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1.
Viruses ; 12(6)2020 05 26.
Article in English | MEDLINE | ID: covidwho-1726015

ABSTRACT

The recent outbreak of the Coronavirus disease 2019 (COVID-19) has quickly spread worldwide since its discovery in Wuhan city, China in December 2019. A comprehensive strategy, including surveillance, diagnostics, research, clinical treatment, and development of vaccines, is urgently needed to win the battle against COVID-19. The past three unprecedented outbreaks of emerging human coronavirus infections at the beginning of the 21st century have highlighted the importance of readily available, accurate, and rapid diagnostic technologies to contain emerging and re-emerging pandemics. Real-time reverse transcriptase-polymerase chain reaction (rRT-PCR) based assays performed on respiratory specimens remain the gold standard for COVID-19 diagnostics. However, point-of-care technologies and serologic immunoassays are rapidly emerging with high sensitivity and specificity as well. Even though excellent techniques are available for the diagnosis of symptomatic patients with COVID-19 in well-equipped laboratories; critical gaps still remain in screening asymptomatic people who are in the incubation phase of the virus, as well as in the accurate determination of live viral shedding during convalescence to inform decisions for ending isolation. This review article aims to discuss the currently available laboratory methods and surveillance technologies available for the detection of COVID-19, their performance characteristics and highlight the gaps in current diagnostic capacity, and finally, propose potential solutions. We also summarize the specifications of the majority of the available commercial kits (PCR, EIA, and POC) for laboratory diagnosis of COVID-19.


Subject(s)
Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Asymptomatic Infections , Betacoronavirus , COVID-19 , COVID-19 Testing , COVID-19 Vaccines , Humans , Immunoenzyme Techniques , Neutralization Tests , Nucleic Acid Amplification Techniques , Pandemics , Point-of-Care Testing , Reagent Kits, Diagnostic/standards , Real-Time Polymerase Chain Reaction , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2 , Sensitivity and Specificity , Serologic Tests , Tomography, X-Ray Computed , Virus Shedding
2.
Anal Bioanal Chem ; 414(5): 1773-1785, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1653430

ABSTRACT

Nucleic acid tests to detect the SARS-CoV-2 virus have been performed worldwide since the beginning of the COVID-19 pandemic. For the quality assessment of testing laboratories and the performance evaluation of molecular diagnosis products, reference materials (RMs) are required. In this work, we report the production of a lentiviral SARS-CoV-2 RM containing approximately 12 kilobases of its genome including common diagnostics targets such as RdRp, N, E, and S genes. The RM was measured with multiple assays using two different digital PCR platforms. To measure the homogeneity and stability of the lentiviral SARS-CoV-2 RM, reverse transcription droplet digital PCR (RT-ddPCR) was used with in-house duplex assays. The copy number concentration of each target gene in the extracted RNA solution was then converted to that of the RM solution. Their copy number values are measured to be from 1.5 × 105 to 2.0 × 105 copies/mL. The RM has a between-bottle homogeneity of 4.80-8.23% and is stable at 4 °C for 1 week and at -70 °C for 6 months. The lentiviral SARS-CoV-2 RM closely mimics real samples that undergo identical pre-analytical processes for SARS-CoV-2 molecular testing. By offering accurate reference values for the absolute copy number of viral target genes, the developed RM can be used to improve the reliability of SARS-CoV-2 molecular testing.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Genome, Viral , RNA, Viral/genetics , Reagent Kits, Diagnostic/standards , SARS-CoV-2/genetics , COVID-19/virology , COVID-19 Nucleic Acid Testing/standards , Coronavirus Envelope Proteins/genetics , Coronavirus Envelope Proteins/metabolism , Coronavirus Nucleocapsid Proteins/genetics , Coronavirus Nucleocapsid Proteins/metabolism , Coronavirus RNA-Dependent RNA Polymerase/genetics , Coronavirus RNA-Dependent RNA Polymerase/metabolism , Gene Dosage , Gene Expression , Humans , Jurkat Cells , Lentivirus/genetics , Lentivirus/metabolism , Phosphoproteins/genetics , Phosphoproteins/metabolism , RNA, Viral/metabolism , RNA, Viral/standards , Reagent Kits, Diagnostic/supply & distribution , Reference Standards , Reproducibility of Results , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/metabolism , Viral Genome Packaging
3.
PLoS One ; 17(1): e0262733, 2022.
Article in English | MEDLINE | ID: covidwho-1643277

