Evaluation of Sample Pooling for Gene Sequencing of SARS-CoV-2: A Simulation Study (preprint)

COVID-19 continues to pose a significant public health threat, requiring ongoing epidemiological and genomic surveillance. Next-generation sequencing (NGS) is commonly utilized for monitoring viral evolution at high-cost. Real-time reverse transcription polymerase chain reaction(RT-qPCR) pooling test have been have been demonstrated to increase molecular testing throughput effectively during the pandemic, while pooling sequencing shows promise as a cost-effective tool for monitoring virus variants. A simulation study was conducted to evaluate the efficacy of sample pooling for viral gene sequencing of SARS-CoV-2. In this study, 72 original raw data of gene sequencing results with different lineages were collected and combined to create simulated samples based on five pooling strategies. A bioinformatics tool based on Freyja was utilized to analyze the variant composition of these 70 simulated pooled samples. The genetic composition of the pooled samples mostly recovered the variant compositions of the original samples, with discrepancies between the top X results (where X is the number of original samples included in the mixture)and the complete results (P < 0.05).Variations were observed in the calculation method for the top X results (P < 0.05) but not in the complete calculation approach (P > 0.05) across the five pooling strategy groups. Some original samples of suboptimal quality were not accurately identified. The present results indicated that sample pooling coupled with streamlined genotyping offers a promising approach for cost-effective gene sequencing of SARS-CoV-2, which will aid in genomic surveillance efforts against COVID-19.

A review on indoor airborne transmission of COVID-19– modelling and mitigation approaches

In the past few years, significant efforts have been made to investigate the transmission of COVID-19. This paper provides a review of the COVID-19 airborne transmission modeling and mitigation strategies. The simulation models here are classified into airborne transmission infectious risk models and numerical approaches for spatiotemporal airborne transmissions. Mathematical descriptions and assumptions on which these models have been based are discussed. Input data used in previous simulation studies to assess the dispersion of COVID-19 are extracted and reported. Moreover, measurements performed to study the COVID-19 airborne transmission within indoor environments are introduced to support validations for anticipated future modeling studies. Transmission mitigation strategies recommended in recent studies have been classified to include modifying occupancy and ventilation operations, using filters and air purifiers, installing ultraviolet (UV) air disinfection systems, and personal protection compliance, such as wearing masks and social distancing. The application of mitigation strategies to various building types, such as educational, office, public, residential, and hospital, is reviewed. Recommendations for future works are also discussed based on the current apparent knowledge gaps covering both modeling and mitigation approaches. Our findings show that different transmission mitigation measures were recommended for various indoor environments;however, there is no conclusive work reporting their combined effects on the level of mitigation that may be achieved. Moreover, further studies should be conducted to understand better the balance between approaches to mitigating the viral transmissions in buildings and building energy consumption.

Development of Physical Activity Guidelines for a Healthy China Using the Life Cycle Concept: The Perspective of Policy Tools from Five Countries

Developing physical activity guidelines based on the life cycle concept is conducive to accelerating the realization of the goal of “all-round, full-cycle maintenance and protection to greatly improve people’s health” in the Healthy China 2030 Planning Outline. Based on a policy tools perspective, this study uses the text analysis method to collect and analyze physical activity guidelines based on the life cycle concept from five economically developed countries: the USA, Japan, Canada, Australia, and the UK. The policy tools, country data, and stages of the life cycle were used to develop physical activity guidelines in China to accelerate the realization of the Healthy China 2030 strategy based on the following principles: (1) Strengthen sectoral cooperation and establish a system of policy instruments;(2) increase publicity and scientific awareness of physical activity and exercise;(3) focus on talent cultivation and improve guideline research and development;and (4) mobilize the power of all sectors to promote the implementation of physical activity guidelines.

