Cold case: COVID-19-triggered type 1 cryoglobulinemia (preprint)

A 42-year-old male was referred to the internal medicine department because of renal failure and persistent malaise after a recent SARS-CoV-2 infection. Blood results showed anemia and severe renal insufficiency (hemoglobin of 6.4 mmol/l and a creatinine of 194 umol/l). Additional tests revealed a type I cryoglobulinemia with a cryoprecipitate composed of biclonal IgM (kappa and lambda). Further investigations on the cryoprecipitate revealed that the immunoglobulins were directed against SARS-CoV-2 antigens. In the meanwhile, our patient noticed improvement of his symptoms accompanied by resolution of laboratory abnormalities. Three months later, the cryoglobulin could no longer be detected. Type 1 cryoglobulinemia is usually associated with lymphoproliferative disorders and is characterized by various symptoms caused by cryoprecipitates occluding small blood vessels. This is, to our knowledge, the first case of type I cryoglobulinemia with proven precipitation of SARS-CoV-19 antibodies. COVID-19 induced cryoglobulinemia appears to have a mild disease course and to be self-limiting upon viral clearance.

Strategies for rapid scale up of laboratory capacity in a public health emergency in a resource-constrained setting: the SARS-CoV-2 Nigeria response experience (preprint)

Introduction: Sufficient laboratory capacity is vital to containing infectious diseases outbreaks. This study was conducted to assess SARS-CoV-2 testing performance, the strategies adopted to scale up laboratory testing capacity, and to highlight challenges and lessons learnt in Nigeria’s response to COVID-19 pandemic regarding testing strategies.Methods This cross-sectional descriptive study adopted a mixed method approach including desk reviews and key informant interviews (KIIs). The KIIs were conducted among actors of the COVID-19 response teams in states (SMoH) and the Federal Ministry of Health (FMoH) in Nigeria. Data extraction tools were populated from the relevant online resources and documents of the FMoH, SMoH and the Nigeria Centre for Disease Control.Results At the beginning of the pandemic in Nigeria, testing performance was poor, but this improved over time. To manage the demand for testing, Nigeria adopted targeted testing with a focus on symptomatic contacts and alerts, returning travelers from high-risk countries who were symptomatic during the quarantine period, among others groups. Strategies to enhance laboratory capacity and improve the turnaround time for results included leveraging on existing tuberculosis laboratory network or building new laboratories where none existed; decentralization of sample collection and testing; staff health workers repurposing and hiring of volunteers; training and retraining of laboratory personnel; adoption of rapid diagnostic testing; and strengthening public-private partnerships to leverage the private sector testing. From an initial three laboratories with capacity to test for SARS-CoV-2 in February, 2020, the number of laboratories increased to 158 by March, 2022. Although laboratory capacity increased, logistics and supply chain disruption was still a challenge.Conclusion Investment in local manufacturing capacities of laboratory consumables such as RDTs and reagents would promote self-reliance and sustainability for a country as populous as Nigeria.

Weight loss treatment of COVID-19 in patients with NCDs: a pilot prospective clinical trial (preprint)

Background COVID-19 in comorbidity with non-communicable chronic diseases (NCDs) complicate the diagnosis, treatment, prognosis, and increase mortality rate.Objective. To evaluate the effects of the weight loss treatment on clinic/laboratory inflammation and metabolic profile, reactive oxygen species (ROS) body composition in patients with COVID-19 in comorbidity with NCDs.Design: A 6-week open, pilot prospective clinical trial.Setting: The study included 72 adult patients with COVID and influenza in comorbidity with type 2 diabetes (T2D), hypertension, and NASH.Interventions: The treatment involved a fast-weight-loss-method (Analimentary detoxication, ANADETO) including calorie restriction to 50–100 kcal/day, salt intake to 5–6 gr/day, hot water drinking 1000–1500 ml/day, walking > 2,000 steps/day, and sexual self-restraint.Main outcome measures: Primary endpoints: Clinic/infectious/inflammation tests for COVID/Influenza; weight loss during 14 days. Secondary endpoints: fasting blood glucose, HbA1c, blood insulin; systolic/diastolic BP; blood lipids; ALT/AST, chest-CT-scan.Results The patients weight lost from baseline (-9,14 − 12,4%; P < 0.001); COVID and Influenza were a negative in > 96.3% patients at the 14 days. Systolic/diastolic BP normalized (P < 0.0001), glucose/lipids metabolism (P < 0.0001); ALT/AST normalized (P < 0.0001), platelets increased from baseline (P < 0.0001), chest-CT (P < 0.0001) at 6-week follow-up. The previous antidiabetic, antihypertensive, anti-inflammatory and hepatoprotective, and other symptomatic medications were adequately decreased in 2–5 days to completely stopping by 5–8 days treatment.Conclusions The non-pharmacological treatment including fast weight loss is clinical/laboratory benefit in treatment of patients with COVID-19 and Influenza in comorbidity with T2D, hypertension, and NASH.Trial Registration: ClinicalTrials.gov NCT05635539 (12/01/2022): https://clinicaltrials.gov/ct2/show/NCT05635539?term=NCT05635539&draw=2&rank=1 .