ABSTRACT

This study aims at establishing specimens pooling approach for the detection of SARS-CoV-2 using the RT-PCR BGI and Sansure-Biotech kits used in Gabon. To validate this approach, 14 positive samples, stored at -20°C for three to five weeks were analyzed individually (as gold standard) and in pools of five, eight and ten in the same plate. We created 14 pools of 5, 8 and 10 samples using 40 µL from each of the selected positive samples mixed with 4, 7 and 9 confirmed negative counterparts in a total volume of 200 µL, 320 µL and 400 µL for the pools of 5, 8 and 10 respectively. Both individual and pooled samples testing was conducted according to the BGI and Sansure-Biotech RT-PCR protocols used at the Professor Daniel Gahouma Laboratory (PDGL). Furthermore, the pooling method was also tested by comparing results of 470 unselected samples tested in 94 pools and individually. Results of our experiment showed that using a BGI single positive sample with cycle threshold (Ct) value of 28.42, confirmed by individual testing, detection occurred in all the pools. On the contrary samples with Ct >31 were not detected in pools of 10 and for these samples (Ct value as high as 37.17) their detection was possible in pool of 8. Regarding the Sansure-Biotech kit, positive samples were detected in all the pool sizes tested, irrespective of their Ct values. The specificity of the pooling method was 100% for the BGI and Sansure-Biotech RT-PCR assays. The present study found an increase in the Ct values with pool size for the BGI and Sansure-Biotech assays. This trend was statistically significant (Pearson's r = 0.978; p = 0,022) using the BGI method where the mean Ct values were 24.04±1.1, 26.74±1.3, 27.91±1.1 and 28.32±1.1 for the individual, pool of 5, 8 and 10 respectively. The testing of the 470 samples showed that one of the 94 pools had a positive test similar to the individual test using the BGI and Sansure-Biotech kits. The saving of time and economizing test reagents by using the pooling method were demonstrated in this study. Ultimately, the pooling method could be used for the diagnosis of SARS-CoV-2 without modifying the accuracy of results in Gabon. We recommend a maximum pool size of 8 for the BGI kit. For the Sansure-Biotech kit, a maximum pool size of 10 can be used without affecting its accuracy compared to the individual testing.


Subject(s)
COVID-19 Nucleic Acid Testing/standards , COVID-19/diagnosis , RNA, Viral/genetics , SARS-CoV-2/genetics , Specimen Handling/methods , COVID-19/epidemiology , Gabon/epidemiology , Health Services , Humans , Reagent Kits, Diagnostic/standards , SARS-CoV-2/classification , Sensitivity and Specificity
4.
J Clin Virol ; 127: 104383, 2020 06.
Article in English | MEDLINE | ID: covidwho-1385847

ABSTRACT

BACKGROUND: Numerous nucleic acid amplification assays have recently received emergency use authorization (EUA) for the diagnosis of SARS-CoV-2 infection, and there is a need to assess their test performance relative to one another. OBJECTIVES: The aim of this study was to compare the test performance of the Hologic Panther Fusion SARS-CoV-2 assay targeting two regions of open reading frame 1ab (ORF1ab) to a high complexity molecular-based, laboratory-developed EUA from Stanford Health Care (SHC) targeting the SARS-CoV-2 envelope (E) gene. STUDY DESIGN: We performed a diagnostic comparison study by testing nasopharyngeal samples on the two assays. Assay agreement was assessed by overall percent agreement and Cohen's kappa coefficient. RESULTS: A total of 184 nasopharyngeal samples were tested using the two assays, of which 180 showed valid results and were included for the comparative analysis. Overall percent agreement between the assays was 98.3 % (95 % confidence interval (CI) 95.2-99.7) and kappa coefficient was 0.97 (95 % CI 0.93-1.0). One sample was detected on the SHC laboratory developed test (LDT) and not on the Panther Fusion, and had a Ct of 35.9. Conversely, 2 samples were detected on the Panther Fusion and not on the LDT, and had Ct values of 37.2 and 36.6. CONCLUSION: The Panther Fusion SARS-CoV-2 assay and the SHC LDT perform similarly on clinical nasopharyngeal swab specimens. Other considerations, including reagent availability, turnaround time, labor requirements, cost and instrument throughput should guide the decision of which assay to perform.


