Effects of the Covid-19 pandemic on the continuity of sexual and reproductive health care in the maternity ward of a health and social promotion centre in Burkina Faso: a qualitative study (preprint)

The COVID-19 pandemic has significantly impacted the continuity of maternity care in Burkina Faso. This study aimed to compare the volumes of in-person visits and explore the experiences of healthcare providers and users regarding the continuity of healthcare in the maternity ward of a Health and Social Promotion Center (HSPC) before, during, and after the lockdown during the COVID-19 pandemic in Ouagadougou, Burkina Faso. Methods We conducted a multimethod, cross-sectional exploratory study with a phenomenological approach. Monthly health administrative data regarding family planning visits, antenatal visits, deliveries, and postnatal care before, during, and after COVID-19 were collected and compared. Qualitative data were collected through semi-structured interviews with family healthcare providers and users and thematically analyzed. Results The study found that the pandemic led to a decline in the demand for healthcare, as people were afraid of contracting COVID-19. This was particularly true for pregnant women who had recently given birth. The study also found that the pandemic disrupted the supply of essential medicines and medical supplies, which made it difficult for healthcare providers to provide quality care. The qualitative analysis allowed us to highlight three themes: the representation of respondents on COVID-19, their perception of the effectiveness of barrier measures and their analysis of the continuity of care in times of COVID-19: the picture of respondents on COVID-19, their perception of the efficacy of barrier measures and their analysis of the continuity of care in times of COVID-19. Despite these challenges, the study found that healthcare providers and users could find ways to maintain continuity of care. Conclusion The study concludes that the COVID-19 pandemic has significantly impacted the continuity of maternity care in Burkina Faso. However, healthcare providers and users have found ways to maintain continuity of care, and the study provides recommendations for improving continuity of care in the future.

CCQM-P199b: Interlaboratory comparability study of SARS-CoV-2 RNA copy number quantification (preprint)

Nucleic acid amplification tests including reverse transcription-quantitative PCR (RT-qPCR) are used to detect RNA from Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of the Coronavirus disease 2019 (COVID-19) pandemic. Standardized measurements of RNA can facilitate comparable performance of laboratory tests in the absence of existing reference measurement systems early on in a pandemic. Interlaboratory study CCQM-P199b 'SARS-CoV-2 RNA copy number quantification' was designed to test the fitness-for-purpose of developed candidate reference measurement procedures (RMPs) for SARS-CoV-2 genomic targets in purified RNA materials, and was conducted under the auspices of the Consultative Committee for Amount of Substance: Metrology in Chemistry and Biology (CCQM) to evaluate the measurement comparability of national metrology institutes (NMIs) and designated institutes (DIs), thereby supporting international standardization. Twenty-one laboratories participated in CCQM-P199b and were requested to report the RNA copy number concentration, expressed in number of copies per microliter, of the SARS-CoV-2 nucleocapsid (N) gene partial region (NC_045512.2: 28274-29239) and envelope (E) gene (NC_045512.2: 26245-26472) (optional measurement) in samples consisting of in vitro transcribed RNA or purified RNA from lentiviral constructs. Materials were provided in two categories: lower concentration (approximately 10 x 1 - 10 x 4/uL in aqueous solution containing human RNA background) and high concentration (approximately 10 x 9/uL in aqueous solution without any other RNA background). For the measurement of N gene concentration in the lower concentration study materials, the majority of laboratories (n = 17) used one-step reverse transcription-digital PCR (RT-dPCR), with three laboratories applying two-step RT-dPCR and one laboratory RT-qPCR. Sixteen laboratories submitted results for E gene concentration. Reproducibility (% CV or equivalent) for RT-dPCR ranged from 19 % to 31 %. Measurements of the high concentration study material by orthogonal methods (isotope dilution-mass spectrometry and single molecule flow cytometry) and a gravimetrically linked lower concentration material were in a good agreement, suggesting a lack of overall bias in RT-dPCR measurements. However methodological factors such as primer and probe (assay) sequences, RT-dPCR reagents and dPCR partition volume were found to be potential sources of interlaboratory variation which need to be controlled when applying this technique. This study demonstrates that the accuracy of RT-dPCR is fit-for-purpose as a RMP for viral RNA target quantification in purified RNA materials and highlights where metrological approaches such as the use of in vitro transcribed controls, orthogonal methods and measurement uncertainty evaluation can support standardization of molecular methods.