Vaccination effects on post-infection outcomes in the Omicron BA.2 outbreak in Shanghai.

Omicron and its sublineages are currently predominant and have triggered epidemiological waves of SARS-CoV-2 around the world due to their high transmissibility and strong immune escape ability. Vaccines are key measures to control the COVID-19 burden. Omicron BA.2 caused a large-scale outbreak in Shanghai since March 2022 and resulted in over 0.6 million laboratory-confirmed infections. The vaccine coverage of primary immunization among residents aged 3 years and older in Shanghai exceeded 90%, and inactivated COVID-19 vaccines were mainly delivered. In the context of high vaccine coverage, we conducted a cohort study to assess vaccine effects on reducing the probability of developing symptoms or severity of disease in infections or nonsevere cases. A total of 48,243 eligible participants were included in this study, the majority of whom had asymptomatic infections (31.0%) and mild-to-moderate illness (67.9%). Domestically developed COVID-19 vaccines provide limited protection to prevent asymptomatic infection from developing into mild-to-moderate illness and durable protection to prevent nonsevere illness from progressing to severe illness caused by Omicron BA.2. Partial vaccination fails to provide effective protection in any situation. The level of vaccine effects on disease progression in the elderly over 80 years old was relatively lower compared with other age groups. Our study results added robust evidence for the vaccine performance against Omicron infection and could improve vaccine confidence.

Weight loss in patients with COVID-19 and Influenza in comorbidity with NCDs: a pilot prospective clinical trial. (preprint)

Background COVID and Influenza with non-communicable chronic diseases (NCDs) complicate the diagnosis, treatment, prognosis, and increase mortality rate. The aim: to evaluate the effects of the fast weight loss on clinic and laboratory inflammation profile, metabolic profile, reactive oxygen species (ROS) and body composition in patients with COVID and Influenza in comorbidity with NCDs. Methods A 6-week open, pilot prospective clinical trial including 62 adult patients with COVID (n=27) and influenza (n=35) in comorbidity with T2D, hypertension, and NASH. Overweight in 33 patients (53.2%) with BMI 28.14{+/-}0.39 kg/m2, and 29 patients without overweight with BMI 23.37 {+/-} 0.38 kg/m2. T2D in 26 (41.9%); Hypertension in 38 (61.3%) (incl. 12 patients with T2D); NASH in 51 patients (82.2%) (incl. 8 patients with NASH, T2D and Hypertension; 6 patients with NASH and T2D; 18 patients with NASH and Hypertension; 19 patients with only NASH). Primary endpoints Clinic/infectious/inflammation tests for COVID and Influenza; weight loss during 14 days. Secondary endpoints: fasting blood glucose, HbA1c, blood insulin; systolic/diastolic BP; blood lipids; ALT, AST, chest CT-scan. Results The patients with overweight lost -12,4% from baseline or BMI= -4.2 kg/m2, and patients without overweight lost -9,14% from baseline or BMI= -2.2 kg/m2 (-9.7{+/-}0.7 kg vs. -6.4{+/-}0.6 kg, respectively; P<0.001) at 14-day of the treatment. Weight loss in both groups was due to reduction of fat mass (P<0.0001). Sputum production increased in 1.0-1.5 liter/day on 2-3 days, decreased in 7-9 days. Body temperature normalized in 6-9 days. On 3-5 days, in most patients their urine became turbid/muddy/intensively colored. Urine microscopy showed organic and non-organic salts, and leukocyturia (20-35/sight). White blood cells, lymphocytes, NLR normalized at 14 days (P<0.0001). Total-fibrinogen, C-reactive-protein, and Erythrocyte-sedimentation-rate, ROS normalized at 14-day of treatment (P<0.0001). COVID and Influenza were a negative in >96.3% patients at 14-day. Systolic/diastolic BP decreased (161.3{+/-}1.31/101.6{+/-}0.85 vs. 118.3{+/-}0.46/80.89{+/-}0.66, P<0.0001), glucose and lipids metabolism in patients with T2D (n=26) (P<0.0001); ALT and AST in patients with NASH (n=51) were significantly normalized (from baseline 134.3{+/-}5.4 and 166.5{+/-}5.5 U/L, respectively, and at 14-day to 78.4{+/-}4.2 and 92.4{+/-}4.9 U/L, respectively (P<0.0001)), platelets increased from baseline (186.5{+/-}4.6, x109/L) at 14-day of treatment (238.5{+/-}5.8, x109/L) (P<0.0001), and at 6-week follow-up (278.3{+/-}6.9, x109/L) (P<0.0001). The mean score of chest-CT for the patients (n=44) was 13.12{+/-}0.38 from baseline, and at 14-day the score was 1.72{+/-}0.12 (P<0.0001). ROS level normalized at 14-day treatment and 6-week follow-up from baseline (P<0.0001). The previous antidiabetic, antihypertensive, antiinflammatory and hepatoprotective, and other symptomatic medications were adequately decreased in 2-5 days to completely stopping by 5-8 days treatment. Conclusions The fast weight loss is clinical/laboratory benefit in treatment of patients with COVID-19 and Influenza in comorbidity with T2D, hypertension, and NASH.