Subject(s)
Coronavirus Infections/diagnosis , Molecular Diagnostic Techniques/methods , Molecular Diagnostic Techniques/standards , Pneumonia, Viral/diagnosis , Reagent Kits, Diagnostic/standards , Viral Envelope Proteins/isolation & purification , Betacoronavirus/genetics , COVID-19 , Coronavirus Envelope Proteins , Humans , Nasopharynx/virology , Pandemics , Reproducibility of Results , SARS-CoV-2 , Viral Envelope Proteins/genetics
5.
Viruses ; 13(7)2021 06 26.
Article in English | MEDLINE | ID: covidwho-1289024

ABSTRACT

The number of serological assays for SARS-CoV-2 has skyrocketed in the past year. Concerns have been raised regarding their performance characteristics, depending on the disease severity and the time of the analysis post-symptom onset (PSO). Thus, independent validations using an unbiased sample selection are required for meaningful serology data interpretation. We aimed to assess the clinical performance of six commercially available assays, the seroconversion, and the dynamics of the humoral response to SARS-CoV-2 infection. The study included 528 serum samples from 156 patients with follow-up visits up to six months PSO and 161 serum samples from healthy people. The IgG/total antibodies positive percentage increased and remained above 95% after six months when chemiluminescent immunoassay (CLIA) IgG antiS1/S2 and electro-chemiluminescent assay (ECLIA) total antiNP were used. At early time points PSO, chemiluminescent microparticle immunoassay (CMIA) IgM antiS achieved the best sensitivity. IgM and IgG appear simultaneously in most circumstances, and when performed in parallel the sensitivity increases. The severe and the moderate clinical forms were significantly associated with higher seropositivity percentage and antibody levels. High specificity was found in all evaluated assays, but the sensitivity was variable depending on the time PSO, severity of disease, detection method and targeted antigen.


Subject(s)
Antibodies, Viral/blood , COVID-19 Serological Testing/methods , COVID-19 Serological Testing/standards , COVID-19/diagnosis , COVID-19/immunology , Reagent Kits, Diagnostic/standards , SARS-CoV-2/immunology , Adult , COVID-19/blood , Female , Humans , Immunoglobulin G/blood , Immunoglobulin M/blood , Longitudinal Studies , Luminescent Measurements , Male , Middle Aged , Prospective Studies , Romania , Sensitivity and Specificity , Time Factors
6.
Am J Trop Med Hyg ; 105(2): 378-386, 2021 Jun 28.
Article in English | MEDLINE | ID: covidwho-1285448

ABSTRACT

Antibody tests can be tools for detecting current or past severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 [coronavirus disease 2019 (COVID-19)]) infections. Independent test evaluations are needed to document the performance with different sample sets. We evaluated six lateral flow assays (LFAs) and two laboratory-based tests (EUROIMMUN-SARS-CoV-2 ELISA and Abbott-Architect-SARS-CoV-2-IgG). We tested 210 plasma samples from 89 patients diagnosed with acute COVID-19. These samples were collected at different time points after the onset of symptoms. In addition, 80 convalescent plasma samples, and 168 pre-pandemic samples collected from adults in the United States and in Africa were tested. LFA performance varied widely, and some tests with high sensitivity had low specificity. LFA sensitivities were low (18.8-40.6%) for samples collected 0 to 3 days after symptom onset, and were greater (80.3-96.4%) for samples collected > 14 days after symptom onset. These results are similar to those obtained by ELISA (15.6% and 89.1%) and chemiluminescent microparticle assay (21.4% and 93.1%). The range of test specificity was between 82.7% and 97%. The combined use of two LFAs can increase specificity to more than 99% without a major loss of sensitivity. Because of suboptimal sensitivity with early COVID-19 samples and background reactivity with some pre-pandemic samples, none of the evaluated tests alone is reliable enough for definitive diagnosis of COVID-19 infection. However, antibody testing may be useful for assessing the status of the epidemic or vaccination campaign. Some of the LFAs had sensitivities and specificities that were comparable to those of more expensive laboratory tests, and these may be useful for seroprevalence surveys in resource-limited settings.


