Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative (preprint)

Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,048 severe disease cases and 571,009 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75-10.05, p=5.41x10-7). These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights.

CoVac501, a self-adjuvanting peptide vaccine conjugated with TLR7 agonists, against SARS-CoV-2 induces protective immunity.

Safe, effective, and economical vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed to achieve adequate herd immunity and end the pandemic. We constructed a novel SARS-CoV-2 vaccine, CoVac501, which is a self-adjuvanting peptide vaccine conjugated with Toll-like receptor 7 (TLR7) agonists. The vaccine contains immunodominant peptides screened from the receptor-binding domain (RBD) and is fully chemically synthesized. It has been formulated in an optimized nanoemulsion formulation and is stable at 40 °C for 1 month. In non-human primates (NHPs), CoVac501 elicited high and persistent titers of protective neutralizing antibodies against multiple RBD mutations, SARS-CoV-2 original strain, and variants (B.1.1.7 and B.1.617.2). Specific peptides booster immunization against the B.1.351 variant has also been shown to be effective in improving protection against B.1.351. Meanwhile, CoVac501 elicited the increase of memory T cells, antigen-specific CD8+ T-cell responses, and Th1-biased CD4+ T-cell immune responses in NHPs. Notably, at an extremely high SARS-CoV-2 challenge dose of 1 × 107 TCID50, CoVac501 provided near-complete protection for the upper and lower respiratory tracts of cynomolgus macaques.

Coping with COVID: Risk and Resilience Factors for Mental Health in a German Representative Panel Study (preprint)

Background: The COVID-19 pandemic might affect mental health. Data from population-representative panel surveys with multiple waves including pre-COVID data investigating risk and protective factors are still rare. Methods: In a stratified random sample of the German household population (n=6,684), we conducted survey-weighted multiple linear regressions to determine the association of various psychological risk and protective factors with changes in psychological distress (PD; measured via PHQ-4) from pre-pandemic (average of 2016 and 2019) to peri-pandemic (both 2020 and 2021) time points. Control analyses on PD change between two pre-pandemic time points (2016 and 2019) were conducted. Regularized regressions were computed to inform on which factors were statistically most influential in the multicollinear setting. Results: PHQ-4 in 2020 (M=2.45) and 2021 (M=2.21) was elevated compared to 2019 (M=1.79). Several risk factors (catastrophizing, neuroticism, asking for instrumental support) and protective factors (perceived stress recovery, positive reappraisal, optimism) were identified for the peri-pandemic outcomes. Control analyses revealed that in pre-pandemic times, neuroticism and optimism were predominantly related to PD changes. Regularized regression mostly confirmed the results and highlighted perceived stress recovery as most consistent influential protective factor across peri-pandemic outcomes. Conclusions: We identified several psychological risk and protective factors related to PD outcomes during the COVID-19 pandemic. Comparison to pre-pandemic data stress the relevance of longitudinal assessments to potentially reconcile contradictory findings. Implications and suggestions for targeted prevention and intervention programs during highly stressful times such as pandemics are discussed.

Parameter Estimation for the One-Term (Multiterm) Fractional-Order SEIAR Models of Norovirus Outbreak

In the paper, we use the Caputo fractional derivative to consider general single-term and multiterm fractional-order SEIAR models for the outbreak of Norovirus. Then, the inverse problem about parameter estimation for these fractional-order SEIAR models of the Norovirus outbreak is studied firstly. To provide the numerical solution of the single-term (or multiterm) fractional-order nonlinear differential equation, the GMMP scheme and Newton method are introduced. Then, we make use of the modified hybrid Nelder-Mead simplex search and particle swarm optimization (MH-NMSS-PSO) algorithm to obtain the fractional orders and parameters for these fractional-order SEIAR models of Norovirus outbreak. To guarantee the correctness and effectiveness of the methods, the data of a 2007 Norovirus outbreak in a middle school in one city is used as the real data to solve the inverse problem of the parameter estimation. With the new parameters, all numerical studies illustrate that the numerical solutions fit very well with the real data, which reveals that the single-term and multiterm fractional-order SEIAR models of Norovirus outbreak all can predict the number of the infectious people accurately. And it also shows that the GMMP scheme and the MH-NMSS-PSO method are efficient and valid for estimating the parameters of the single-term (or multiterm) fractional-order nonlinear equations. Then, we research the impact of changes in each parameter on the amount of infected humans It when the remaining parameters are unchanged. All results of numerical simulation reveal that the single-term and multiterm fractional-order SEIAR model of Norovirus can provide better results than other models. And we also study the effect of the isolation on different days. The conclusion is obtained that the earlier the isolation is taken, the less the infected people are. Hence, for a fractional-order application in the SEIAR model of Norovirus outbreak, we establish the effective parameter estimation methods.

High concentrations of hypochlorous acid-based disinfectant in the environment reduced the load of SARS-CoV-2 in nucleic acid amplification testing.

