SARS-CoV-2: An insight into detection tools

2021 ◽  
Vol 20 ◽  
Author(s):  
Shaghayegh Khanmohammadi ◽  
Mohammadreza Tabary ◽  
Farnaz Araghi ◽  
Seyed Mohammad Tavangar
Keyword(s):  
Nucleic Acid ◽  
Genome Sequencing ◽  
Nucleic Acid Amplification ◽  
Diagnostic Tools ◽  
Serological Tests ◽  
Diagnostic Laboratory ◽  
Advantages And Disadvantages ◽  
Pros And Cons ◽  
Novel Coronavirus ◽  
Diagnostic Laboratory Tests

: The novel coronavirus disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), was announced as a pandemic in March 2020. Different diagnostic laboratory tests have been used to detect the infection. Each diagnostic tool, such as Chest Computed tomography (CT) imaging, genome sequencing, nucleic acid amplification methods, whole genome sequencing, microarray, and serology testing have several advantages and disadvantages. Nucleic acid amplification methods are better diagnostic tools for the detection of SARS-CoV-2 in early stages of the infection, while serological tests are more appropriate for the recognition of previously infected patients. In this review, we will briefly consider each diagnostic method, and discuss its pros and cons.

Laboratory Diagnosis of Zika Virus Infection

2016 ◽  
Vol 141 (1) ◽  
pp. 60-67 ◽  
Author(s):  
Marie Louise Landry ◽  
Kirsten St. George
Keyword(s):  
Public Health ◽  
Nucleic Acid ◽  
Virus Infection ◽  
Zika Virus ◽  
Laboratory Diagnosis ◽  
Government Support ◽  
Nucleic Acid Amplification ◽  
Diagnostic Tools ◽  
Nucleic Acid Amplification Tests ◽  
Zika Virus Infection

Context.—The rapid and accurate diagnosis of Zika virus infection is an international priority. Objective.—To review current recommendations, methods, limitations, and priorities for Zika virus testing. Data Sources.—Sources include published literature, public health recommendations, laboratory procedures, and testing experience. Conclusions.—Until recently, the laboratory diagnosis of Zika infection was confined to public health or research laboratories that prepared their own reagents, and test capacity has been limited. Furthermore, Zika cross-reacts serologically with other flaviviruses, such as dengue, West Nile, and yellow fever. Current or past infection, or even vaccination with another flavivirus, will often cause false-positive or uninterpretable Zika serology results. Detection of viral RNA during acute infection using nucleic acid amplification tests provides more specific results, and a number of commercial nucleic acid amplification tests have received emergency use authorization. In addition to serum, testing of whole blood and urine is recommended because of the higher vial loads and longer duration of shedding. However, nucleic acid amplification testing has limited utility because many patients are asymptomatic or present for testing after the brief period of Zika shedding has passed. Thus, the greatest need and most difficult challenge is development of accurate antibody tests for the diagnosis of recent Zika infection. Research is urgently needed to identify Zika virus epitopes that do not cross-react with other flavivirus antigens. New information is emerging at a rapid pace and, with ongoing public-private and international collaborations and government support, it is hoped that rapid progress will be made in developing robust and widely applicable diagnostic tools.

scholarly journals Point-of-Care Diagnostic Tools for Surveillance of SARS-CoV-2 Infections

2021 ◽  
Vol 9 ◽  
Author(s):  
Dhanasekaran Sakthivel ◽  
David Delgado-Diaz ◽  
Laura McArthur ◽  
William Hopper ◽  
Jack S. Richards ◽  
...  
Keyword(s):  
Large Scale ◽  
Clinical Symptoms ◽  
Point Of Care ◽  
Cost Effective ◽  
Nucleic Acid Amplification ◽  
Diagnostic Tools ◽  
Rt Pcr ◽  
Serological Tests ◽  
Polymerase Chain ◽  
Effective Public Health

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a recently emerged and highly contagious virus that causes coronavirus disease 2019 (COVID-19). As of August 24, 2021, there were more than 212 million confirmed COVID-19 cases and nearly 4.4 million deaths reported globally. Early diagnosis and isolation of infected individuals remains one of the most effective public health interventions to control SARS-CoV-2 spread and for effective clinical management of COVID-19 cases. Currently, SARS-CoV-2 infection is diagnosed presumptively based on clinical symptoms and confirmed by detecting the viral RNA in respiratory samples using reverse transcription polymerase chain reaction (RT-PCR). Standard RT-PCR protocols are time consuming, expensive, and technically demanding, which makes them a poor choice for large scale and point-of-care screening in resource-poor settings. Recently developed isothermal nucleic acid amplification tests (iNAAT), antigen and/or serological tests are cost-effective to scale COVID-19 testing at the point-of-care (PoC) and for surveillance activities. This review discusses the development of rapid PoC molecular tools for the detection and surveillance of SARS-CoV-2 infections.