Subject(s)
Antibodies, Viral/blood , COVID-19 Serological Testing/standards , COVID-19/diagnosis , Immunoassay/standards , Reagent Kits, Diagnostic/standards , SARS-CoV-2/immunology , Africa , COVID-19/blood , COVID-19/immunology , COVID-19 Serological Testing/instrumentation , COVID-19 Serological Testing/methods , Humans , Immunoassay/instrumentation , Immunoassay/methods , Immunoglobulin G/blood , Immunoglobulin M/blood , Retrospective Studies , Sensitivity and Specificity
7.
EBioMedicine ; 69: 103455, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-1284047

ABSTRACT

BACKGROUND: Antigen rapid diagnostic tests (RDT) for SARS-CoV-2 are fast, broadly available, and inexpensive. Despite this, reliable clinical performance data from large field studies is sparse. METHODS: In a prospective performance evaluation study, RDT from three manufacturers (NADAL®, Panbio™, MEDsan®, conducted on different samples) were compared to quantitative reverse transcription polymerase chain reaction (RT-qPCR) in 5 068 oropharyngeal swabs for detection of SARS-CoV-2 in a hospital setting. Viral load was derived from standardised RT-qPCR Cycle threshold (Ct) values. The data collection period ranged from November 12, 2020 to February 28, 2021. FINDINGS: The sensitivity of RDT compared to RT-qPCR was 42·57% (95% CI 33·38%-52·31%). The specificity was 99·68% (95% CI 99·48%-99·80%). Sensitivity declined with decreasing viral load from 100% in samples with a deduced viral load of ≥108 SARS-CoV-2 RNA copies per ml to 8·82% in samples with a viral load lower than 104 SARS-CoV-2 RNA copies per ml. No significant differences in sensitivity or specificity could be observed between samples with and without spike protein variant B.1.1.7. The NPV in the study cohort was 98·84%; the PPV in persons with typical COVID-19 symptoms was 97·37%, and 28·57% in persons without or with atypical symptoms. INTERPRETATION: RDT are a reliable method to diagnose SARS-CoV-2 infection in persons with high viral load. RDT are a valuable addition to RT-qPCR testing, as they reliably detect infectious persons with high viral loads before RT-qPCR results are available. FUNDING: German Federal Ministry for Education and Science (BMBF), Free State of Bavaria.


Subject(s)
COVID-19 Serological Testing/standards , COVID-19/diagnosis , Point-of-Care Testing/standards , Adult , Aged , COVID-19/immunology , COVID-19/virology , COVID-19 Nucleic Acid Testing/methods , COVID-19 Nucleic Acid Testing/standards , COVID-19 Serological Testing/methods , Female , Humans , Male , Middle Aged , Reagent Kits, Diagnostic/standards , Sensitivity and Specificity , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology , Viral Load
8.
Diagn Microbiol Infect Dis ; 100(4): 115381, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-1269260

ABSTRACT

To compare the practicability (usability and satisfaction) and analytical performances of VitaPCR™ Flu A&B Assay (Credo Diagnostics Biomedical Pte. Ltd., Singapore, Republic of Singapore) and Xpert® Xpress Flu/RSV kit (Cepheid, Sunnyvale, USA), two rapid point-of-care (POC) nucleic acid amplification tests (NAATs) by reference to multiplex RT-PCR for respiratory viruses. Nasopharyngeal swabs (n=117) were collected from patients with influenza-like illness in Paris, France. Thawed specimens were further analyzed with both NAATs. The usability was comparable for both NAATs. Satisfaction questionnaire was better for the VitaPCR™ platform for the short time of test result in 20 minutes. Both NAATs showed comparable sensitivities (VitaPCRTM: 95.0%; Xpert® Xpress: 97.5%) and specificities (100%) for influenza A/B RNA detection, with excellent reliability and accuracy between both NAATs. Both VitaPCR™ and Xpert® Xpress NAATs can be implemented in hospital setting as POC NAATs to rapidly detect influenza A/B RNA in symptomatic patients.