SARS-CoV-2 variant transition dynamics are associated with vaccination rates, number of co-circulating variants, and natural immunity (preprint)

Background: Throughout the COVID-19 pandemic, the SARS-CoV-2 virus has continued to evolve, with new variants outcompeting existing variants and often leading to different dynamics of disease spread. Methods: In this paper, we performed a retrospective analysis using longitudinal sequencing data to characterize differences in the speed, calendar timing, and magnitude of 13 SARS-CoV-2 variant waves/transitions for 215 countries and sub-country regions, between October 2020 and October 2022. We then clustered geographic locations in terms of their variant behavior across all Omicron variants, allowing us to identify groups of locations exhibiting similar variant transitions. Finally, we explored relationships between heterogeneity in these variant waves and time-varying factors, including vaccination status of the population, governmental policy, and the number of variants in simultaneous competition. Findings: This work demonstrates associations between the behavior of an emerging variant and the number of co-circulating variants as well as the demographic context of the population. We also observed an association between high vaccination rates and variant transition dynamics prior to the Mu and Delta variant transitions. Interpretation: These results suggest the behavior of an emergent variant may be sensitive to the immunologic and demographic context of its location. Additionally, this work represents the most comprehensive characterization of variant transitions globally to date. Funding: Laboratory Directed Research and Development (LDRD), Los Alamos National Laboratory

Methylprednisolone use in children with severe pneumonia caused by SARS-CoV-2 (preprint)

Objective: This study aimed to evaluate the effectiveness and optimal use of corticosteroids in children with severe coronavirus disease 2019 (COVID-19) pneumonia. Methods: We conducted a retrospective study and included patients (aged<18 years) with severe COVID-19 pneumonia and/or acute respiratory distress syndrome (ARDS) who received standard doses (2–4 mg/kg/day) and high doses (>250 mg/day) of methylprednisolone (MPZ). We adjusted for patients on steroid treatments with a propensity score and patient survival. Results: Fifty-nine patients were included: 61% were male, the median age was 8 (interquartile range [IQR], 2–15) years. The overall survival was 84.4% in patients treated with standard-dose MPZ (n = 45, 76.3%) and 92.2% in patients treated with high-dose MPZ (n = 14, 23.7%; p = 0.67). The demographic, clinical, and laboratory data didn’t differ significantly after propensity score matching, apart from bradycardia, which was a prominent feature of the high-dose group. The clinical and radiological response rates on Day 7 were higher and the need for invasive mechanical ventilation (IMV) was lower in the high-dose group. Conclusion: Pulse MPZ treatment seems to result in better clinical and radiological responses, with less need for IMV, although the mortality rate doesn’t differ between standard and high-dose regimens of MPZ.

Clinical Subphenotypes of Multisystem Inflammatory Syndrome in Children: An EHR-based cohort study from the RECOVER program (preprint)