Neutralisation sensitivity of the SARS-CoV-2 BA.2.87.1 variant (preprint)

Against the backdrop of the rapid global takeover and dominance of BA.1/BA.2 and subsequently BA.2.86 lineages, the emergence of a highly divergent SARS-CoV-2 variant warrants characterization and close monitoring. Recently, another such BA.2 descendent, designated BA.2.87.1, was detected in South Africa. Here, we show using spike-pseudotyped viruses that BA.2.87.1 is less resistant to neutralisation by prevailing antibody responses in Sweden than other currently circulating variants such as JN.1. Further we show that a monovalent XBB.1.5-adapted booster enhanced neutralising antibody titers to BA.2.87.1 by almost 4-fold. While BA.2.87.1 may not outcompete other currently-circulating lineages, the repeated emergence and transmission of highly diverged variants suggests that another large antigenic shift, similar to the replacement by Omicron, may be likely in the future.

COVID-19 Impact on Patients with Immune-Mediated Rheumatic Disease: A Comparative Study of Disease Activity and Psychological Well-Being Over Six Months (preprint)

Objectives: To compare the impact of COVID-19 on clinical status and psychological condition in patients with immune-mediated rheumatic diseases (IMRD) infected by SARS-CoV-2 with IMRD controls not infected, during a 6-month follow-up. Methods: The ReumaCoV Brasil is a longitudinal study designed to follow-up IMRD patients for 6 months after COVID-19 (cases) compared with IMRD patients no COVID-19 (controls). Clinical data, disease activity measurements and current treatment regarding IMRD, and COVID-19 outcomes were evaluated in all patients. Disease activity was assessed through validated tools at inclusion and at 3 and 6 months post-COVID-19. The FACIT-F (Functional Assessment of Chronic Illness Therapy) and DASS 21 (Depression, Anxiety and Stress Scale - 21 Items) questionnaires were also applied at 6 months after COVID-19 in both groups before large-scale vaccination. The significance level was set as p<0.05, with a 95% confidence interval. Results: A total of 601 patients were evaluated, being 321 cases (IMRD COVID-19+) and 280 controls (IMRD COVID-19 -), predominantly female with similar median age. No significant differences were noted in demographic data between the groups, including comorbidities, disease duration, and IMRD. Disease activity assessment over a 6-month follow-up showed no significant difference between cases and controls. While mean activity scores did not differ significantly, some patients reported worsened disease activity post-COVID-19, particularly in rheumatoid arthritis (RA) (32.2%) and systemic lupus erythematosus (SLE) (23.3%). Post-COVID-19 worsening in RA patients correlated with medical global assessment (MGA) and CDAI scores, with a moderate to large effect size. Diabetes mellitus showed a positive association (OR=7.15), while TNF inhibitors showed a protective effect (OR=0.51). Comparing SLEDAI pre- and post-COVID-19, a minority showed increased scores, with few requiring treatment changes. Fatigue, depression, anxiety, and stress were significantly higher in cases compared to controls. Worsening disease activity post-COVID correlated with worsened FACIT-F and DASS-21 stress scale in RA patients. No significant associations were found between COVID-19 outcomes and post-COVID-19 disease activity or psychological assessments. Conclusions: Post-COVID-19 IMRD patients show significant psychological well-being deterioration despite similar disease activity scores. The variability in reports on IMRD flares and the potential trigger of SARS-CoV-2 for autoimmune manifestations underline the need for detailed clinical assessment and a comprehensive approach to managing them.

Cell culture differentiation and proliferation conditions influence the in vitro regeneration of the human airway epithelium (preprint)

The human airway mucociliary epithelium can be recapitulated in vitro using primary cells cultured in an Air-Liquid Interface (ALI), a reliable surrogate to perform pathophysiological studies. As tremendous variations exist between media used for ALI-cultured human airway epithelial cells, our study aimed to evaluate the impact of several media (BEGM, PneumaCult, "Half&Half" and "Clancy") on cell type distribution using single-cell RNA sequencing and imaging. Our work revealed the impact of these media on cell composition, gene expression profile, cell signaling or epithelial morphology. We found higher proportions of multiciliated cells in PneumaCult-ALI and Half&Half, stronger EGF signaling from basal cells in BEGM-ALI, differential expression of the SARS-CoV-2 entry factor ACE2, and distinct secretome transcripts depending on media used. We also established that proliferation in PneumaCult-Ex Plus favored secretory cell fate, showing the key influence of proliferation media on late differentiation epithelial characteristics. Altogether, our data offer a comprehensive repertoire for evaluating the effects of culture conditions on airway epithelial differentiation and will help to choose the most relevant medium according to the processes to be investigated such as cilia, mucus biology or viral infection. We detail useful parameters that should be explored to document airway epithelial cell fate and morphology.

