TREM-1, TREM-2 and their association with disease severity in patients with COVID-19 (preprint)

Background Delayed diagnosis and inadequate treatment caused by limited biomarkers were associated with outcomes of COVID-19 patients. It is necessary to find other promising biomarkers and candidate targets for defining dysregulated inflammatory state besides the typical biomarkers and drug targets have been used clinically.Methods In a cohort of hospitalized COVID-19 patients with varying degrees of illness severity, we characterized TREM-1 and TREM-2 expression in plasma and on the surface of cell subpopulations using ELISA and flow cytometry, respectively. And their correlations with disease severity and contrast with main clinical indicators were evaluated.Results We found the increased expression of soluble TREM-1 and TREM-2 in plasma from COVID-19 patients compared to the control group. Moreover, membrane-bound TREM-1 and TREM-2 expression was also upregulated on the cell surface of circulating blood T cells from COVID-19 patients. Correlation analysis results showed the sTREM-2 level was negatively correlated with PaO2/FiO2, but positively correlated with CRP, PCT and IL-6 level. Receiver operating characteristic (ROC) curves presented that TREM-1 and TREM-2 exhibited strong predictive abilities, and their expression was equal to CRP and IL-6, and better than leukocytes or neutrophil absolute count and PCT in distinguishing disease severity.Conclusion These results highlighted the important role of TREM-1 and TREM-2 in viral infection. TREM-2 and TREM-1 were critical host immune factors in response to SARS-COV-2 infection and could serve as potential diagnostic and therapeutic biomarkers of COVID-19.

Transmission pattern of shigellosis in Wuhan City, China: a modelling study

The article aims to estimate and forecast the transmissibility of shigellosis and explore the association of meteorological factors with shigellosis. The mathematical model named Susceptible–Exposed–Symptomatic/Asymptomatic–Recovered–Water/Food (SEIARW) was used to explore the feature of shigellosis transmission based on the data of Wuhan City, China, from 2005 to 2017. The study applied effective reproduction number (Reff) to estimate the transmissibility. Daily meteorological data from 2008 to 2017 were used to determine Spearman's correlation with reported new cases and Reff. The SEIARW model fit the data well (χ2 = 0.00046, p > 0.999). The simulation results showed that the reservoir-to-person transmission of the shigellosis route has been interrupted. The Reff would be reduced to a transmission threshold of 1.00 (95% confidence interval (CI) 0.82–1.19) in 2035. Reducing the infectious period to 11.25 days would also decrease the value of Reff to 0.99. There was a significant correlation between new cases of shigellosis and atmospheric pressure, temperature, wind speed and sun hours per day. The correlation coefficients, although statistically significant, were very low (<0.3). In Wuhan, China, the main transmission pattern of shigellosis is person-to-person. Meteorological factors, especially daily atmospheric pressure and temperature, may influence the epidemic of shigellosis.

Self-assessment of COVID-19 vaccination efficacy using a simple POCT for SARS-CoV-2 S1 protein antibody IgG-IgM (preprint)

1. A highly specific lateral flow test kit for SARS-CoV-2 S1 IgG+IgM antibodies was developed as a home-test assay with a LOD at 50IU/mL of pseudovirus neutralizing titer (PVNT). 2. After full vaccination with COVID-19 vaccines, 96.6% of the vaccinees successfully achieved the seroconversion of SARS-CoV-2 S1 IgG+IgM antibody. 3. Even though the S1 antibody level in 88% of the vaccinees vaccinated with inactivated virus vaccines dropped below the detection 2-6 months layer, one boost could quickly raise the S1 antibody titer above 50IU/mL, indicating the initial vaccination was successful and immunization memory was developed. Abstract Background: More than ten novel COVID-19 vaccines have been approved with protections against SARS-CoV-2 infections ranges between 52-95%. It is of great interest to the vaccinees who have received the COVID-19 vaccines, vaccine developers and authorities to identify the non-responders in a timely manner so intervention can take place by either giving additional boosts of the same vaccine or switching to a different vaccine to improve the protection against the SARS-CoV-2 infections. A robust correlation was seen between binding antibody titer and efficacy (p=0.93) in the clinic studies of 7 COVID-19 vaccines, so it is of urgency to develop a simple POCT for vaccinees to self-assess their immune response at home. Methods. Using CHO cell-expressed full length SARS-CoV2 S1 protein as coating antigen on colloidal gold particles, a SARS-CoV-2 S1 IgG-IgM antibody lateral flow test kit (POCT) was developed. The test was validated with negative human sera collected prior to the COVID-19 outbreaks, and blood samples from human subjects prior, during, and post-immunization of COVID-19 vaccines. Results. The specificity of the POCT was 99.0%, as examined against 947 normal human sera and 20 whole blood samples collected pre-immunization. The limit of detection was 50 IU/mL of pseudovirus neutralizing titer (PVNT) using human anti-SARS-2 neutralizing standards from convalescent sera. The sensitivity of POCT for SARS-CoV-2 S1 protein antibody IgG-IgM was compared with SARS-CoV-2 RBD antibody ELISA and determined to be 100% using 23 blood samples from vaccinated human subjects and 10 samples from non-vaccinated ones. Whole blood samples were collected from 119 human subjects (ages between 22-61 years) prior to, during, and post-vaccination of five different COVID-19 vaccines. Among them, 115 people tested positive for SARS-CoV-2 S1 antibodies (showing positive at least once) and 4 people tested negative (tested negative at least twice on different days), demonstrating 96.64% of seroconversion after full-vaccination. 92.3% (36/39) of the human subjects who were younger than 45 achieved seroconversion within 2 weeks while only 57.1% (4/7) of subjects older than 45 tested positive for S1 antibodies, suggesting that younger people develop protection much faster than older ones. Even though the S1 antibody level in 88% of human subjects vaccinated with inactivated virus dropped below 50 IU/mL two months later, one boost could quickly raise the S1 antibody titer above 50 IU/mL of PVNT, indicates that the initial vaccination was successful and immunization memory was developed. Conclusion: Using the lateral flow tests of SARS-CoV2 S1 IgG+IgM, vaccinated human subjects can easily self-assess the efficacy of their vaccination at home. The vaccine developer could quickly identify those non-responders and give them an additional boost to improve the efficacy of their vaccines. Vaccinees who failed in response could switch to different types of COVID-19 vaccines since there are more than 10 COVID-19 vaccines approved using three different platform technologies.