Background: Multi-system inflammatory syndrome in children (MIS-C) represents one of the most severe post-acute sequelae of SARS-CoV-2 infection in children, and there is a critical need to characterize its disease patterns for improved recognition and management. Our objective was to characterize subphenotypes of MIS-C based on presentation, demographics and laboratory parameters. Methods: We conducted a retrospective cohort study of children with MIS-C from March 1, 2020 - April 30, 2022 and cared for in 8 pediatric medical centers that participate in PEDSnet. We included demographics, symptoms, conditions, laboratory values, medications and outcomes (ICU admission, death), and grouped variables into eight categories according to organ system involvement. We used a heterogeneity-adaptive latent class analysis model to identify three clinically-relevant subphenotypes. We further characterized the sociodemographic and clinical characteristics of each subphenotype, and evaluated their temporal patterns. Findings: We identified 1186 children hospitalized with MIS-C. The highest proportion of children (44.4%) were aged between 5-11 years, with a male predominance (61.0%), and non-Hispanic white ethnicity (40.2%). Most (67.8%) children did not have a chronic condition. Class 1 represented children with a severe clinical phenotype, with 72.5% admitted to the ICU, higher inflammatory markers, hypotension/shock/dehydration, cardiac involvement, acute kidney injury and respiratory involvement. Class 2 represented a moderate presentation, with 4-6 organ systems involved, and some overlapping features with acute COVID-19. Class 3 represented a mild presentation, with fewer organ systems involved, lower CRP, troponin values and less cardiac involvement. Class 1 initially represented 51.1% of children early in the pandemic, which decreased to 33.9% from the pre-delta period to the omicron period. Interpretation: MIS-C has a spectrum of clinical severity, with degree of laboratory abnormalities rather than the number of organ systems involved providing more useful indicators of severity. The proportion of severe/critical MIS-C decreased over time.

Biosafety of personnel of microbiological laboratories in the context of the Federal Law of the Russian Federation № 492-FZ of December 30, 2020 «On the biological safety of the Russian Federation¼.

One of the most important requirements for the personnel of microbiological laboratories working with pathogenic and infectious agents is the observance of precautionary measures and the implementation of a set of preventive measures, collectively interpreted as biological safety (biosafety). To a large extent, biosafety problems are also relevant for all clinical laboratories working with biosubstrates, with the potential threat of containing pathogens of bloodborne infections in them. On December 30, 2020, the President of the Russian Federation signed Federal Law № 492 «On the Biological Safety of the Russian Federation¼ (№ 492-FZ), which regulates the basic legal norms and regulation of biosafety issues, as well as a list of measures to prevent the risks of the spread of infections due to accidents, bioterrorist acts and sabotage. The current pandemic of the coronavirus infection COVID-19 has demonstrated, on the one hand, the epidemiological vulnerability of the single world space, and on the other hand, the decisive influence of biological emergencies on the emergence of negative political and economic processes in the world community. In this regard, the issues of ensuring biosafety in the work of microbiological laboratories in the context of protecting personnel and the environment from accidental or unintentional spread of infections are relevant. Working with pathogenic biological agents in microbiological laboratories is constantly associated with the risk of accidents and possible laboratory infection (laboratory-acquired infections) of employees, environmental pollution if the requirements of regulatory documents on biological safety are not met. In accordance with the requirements of № 492-FZ, in order to prevent biological threats, it is necessary to create a system for monitoring biological risks in microbiological laboratories when working with any infected material.

Biomarkers and Outcomes in Hospitalized Covid-19 Patients: A Prospective Registry (preprint)

ABSTRACT Objectives: To determine association of biomarkers high sensitivity C-reactive protein (hsCRP), D-dimer, interleukin-6 (IL-6), lactic dehydrogenase (LDH), ferritin and neutrophil-lymphocyte ratio (NLR) at hospital admission with clinical features and outcomes in Covid-19. Methods: Successive virologically confirmed Covid-19 patients hospitalized from April 2020 to July 2021 were recruited in a prospective registry. Details of clinical presentation, investigations, management and outcomes were recorded. All the biomarkers were divided into tertiles to determine associations with clinical features and outcomes. Numerical data are presented in median and interquartile range (IQR 25-75). Univariate and multivariate (age, sex, risk factor, comorbidity adjusted) odds ratio (OR) and 95% confidence intervals (CI) were calculated to determine association of deaths with each biomarker. Results: We identified 3036 virologically confirmed Covid-19 patients during the study period, 1215 were hospitalized and included in the present study. Men were 70.0%, aged >60y 44.8%, hypertension 44.8% diabetes 39.6% and cardiovascular disease 18.9%. Median symptom duration was 5 days (IQR 4-7) and SpO2 95% (90-97). Total white cell count was 6.9x103/micro-litre, (5.0-9.8), neutrophils 79.2% (68.1-88.2) and lymphocytes 15.8% (8.7-25.5). Medians (IQR) for biomarkers were hsCRP 6.9 mg/dl (2.2-18.9), D-dimer 464 ng/dl (201-982), IL-6 20.1 ng/dl (6.5-60.4), LDH 284 mg/dl (220-396) and ferritin 351 mg/dl (159-676). Oxygen support at admission was in 38.6%, and non-invasive or invasive ventilatory support in 11.0% and 11.6% respectively. 173 (13.9%) patients died and 15 (1.2%) transferred to hospice care. For each biomarker, those in the second and third tertiles, compared to the first, had worse clinical and laboratory abnormalities, and greater oxygen and ventilatory support. Multivariate adjusted OR (95% CI) for deaths in second and third vs first tertiles, respectively, were for hsCRP 2.29(1.14-4.60) and 13.39(7.23-24.80); D-dimer 3.26(1.31-7.05) and 13.89(6.87-28.27); IL-6 2.61(1.31-5.18) and 10.96(5.88-20.43); ferritin 3.19(1.66-6.11) and 9.13(4.97-16.78); LDH 1.85(0.87-3.97) and 10.51(5.41-20.41); and NLR 3.34(1.62-6.89) and 17.52(9.03-34.00) (p<0.001). Conclusions: In Covid-19, high levels of biomarkers- hsCRP, D-dimer, IL-6, LDH, ferritin and NLR are associated with more severe illness and significantly greater in-hospital mortality. NLR, a simple, widely available and inexpensive investigation provides prognostic information similar to the more expensive biomarkers.

