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1.
Bioinformatics ; 2022 Mar 24.
Article in English | MEDLINE | ID: covidwho-1758637

ABSTRACT

SUMMARY: Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A 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. A fully integrated analytical process for raw sequence to consensus genome determination, suited to outbreaks such as the ongoing COVID-19 pandemic, is critical to provide a solid genomic basis for epidemiological analyses and well-informed decision making. We have developed a web-based platform and integrated bioinformatic workflows that help to provide consistent high-quality analysis of SARS-CoV-2 sequencing data generated with either the Illumina or Oxford Nanopore Technologies (ONT). Using an intuitive web-based interface, this workflow automates data quality control, SARS-CoV-2 reference-based genome variant and consensus calling, lineage determination, and provides the ability to submit the consensus sequence and necessary metadata to GenBank, GISAID, and INSDC raw data repositories. We tested workflow usability using real world data and validated the accuracy of variant and lineage analysis using several test datasets, and further performed detailed comparisons with results from the COVID-19 Galaxy Project workflow. Our analyses indicate that EC-19 workflows generate high quality SARS-CoV-2 genomes. Finally, we share a perspective on patterns and impact observed with Illumina vs ONT technologies on workflow congruence and differences. AVAILABILITY: https://edge-covid19.edgebioinformatics.org, and https://github.com/LANL-Bioinformatics/EDGE/tree/SARS-CoV2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

2.
Trends Analyt Chem ; 151: 116600, 2022 Jun.
Article in English | MEDLINE | ID: covidwho-1735015

ABSTRACT

Since the COVID-19 pandemic, the unprecedented use of facemasks has been requiring for wearing in daily life. By wearing facemask, human exhaled breath aerosols and inhaled environmental exposures can be efficiently filtered and thus various filtration residues can be deposited in facemask. Therefore, facemask could be a simple, wearable, in vivo, onsite and noninvasive sampler for collecting exhaled and inhalable compositions, and gain new insights into human health and environmental exposure. In this review, the recent advances in developments and applications of in vivo facemask sampling of human exhaled bacteria, viruses, proteins, and metabolites, and inhalable facemask contaminants and air pollutants, are reviewed. New features of facemask sampling are highlighted. The perspectives and challenges on further development and potential applications of facemask devices are also discussed.

3.
J Anal Test ; 5(4): 287-297, 2021.
Article in English | MEDLINE | ID: covidwho-1694113

ABSTRACT

COVID-19 is a highly contagious respiratory disease that can be infected through human exhaled breath. Human breath analysis is an attractive strategy for rapid diagnosis of COVID-19 in a non-invasive way by monitoring breath biomarkers. Mass spectrometry (MS)-based approaches offer a promising analytical platform for human breath analysis due to their high speed, specificity, sensitivity, reproducibility, and broad coverage, as well as its versatile coupling methods with different chromatographic separation, and thus can lead to a better understanding of the clinical and biochemical processes of COVID-19. Herein, we try to review the developments and applications of MS-based approaches for multidimensional analysis of COVID-19 breath samples, including metabolites, proteins, microorganisms, and elements. New features of breath sampling and analysis are highlighted. Prospects and challenges on MS-based breath analysis related to COVID-19 diagnosis and study are discussed.

4.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-308289

ABSTRACT

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.

5.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-315740

ABSTRACT

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

6.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-315271

ABSTRACT

Summary: Polymerase chain reaction-based assays are the current gold standard for detecting and diagnosing SARS-CoV-2. However, as SARS-CoV-2 mutates, we need to constantly assess whether existing PCR-based assays will continue to detect all known viral strains. To enable the continuous monitoring of SARS-CoV-2 assays, we have developed a web-based assay validation algorithm that checks existing PCR-based assays against the ever-expanding genome databases for SARS-CoV-2 using both thermodynamic and edit-distance metrics. The assay screening results are displayed as a heatmap, showing the number of mismatches between each detection and each SARS-CoV-2 genome sequence. Using a mismatch threshold to define detection failure, assay performance is summarized with the true positive rate (recall) to simplify assay comparisons. Availability: https://covid19.edgebioinformatics.org/#/assayValidation. Contact: Jason Gans (jgans@lanl.gov) and Patrick Chain (pchain@lanl.gov)

