows Th22 cells to be recruited along this axis

Th22 cells are efficiently recruited in the gut by CCL28 as an alternative to CCL20 but do not compensate for the loss of Th17 cells in treated HIV-1-infected individuals

International audienceGut CD4+ T cells are incompletely restored in most HIV-1-infected individuals on antiretroviral therapy, notably Th17 cells, a key subset in mucosal homeostasis. By contrast, gut Th22 cells are usually restored at normal frequencies. Th22 cells display a CCR6+CCR10+ phenotype and could thus respond to CCL20- and CCL28-mediated chemotaxis, while Th17 cells, which express CCR6 but not CCR10, depend on CCL20. Herein, we found that CCL28 is normally expressed by duodenal enterocytes of treated HIV-1-infected individuals, while CCL20 expression is blunted. Ex vivo, we showed that Th22 cells contribute to the reduction of CCL20 production by enterocytes through an IL-22- and IL-18-dependent mechanism. Th22 cells preferentially migrate via CCL20- rather than CCL28-mediated chemotaxis when both chemokines are available in the microenvironment. However, when the CCL20/CCL28 ratio drops, as in treated HIV-1-infected individuals, Th22 cells can migrate via the CCR10-CCL28 axis, as an alternative to CCR6-CCL20. This could explain the better reconstitution of gut Th22 compared with Th17 cells on antiretroviral therapy. Lastly, we assessed the relationships between the frequencies of gut Th17 and Th22 cells and inflammatory markers related to microbial translocation, and showed that Th22 cells do not compensate for the loss of Th17 cells in treated HIV-1-infected individuals

Evolution of Anti-RBD IgG Avidity following SARS-CoV-2 Infection

SARS-CoV-2 infection rapidly elicits anti-Spike antibodies whose quantity in plasma gradually declines upon resolution of symptoms. This decline is part of the evolution of an immune response leading to B cell differentiation into short-lived antibody-secreting cells or resting memory B cells. At the same time, the ongoing class switch and antibody maturation processes occurring in germinal centers lead to the selection of B cell clones secreting antibodies with higher affinity for their cognate antigen, thereby improving their functional activity. To determine whether the decline in SARS-CoV-2 antibodies is paralleled with an increase in avidity of the anti-viral antibodies produced, we developed a simple assay to measure the avidity of anti-receptor binding domain (RBD) IgG elicited by SARS-CoV-2 infection. We longitudinally followed a cohort of 29 convalescent donors with blood samples collected between 6- and 32-weeks post-symptoms onset. We observed that, while the level of antibodies declines over time, the anti-RBD avidity progressively increases and correlates with the B cell class switch. Additionally, we observed that anti-RBD avidity increased similarly after SARS-CoV-2 mRNA vaccination and after SARS-CoV-2 infection. Our results suggest that anti-RBD IgG avidity determination could be a surrogate assay for antibody affinity maturation and, thus, suitable for studying humoral responses elicited by natural infection and/or vaccination

Hepatitis E virus replication in human intestinal cells

International audienceHepatitis E virus (HEV), one of the most common agent of acute hepatitis worldwide, is mainly transmitted enterically, via contaminated water for HEV genotypes 1 (HEV1) and HEV2, or by eating raw or undercooked infected meat for HEV genotype 3 (HEV3) and HEV4. However, little is known about how the ingested HEV reaches the liver or its ability to replicate in intestinal cells. We developed human primary cultures of small intestine epithelial cells and intestinal explants obtained from small bowel resections. The epithelial cells were also polarised on transwells. Cells were infected with Kernow-p6 strain or clinically derived virions. Primary intestinal cells supported the growth of Kernow-p6 strain and HEV1 and HEV3 clinically derived virions. Polarised enterocytes infected with HEV1 and HEV3 strains released HEV particles vectorially: mostly into the apical compartment with a little basally. Iodixanol density gradient centrifugation of enterocyte-derived HEV virions gave bands at a density of 1.06-1.08 g/cm3, corresponding to that of quasi-enveloped HEV particles. Ribavirin therapy inhibited HEV excretion from the basal surface but not from the apical side of infected human enterocytes. HEV virions also infected intestinal tissue explants. Lastly, HEV RNA and antigen were detected in the intestinal crypts of a chronically infected patient. HEV can replicate in intestinal cells and reaches the liver as quasi-enveloped virions