More severe pneumonitis in children predicts the need for admission and elevation of some but not all markers of severe Covid-19. (preprint)

Unlike most other viral pneumonitis, SARS-CoV-2 often causes hyperferritinemia, elevations in D-dimer, lactate dehydrogenase (LDH), transaminases, troponin, CRP, and other inflammatory markers. We questioned (1) if the severity of pneumonitis observed on lung ultrasound was associated with hospitalization and (2) could lung ultrasound be used to stratify which children needed blood tests? Methods We did a retrospective cross-sectional review of children aged between 14 days and 21 years of age being evaluated for Covid-19 in our pediatric emergency department from 30/November/2019 to 14/August/2021 who had had a point-of-care lung ultrasound. Lung ultrasounds were categorized using a 6-point ordinal scale. We used logistic regression to estimate the adjusted effect of lung ultrasound on hospital admission. We performed ordinary least square regression for the association between lung ultrasound severity and laboratory abnormalities. We adjusted these using propensity score derived inverse probability weighting to account for the non-random decision to obtain laboratory investigations. Results We identified 500 point-of-care lung ultrasounds of which 427 could be assigned a severity category. Increasing lung ultrasound severity was associated with increased hospital admission OR 1.36( 95% CI 1.08, 1.72.) Ferritin, LDH, transaminases, and D-dimer, but not CRP or troponin were significantly associated with more than moderately severe lung ultrasounds. D-Dimer, CRP, and troponin were sometimes elevated even when lung ultrasound was normal. Conclusion Severity of pneumonitis was associated with hospital admission. Ferritin, LDH, transaminases, and D-dimer were increased in more than moderately severe pneumonitis but lung ultrasound did not predict elevation of other markers.

Improvement of field-deployable metagenomic virus detection by a simple pretreatment method (preprint)

As both the current COVID-19 pandemic and earlier pandemics have shown, animals are the source for some of the deadliest viral pathogens, which can spread to humans. Therefore, early detection at the point of incidence is crucial to both prevent and understand the threats posed to human health from pathogens in animal reservoirs. Often, the exact genetic nature of these zoonotic pathogens is unknown and advanced laboratory facilities do not exist in most field settings and therefore the development of methods for unbiased metagenomic and point of incidence detection is crucial in order to identify novel viral pathogens in animals with zoonotic and pandemic potential. Here we addressed some of these issues by developing a metagenomic Nanopore next-generation sequencing (mNGS) method for nucleic acids extracted from clinical samples from patients with SARS-CoV-2. To reduce the non-RNA viral genetic components in the samples, we used DNase pretreatment in a syringe followed by filtration and found that these pretreatments increased the number of SARS-CoV2 reads by > 500-fold compared with no pretreatment. The simple protocol, described here, allows for fast (within 6 hours) metagenomic detection of RNA viruses in biological samples exemplified by SARS-CoV-2 detection in clinical throat swabs. This method could also be applied in field settings for point of incidence detection of virus pathogens, thus eliminating the need for transport of infectious samples, cold storage and a specialized laboratory. Highlights Here we present a field-deployable metagenomic Nanopore protocol for RNA virus detection. SARS-CoV-2 detection used as proof-of-concept. Analysis of simple methods for non-viral nucleic acid depletion were tested on SARS-CoV-2 clinical samples. DNase I treatment followed by 0.22µM syringe filtration dramatically increased the number of SARS-CoV-2 reads and virus genome coverage.