Physiology of cardiomyocyte injury in COVID-19 (preprint)

COVID-19 affects multiple organs. Clinical data from the Mount Sinai Health System shows that substantial numbers of COVID-19 patients without prior heart disease develop cardiac dysfunction. How COVID-19 patients develop cardiac disease is not known. We integrate cell biological and physiological analyses of human cardiomyocytes differentiated from human induced pluripotent stem cells (hiPSCs) infected with SARS-CoV-2 in the presence of interleukins, with clinical findings, to investigate plausible mechanisms of cardiac disease in COVID-19 patients. We infected hiPSC-derived cardiomyocytes, from healthy human subjects, with SARS-CoV-2 in the absence and presence of interleukins. We find that interleukin treatment and infection results in disorganization of myofibrils, extracellular release of troponin-I, and reduced and erratic beating. Although interleukins do not increase the extent, they increase the severity of viral infection of cardiomyocytes resulting in cessation of beating. Clinical data from hospitalized patients from the Mount Sinai Health system show that a significant portion of COVID-19 patients without prior history of heart disease, have elevated troponin and interleukin levels. A substantial subset of these patients showed reduced left ventricular function by echocardiography. Our laboratory observations, combined with the clinical data, indicate that direct effects on cardiomyocytes by interleukins and SARS-CoV-2 infection can underlie the heart disease in COVID-19 patients.

EDGE COVID-19: A Web Platform to generate submission-ready genomes for SARS-CoV-2 sequencing efforts (preprint)

Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A wide range of technologies and strategies for pathogen genome enrichment and sequencing are being used by laboratories worldwide, together with different, and sometimes ad hoc, analytical procedures for generating genome sequences. As a result, public repositories now contain non-standard entries of varying quality. A standardized analytical process for consensus genome sequence determination, particularly for outbreaks such as the ongoing COVID-19 pandemic, is critical to provide a solid genomic basis for epidemiological analyses and well-informed decision making. To address this need, we have developed a bioinformatic workflow to standardize the analysis of SARS-CoV-2 sequencing data generated with either the Illumina or Oxford Nanopore platforms. Using an intuitive web-based interface, this workflow automates SARS-CoV-2 reference-based genome assembly, variant calling, lineage determination, and provides the ability to submit the consensus sequence and necessary metadata to GenBank or GISAID. Given a raw Illumina or Oxford Nanopore FASTQ read file, this web-based platform enables non-bioinformatics experts to automatically produce a SARS-CoV-2 genome that is ready for submission to GISAID or GenBank. Availability:https://edge-covid19.edgebioinformatics.org;https://github.com/LANL-Bioinformatics/EDGE/tree/SARS-CoV2

Uncovering the underlying mechanisms of Compound Yuxingcao Mixture in the treatment of COVID-19 based on network pharmacology (preprint)

Background and objective: The novel coronavirus named COVID-19 emerged in Wuhan, China in December, 2019 and has spread rapidly in China and around the world. The traditional Chinese medicine Compound Yuxingcao Mixture (CYM) has been recommended in recent editions of the national guideline while the underlying mechanisms are still unclear. In this study, we analyzed the effectiveness and potential mechanisms of CYM on COVID-19 based on network pharmacology and molecular docking approach. Methods: The active ingredients and potential targets of CYM were screened using TCMSP and STITCH databases. Genes related severe acute respiratory syndromes (SARS) and Middle East respiratory syndrome (MERS) were queried on the DisGeNET and MalaCards databases. CYM-COVID-19 common target protein interaction network was established by STRING database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted to generate the relative pathways based on KOBAS databases. In addition, the possible binding site of screened compounds were also predicted by Autodock vina software. Results: A total of 103 active ingredients and 205 putative targets were screened from CYM, of which 32 overlapped with the targets of COVID-19 and were considered therapeutic targets. The analysis of the network diagram demonstrated that the CYM activity of ingredients of quercetin, luteolin, β-sitosterol and kaempferol may play a crucial role in treating COVID-19 by regulating TNF, IL-6, IL-1β, etc. The analysis of molecular binding energy showed that β-sitosterol had the lowest binding energy with COVID-19 3CLpro (-8.63 kJ/mol). GO and KEGG enrichment analysis revealed that these targets were closely associated with inflammatory responses and immune defense processes. Conclusion: In summary, our study identified the potential mechanisms and targets of CYM for the prevention of COVID-19, providing directions for further clinical research.