7.
2021.
Preprint in English | Other preprints | ID: ppcovidwho-295296

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. Highlights 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. A highly specific and very simple lateral flow test kit for measurement of SARS-CoV-2 S1IgG+IgM antibodies post-immunization of COVID-19 vaccine using peripheral blood was developed as a home-test assay with a limit of detection (LOD) at 50 IU/mL of pseudovirus neutralizing titer (PVNT). After full vaccinations with COVID-19 vaccines, 96.6% of the volunteers successfully achieved the seroconversion of SARS-CoV-2 S1 IgG+IgM antibody. 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 peopl develop protection much faster than older ones. Even though the S1 antibody level in 88% of human subjects vaccinated with inactivated virus dropped below the detection 2-6 months later, one boost could quickly raise the S1 antibody titer above 50 IU/mL of PVNT, indicating that the initial vaccination was successful and immunization memory was developed.

8.
Int J Gen Med ; 14: 8301-8309, 2021.
Article in English | MEDLINE | ID: covidwho-1523539

ABSTRACT

PURPOSE: Studies regarding death risk factors of disseminated intravascular coagulation (DIC) patients were limited. We conducted this study to investigate whether red blood cell distribution width (RDW) was independently related to all-cause mortality of DIC patients. METHODS: We used data from the Medical Information Mart for Intensive Care III version 1.4 (MIMIC-III v1.4). A total of 2098 patients with DIC were included. The main outcome was in-hospital all-cause mortality. RESULTS: After adjusting for potential covariates, the in-hospital all-cause mortality was positively correlated with RDW. The hazard ratio (HR), 95% confidence intervals (CI), and P-value were 1.08, (1.05, 1.12), and P<0.0001, respectively. The Kaplan-Meier curve found DIC patients with elevated RDW had a lower survival rate than patients with normal RDW (P<0.0001). A nonlinear relationship between RDW and mortality was found with the inflection point 19.2%. When RDW <19.2%, RDW was positively correlated with in-hospital all-cause mortality of DIC patients (HR (95% CI): 1.17 (1.11, 1.24), P<0.0001). An elevation in RDW greater than 19.2% did not result in an additional increased risk of mortality (HR=0.97, 95% CI: 0.91-1.04, P=0.4617). CONCLUSION: RDW is an independent predictor of all-cause mortality in DIC patients. Furthermore, there is a nonlinear association between RDW and all-cause mortality of DIC patients.

9.
IEEE Internet of Things Journal ; 8(21):15649-15651, 2021.
Article in English | ProQuest Central | ID: covidwho-1494325

ABSTRACT

The Internet of Medical Things (IoMT) is an extension and specialization of that original Internet of Things (IoT) concept, and applies to the interconnectedness of devices, software applications, and data which are specific to the medical industry. IoMT can add smart technologies to medical devices to monitor the progression of a disease away from the doctor’s office and learn things that could impact future care guidelines and patients. It can also provide a better way to care for our elderly by tracking vitals and heart performance, glucose and other body systems, and activity and sleeping levels. During the outbreak of pandemic (e.g., COVID-19), IoMT can even be used to detect main symptoms ubiquitously using intelligent sensors and trace the origin of the outbreak based on aggregated IoT data (e.g., geographic mobile data and purchase history). Although most of the contemporary IoMT systems can measure risks, make decisions, and take actions automatically, the lack of emotion-aware abilities will be an obstacle to more harmonious human–machine interaction and more efficient medical process. Besides, mental disorders, such as depression, schizophrenia, and anxiety, have become a more noticeable cause of suffering. The integration of emotion-aware abilities into IoMT can also contribute to monitor emotional dysregulation continuously in subjects with mental disorders or undergoing serious pandemic such as COVID-19, and give these patients personalized therapy recommendations. Research on affective computing has defined a framework to recognize, interpret, and process human affects, but more research is needed to investigate its application to biomedical applications, especially “in the wild” and over extended periods of time, and how to integrate emotion-aware abilities into IoMT organically is still an open question. This special issue aims to create a platform for researchers, developers, and practitioners from both academia and industry to disseminate the state-of-the-art results and to advance the Emotion-Aware ubiquitous computing in IoMT.