COVID-19 Patients’ Symptoms: Gastrointestinal Presentations, Comorbidities and Outcomes in a Canadian Hospital Setting (preprint)

ABSTRACT Background The Coronavirus disease 2019 (COVID-19) pandemic has had significant global impact. While public health interventions and universal health insurance has been credited with minimizing transmission rates in Canada relative to neighboring countries, significant morbidity and mortality have occurred nationwide. We sought to determine factors associated with differences in gastrointestinal outcomes in COVID-19 patients at a Canadian hospital. Methods We collected data from 192 hospital records of COVID-19 patients across seven Hamilton Health Sciences hospitals, a network of academic health centres serving one of the largest metropolitan areas in Canada. Statistical and correlative analysis of symptoms, comorbidities, and mortality were performed. Results There were 192 patients. The mean age was 57.6 years (SD=21.0). For patients who died (n=27, 14%), mean age was 79.2 years old (SD=10.6) versus 54 years for survivors (SD=20.1). There was a higher mortality among patients with older age ( p= 0.000), long hospital stay ( p= 0.004), male patients ( p= 0.032), and patients in nursing homes ( p= 0.000). Patients with dyspnea ( p= 0.028) and hypertension ( p= 0.004) were more likely to have a poor outcome. Laboratory test values that were significant in determining outcomes were an elevated INR ( p= 0.007) and elevated creatinine ( p= 0.000). Cough and hypertension were the most common symptom and comorbidity, respectively. Diarrhea was the most prevalent (14.5%) gastrointestinal symptom. Impaired liver function was related to negative outcome (LR 5.6; p =0.018). Conclusions In a Canadian cohort, elevated liver enzymes, prolonged INR and elevated creatinine were associated with poor prognosis. Hypertension was also linked to a higher likelihood of negative outcome. SUMMARY BOX What is already known about this subject? The prevalence of gastrointestinal symptoms in COVID-19 patients across Canada is lacking Gastrointestinal manifestations of COVID-19 are well described, and longterm sequelae of gastrointestinal tract involvement are an ongoing concern What are the new findings? There was a significant prevalence of gastrointestinal symptoms in patients with a confirmed diagnosis of COVID-19 at one of the largest metropolitan regions across Canada Liver enzyme abnormalities were common in patients at diagnosis This report, over an 8-month period, represents the largest cohort of COVID-19 patients reported in Canada How might these results impact on clinical practice in the foreseeable future? Baseline gastrointestinal symptoms and laboratory abnormalities correlate with patient outcome in Canadian COVID-19 patients These results enhance our knowledge of the prevalence of gastrointestinal symptoms and laboratory abnormalities in Canadian patients and offer important baseline data for longitudinal studies in these patients Our findings increase our knowledge of the epidemiology of COVID-19 in Canada and allow future comparison with international data

Impaired Immunogenicity to COVID-19 Vaccines in Autoimmune Systemic Diseases - High Prevalence of Non-Response in Different Patients’ Subgroups (preprint)

Background: Autoimmune systemic diseases (ASD) may show impaired immunogenicity to COVID-19 vaccines . Our prospective observational multicenter study aimed to evaluate the seroconversion after the vaccination cycle and at 6-12-month follow-up, as well the safety and efficacy of vaccines in preventing COVID-19.Methods: The study included 478 unselected ASD patients (mean age 59±15 years), namely 101 rheumatoid arthritis (RA), 38 systemic lupus erythematosus (SLE), 265 systemic sclerosis (SSc), 61 cryoglobulinemic vasculitis (CV), and a miscellanea of 13 systemic vasculitis. The control group included 502 individuals from the general population (mean age 59±14SD years). The immunogenicity of mRNA COVID-19 vaccines (BNT162b2 and mRNA-1273) was evaluated by measuring serum IgG-neutralizing antibody (NAb) (SARS-CoV-2 IgG II Quant antibody test kit; Abbott Laboratories, Chicago, IL) on samples obtained within 3 weeks after vaccination cycle.Findings: The short-term results of our prospective study revealed significantly lower NAb levels in ASD series compared to controls [286 (53-1203) vs 825 (451-1542) BAU/mL, p<0.0001], as well as between single ASD subgroups and controls. More interestingly, higher percentage of non-responders to vaccine was recorded in ASD patients compared to controls [13.2% (63/478), vs 2.8% (14/502); p<0.0001]. Increased prevalence of non-response to vaccine was also observed in different ASD subgroups, in patients with ASD-related interstitial lung disease (p=.009), and in those treated with glucocorticoids (p=.002), mycophenolate-mofetil (pInterpretations: Patients with weak/absent seroconversion, believed to be immune to SARS-CoV-2 infection, are at high risk to develop COVID-19. Early determination of serum NAb after vaccination cycle may allow to identify three main groups of ASD patients: responders, subjects with suboptimal response, non-responders. Patients with suboptimal response should be prioritized for a booster-dose of vaccine; while a different type of vaccine could be administered to non-responder individuals.Funding Information: None.Declaration of Interests: The authors do not have conflict of interest.Ethics Approval Statement: The study protocol was approved by local ethic committee (RETRO-CoV2 study code #17886_bio); informed consent was obtained from all patients before participation.