scholarly journals A systematic review and meta-analysis of the sensitivity of antibody tests for the laboratory confirmation of COVID-19

2021 ◽  
Author(s):  
Nigel A Makoah ◽  
Thomas Tipih ◽  
Matefo M Litabe ◽  
Mareza Brink ◽  
Joseph B Sempa ◽  
...  
Keyword(s):  
Systematic Review ◽  
Nucleic Acid ◽  
Symptom Onset ◽  
Meta Analysis ◽  
Nucleic Acid Amplification ◽  
Serological Tests ◽  
Nucleic Acid Amplification Tests ◽  
Laboratory Confirmation ◽  
Using Data ◽  
Low Sensitivity

Aim: The aim of this study was to investigate the utility of serological tests for the diagnosis of COVID-19 during the first week of symptom onset in patients confirmed with the real-time RT-PCR. Materials & methods: A systematic review and meta-analysis of 58 publications were performed using data obtained from Academic Search Ultimate, Africa-wide, Scopus, Web of Science and MEDLINE. Results: We found that the highest pooled sensitivities were obtained with ELISA IgM-IgG and chemiluminescence immunoassay IgM tests. Conclusion: Serological tests have low sensitivity within the first week of symptom onset and cannot replace nucleic acid amplification tests. However, serological assays can be used to support nucleic acid amplification tests.

scholarly journals Multiplex SARS-CoV-2 Genotyping PCR for Population-Level Variant Screening and Epidemiologic Surveillance

2021 ◽  
Author(s):  
Hannah Wang ◽  
Jacob A. Miller ◽  
Michelle Verghese ◽  
Mamdouh Sibai ◽  
Daniel Solis ◽  
...  
Keyword(s):  
Public Health ◽  
Nucleic Acid ◽  
Whole Genome Sequencing ◽  
San Francisco ◽  
Genome Sequencing ◽  
High Throughput ◽  
Population Level ◽  
Nucleic Acid Amplification ◽  
Whole Genome ◽  
Epidemiologic Surveillance

ABSTRACTBackgroundEmergence of SARS-CoV-2 variants with concerning phenotypic mutations is of public health interest. Genomic surveillance is an important tool for pandemic response, but many laboratories do not have the resources to support population-level sequencing. We hypothesized that a spike genotyping nucleic acid amplification test (NAAT) could facilitate high-throughput variant surveillance.MethodsWe designed and analytically validated a one-step multiplex allele-specific reverse transcriptase polymerase chain reaction (RT-qPCR) to detect three non-synonymous spike protein mutations (L452R, E484K, N501Y). Assay specificity was validated with next-generation whole-genome sequencing. We then screened a large cohort of SARS-CoV-2 positive specimens from our San Francisco Bay Area population.ResultsBetween December 1, 2020 and March 1, 2021, we screened 4,049 unique infections by genotyping RT-qPCR, with an assay failure rate of 2.8%. We detected 1,567 L452R mutations (38.7%), 34 N501Y mutations (0.84%), 22 E484K mutations (0.54%), and 3 (0.07%) E484K+N501Y mutations. The assay had near-perfect (98-100%) concordance with whole-genome sequencing in a validation subset of 229 specimens, and detected B.1.1.7, B.1.351, B.1.427, B.1.429, B.1.526, and P.2 variants, among others. The assay revealed rapid emergence of L452R in our population, with a prevalence of 24.8% in December 2020 that increased to 62.5% in March 2021.ConclusionsWe developed and clinically implemented a genotyping RT-qPCR to conduct high-throughput SARS-CoV-2 variant screening. This approach can be adapted for emerging mutations and immediately implemented in laboratories already performing NAAT worldwide using existing equipment, personnel, and extracted nucleic acid.Summary / Key PointsEmergence of SARS-CoV-2 variants with concerning phenotypes is of public health interest. We developed a multiplex genotyping RT-qPCR to rapidly detect L452R, E484K, and N501Y with high sequencing concordance. This high-throughput alternative to resource-intensive sequencing enabled surveillance of L452R emergence.

scholarly journals Symptomatic SARS-CoV-2 Reinfection in a Healthy Healthcare Worker in Italy Confirmed by Whole-Genome Sequencing