10.
IEEE Internet of Things Journal ; 8(21):15892-15905, 2021.
Article in English | ProQuest Central | ID: covidwho-1494319

ABSTRACT

The Internet of Medical Things (IoMT) aims to exploit the Internet-of-Things (IoT) techniques to provide better medical treatment scheme for patients with smart, automatic, timely, and emotion-aware clinical services. One of the IoMT instances is applying IoT techniques to sleep-aware smartphones or wearable devices’ applications to provide better sleep healthcare services. As we all know, sleep is vital to our daily health. What is more, studies have shown a strong relationship between sleep difficulties and various diseases such as COVID-19. Therefore, leveraging IoT techniques to develop a longer lifetime sleep healthcare IoMT system, with a tradeoff between data transferring/processing speed and battery energy efficiency, to provide longer time services for bad sleep condition persons, especially the COVID-19 patients or survivors, is a meaningful research topic. In this study, we propose an IoT-enabled sleep data fusion networks (SDFN) module with a star topology Bluetooth network to fuse data of sleep-aware applications. A machine learning model is built to detect sleep events through an audio signal. We design two data reprocessing mechanisms running on our IoT devices to alleviate the data jam problem and save the IoT devices’ battery energy. The experiments manifest that the presented module and mechanisms can save the energy of the system and alleviate the data jam problem of the device.

11.
J Virol ; 96(2): e0106321, 2022 01 26.
Article in English | MEDLINE | ID: covidwho-1476388

ABSTRACT

COVID-19 affects multiple organs. Clinical data from the Mount Sinai Health System show 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 integrated cell biological and physiological analyses of human cardiomyocytes differentiated from human induced pluripotent stem cells (hiPSCs) infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the presence of interleukins (ILs) with clinical findings related to laboratory values in COVID-19 patients to identify 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 IL-6 and IL-1ß. Infection resulted in increased numbers of multinucleated cells. Interleukin treatment and infection resulted in disorganization of myofibrils, extracellular release of troponin I, and reduced and erratic beating. Infection resulted in decreased expression of mRNA encoding key proteins of the cardiomyocyte contractile apparatus. Although interleukins did not increase the extent of infection, they increased the contractile dysfunction associated with 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 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 might underlie heart disease in COVID-19 patients. IMPORTANCE SARS-CoV-2 infects multiple organs, including the heart. Analyses of hospitalized patients show that a substantial number without prior indication of heart disease or comorbidities show significant injury to heart tissue, assessed by increased levels of troponin in blood. We studied the cell biological and physiological effects of virus infection of healthy human iPSC-derived cardiomyocytes in culture. Virus infection with interleukins disorganizes myofibrils, increases cell size and the numbers of multinucleated cells, and suppresses the expression of proteins of the contractile apparatus. Viral infection of cardiomyocytes in culture triggers release of troponin similar to elevation in levels of COVID-19 patients with heart disease. Viral infection in the presence of interleukins slows down and desynchronizes the beating of cardiomyocytes in culture. The cell-level physiological changes are similar to decreases in left ventricular ejection seen in imaging of patients' hearts. These observations suggest that direct injury to heart tissue by virus can be one underlying cause of heart disease in COVID-19.