During the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) pandemic, chlorine-containing disinfectants have been widely used in nucleic acid amplification testing laboratories. Whether the use of disinfectants affect the results of viral nucleic acid amplification is unknown. We examined the impact of different hypochlorous acid (HOCl) concentrations on the quantitative results of SARS-CoV-2 by real-time reverse-transcription polymerase chain reaction (RT-PCR). We also explored the mechanisms and models of action of chlorine-containing disinfectants that affected the detection of SARS-CoV-2. The results showed that different HOCl concentrations and different action times had an impact on the SARS-CoV-2 results. High concentrations of ambient HOCl have a greater impact than low concentrations, and this effect will increase with the extension of the action time and with the increase in ambient humidity. Compared with the enzymes or the extracted RNA required for RT-PCR, the impact of HOCl on the SARS-CoV-2 detection is more likely to be caused by damage to primers and probes in the PCR system. The false negative result still existed after changing the ambient disinfectant to ethanol but not peracetic acid. The use of HOCl in the environment will have an unpredictable impact on the nucleic acid test results of SARS-CoV-2. In order to reduce the possibility of false negative of SARS-CoV-2 nucleic acid test and prevent the spread of epidemic disease, environmental disinfectants should be used at the beginning and end of the experiment rather than during the experimental operation.

Development and Clinical Application of a Rapid and Sensitive Loop-Mediated Isothermal Amplification Test for SARS-CoV-2 Infection.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak urgently necessitates sensitive and convenient COVID-19 diagnostics for the containment and timely treatment of patients. We aimed to develop and validate a novel reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay to detect SARS-CoV-2. Patients with suspected COVID-19 and close contacts were recruited from two hospitals between 26 January and 8 April 2020. Respiratory samples were collected and tested using RT-LAMP, and the results were compared with those obtained by reverse transcription-quantitative PCR (RT-qPCR). Samples yielding inconsistent results between these two methods were subjected to next-generation sequencing for confirmation. RT-LAMP was also applied to an asymptomatic COVID-19 carrier and patients with other respiratory viral infections. Samples were collected from a cohort of 129 cases (329 nasopharyngeal swabs) and an independent cohort of 76 patients (152 nasopharyngeal swabs and sputum samples). The RT-LAMP assay was validated to be accurate (overall sensitivity and specificity of 88.89% and 99.00%, respectively) and diagnostically useful (positive and negative likelihood ratios of 88.89 and 0.11, respectively). RT-LAMP showed increased sensitivity (88.89% versus 81.48%) and high consistency (kappa, 0.92) compared to those of RT-qPCR for SARS-CoV-2 screening while requiring only constant-temperature heating and visual inspection. The time required for RT-LAMP was less than 1 h from sample preparation to the result. In addition, RT-LAMP was feasible for use with asymptomatic patients and did not cross-react with other respiratory pathogens. The developed RT-LAMP assay offers rapid, sensitive, and straightforward detection of SARS-CoV-2 infection and may aid the expansion of COVID-19 testing in the public domain and hospitals.IMPORTANCE We developed a visual and rapid reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay targeting the S gene for SARS-CoV-2 infection. The strength of our study was that we validated the RT-LAMP assay using 481 clinical respiratory samples from two prospective cohorts of suspected COVID-19 patients and on the serial samples from an asymptomatic carrier. The developed RT-LAMP approach showed an increased sensitivity (88.89%) and high consistency (kappa, 0.92) compared with those of reverse transcription-quantitative PCR (RT-qPCR) for SARS-CoV-2 screening while requiring only constant-temperature heating and visual inspection, facilitating SARS-CoV-2 screening in well-equipped labs as well as in the field. The time required for RT-LAMP was less than 1 h from sample preparation to the result (more than 2 h for RT-qPCR). This study showed that the RT-LAMP assay was a simple, rapid, and sensitive approach for SARS-CoV-2 infection and can facilitate COVID-19 diagnosis, especially in resource-poor settings.

Clinical Features and Histopathological Changes of Skeletal Muscle in Patients with COVID-19: Two Case reports (preprint)

BackgroundTo the best of our knowledge, muscle soreness is a common manifestation for the coronavirus disease-19 (COVID-19) patients, but the mechanism of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) injury to skeletal muscle remains unclear, there has been no publication focused on muscle involvement in COVID-19 patients.Case presentationWe present the case of two Chinese men with COVID-19, whose common symptoms were fatigue and muscle soreness. They went through different treatments, patient 1, 81-year-old, eventually died of multi-organ failure, and patient 2, 53-year-old, underwent amputation of the mid-lower section of left thigh. Laboratory tests in both patients showed abnormal biochemical parameters associated with skeletal muscle injury. We obtained skeletal muscle samples from these two patients, one from postmortem biopsy of gastrocnemius muscle and the other from a resected left lower limb due to thrombosis. The pathological findings in patient 1 were mainly scattered atrophic muscles, while fiber necrosis and minor inflammation were identified in patient 2, and the mild infiltrations were confirmed by CD68 and LCA staining to be predominantly macrophages and lymphocytes.ConclusionsWe report the clinical and laboratory features together with histopathological findings in skeletal muscle tissues from two COVID-19 cases and speculate that the SARS-CoV-2 may cause skeletal muscle injury. Due to the particularity of individual differences in case reports, the background of chronic neuromuscular disease in patient 1 and a minimal compartment syndrome caused by thrombosis in patient 2 need to be excluded prior to the conclusion that the skeletal muscles have been involved in COVID-19.