Evaluating the Impact of Vaccine Hesitancy on the Allocation of Vital Resources During COVID-19 Pandemic (preprint)

The COVID-19 pandemic highlighted significant challenges in the allocation of vital healthcare resources. Existing epidemiological models, specifically compartmental models, aimed to predict the spread of the COVID-19 virus and its impact on the population, but they overlooked the influence of \ac{VH} on disease dynamics, including the expected number of hospitalizations and fatalities. We propose improvements to the \ac{SEIR} model for COVID-19 by incorporating the influence of vaccination, \ac{VH}, and resource availability on the disease dynamics. We collect publicly available data and perform data analysis to capture \ac{VH} dynamic changes over time and develop scenario paths for \ac{VH}. We simulate the proposed compartmental model for each \ac{VH} path to explain the impacts of public attitudes toward vaccination, the impacts of healthcare resources on patient outcomes, and the timing of vaccination rollout on the progression and severity of the epidemic. Our analysis demonstrates that reducing \ac{VH} improves health outcomes, reinforcing the importance of addressing \ac{VH} to curb the spread of infectious diseases. Our results show that adequate levels of critical healthcare resources are crucial for minimizing fatalities and also highlight the life-saving impact of timely and effective vaccination programs.

Computing psycholinguistic analysis by examining topic modelling and sentiment analysis during COVID-19: changes in wording and emotions for public health (preprint)

Between 2020 and 2022, lockdown and restraining measures as a result of the COVID-19 pandemic led to changes in daily routines and also in language usage. At certain points during the pandemic, populations in some countries were unwilling or unlikely to respond to government messages, either because of the tone and analytic discourse used by leaders, or because they did not understand the messages. Linguistic markers and meanings were therefore linked to low levels of engagement, negative emotions and high levels of analytical thinking, especially in relation to the discourses of influential global speakers. We subjected sixteen speeches by eight country leaders to topic modelling and sentiment analysis in order to understand how the psychological functions of language were affected during two different periods of the COVID-19 pandemic. In this topic analysis we organize 39,073 words collected from sixteen authentic speeches delivered in two different periods of the acute phase of the pandemic. These were encoded in the Linguistic Inquiry Word Count program (LIWC), with the main aim being to identify differences between the periods. We examined the following aspects: (1) the emotional tone, analytical thinking and clout (empathy dimension); (2) the changes in these three dimensions or factors between periods 1 and 2 (February and May 2020). We observed a negative relationship between emotional tone and analytical thinking and a positive relationship between clout and emotional tone. When we considered the changes in pandemic circumstances, the psycholinguistic profiles of eight country leaders demonstrated fluctuations in language and emotions. Further reviews and research should focus on the current language and deficit wording of this population (leaders). We also note that psychologists and schoolteachers can play an important role in supporting language programmes with positive wording and by emphasising the collateral effects of face-to-face classes when teaching children to read and write.

Slight recovery of brain metabolic impairment in patients with persistent long COVID: a nine-month follow-up [18F]FDG-PET study (preprint)

Purpose A hypometabolic profile involving the limbic areas, brainstem and cerebellum has been identified in long COVID patients via cerebral [18F]fluorodeoxyglucose (FDG)-PET. This study was conducted to evaluate possible recovery of brain metabolism during the follow-up of patients with prolonged symptoms.Methods Fifty-six adults with long COVID who underwent two brain [18F]FDG-PET scans in our department in May 2020–October 2022 were retrospectively analysed and compared to 51 healthy subjects. On average, PET1 was performed 7 (range 3–17) months after acute COVID-19 infection, and PET2 was performed 16 (range 8–32) months after acute infection. PET was performed because of persistent symptoms, including the following conditions: asthenia, cognitive complaints, dyspnoea, and sleep disorders. Whole-brain voxel-based analysis compared PET1 and PET2 from long COVID patients to scans from healthy subjects (p-voxel < 0.001 uncorrected, p-cluster < 0.05 FWE-corrected) and PET1 to PET2 (with the same threshold and with a less constrained threshold of p-voxel < 0.005 uncorrected, p-cluster < 0.05 uncorrected).Results PET1 and PET2 scans revealed hypometabolism in the previously reported profile. The between-group analysis comparing PET1 and PET2 showed minor improvements in the pons and cerebellum (8.4 and 5.2%, respectively, only significant under the less constrained uncorrected p-threshold); for the pons, the improvement was correlated with the PET1-PET2 interval (r = 0.21, p < 0.05). Of the 14,068 hypometabolic voxels identified on PET1, 6,503 were also hypometabolic on PET2 (46%). Of the 7,732 hypometabolic voxels identified on PET2, 6,094 were also hypometabolic on PET1 (78%).Conclusion Subjects with persistent symptoms of long COVID exhibit durable changes in brain metabolism, with only slight improvement 9 months later.

