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2.
Clin Chem ; 68(1): 143-152, 2021 12 30.
Article in English | MEDLINE | ID: covidwho-20243230

ABSTRACT

BACKGROUND: The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse-transcription PCR (RT-qPCR). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce. To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction. METHODS: We evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT-qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral inactivation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance. RESULTS: After optimization, SwabExpress has a low limit of detection at 2-4 molecules/µL, 100% sensitivity, and 99.4% specificity when compared side by side with a traditional RT-qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time. CONCLUSION: SwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19 , COVID-19/diagnosis , Clinical Laboratory Techniques , Humans , RNA, Viral/isolation & purification , Real-Time Polymerase Chain Reaction , SARS-CoV-2/isolation & purification , Sensitivity and Specificity , Specimen Handling
4.
Analyst ; 148(12): 2758-2766, 2023 Jun 12.
Article in English | MEDLINE | ID: covidwho-2323689

ABSTRACT

This paper introduces an enclosed microfluidic chip that integrates sample preparation and the chamber-based digital polymerase chain reaction (cdPCR). The sample preparation of the chip includes nucleic acid extraction and purification based on magnetic beads, which adsorb nucleic acids by moving around the reaction chambers to complete the reactions including lysis, washing, and elution. The cdPCR area of the chip consists of tens of thousands of regularly arranged microchambers. After the sample preparation processes are completed, the purified nucleic acid can be directly introduced into the microchambers for amplification and detection on the chip. The nucleic acid extraction performance and digital quantification performance of the system were examined using synthetic SARS-CoV-2 plasmid templates at concentrations ranging from 101-105 copies per µL. Further on, a simulated clinical sample was used to test the system, and the integrated chip was able to accurately detect SARS-CoV-2 virus particle samples doped with interference (saliva) with a detection limit of 10 copies per µL. This integrated system could provide a promising tool for point-of-care testing of pathogenic infections.


Subject(s)
Microfluidics , Microfluidics/methods , Polymerase Chain Reaction , Nucleic Acids/analysis , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification
6.
Curr Opin Gastroenterol ; 37(1): 4-8, 2021 01.
Article in English | MEDLINE | ID: covidwho-2318694

ABSTRACT

PURPOSE OF REVIEW: We discuss the potential role of the faecal chain in COVID-19 and highlight recent studies using waste water-based epidemiology (WBE) to track severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RECENT FINDINGS: WBE has been suggested as an adjunct to improve disease surveillance and aid early detection of circulating disease. SARS-CoV-2, the aetiological agent of COVID-19, is an enveloped virus, and as such, typically not associated with the waste water environment, given high susceptibility to degradation in aqueous conditions. A review of the current literature supports the ability to detect of SARS-CoV-2 in waste water and suggests methods to predict community prevalence based on viral quantification. SUMMARY: The summary of current practices shows that while the isolation of SARS-CoV-2 is possible from waste water, issues remain regarding the efficacy of virial concentration and subsequent quantification and alignment with epidemiological data.


Subject(s)
COVID-19/epidemiology , Public Health Surveillance/methods , SARS-CoV-2/isolation & purification , Sewage/virology , COVID-19/diagnosis , Feces/virology , Global Health , Humans
8.
J Appl Microbiol ; 130(1): 2-13, 2021 Jan.
Article in English | MEDLINE | ID: covidwho-2299665

ABSTRACT

AIMS: Providing a ready-to-use reverse transcriptase qPCR (RT-qPCR) method fully validated to detect the SARS-CoV-2 with a higher exclusivity than this shown by early published RT-qPCR designs. METHODS AND RESULTS: The specificity of the GPS™ CoVID-19 dtec-RT-qPCR test by analysis of sequence alignments was approached and compared with other RT-qPCR designs. The GPS™ CoVID-19 dtec-RT-qPCR test was validated following criteria of UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012. Diagnostic validation was achieved by two independent reference laboratories, the Instituto de Salud Carlos III, (Madrid, Spain), the Public Health England (Colindale, London, UK), and received the label CE-IVD. The GPS design showed the highest exclusivity and passed all parameters of validation with strict acceptance criteria. Results from reference laboratories 100% correlated with these obtained by using reference methods and showed 100% of diagnostic sensitivity and specificity. CONCLUSIONS: The CE-IVD GPS™ CoVID-19 dtec-RT-qPCR test, available worldwide with full analytical and diagnostic validation, is the more exclusive for SARS-CoV-2 by far. SIGNIFICANCE AND IMPACT OF THE STUDY: Considering the CoVID-19 pandemic status, the exclusivity of RT-qPCR tests is crucial to avoid false positives due to related coronaviruses. This work provides of a highly specific and validated RT-qPCR method for detection of SARS-CoV-2, which represents a case of efficient transfer of technology successfully used since the pandemic was declared.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , SARS-CoV-2/isolation & purification , COVID-19 Nucleic Acid Testing/standards , Computer Simulation , Humans , Pandemics , Real-Time Polymerase Chain Reaction , Reproducibility of Results , SARS-CoV-2/classification , SARS-CoV-2/genetics , Sensitivity and Specificity , Sequence Alignment
9.
Orv Hetil ; 163(25): 975-983, 2022 Jun 19.
Article in English | MEDLINE | ID: covidwho-2276268