Clinical Efficacy and Adverse Events of Baricitinib Treatment for Coronavirus Disease-2019 (COVID-19): A Systematic Review and Meta-Analysis (preprint)

Background: The benefits of baricitinib, which is a Janus kinase inhibitor, in coronavirus disease-2019 (COVID-19) are inadequately defined. We performed a systematic review and meta-analysis of randomised, controlled trials and observational studies of baricitinib to determine its clinical efficacy and adverse events in patients with COVID-19.Methods: Major databases were searched from 2019 to 2021 inclusive. The primary outcome was the coefficient of mortality. We also compared increasing different doses of baricitinib, intensive care unit admission, the requirement for mechanical ventilation, the oxygenation index, and adverse events between baricitinib treatment and placebo or other treatments.Findings: Twelve studies of 3564 patients were included and assessed qualitatively (Jadad and Newcastle–Ottawa Scale scores). Baricitinib effectively improved the mortality rate (relative risk of mortality = 0.56; 95% confidence interval: 0.46–0.69; P < 0.00001; I2 = 2%), and this result was unchanged by subgroup analysis. Baricitinib also improved intensive care unit admission, the requirement for invasive mechanical ventilation, and the oxygenation index. Data from these studies also showed that baricitinib slightly reduced the risk of adverse events. With regard to the choice of the drug dosage of baricitinib, the high-dose group appeared to have additional benefits for clinical efficacy.Interpretation: Our study shows that baricitinib may be a promising, safe, and effective anti-severe acute respiratory syndrome-coronavirus-2 drug candidate, with the advantages of a low cost, easy production, and convenient storage.Funding Information: We gratefully acknowledge the financial supports by the Basic research program of Guangzhou (202102010224), Clinical Transformation program of the first affiliated hospital of Guangzhou medical university (ZH201802, ZH201914), High-level university program of Guangzhou medical university (2017(160)) and Opening Project of State Key Laboratory of Respiratory Disease (SKLRD-0P-202115).Declaration of Interests: The authors have no potential conflict of interest to disclose.

Robust and Functional Immunity up to 9 months after SARS-CoV-2 infection: a Southeast Asian longitudinal cohort (preprint)

Assessing the duration of humoral and cellular immunity remains key to overcome the current SARS-CoV-2 pandemic, especially in understudied populations in least developed countries. Sixty-four Cambodian individuals with laboratory-confirmed infection with asymptomatic or mild/moderate clinical presentation were evaluated for humoral immune response to the viral spike protein and antibody effector functions during acute phase of infection and at 6-9 months follow-up. Antigen-specific B cells, CD4+ and CD8+ T cells were characterized, and T cells were interrogated for functionality at late convalescence. Anti-spike (S) antibody titers decreased over time, but effector functions mediated by S-specific antibodies remained stable. S- and nucleocapsid (N)-specific B cells could be detected in late convalescence in the activated memory B cell compartment and are mostly IgG+. CD4+ and CD8+ T cell immunity was maintained to S and membrane (M) protein. Asymptomatic infection resulted in decreased ADCC and frequency of SARS-CoV-2-specific CD4+ T cells at late convalescence. Whereas anti-S antibodies correlated with S-specific B cells, there was no correlation between T cell response and humoral immunity. Hence, all aspects of a protective immune response are maintained up to nine months after SARS-CoV-2 infection in the absence of re-infection. One sentence summaryFunctional immune memory to SARS-CoV-2, consisting of polyfunctional antibodies, memory B cells and memory T cells are maintained up to nine months in a South-East Asian cohort in the absence of re-infection.