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 899
Author(s):  
Daniela Loconsole ◽  
Anna Sallustio ◽  
Marisa Accogli ◽  
Francesca Centrone ◽  
Daniele Casulli ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Healthcare Worker ◽  
Genome Sequencing ◽  
Genomic Analysis ◽  
Nucleic Acid Amplification ◽  
Whole Genome ◽  
Serological Tests ◽  
Routine Surveillance ◽  
Two Samples ◽  
Genomic Analyses

This study describes a case of SARS-CoV-2 reinfection confirmed by whole-genome sequencing in a healthy physician who had been working in a COVID-19 hospital in Italy since the beginning of the pandemic. Nasopharyngeal swabs were obtained from the patient at each presentation as part of routine surveillance. Nucleic acid amplification testing was performed on the two samples to confirm SARS-CoV-2 infection, and serological tests were used to detect SARS-CoV-2 IgG antibodies. Comparative genome analysis with whole-genome sequencing was performed on nasopharyngeal swabs collected during the two episodes of COVID-19. The first COVID-19 episode was in March 2020, and the second was in January 2021. Both SARS-CoV-2 infections presented with mild symptoms, and seroconversion for SARS-CoV-2 IgG was documented. Genomic analysis showed that the viral genome from the first infection belonged to the lineage B.1.1.74, while that from the second infection to the lineage B.1.177. Epidemiological, clinical, serological, and genomic analyses confirmed that the second episode of SARS-CoV-2 infection in the healthcare worker met the qualifications for “best evidence” for reinfection. Further studies are urgently needed to assess the frequency of such a worrisome occurrence, particularly in the light of the recent diffusion of SARS-CoV-2 variants of concern.

scholarly journals 1029. Torus Synestia Nucleic Acid Analysis Platform for Fast, High Multiplex Analysis of Nucleic Acids With Single-Nucleotide Discrimination Level

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S605-S605
Author(s):  
Tyler Rockwood ◽  
Andrew Sullivan ◽  
Jahnavi Gandhi ◽  
Sarah Gruszka ◽  
Brian Turczyk ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Target Detection ◽  
Bacterial Species ◽  
Nucleic Acid Amplification ◽  
Detection Sensitivity ◽  
Label Free ◽  
Single Nucleotide ◽  
Advantages And Disadvantages ◽  
Tract Infections ◽  
Dna 2

Abstract Background Nucleic acid amplification testing (NAAT) is an essential tool both for biomedical research and for clinical molecular diagnostics. Currently, there are multiple NAAT platforms available, each offering certain performance and utility advantages and disadvantages as compared to each other. Next generation NAAT platforms aim to deliver increased target detection sensitivity and specificity, low limits of target detection, quantitative high multiplex target capacity, rapid time to results, and simple sample-to-answer workflow. Methods Here we describe the Torus Synestia System, a NAAT platform capable of rapid, highly multiplexed amplification and detection of both DNA and RNA targets. The platform comprises a small, portable (~ 2kg) amplification and detection device and a disposable single-use cartridge housing a PCR amplification chamber with an integrated label-free microarray for real-time data acquisition and interpretation. The platform offers a 30-min turnaround time with a detection limit of 10 DNA/RNA molecules per assay and single nucleotide discrimination. Results We demonstrate the Synestia System performance and utility with three distinct molecular applications: 1) detection of 20 genetic loci and 30 single nucleotide polymorphisms in human genomic DNA; 2) detection and genotyping of 43 unique bacterial species associated with human urinary tract infections; and 3) detection and profiling human respiratory viral pathogens including SARS-CoV-1/2, seasonal coronaviruses, Influenza A/B, and human respiratory syncytial viruses. In addition, the single-nucleotide specificity of our label-free microarray probes allowed for robust identification and discrimination of newly emerging SARS-CoV-2 lineages, such as B.1.1.7 (a.k.a. UK), B.1.351 (a.k.a. South African), P.1 (a.k.a. Brazilian), and B.1.617 (a.k.a. Indian). Conclusion The Torus Synestia System has broad applicability in both clinical and research environments. We are confident that the Torus Synestia System will revolutionize syndromic diagnostics at the point of care (PoC) and lead to improved response times during future epidemic and pandemic pathogen outbreaks. Disclosures All Authors: No reported disclosures

Diagnostic laboratory tests for systemic autoimmune rheumatic diseases: unmet needs towards harmonization

2018 ◽  
Vol 56 (10) ◽  
pp. 1743-1748 ◽  
Author(s):  
Pier Luigi Meroni ◽  
Maria Orietta Borghi
Keyword(s):  
Rheumatic Diseases ◽  
Laboratory Tests ◽  
Solid Phase ◽  
Organ Damage ◽  
Diagnostic Tools ◽  
Lower Sensitivity ◽  
Diagnostic Laboratory ◽  
Disease Evolution ◽  
Autoimmune Rheumatic Diseases ◽  
Diagnostic Laboratory Tests