Intact proviruses are enriched in the colon and associated with PD-1+TIGIT− mucosal CD4+ T cells of people with HIV-1 on antiretroviral therapyResearch in context

Summary: Background: The persistence of intact replication-competent HIV-1 proviruses is responsible for the virological rebound off treatment. The gut could be a major reservoir of HIV-1 due to the high number of infected target cells. Methods: We collected blood samples and intestinal biopsies (duodenum, ileum, colon) from 42 people with HIV-1 receiving effective antiretroviral therapy. We used the Intact Proviral DNA Assay to estimate the frequency of intact HIV-1 proviruses in the blood and in the intestinal mucosa of these individuals. We analyzed the genetic complexity of the HIV-1 reservoir by performing single-molecule next-generation sequencing of HIV-1 env DNA. The activation/exhaustion profile of mucosal T lymphocytes was assessed by flow cytometry. Findings: Intact proviruses are particularly enriched in the colon. Residual HIV-1 transcription in the gut is associated with persistent mucosal and systemic immune activation. The HIV-1 intestinal reservoir appears to be shaped by the proliferation of provirus-hosting cells. The genetic complexity of the viral reservoir in the colon is positively associated with TIGIT expression but negatively with PD-1, and inversely related to its intact content. The size of the intact reservoir in the colon is associated with PD-1+TIGIT− mucosal CD4+ T cells, particularly in CD27+ memory cells, whose proliferation and survival could contribute to the enrichment of the viral reservoir by intact proviruses. Interpretation: Enrichment in intact proviruses makes the gut a key compartment for HIV-1 persistence on antiretroviral therapy. Funding: This project was supported by grants from the ANRS-MIE (ANRS EP61 GALT), Sidaction, and the Institut Universitaire de France

Humoral Responses Elicited after a Fifth Dose of SARS-CoV-2 mRNA Bivalent Vaccine

While an important part of the world’s population is vaccinated against SARS-CoV-2, new variants continue to emerge. We observe that even after a fifth dose of the mRNA bivalent vaccine, most vaccinated individuals have antibodies that poorly neutralize several Omicron subvariants, including BQ.1.1, XBB, XBB.1.5, FD.1.1, and CH.1.1. However, Fc-effector functions remain strong and stable over time against new variants, which may partially explain why vaccines continue to be effective. We also observe that donors who have been recently infected have stronger antibody functional activities, including neutralization and Fc-effector functions, supporting the observations that hybrid immunity leads to better humoral responses

An extended SARS-CoV-2 mRNA vaccine prime-boost interval enhances B cell immunity with limited impact on T cells

Summary: Spacing the first two doses of SARS-CoV-2 mRNA vaccines beyond 3–4 weeks raised initial concerns about vaccine efficacy. While studies have since shown that long-interval regimens induce robust antibody responses, their impact on B and T cell immunity is poorly known. Here, we compare SARS-CoV-2 naive donors B and T cell responses to two mRNA vaccine doses administered 3–4 versus 16 weeks apart. After boost, the longer interval results in a higher magnitude and a more mature phenotype of RBD-specific B cells. While the two geographically distinct cohorts present quantitative and qualitative differences in T cell responses at baseline and after priming, the second dose led to convergent features with overall similar magnitude, phenotype, and function of CD4+ and CD8+ T cell responses at post-boost memory time points. Therefore, compared to standard regimens, a 16-week interval has a favorable impact on the B cell compartment but minimally affects T cell immunity