Subject(s)
Molecular Diagnostic Techniques/instrumentation , Reagent Kits, Diagnostic/standards , Real-Time Polymerase Chain Reaction/instrumentation , Viruses/genetics , Humans , Influenza A virus/genetics , Influenza, Human/diagnosis , Influenza, Human/virology , Molecular Diagnostic Techniques/methods , Nasopharynx/virology , Point-of-Care Testing/standards , Real-Time Polymerase Chain Reaction/standards , Reproducibility of Results , Sensitivity and Specificity , Viruses/classification , Viruses/isolation & purification
9.
PLoS One ; 16(5): e0251661, 2021.
Article in English | MEDLINE | ID: covidwho-1238764

ABSTRACT

BACKGROUND: Understanding the false negative rates of SARS-CoV-2 RT-PCR testing is pivotal for the management of the COVID-19 pandemic and it has implications for patient management. Our aim was to determine the real-life clinical sensitivity of SARS-CoV-2 RT-PCR. METHODS: This population-based retrospective study was conducted in March-April 2020 in the Helsinki Capital Region, Finland. Adults who were clinically suspected of SARS-CoV-2 infection and underwent SARS-CoV-2 RT-PCR testing, with sufficient data in their medical records for grading of clinical suspicion were eligible. In addition to examining the first RT-PCR test of repeat-tested individuals, we also used high clinical suspicion for COVID-19 as the reference standard for calculating the sensitivity of SARS-CoV-2 RT-PCR. RESULTS: All 1,194 inpatients (mean [SD] age, 63.2 [18.3] years; 45.2% women) admitted to COVID-19 cohort wards during the study period were included. The outpatient cohort of 1,814 individuals (mean [SD] age, 45.4 [17.2] years; 69.1% women) was sampled from epidemiological line lists by systematic quasi-random sampling. The sensitivity (95% CI) for laboratory confirmed cases (repeat-tested patients) was 85.7% (81.5-89.1%) inpatients; 95.5% (92.2-97.5%) outpatients, 89.9% (88.2-92.1%) all. When also patients that were graded as high suspicion but never tested positive were included in the denominator, the sensitivity (95% CI) was: 67.5% (62.9-71.9%) inpatients; 34.9% (31.4-38.5%) outpatients; 47.3% (44.4-50.3%) all. CONCLUSIONS: The clinical sensitivity of SARS-CoV-2 RT-PCR testing was only moderate at best. The relatively high false negative rates of SARS-CoV-2 RT-PCR testing need to be accounted for in clinical decision making, epidemiological interpretations, and when using RT-PCR as a reference for other tests.


Subject(s)
COVID-19 Nucleic Acid Testing/standards , Adult , Aged , COVID-19 Nucleic Acid Testing/methods , False Negative Reactions , Female , Humans , Male , Middle Aged , Random Allocation , Reagent Kits, Diagnostic/standards
10.
Sex Transm Infect ; 97(4): 276-281, 2021 06.
Article in English | MEDLINE | ID: covidwho-1232365

ABSTRACT

OBJECTIVES: 1.5 million people in the UK have mild to moderate learning disabilities. STIs and bloodborne viruses (BBVs) are over-represented in people experiencing broader health inequalities, which include those with mild learning disabilities. Self-managed care, including self-sampling for STIs/BBVs, is increasingly commonplace, requiring agency and health literacy. To inform the development of a partner notification trial, we explored barriers and facilitators to correct use of an STI/BBV self-sampling pack among people with mild learning disabilities. METHODS: Using purposive and convenience sampling we conducted four interviews and five gender-specific focus groups with 25 people (13 women, 12 men) with mild learning disabilities (July-August 2018) in Scotland. We balanced deductive and inductive thematic analyses of audio transcripts to explore issues associated with barriers and facilitators to correct use of the pack. RESULTS: All participants found at least one element of the pack challenging or impossible, but welcomed the opportunity to undertake sexual health screening without attending a clinic and welcomed the inclusion of condoms. Reported barriers to correct use included perceived overly complex STI/BBV information and instructions, feeling overwhelmed and the manual dexterity required for blood sampling. Many women struggled interpreting anatomical diagrams depicting vulvovaginal self-swabbing. Facilitators included pre-existing STI/BBV knowledge, familiarity with self-management, good social support and knowing that the service afforded privacy. CONCLUSION: In the first study to explore the usability of self-sampling packs for STI/BBV in people with learning disabilities, participants found it challenging to use the pack. Limiting information to the minimum required to inform decision-making, 'easy read' formats, simple language, large font sizes and simpler diagrams could improve acceptability. However, some people will remain unable to engage with self-sampling at all. To avoid widening health inequalities, face-to-face options should continue to be provided for those unable or unwilling to engage with self-managed care.