Subject(s)
COVID-19/immunology , Induced Pluripotent Stem Cells , Interleukin-10/immunology , Interleukin-1beta/immunology , Interleukin-6/immunology , Myocytes, Cardiac , Cells, Cultured , Humans , Induced Pluripotent Stem Cells/immunology , Induced Pluripotent Stem Cells/pathology , Induced Pluripotent Stem Cells/virology , Myocytes, Cardiac/immunology , Myocytes, Cardiac/pathology , Myocytes, Cardiac/virology
12.
Anal Chim Acta ; 1186: 339134, 2021 Nov 22.
Article in English | MEDLINE | ID: covidwho-1446328

ABSTRACT

In recent years, single particle inductively coupled plasma mass spectrometry (SP-ICP-MS) has become a powerful tool for biological quantitative analysis. Homogeneous analysis method requires no separation and washing steps, which is suited for the analysis of highly infectious pathogens, so as to reduce the risk of infection during the operation. SARS-CoV-2 spreads all over the world, and its early infection symptoms are similar to influenza, which brings inconvenience to triage. Therefore, developing novel analytical method for simultaneous detection of multiple viral nucleic acids is essential. Taking the advantages of SP-ICP-MS and homogeneous analysis strategy, a SP-ICP-MS homogeneous nucleic acid assay by using gold nanoparticles (Au NPs) and silver nanoparticles (Ag NPs) probes was established for simultaneous sensitive analysis of SARS-CoV-2 and influenza A (H3N2). In the present of target SARS-CoV-2 or H3N2 nucleic acids, corresponding Au NPs or Ag NPs probes form larger aggregates, resulting in increased pulse signal intensity and reduced pulse signal frequency of the corresponding NPs in SP-ICP-MS measurement. In this assay, the reaction system of Au NPs and Ag NPs probes does not interfere with each other, and there was no separation and washing procedure, which facilitates operation, saves the analysis time, and improves the analysis efficiency. The linear range of this method is 5-1000 pmol L-1, with low-level limits of quantification of target nucleic acid. The developed SP-ICP-MS simultaneous homogeneous detection method has a good potential for detecting nucleic acid, protein, cell and other biological samples by changing different modification sequences on the NPs probes.


Subject(s)
COVID-19 , Influenza, Human , Metal Nanoparticles , Nucleic Acids , Gold , Humans , Influenza A Virus, H3N2 Subtype , Mass Spectrometry , SARS-CoV-2 , Silver
13.
J Anal Test ; 5(4): 287-297, 2021.
Article in English | MEDLINE | ID: covidwho-1363822

ABSTRACT

COVID-19 is a highly contagious respiratory disease that can be infected through human exhaled breath. Human breath analysis is an attractive strategy for rapid diagnosis of COVID-19 in a non-invasive way by monitoring breath biomarkers. Mass spectrometry (MS)-based approaches offer a promising analytical platform for human breath analysis due to their high speed, specificity, sensitivity, reproducibility, and broad coverage, as well as its versatile coupling methods with different chromatographic separation, and thus can lead to a better understanding of the clinical and biochemical processes of COVID-19. Herein, we try to review the developments and applications of MS-based approaches for multidimensional analysis of COVID-19 breath samples, including metabolites, proteins, microorganisms, and elements. New features of breath sampling and analysis are highlighted. Prospects and challenges on MS-based breath analysis related to COVID-19 diagnosis and study are discussed.