Time-to-event assessment for the discovery of the proper prognostic value of clinical biomarkers optimized for COVID-19 (preprint)

In the early days of the pandemic, clinical biomarkers for COVID -19 have been investigated to predict patient mortality. A decision tree has been proposed previously comprising three variables, i.e., lactic dehydrogenase (LDH), high-sensitivity C-reactive protein (CRP), and lymphocyte percentage, with more than 90% accuracy in a public cohort. In this work, we highlighted the importance of the cohort made publicly available and complemented the findings by incorporating further evaluation. Results confirmed poor short-term prognosis to abnormal levels of some laboratorial indicators, such as LDH, CRP, lymphocytes, interleukin-6, and procalcitonin. In addition, our findings provide insights into COVID-19 research, such as key levels of fibrin degradation products, which are directly associated with the Dimerized plasmin fragment D and could indicate active coagulation and thrombosis. Still, we highlight here the prognostic value of interleukin-6, a cytokine that induces inflammatory response and may serve as a predictive biomarker.

A suitable murine model for studying respiratory coronavirus infection and therapeutic countermeasures in BSL-2 laboratories (preprint)

Several animal models are being used to explore important features of COVID-19, nevertheless none of them recapitulates all aspects of the disease in humans. The continuous refinement and development of other options of in vivo models are opportune, especially ones that are carried out at BSL-2 (Biosafety Level 2) laboratories. In this study, we investigated the suitability of the intranasal infection with the murine betacoronavirus MHV-3 to recapitulate multiple aspects of the pathogenesis of COVID-19 in C57BL/6J mice. We demonstrate that MHV-3 replicated in lungs 1 day after inoculation and triggered respiratory inflammation and dysfunction. This MHV-model of infection was further applied to highlight the critical role of TNF in cytokine-mediated coronavirus pathogenesis. Blocking TNF signaling by pharmacological and genetic strategies greatly increased the survival time and reduces lung injury of MHV-3-infected mice. In vitro studies showed that TNF blockage decreased SARS-CoV-2 replication in human epithelial lung cells and resulted in the lower release of IL-6 and IL-8 cytokines beyond TNF itself. Taken together, our results demonstrate that this model of MHV infection in mice is a useful BSL-2 screening platform for evaluating pathogenesis for human coronaviruses infections, such as COVID-19.

Patients With A High-Risk Common Type COVID-19 Pneumonia May Be the Optimal Time for Methylprednisolone Therapy: A Retrospective Cohort Study (preprint)

Background: The optimal timing of corticosteroid treatment for coronavirus disease 2019(COVID-19) pneumonia is uncertain. We evaluated the clinical outcomes of methylprednisolone therapy (MPT) for patients with a high-risk common type(HRCT) COVID-19 pneumonia. Methods: We conducted a multi-centre retrospective cohort study in northeast China. A comparison was performed between the standard treatment (SDT) group and the SDT+MPT group to determine the efficacy of methylprednisolone in treating HRCT COVID-19 pneumonia. Results: We collected the medical records of 403 patients with HRCT COVID-19 pneumonia (127 in the SDT+MPT group and 276 in the SDT group). None of the patients had received mechanical ventilation or died. Further, there had been no side-effects associated with of MPT. Patients in the SDT+MPT group treated with methylprednisolone received an intravenous injection for a median interval of five days (interquartile range of three to seven days). The trends in lymphocyte count, C-reactive protein, interleukin 6, lactic acid dehydrogenase, respiratory rate, SpO2, PaO2, D-dimer and body temperature were similar between the SDT+MPT and SDT groups. The results for the SDT+MPT group seems to be faster improved than the SDT group; however, the results were not statistically significant. Clinical outcomes revealed that the average hospitalisation days and the rate of progression to severe type COVID-19 pneumonia in both the SDT+MPT group and the SDT group were present in 14.56±0.57days vs 16.55±0.3days(p=0.0009) and 21.26%(27/127) vs 32.4%(89/276)(p=0.0254), respectively. The 16-day nucleic acid negative rate was higher in the SDT+MPT group than the SDT group, 81.73% (104/127) vs 65.27% (180/276) (p = 0.0014). Conclusions: MPT effectively prevents patients with HRCT COVID-19 pneumonia from progressing to the severe stage. Therefore, patients with HRCT may be the optimal timing for MPT.Funding Statement: 1.The National Key Laboratory of Sponsored by Open Project of State Key Laboratory of Respiratory Disease (Project Funding Number：SKLRD-OP-201902)” 2.The National Key Laboratory of Urban Water Resources and Water Environment Full Funds. (Project Funding Number：ESK201602.)Declaration of Interests: We have not any conflict of interests to declare.Ethics Approval Statement: Ethical approval by the institutional ethics board of the Qun'li branch of the First Affiliated Hospital of Harbin Medical University and Kang'an Hospital of Mudanjiang was obtained for the analysis and summary of clinical data from COVID-19-infected inpatients.