Subject(s)
Blood-Borne Infections/diagnosis , Disabled Persons/psychology , Learning Disabilities/psychology , Reagent Kits, Diagnostic/standards , Sexually Transmitted Diseases/diagnosis , Adult , Female , Health Literacy , Humans , Male , Middle Aged , Qualitative Research , Scotland/epidemiology , Self Care , Specimen Handling
11.
J Virol Methods ; 294: 114182, 2021 08.
Article in English | MEDLINE | ID: covidwho-1225321

ABSTRACT

The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic requires fast and accurate high-throughput diagnostic tools. To evaluate the analytical performance of the Hologic Aptima transcription-mediated amplification (TMA) assay for detection of SARS-CoV-2 RNA from respiratory samples we analysed 103 clinical and proficiency panel samples pre-tested by real-time RT-PCR (Altona, RealStar) and found a positive percent agreement (sensitivity) of 95.7 % and a negative percent agreement (specificity) of 100 %. The limit of detection of the Aptima test was 150 copies/mL determined as 95 % detection probability. To further assess the Aptima assay's specificity we prospectively analysed 7545 clinical specimens from the upper and lower respiratory tract sent for the purpose of routine SARS-CoV-2 screening. SARS-CoV-2 RNA was detected in 16/7545 (0.2 %) samples by the TMA assay and confirmed independently by the Xpert SARS-CoV-2 RT-PCR (Cepheid); in one case a previous discrepant result was confirmed as true SARS-CoV-2 infection in a subsequent sample from the same patient. Results from the Aptima SARS-CoV-2 TMA assay agreed well with RT-PCR and showed an excellent specificity in a large number of routine specimens despite the low prevalence at that time of the pandemic, indicating that this assay can be used even for screening purposes.


Subject(s)
COVID-19 Testing/standards , Nucleic Acid Amplification Techniques/standards , RNA, Viral/genetics , Reagent Kits, Diagnostic/standards , SARS-CoV-2/genetics , Asymptomatic Infections , COVID-19 Testing/methods , Clinical Laboratory Techniques/methods , Clinical Laboratory Techniques/standards , Humans , Limit of Detection , Nasopharynx/virology , Nucleic Acid Amplification Techniques/methods , Prospective Studies , Retrospective Studies , Sensitivity and Specificity
12.
J Virol Methods ; 294: 114178, 2021 08.
Article in English | MEDLINE | ID: covidwho-1213408

ABSTRACT

The aim of this study was to evaluate the diagnostic performance of Simtomax® CoronaCheck, a serology rapid diagnostic test (RDT) for the detection of IgG and IgM against SARS-CoV-2. 48 plasma samples positive for SARS-CoV-2 based on RT-PCR and 98 negative control samples were studied. Diagnostic performance of the IgG/IgM RDT was assessed against RT-PCR and the electro-chemiluminescence immunoassay (ECLIA) Elecsys® Anti-SARS-CoV-2 total Ig. Overall, the RDT sensitivity was 92 % (95 % confidence interval [95 %CI]: 79-97), specificity 97 % (95 % CI: 91-99 %), PPV 94 % (95 % CI: 81-98) and the NPV 96 % (95 % CI: 89-99). When considering only samples collected ≥ 15 days post-symptoms (DPS), the sensitivity increased to 98 % (95 %CI: 86-100) and the specificity was 97 % (95 % CI: 91-99 %). Two samples with 180 DPS were still positive for IgG. Globally, this IgG/IgM RDT displayed a high diagnostic accuracy for SARS-CoV-2 IgG/IgM detection in plasma samples in high COVID-19 prevalence settings. It could be effectively used, in absence of facilities for routine diagnostic serology, for samples with a DPS between 15 and 180 days.


Subject(s)
Antibodies, Viral/blood , COVID-19 Serological Testing/standards , COVID-19/diagnosis , Immunoassay/standards , Reagent Kits, Diagnostic/standards , Adolescent , Adult , COVID-19/immunology , COVID-19 Serological Testing/methods , Female , Humans , Immunoassay/methods , Immunoglobulin G/blood , Immunoglobulin M/blood , Male , Middle Aged , SARS-CoV-2/immunology , Sensitivity and Specificity , Young Adult
13.
J Med Virol ; 93(9): 5618-5622, 2021 09.
Article in English | MEDLINE | ID: covidwho-1206843

ABSTRACT

The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has led to the design and development of multiple reverse-transcription polymerase chain reaction kits aimed to facilitate the rapid scale-up of molecular testing for massive screening. We evaluated the diagnostic performance of nine commercial kits, which showed optimal performance and high discriminatory power. However, we observed differences in terms of sensitivity, specificity, and E gene Ct Values and discuss these results in light of the influence of SARS-CoV-2 genetic variability and its potential impact in current molecular diagnostic assays.