14.
J Clin Invest ; 131(11)2021 06 01.
Article in English | MEDLINE | ID: covidwho-1249494

ABSTRACT

With increasing age, individuals are more vulnerable to viral infections such as with influenza or the SARS-CoV-2 virus. One age-associated defect in human T cells is the reduced expression of miR-181a. miR-181ab1 deficiency in peripheral murine T cells causes delayed viral clearance after infection, resembling human immune aging. Here we show that naive T cells from older individuals as well as miR-181ab1-deficient murine T cells develop excessive replication stress after activation, due to reduced histone expression and delayed S-phase cell cycle progression. Reduced histone expression was caused by the miR-181a target SIRT1 that directly repressed transcription of histone genes by binding to their promoters and reducing histone acetylation. Inhibition of SIRT1 activity or SIRT1 silencing increased histone expression, restored cell cycle progression, diminished the replication-stress response, and reduced the production of inflammatory mediators in replicating T cells from old individuals. Correspondingly, treatment with SIRT1 inhibitors improved viral clearance in mice with miR-181a-deficient T cells after LCMV infection. In conclusion, SIRT1 inhibition may be beneficial to treat systemic viral infection in older individuals by targeting antigen-specific T cells that develop replication stress due to miR-181a deficiency.


Subject(s)
COVID-19/immunology , Cellular Senescence/immunology , Histones/deficiency , MicroRNAs/immunology , SARS-CoV-2/immunology , T-Lymphocytes/immunology , Animals , COVID-19/genetics , Cellular Senescence/genetics , Female , Histones/immunology , Humans , Male , Mice, Knockout , MicroRNAs/genetics , SARS-CoV-2/genetics , Sirtuin 1/genetics , Sirtuin 1/immunology
15.
Renewable and Sustainable Energy Reviews ; 145:111026, 2021.
Article in English | ScienceDirect | ID: covidwho-1188985

ABSTRACT

Sterilization is of great importance to prevent the spread and resurgence of the COVID-19, yet sterilization methods are all energy intensive in general. Steam sterilization is easily maintained and can be applied in various scenarios with less residual pollution. However, the current steam generator (so called boiler) has brought many energy and environmental concerns. With the investigation on steam sterilization's features, this study proposed a clean and flexible steam generation system with the air source heat pump and water vapor compressor, and the system can be further simplified through the combination with district heating pipeline. The critical design parameters and simulated performance of the system are evaluated and optimized through a MATLAB simulation, and a prototype was built with experimental performance assessing. The results show the system has an average boiler efficiency of over 170% when the ambient temperature varies from 5 °C to 35 °C and the temperature of outlet steam is above 110 °C, and has the best economic performance when the operating period is above 3 years. Furthermore, the air-source heat pump boiler system is proved to effectively respond to the surging sterilization demands during the peaks of the COVID-19 pandemic and is well consistent with the UN Sustainable Development Goals.

16.
Arch Pathol Lab Med ; 144(10): 1217-1222, 2020 10 01.
Article in English | MEDLINE | ID: covidwho-1016380

ABSTRACT

CONTEXT.­: The pandemic of a novel coronavirus, termed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has created an unprecedented global health burden. OBJECTIVE.­: To investigate the effect of the SARS-CoV-2 infection on maternal, fetal, and neonatal morbidity and other poor obstetrical outcomes. DESIGN.­: All suspected cases of pregnant women with coronavirus disease 2019 (COVID-19) admitted into one center in Wuhan from January 20 to March 19, 2020, were included. Detailed clinical data of those pregnancies with COVID-19 were retrospectively collected and analyzed. RESULTS.­: Twenty-seven pregnant women (4 early pregnancies included) with laboratory or clinically confirmed SARS-CoV-2 infection and 24 neonates born to the 23 women in late pregnancy were analyzed. On admission, 46.2% (13 of 27) of the patients had symptoms, including fever (11 of 27), cough (9 of 27), and vomiting (1 of 27). Decreased total lymphocytes count was observed in 81.5% (22 of 27) of patients. Twenty-six patients showed typical viral pneumonia by chest computed tomography scan, whereas 1 patient confirmed with COVID-19 infection showed no abnormality on chest computed tomography. One mother developed severe pneumonia 3 days after her delivery. No maternal or perinatal death occurred. Moreover, 1 early preterm newborn born to a mother with the complication of premature rupture of fetal membranes, highly suspected to have SARS-CoV-2 infection, was SARS-CoV-2 negative after repeated real-time reverse transcriptase polymerase chain reaction testing. Statistical differences were observed between the groups of women in early and late pregnancy with COVID-19 in the occurrence of lymphopenia and thrombocytopenia. CONCLUSIONS.­: No major complications were reported among the studied cohort, though 1 serious case and 1 perinatal infection were observed. Much effort should be made to reduce the pathogenic effect of COVID-19 infection in pregnancies.