Abstract Autoantibodies are helpful tools not only for the diagnosis and the classification of systemic autoimmune rheumatic diseases (SARD) but also for sub-grouping patients and/or for monitoring disease activity or specific tissue/organ damage. Consequently, the role of the diagnostic laboratory in the management of SARD is becoming more and more important. The advent of new techniques raised the need of updating and harmonizing our use/interpretation of the assays. We discuss in this opinion paper some of these issues. Indirect immunofluorescence (IIF) was originally suggested as the reference technique for anti-nuclear antibody (ANA) detection as previous solid phase assays (SPA) displayed lower sensitivity. The new available SPA are now offering better results and can represent alternative or even complementary diagnostic tools for ANA detection. The improved sensitivity of SPA technology is also changing our interpretation of the results for other types of autoantibody assays, but we need updating their calibration and new reference materials are going to be obtained in order to harmonize the assays. There is growing evidence that the identification of autoantibody combinations or profiles is helpful in improving diagnosis, patients’ subgrouping and predictivity for disease evolution in the field of SARD. We report some explanatory examples to support the idea to make the use of these autoantibody profiles more and more popular. The technological evolution of the autoimmune assays is going to change our routine diagnostic laboratory tests for SARD and validation of new algorithms is needed in order to harmonize our approach to the issue.

scholarly journals Insights into the SARS-CoV-2 Diagnosis in India: Present Status and Future Prospects

2021 ◽  
pp. 38-53
Author(s):  
Laxmipreeya Behera ◽  
Jyoti Prakash Sahoo ◽  
Sushree Suparna Mahapatra ◽  
Jannila Praveena ◽  
Trupti Dash ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Rna Virus ◽  
Surface Protein ◽  
Nucleic Acid Amplification ◽  
Serological Tests ◽  
Test Loop ◽  
In Vitro Diagnostic ◽  
Lateral Flow Assays ◽  
Antigen Tests

COVID-19, the infectious pandemic disease is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This deadly disease was unknown before its catastrophic outbreak of the infection in Wuhan city of China, in December 2019. The pandemic situation has increased the demand of rapid enhancement of the in-vitro diagnostic assays which would enable the mass screening and testing. Several molecular and serological diagnostics assays such as direct viral antigen tests, nucleic acid amplification tests and serological tests were developed. Nucleic acid tests such as RT-PCR. TrueNAT, Feluda Test, loop-mediated isothermal amplification (LAMP) etc. detect the presence of RNA virus in the nasal or throat swab or from saliva. Antigen tests detect the presence of a virus as the antigen, which is a surface protein. Antibody tests such as enzyme-linked immunosorbent assays (ELISA), lateral flow assays (LFA), chemiluminescence assays (CLIA) etc. detect the presence of antibodies generated against SARS-CoV-2 in the blood samples.

scholarly journals Direct RT-PCR amplification of SARS-CoV-2 from clinical samples using a concentrated viral Lysis-Amplification Buffer prepared with IGEPAL-630.

2020 ◽  
Author(s):  
Alejandro Castellanos-Gonzalez ◽  
Thomas Shelite ◽  
Lloyd Nicole ◽  
Sadiqova Aygul ◽  
Ping Ren ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Pcr Amplification ◽  
Nucleic Acid Amplification ◽  
Clinical Samples ◽  
Viral Lysis ◽  
Gold Standard Method ◽  
Nucleic Acid Isolation ◽  
Qualitative Detection ◽  
Nonionic Detergent ◽  
Novel Coronavirus

Abstract The pandemic of 2019 caused by the novel coronavirus (SARS-CoV-2) is still rapidly spreading worldwide. Nucleic acid amplification serves as the gold standard method for confirmation of COVID-19 infection. However, challenges faced for diagnostic laboratories from undeveloped countries includes shortage of kits and supplies to purify viral RNA. Therefore, it is urgent to validate alternative nucleic acid isolation methods for SARS-CoV-2. Our results demonstrate that a concentrated viral lysis amplification buffer (vLAB) prepared with the nonionic detergent IGEPAL enables qualitative detection of SARS-CoV-2 by direct Reverse Transcriptase-Polymerase Chain Reaction (dRT-PCR). Furthermore, vLAB was effective in inactivating SARS-CoV-2. Since this method is inexpensive and no RNA purification equipment or additional cDNA synthesis is required, this dRT-PCR with vLAB should be considered as an alternative method for COVID-19 detection.

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