Correlating Quantitative and Genomic SARS-CoV-2 Wastewater Data with Clinical Metrics in Metropolitan Perth, Western Australia (preprint)

Wastewater-based epidemiology (WBE) has emerged as a key method for continuous monitoring of COVID-19 prevalence including circulating SARS-CoV-2 lineages. WBE addresses limitations of traditional clinical COVID-19 surveillance such as clinical test availability, fluctuating testing rates and increased reliance on rapid antigen tests. Our study in Perth, Western Australia, found a significant positive correlation between SARS-CoV-2 concentrations in wastewater and clinical PCR positivity rates (rs = 0.772; p < 0.001) over an 18-month period that included four successive COVID-19 waves. A strong positive correlation was apparent between the proportions of SARS-CoV-2 lineages in wastewater and clinical cases within the same region (rs = 0.728; p < 0.001), including earlier detection of Omicron and recombinant lineages in wastewater before clinical case confirmation. The successful integration of WBE with healthcare data underscores its critical role in enhancing public health decision-making and pandemic management. This approach not only demonstrates the value of WBE in current global health surveillance efforts but also highlights the potential of WBE to address future public health challenges, as a comprehensive disease monitoring and response approach.

Fluoxetine and Sertraline Potently Neutralize the Replication of Distinct SARS-CoV-2 Variants (preprint)

The pandemic caused by SARS-CoV-2 is still a major health problem. Newly emerging variants and long-COVID-19 represent a challenge for the global health system. In particular, individuals in developing countries with insufficient health care need easily accessible, affordable and effective treatments of COVID-19. Previous studies have demonstrated the efficacy of functional inhibitors of acid sphingomyelinase (FIASMA) against infections with various viruses, including early variants of SARS-CoV-2. This work investigated whether the acid sphingomyelinase inhibitors fluoxetine and sertraline, usually used as antidepressant molecules in clinical practice, can inhibit the replication of the former and recently emerged SARS-CoV-2 variants in vitro. Fluoxetine and sertraline potently inhibited the infection with pseudotyped virus like particles and SARS-CoV-2 variants D614G, alpha, delta, omicron BA.1 and omicron BA.5. These results highlight fluoxetine and sertraline as priority candidates for large-scale phase 3 clinical trials at different stages of SARS-CoV-2 infections, either alone or in combination with other medications.

Retrospective analysis of telematic glaucoma clinic as a consequence of COVID-19 pandemic (preprint)

PURPOSE Due to COVID-19 pandemic, the glaucoma clinic had to adapt to meet the needs of this chronic disease. New technologies allowed us to monitor some of these patients in a telematic way.  METHODS We retrospectively analyzed patients with-open angle glaucoma who were visited between September 2021 and March 2022, and compared Visual Field (VF) and Optical Coherence Tomography (OCT) parameters depending on whether they had telematic or only face-to-face controls. All patients were stratified in each group according to glaucoma severity.  RESULTS A total of 204 eyes from 118 patients were included in the analysis, with 100 in the group with only face-to-face controls (group 1/FTF) and 104 with some telematic control (group 2/HG). In group 2/HG, an average of 3.37 face-to-face visits and 1.27 telematic visits were made, while group 1/FTF had 4.4 face-to-face visits. There was no significant difference between the pre-pandemic and 2 years after it visits, neither in Visual Accuity, OCT and VF parameters. Regarding glaucoma severity, there were more cases of severe glaucoma in group 1/FTF and more cases of mild glaucoma in group 2/HG.  CONCLUSIONS Telematic management of the glaucoma clinic, with the use of appropriate tools, can be useful for maintaining the quality of care during periods of face-to-face consultations saturation or when face-to-face control is completely impossible.