Development of a Bayesian inference model for assessing ventilation condition based on CO2 meters in primary schools

Outdoor fresh air ventilation plays a significant role in reducing airborne transmission of diseases in indoor spaces. School classrooms are considerably challenged during the COVID-19 pandemic because of the increasing need for in-person education, untimely and incompleted vaccinations, high occupancy density, and uncertain ventilation conditions. Many schools started to use CO2 meters to indicate air quality, but how to interpret the data remains unclear. Many uncertainties are also involved, including manual readings, student numbers and schedules, uncertain CO2 generation rates, and variable indoor and ambient conditions. This study proposed a Bayesian inference approach with sensitivity analysis to understand CO2 readings in four primary schools by identifying uncertainties and calibrating key parameters. The outdoor ventilation rate, CO2 generation rate, and occupancy level were identified as the top sensitive parameters for indoor CO2 levels. The occupancy schedule becomes critical when the CO2 data are limited, whereas a 15-min measurement interval could capture dynamic CO2 profiles well even without the occupancy information. Hourly CO2 recording should be avoided because it failed to capture peak values and overestimated the ventilation rates. For the four primary school rooms, the calibrated ventilation rate with a 95% confidence level for fall condition is 1.96±0.31 ACH for Room #1 (165 m3 and 20 occupancies) with mechanical ventilation, and for the rest of the naturally ventilated rooms, it is 0.40±0.08 ACH for Room #2 (236 m3 and 21 occupancies), 0.30±0.04 or 0.79±0.06 ACH depending on occupancy schedules for Room #3 (236 m3 and 19 occupancies), 0.40±0.32,0.48±0.37,0.72±0.39 ACH for Room #4 (231 m3 and 8–9 occupancies) for three consecutive days.

Microplastics interact with SARS-CoV-2 and facilitate host cell infection

Microplastics (MP) pollution is a global issue that raises concerns about potential toxicity for environmental and human health. The notion that SARS-CoV-2 is more stable when adsorbed on plastic surfaces urged us to examine whether the virus can attach to MP, which may facilitate infection upon inhalation or ingestion. Here, we describe that MP can bind SARS-CoV-2 pseudovirus on their surface and enhance infection of human cells in vitro. This enhanced in vitro infectivity was confirmed with authentic SARS-CoV-2, in parallel with increased expression of inflammation-related caspase-3, IL-8 and TNF-alpha genes. These results suggest that the presence of MP in the environment or in our respiratory or gastrointestinal tracts has the potential to interact with SARS-CoV-2, and potentially increase viral infectivity and spreading.

Micronutrient Level Is Negatively Correlated with the Neutrophil-Lymphocyte Ratio in Patients with Severe COVID-19

Aim To explore the potential relationship between NLR and micronutrient deficiency in patients with severe COVID-19 infection. Methods Sixteen patients were categorized into the mild group (mild COVID-19) and severe group (severe COVID-19) based on the guideline of the management of COVID-19. The lactate dehydrogenase (LDH);superoxide dismutase (SOD), the inflammatory markers (neutrophil lymphocyte ratio (NLR)), erythrocyte sedimentation rate (ESR), c-reactive protein (CRP), selenium (Se), iron (Fe), zinc (Zn), nickel (Ni), copper (Cu), chromium (Cr), cadmium (Cd), arsenic (As), and manganese (Mn) were measured in the blood. Results Compared to the mild group, the NLR (P < 0.05) and the level of Se (P < 0.01), Fe (P < 0.05), and Zn (P < 0.05) were significantly decreased in the severe group. The level of Se, Fe, and Zn was significantly correlated to NLR levels. Furthermore, close positive correlation was found between NLR and severity of COVID-19. Conclusion The micronutrient deficiency in the blood is associated with NLR in the severity of COVID-19 patients.