ABSTRACT

INTRODUCTION: The COVID-19 (coronavirus disease 2019) caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is associated with high mortality rates worldwide. Polymerase chain reaction (PCR) is extensively used for virus detection in both infected patients and deceased persons. PCR, however, gives no information about the localization of the virus in cells and tissues. Detection of spike and nucleocapsid proteins and viral ribonucleic acid (RNA) of the SARS-CoV-2 in situ might provide more information and aid in the discovery of the pathomechanism of cellular damage. There are several commercially available anti-spike and anti-nucleocapsid antibodies used to detect immunohistochemical reactions, though each gives different results. OBJECTIVE: The goal of the present study was to compare the intensity and specificity of several anti-spike and anti-nucleocapsid antibodies in different dilutions in four Hungarian university departments. METHOD: Immunohistochemical reactions were performed on coded slides taken from infected lungs of 3 deceased and placenta samples with appropriate negative controls of formalin-fixed paraffin-embedded tissues, scanned, evaluated unanimously and analysed statistically by the assessors. RESULTS: By comparing the intensity, dilution, background and reproducibility of the different primary antibodies, it was possible to select the antibodies with the best results. CONCLUSION: The antibodies selected with established dilutions can be used in further studies to detect SARS-CoV-2 proteins in surgical materials and in samples obtained during autopsy. Orv Hetil. 2022; 163(25): 975-983.


Subject(s)
COVID-19 Testing , COVID-19 , SARS-CoV-2 , Antibodies, Viral , COVID-19/diagnosis , COVID-19 Testing/methods , Female , Humans , Nucleocapsid Proteins/analysis , Pregnancy , Reproducibility of Results , SARS-CoV-2/isolation & purification , Spike Glycoprotein, Coronavirus/analysis
10.
Science ; 380(6640): 11, 2023 04 07.
Article in English | MEDLINE | ID: covidwho-2285172

ABSTRACT

When the first cases of human infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were reported from Wuhan, China, in December 2019, there was quick agreement across scientific and health communities that understanding the facts about its emergence would help prevent future outbreaks. Never could I have imagined the degree of politicization that would cloud this quest. Over the past 39 months, while reported deaths from COVID-19 increased to nearly 7 million worldwide, science on the virus's origins has gotten smaller while the politics surrounding this question has grown ever bigger. Last month, the World Health Organization (WHO) learned that scientists in China possessed data on viral samples from Wuhan that had been gathered in January 2020, which should have been shared immediately-not 3 years later-with the global research community. The lack of data disclosure is simply inexcusable. The longer it takes to understand the origins of the pandemic, the harder it becomes to answer the question, and the more unsafe the world becomes.


Subject(s)
COVID-19 , Information Dissemination , Pandemics , SARS-CoV-2 , Humans , COVID-19/epidemiology , Pandemics/prevention & control , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , World Health Organization
11.
Nat Commun ; 14(1): 1541, 2023 03 27.
Article in English | MEDLINE | ID: covidwho-2273491

ABSTRACT

Several studies have reported associations between COVID-19 vaccination and risk of cardiac diseases, especially in young people; the impact on mortality, however, remains unclear. We use national, linked electronic health data in England to assess the impact of COVID-19 vaccination and positive SARS-CoV-2 tests on the risk of cardiac and all-cause mortality in young people (12 to 29 years) using a self-controlled case series design. Here, we show there is no significant increase in cardiac or all-cause mortality in the 12 weeks following COVID-19 vaccination compared to more than 12 weeks after any dose. However, we find an increase in cardiac death in women after a first dose of non mRNA vaccines. A positive SARS-CoV-2 test is associated with increased cardiac and all-cause mortality among people vaccinated or unvaccinated at time of testing.


Subject(s)
COVID-19 Testing , COVID-19 Vaccines , COVID-19 , Cause of Death , SARS-CoV-2 , Vaccination , Adolescent , Adult , Female , Humans , Male , Young Adult , Age Factors , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/mortality , COVID-19/virology , COVID-19 Vaccines/administration & dosage , COVID-19 Vaccines/adverse effects , Electronic Health Records , England/epidemiology , Heart Diseases/epidemiology , Heart Diseases/mortality , Incidence , mRNA Vaccines/administration & dosage , mRNA Vaccines/adverse effects , Risk Assessment , SARS-CoV-2/isolation & purification , Sex Factors , Time Factors , Vaccination/adverse effects , Child , Hospitalization
20.
Science ; 380(6640): 16-17, 2023 04 07.
Article in English | MEDLINE | ID: covidwho-2258278

ABSTRACT

Scientists suggest that GISAID, a prominent database of virus sequences, is rewriting pandemic history.


Subject(s)
COVID-19 , Genome, Viral , Information Dissemination , SARS-CoV-2 , Humans , COVID-19/virology , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification
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