SARS-CoV-2 Neutralizing Antibodies in Three African Countries Following Multiple Distinct Immune Challenges (preprint)

Background: The COVID-19 pandemic has affected Madagascar, Cameroon, and the Central African Republic (CAR), with each experiencing multiple waves by mid-2022. This study aimed to evaluate immunity against SARS-CoV-2 strains Wuhan (W) and BA.2 (BA.2) among healthcare workers (HCWs) in these countries, focusing on vaccination and natural infection effects. Methods: HCWs' serum samples were analyzed for neutralizing antibodies (nAbs) against W and BA.2 variants, with statistical analyses comparing responses between countries and vaccination statuses. Results: Madagascar showed significantly higher nAb titers against both strains compared to CAR and Cameroon. Vaccination notably increased nAb levels against W by 2.6-fold in CAR and 1.8-fold in Madagascar, and against BA.2 by 1.6-fold in Madagascar and 1.5-fold in CAR. However, in Cameroon, there was no significant difference in nAb levels between vaccinated and unvaccinated groups. Conclusion: The study highlights the complex relationship between natural and vaccine-induced immunity, emphasizing the importance of assessing immunity in regions with varied epidemic experiences and low vaccination rates.

Sewage reclamation process as multifactorial public health risk concern: a longitudinal study. (preprint)

This year-long research analysed emerging risks in influent, effluent wastewaters and biosolids from six wastewater treatment plants in Spain's Valencian Region. Specifically, it focused on human enteric and respiratory viruses, bacterial and viral faecal contamination indicators, extended spectrum beta-lactamases-producing Escherichia coli and antibiotic resistance genes. Additionally, particles and microplastics in biosolid and wastewater samples were assessed. Human enteric viruses were prevalent in influent wastewater, with limited post-treatment reduction. Wastewater treatment effectively eliminated respiratory viruses, except for low levels of SARS-CoV-2 in effluent and biosolid samples, suggesting minimal public health risk. Antibiotic resistance genes and microplastics were persistently found in effluent and biosolids, thus indicating treatment inefficiencies and potential environmental dissemination. This multifaced research sheds light on diverse contaminants present after water reclamation, emphasizing the interconnectedness of human, animal, and environmental health in wastewater management. It underscores the need for a One Health approach to address the United Nations Sustainable Development Goals.

The relationship between neighbourhood income and youth mental health service use differs by immigration: Analysis of population-based data in British Columbia, Canada (preprint)

Purpose We investigated the relationship between neighbourhood income quintile and mental health service use by immigration among youth and explored changes during the COVID-19 pandemic. Method We used administrative data to examine mental health service use in British Columbia, Canada, among youth aged 10 to 24 between April 1, 2019, and March 31, 2022. We compared rates of community-based service use, emergency department visits, and hospitalizations and the proportion of involuntary admissions by neighbourhood income quintile and immigration. We used models stratified by immigration to estimate the relationship with income. Results Non-immigrant youth used substantially more services than immigrant youth. Service use increased following the pandemic's start and peaked between January and March 2021. We observed a clear income gradient for community-based service use among both immigrant and non-immigrant youth, but the direction of the gradient was reversed. Service use was highest among non-immigrant youth in lower-income neighbourhoods and lowest for immigrant youth in lower-income neighbourhoods. We observed similar patterns of income gradient for non-immigrant youth for emergency department visits and hospitalization. The proportion of involuntary admissions was higher for immigrant youth. Conclusions Mental health service use was substantially lower among immigrant youth than non-immigrant youth, but higher proportions of immigrant youth were hospitalized involuntarily. The reverse income gradient patterns observed for community-mental health service use are noteworthy and suggest significant barriers to accessing preventable care among immigrant youth, particularly those living in lower-income neighbourhoods.

Impact of the COVID-19 Pandemic on the Diagnosis of Malignant Neoplasia of the Bronchus and Lung in the Burgos Region (preprint)

Purpose: This study analysed the impact of the COVID-19 pandemic on the diagnosis of malignant neoplasia of the bronchus and lung. Cases diagnosed in the Burgos region in the year prior to the official declaration of the pandemic were compared with those in the year after the pandemic. The research sought to identify whether there was a decrease in the number of cases during the pandemic, and whether this may have led to a delay in diagnosis, reflected in more advanced stages of the disease. Mortality and survival time in each of the periods were also analysed.