Impact of COVID-19 pandemic on the psychosocial well-being of children with neuromuscular disorders (preprint)

To examine the impact of COVID-19 on the psychosocial wellbeing in children with neuromuscular disorders (NMD), the parents of 41 children with NMD aged 3-12 years completed a survey during COVID-19 pandemic. The findings were compared to those of the parents of 164 matched typically-developed (TD) children. Health-related quality of life and lifestyle habits of the NMD group were compared with the TD group using independent two-sample t-test. Children with NMD with uninterrupted disease-modifying treatments showed higher PedsQL total scores during the pandemic compared to the pre-pandemic state (p=0.012). PedsQL total score in the NMD group was significantly lower than the TD group (p<0.001). Those with disrupted rehabilitation training (73.8% of NMD group) had significant lower PedsQL scores compared to those with continuous training (p = 0.012). Parental guidance on the usage of electronic devices was significantly associated with the total score of PedsQL, particularly in the NMD group (p=0.007). In conclusion, children with NMD have had a poorer quality of life than TD children during the COVID-19 pandemic. Our study highlights the importance of parental guidance on electronic device usage, the continuation of drug treatment, and rehabilitation training for the psychosocial wellbeing of children with NMD during the pandemic.

Severe novel coronavirus pneumonia: a case report and literature review

Objective To describe the diagnosis and treatment of a patient with severe novel coronavirus pneumonia, and to improve the understanding and management of clinicians on novel coronavirus pneumonia. Methods The onset, development, treatment and outcome of a patient with severe 2019 novel coronavirus pneumonia were retrospectively analyzed and relevant literatures were reviewed. Results At the beginning of the disease, the patient presented fever and dry cough, and later the disease progressed to dyspnea. Chest CT showed bilateral exudation of the lung. Lopinavir/ritonavir, IFN-a and immunoglobulin were given to the patient according to the expert group's opinion. The pneumonia was cured and the patient was discharged two weeks later. Conclusion Appropriate management strategies are effective on diagnosis and treatment of new coronavirus pneumonia.

Chest CT features of 105 patients with COVID-19: a multicenter retrospective study in Shandong Province

Objective: To explore the chest CT features of patients with coronavirus disease 19 (COVID-19) and the clinical application value.

Research priorities to reduce the impact of COVID-19 in low- and middle-income countries

Background The COVID-19 pandemic has caused disruptions to the functioning of societies and their health systems. Prior to the pandemic, health systems in low- and middle-income countries (LMIC) were particularly stretched and vulnerable. The International Society of Global Health (ISoGH) sought to systematically identify priorities for health research that would have the potential to reduce the impact of the COVID-19 pandemic in LMICs. Methods The Child Health and Nutrition Research Initiative (CHNRI) method was used to identify COVID-19-related research priorities. All ISoGH members were invited to participate. Seventy-nine experts in clinical, translational, and population research contributed 192 research questions for consideration. Fifty-two experts then scored those questions based on five pre-defined criteria that were selected for this exercise: 1) feasibility and answerability;2) potential for burden reduction;3) potential for a paradigm shift;4) potential for translation and implementation;and 5) impact on equity. Results Among the top 10 research priorities, research questions related to vaccination were prominent: health care system access barriers to equitable uptake of COVID-19 vaccination (ranked 1st), determinants of vaccine hesitancy (4th), development and evaluation of effective interventions to decrease vaccine hesitancy (5th), and vaccination impacts on vulnerable population/s (6th). Health care delivery questions also ranked highly, including: effective strategies to manage COVID-19 globally and in LMICs (2nd) and integrating health care for COVID-19 with other essential health services in LMICs (3rd). Additionally, the assessment of COVID-19 patients’ needs in rural areas of LMICs was ranked 7th, and studying the leading socioeconomic determinants and consequences of the COVID-19 pandemic in LMICs using multi-faceted approaches was ranked 8th. The remaining questions in the top 10 were: clarifying paediatric case-fatality rates (CFR) in LMICs and identifying effective strategies for community engagement against COVID-19 in different LMIC contexts. Interpretation Health policy and systems research to inform COVID-19 vaccine uptake and equitable access to care are urgently needed, especially for rural, vulnerable, and/or marginalised populations. This research should occur in parallel with studies that will identify approaches to minimise vaccine hesitancy and effectively integrate care for COVID-19 with other essential health services in LMICs. ISoGH calls on the funders of health research in LMICs to consider the urgency and priority of this research during the COVID-19 pandemic and support studies that could make a positive difference for the populations of LMICs.