Subject(s)
Coronavirus Infections/complications , Pneumonia, Viral/complications , Pregnancy Complications, Infectious/virology , Adult , Betacoronavirus , COVID-19 , China , Coronavirus Infections/pathology , Female , Humans , Infant, Newborn , Pandemics , Pneumonia, Viral/pathology , Pregnancy , Pregnancy Complications, Infectious/pathology , Pregnancy Outcome , Retrospective Studies , SARS-CoV-2 , Young Adult
17.
Bioinformatics ; 37(7): 1024-1025, 2021 05 17.
Article in English | MEDLINE | ID: covidwho-706027

ABSTRACT

SUMMARY: Polymerase chain reaction-based assays are the current gold standard for detecting and diagnosing SARS-CoV-2. However, as SARS-CoV-2 mutates, we need to constantly assess whether existing PCR-based assays will continue to detect all known viral strains. To enable the continuous monitoring of SARS-CoV-2 assays, we have developed a web-based assay validation algorithm that checks existing PCR-based assays against the ever-expanding genome databases for SARS-CoV-2 using both thermodynamic and edit-distance metrics. The assay-screening results are displayed as a heatmap, showing the number of mismatches between each detection and each SARS-CoV-2 genome sequence. Using a mismatch threshold to define detection failure, assay performance is summarized with the true-positive rate (recall) to simplify assay comparisons. AVAILABILITY AND IMPLEMENTATION: The assay evaluation website and supporting software are Open Source and freely available at https://covid19.edgebioinformatics.org/#/assayValidation, https://github.com/jgans/thermonucleotide BLAST and https://github.com/LANL-Bioinformatics/assay_validation. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19 Testing , Humans , Polymerase Chain Reaction , Sensitivity and Specificity
18.
Anal Chem ; 92(17): 11543-11547, 2020 09 01.
Article in English | MEDLINE | ID: covidwho-677479

ABSTRACT

Molecular analysis of exhaled breath aerosol (EBA) with simple procedures represents a key step in clinical and point-of-care applications. Due to the crucial health role, a face mask now is a safety device that helps protect the wearer from breathing in hazardous particles such as bacteria and viruses in the air; thus exhaled breath is also blocked to congregate in the small space inside of the face mask. Therefore, direct sampling and analysis of trace constituents in EBA using a face mask can rapidly provide useful insights into human physiologic and pathological information. Herein, we introduce a simple approach to collect and analyze human EBA by combining a face mask with solid-phase microextraction (SPME) fiber. SPME fiber was inserted into a face mask to form SPME-in-mask that covered nose and mouth for in vivo sampling of EBA, and SPME fiber was then coupled with direct analysis in real-time mass spectrometry (DART-MS) to directly analyze the molecular compositions of EBA under ambient conditions. The applicability of SPME-in-mask was demonstrated by direct analysis of drugs and metabolites in oral and nasal EBA. The unique features of SPME-in-mask were also discussed. Our results showed that this method is enabled to analyze volatile and nonvolatile analytes in EBA and is expected to have a significant impact on human EBA analysis in clinical applications. We also hope this method will inspire biomarker screening of some respiratory diseases that usually required wearing of a face mask in daily life.


Subject(s)
Aerosols/chemistry , Biomarkers/analysis , Body Fluids/chemistry , Body Fluids/metabolism , Mass Spectrometry/methods , Organic Chemicals/analysis , Solid Phase Microextraction/methods , Biosensing Techniques , Breath Tests , Exhalation , Humans , Imidazoles/chemistry , In Vitro Techniques , Masks , Metabolomics , Specimen Handling/methods
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