Mosaic sarbecovirus vaccination elicits cross-reactive responses in pre-immunized animals (preprint)

Immunization with mosaic-8b [60-mer nanoparticles presenting 8 SARS-like betacoronavirus (sarbecovirus) receptor-binding domains (RBDs)] elicits more broadly cross-reactive antibodies than homotypic SARS-CoV-2 RBD-only nanoparticles and protects against sarbecoviruses. To investigate original antigenic sin (OAS) effects on mosaic-8b efficacy, we evaluated effects of prior COVID-19 vaccinations in non-human primates and mice on sarbecovirus response breadths elicited by mosaic-8b, admix-8b (8 homotypics), and homotypic SARS-CoV-2, finding greatest cross-reactivity for mosaic-8b. As demonstrated by molecular fate-mapping in which antibodies derived from specific cohorts of B cells are differentially detected, B cells primed by WA1 spike mRNA-LNP dominated antibody responses after RBD-nanoparticle boosting. While mosaic-8b and homotypic-nanoparticles boosted cross-reactive antibodies, de novo antibodies were predominantly induced with mosaic-8b boosting, and these were specific for variant RBDs with increased identity to RBDs on mosaic-8b. These results inform OAS mechanisms and support using mosaic-8b to protect COVID-19 vaccinated/infected humans against as-yet-unknown SARS-CoV-2 variants and animal sarbecoviruses with human spillover potential.

Impact of mechanical power on mortality in ventilated critically ill patients. Retrospective study with continuous real-life data (preprint)

Background Over the past decade, numerous studies on potential factors contributing to ventilation-induced lung injury have been carried out. Mechanical power has been pointed out as the parameter that encloses all ventilation-induced lung injury-contributing factors. However, studies conducted to date provide data regarding mechanical power during the early hours of mechanical ventilation that may not correspond to the real scenario. Methods Retrospective observational study conducted at a single center in Spain. Patients admitted to the intensive care unit, > o = 18 years of age, and ventilated for over 24 hours were included. We extracted the mechanical power values throughtout the entire mechanical ventilation period from the clinical information system every two minutes. First, we calculate the cutoff-point for mechanical power beyond which there was a greater change in the probability of death. After, the sum of time values above the safe cut-off point was calculated to obtain the value in hours. We analyzed if the number of hours the patient was under ventilation with a mechanical power above the safe threshold was associated with mortality, invasive mechanical ventilation days, and intensive care unit length of stay. We repeated the analysis in different subgroups based on the degree of hypoxemia and in patients with SARS CoV-2 pneumonia. Results The cut-off point of mechanical power at with there is a higher increase in mortality was 18J/min. The greater the number or hours patients were under mechanical power > 18 J/min the higher the mortality in all the study population, in patients with SARS CoV-2 pneumonia and in mild to moderate hyopoxemic respiratory failure. The risk of death inceases 0.1% for each our with mechanical power exceeding 18 J/min. The number of hours with mechanical power > 18 J/min also affected the days of invasive mechanical ventilation and intensive care unit length of stay. Conclusions Continuous monitoring of mechanical power using an automated clinical information system shows that the number of hours with mechanical power > 18 J/min increases mortality in critically ill patients.

A genetically modulated Toll-like-receptor-tolerant phenotype in peripheral blood cells of children with multisystem inflammatory syndrome. (preprint)

Dysregulated innate immune responses contribute to multisystem inflammatory syndrome in children (MIS-C), characterized by gastrointestinal, mucocutaneous, and/or cardiovascular injury occurring weeks after SARS-CoV-2 exposure. To investigate innate immune functions in MIS-C, we stimulated ex vivo peripheral blood cells from MIS-C patients with agonists of Toll-like receptors (TLR), key innate immune response initiators. We found severely dampened cytokine responses and elevated gene expression of negative regulators of TLR signaling. Increased plasma levels of zonulin, a gut leakage marker, were also detected. These effects were also observed in children enrolled months after MIS-C recovery. Moreover, cells from MIS-C children carrying rare genetic variants of lysosomal trafficking regulator (LYST) were less refractory to TLR stimulation and exhibited lysosomal and mitochondrial abnormalities with altered energy metabolism. Our results strongly suggest that MIS-C hyperinflammation and/or excessive or prolonged stimulation with gut-originated TLR ligands drive immune cells to a lasting refractory state. TLR hyporesponsiveness is likely beneficial, as suggested by excess lymphopenia among rare LYST variant carriers. Our findings point to cellular mechanisms underlying TLR hyporesponsiveness; identify genetic determinants that may explain the MIS-C clinical spectrum; suggest potential associations between innate refractory states and long COVID; and highlight the need to monitor long-term consequences of MIS-C.