To Explore the Network Pharmacology and Molecular Docking Mechanism of Chaihu Shugan Powder with the “Same Treatment for Different Diseases” for Insomnia and Depression Based on the COVID-19 Pandemic (preprint)

Background: The classic prescription Chaihu Shugan Powder (CHSGP) has been widely used in clinical Chinese medicine treatment and has clear clinical effects in the treatment of emotional diseases. Based on the increasing incidence of emotional diseases such as insomnia and depression in the population during the COVID-19 pandemic, we will explore the mechanism of CHSGP in the treatment of insomnia and depression with “Same Treatment for Different Diseases”. Methods: Using a bioinformatics and network pharmacology platform, protein database and STRING database, we collected CHSGP chemical composition and related target data and constructed a "component-target" action network through Gene Ontology and Kyoto Encyclopedia of Genes and Genome pathway enrichment analysis. Molecular docking technology was used to verify key active ingredients and core targets. Results: A total of 119 active compounds of CHSGP were screened, such as quercetin, kaempferol, and β-sitosterol, and 113 common related targets overlapped with insomnia and depression. GO enrichment and KEGG pathway analysis mainly involved immune, inflammation, cell proliferation, apoptosis, endocrine and other related targets and signaling pathways. Molecular docking showed that small molecular compounds (kaempferol, luteolin, quercetin, 7-methoxy-2-methyl isoflavone and beta-sitosterol) had good binding effects with five target proteins (AKT1, IL1B, IL-6, FOS, GSK3B) to play a role in regulating immunity, the inflammatory response, cell proliferation, apoptosis, and endocrine signaling. Conclusions: Under the context of the COVID-19 pandemic, it revealed the complex mechanism of multicomponent, multitarget, and multipathway of the classic CHSGP for insomnia and depression, laying a theoretical foundation for its clinical application of its "same treatment for different diseases".

Interferon-induced transmembrane protein 3 (IFITM3) limits lethality of SARS-CoV-2 in mice (preprint)

Interferon-induced transmembrane protein 3 (IFITM3) is a host antiviral protein that alters cell membranes to block fusion of viruses. Published reports have identified conflicting pro- and anti-viral effects of IFITM3 on SARS-CoV-2 in cultured cells, and its impact on viral pathogenesis in vivo remains unclear. Here, we show that IFITM3 knockout (KO) mice infected with mouse-adapted SARS-CoV-2 experienced extreme weight loss and lethality, while wild type (WT) mice lost minimal weight and recovered. KO mice had higher lung viral titers and increases in lung inflammatory cytokine levels, CD45-positive immune cell infiltration, and histopathology, compared to WT mice. Mechanistically, we observed disseminated viral antigen staining throughout the lung tissue and pulmonary vasculature in KO mice, while staining was observed in confined regions in WT lungs. Global transcriptomic analysis of infected lungs identified upregulation of gene signatures associated with interferons, inflammation, and angiogenesis in KO versus WT animals, highlighting changes in lung gene expression programs that precede severe lung pathology and fatality. Corroborating the protective effect of IFITM3 in vivo, K18-hACE2/IFITM3 KO mice infected with non-adapted SARS-CoV-2 showed enhanced, rapid weight loss and early death compared to control mice. Increased heart infection was observed in both mouse models in the absence of IFITM3, indicating that IFITM3 constrains extrapulmonary dissemination of SARS-CoV-2. Our results establish IFITM3 KO mice as a new animal model for studying severe SARS-CoV-2 infection of the lung and cardiovascular system, and overall demonstrate that IFITM3 is protective in SARS-CoV-2 infections of mice.

Identify potential treatments of COVID-19 from Tibetan medicine Hippophae Fructus using a network pharmacological approach

OBJECTIVE Since the coronavirus disease 2019(COVID-19) outbreak in December 2019, the search for a potential treatment for COVID-19 has been a constant focus. Therefore, we identified potential treatments for COVID-19 from Hippophae Fructus, a Tibetan medicine that may act on COVID-19, using a network pharmacology approach.METHODS We collected the chemical constituents and corresponding targets of Hippophae Fructus from traditional Chinese medicine system pharmacology(TCMSP). COVID-19 related genes were predicted in pubmed-Gene, OMIM and GeneCards databases. Then, protein-protein interactions(PPIs) of key genes were analyzed by STRING database.Compound-target-diseases network was constructed using Cytoscape software. The potential pathways were determined by Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analyses. Additionally,molecular docking was used to verify the binding effect between the active component and the target. RESULTS A total of 33 components and 192 corresponding targets in Hippophae Fructus were found. 50 genes were obtained from the intersection of component targets and disease targets. These genes include IL-6, TNF, MAPK8 and PTGS2, which regulate several pathways associated with COVID-19, involving Hepatitis B, Influenza A, TNF signaling pathway and Tuberculosis. More importantly, high-node compounds such as quercetin and beta-sitosterol can well bind to key targets.CONCLUSION Some components in Hippophae Fructus can act on COVID-19 related genes and regulate multiple pathways. Perhaps Hippophae Fructus has the effect in treating COVID-19.

Comparative evaluation of the transmissibility of SARS-CoV-2 variants of concern (preprint)

Since the start of the SARS-CoV-2 pandemic in late 2019, several variants of concern (VOC) have been reported, such as B.1.1.7, B.1.351, P.1, and B.1.617.2. The exact reproduction number Rt for these VOCs is important to determine appropriate control measures. Here, we estimated the transmissibility for VOCs and lineages of SAR-CoV-2 based on genomic data and Bayesian inference under an epidemiological model to infer the reproduction number (Rt). We analyzed data for multiple VOCs from the same time period and countries, in order to compare their transmissibility while controlling for geographical and temporal factors. The lineage B had a significantly higher transmissibility than lineage A, and contributed to the global pandemic to a large extent. In addition, all VOCs had increased transmissibility when compared with other lineages in each country, indicating they are harder to control and present a high risk to public health. All countries should formulate specific prevention and control policies for these VOCs when they are detected to curve their potential for large-scale spread.

The molecular basis for SARS-CoV-2 recognized by dog ACE2 (preprint)

SARS-CoV-2 can infect many domestic animals, including dogs. Herein, we show that dog angiotensin converting enzyme 2 (dACE2) can bind to SARS-CoV-2 spike (S) protein receptor binding region (RBD), and that both pseudotyped and authentic SARS-CoV-2 can infect dACE2-expressing cells. we solved the crystal structure of RBD in complex with dACE2 and found that the total numbers of contact residues, contact atoms, hydrogen bonds and salt bridges at the binding interface in this complex are slightly fewer than those in the complex of the RBD and human ACE2 (hACE2). This result is consistent with the fact that the binding affinity of RBD to dACE2 is lower than that to hACE2. We further show that a few important mutations in the RBD binding interface play a pivotal role in the binding affinity of RBD to both dACE2 and hACE2, and need intense monitoring and controlling.

Stigma and Misconceptions in the Time of the Covid-19 Pandemic: A Field Experiment in India (preprint)

A hidden cost of the COVID-19 pandemic is the stigma associated with the disease for those infected and groups that are considered as more likely to be infected. This paper examines whether the provision of accurate and focused information about COVID-19 from a reliable source can reduce stigmatization. We carry out a randomized field experiment in the state of Uttar Pradesh, India, in which we provide an information brief about COVID-19 by phone to a random subsample of participants to address stigma and misconceptions. We find that the information brief decreases stigmatization of COVID-19 patients and certain groups such as religious minorities, lower-caste groups, and frontline workers (healthcare, police), and reduces the belief that infection cases are more prevalent among certain marginalized social and economic groups (Muslims, low caste, rural-poor population). We provide suggestive evidence that improved knowledge about the prevention and transmission of COVID-19 and reduced stress about the disease are important channels for these effects.