Subject(s)
COVID-19/diagnosis , Reagent Kits, Diagnostic/standards , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , COVID-19/virology , COVID-19 Testing , Colombia , Humans , Molecular Diagnostic Techniques , Sensitivity and Specificity
14.
J Mol Diagn ; 23(6): 665-670, 2021 06.
Article in English | MEDLINE | ID: covidwho-1171781

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is spreading all over the world and has caused millions of deaths. Several sample-to-answer platforms, including Cepheid Xpert Xpress SARS-CoV-2 (Xpert Xpress), have received emergency use authorization for SARS-CoV-2 nucleic acid detection as a point of care test in the United States. However, their application niche is unclear when compared with real-time RT-PCR assays cleared by the National Medical Products Administration in China. In this study, the clinical performance, sensitivity, and workflow of Xpert Xpress and two real-time RT-PCR kits (BioGerm kit and Sansure kit) were evaluated by the specimens from 86 symptomatic patients. The positive percent agreement of Xpert Xpress was 100% compared with 96.15% for the BioGerm kit and 90% for the Sansure kit. The negative percent agreement was 100% for all three assays. The limit of detection is 100 copies/mL for Xpert Xpress and 500 copies/mL for the BioGerm kit and Sansure kit. By serially diluting five positive specimens, the Xpert Xpress had better detection capability. In the workflow and throughput analysis, the turnaround time was 51 minutes for Xpert Xpress, 150 minutes for the BioGerm kit, and 210 minutes for the Sansure kit. This study provides some indication for diagnosis methods selection.


Subject(s)
COVID-19 Nucleic Acid Testing/standards , COVID-19/diagnosis , RNA, Viral/genetics , Reagent Kits, Diagnostic/standards , Real-Time Polymerase Chain Reaction/standards , SARS-CoV-2/genetics , Benchmarking , COVID-19/epidemiology , COVID-19 Nucleic Acid Testing/instrumentation , COVID-19 Nucleic Acid Testing/methods , China/epidemiology , Humans , Limit of Detection , Point-of-Care Testing , United States/epidemiology
15.
J Med Virol ; 93(5): 3219-3226, 2021 May.
Article in English | MEDLINE | ID: covidwho-1100914

ABSTRACT

The emergence of the novel coronavirus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the late months of 2019 had the officials to declare a public health emergency leading to a global response. Public measurements rely on an accurate diagnosis of individuals infected with the virus by using real-time reverse transcriptase-polymerase chain reaction (RT-PCR). The aim of our study is to relate the fundamental clinical and analytical performance of SARS-CoV-2 (RT-PCR) commercial kits. A total of 94 clinical samples were selected. Generally, 400 µl of each respiratory specimen was subjected to extraction using ExiPrep 96 Viral RNA Kit. All kits master mix preparation, cycling protocol, thermocycler, and results interpretation were carried out according to the manufacturer's instructions of use and recommendations. The performance of the kits was comparable except for the LYRA kit as it was less sensitive (F = 67, p < .001). Overall, four kits scored a sensitivity of 100% including: BGI, IQ Real, Sansure, and RADI. For specificity, all the tested kits scored above 95%. The performance of these commercial kits by gene target showed no significant change in CT values which indicates that kits disparities are mainly linked to the oligonucleotide of the gene target. We believe that most of the commercially available RT-PCR kits included in this study can be used for routine diagnosis of patients with SARS-CoV-2. We recommend including kits with multiple targets in order to monitor the virus changes over time.


Subject(s)
COVID-19/diagnosis , Reagent Kits, Diagnostic , Real-Time Polymerase Chain Reaction/methods , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2 , COVID-19/virology , Humans , Reagent Kits, Diagnostic/standards , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Sensitivity and Specificity
16.
Clin Lab ; 67(2)2021 Feb 01.
Article in English | MEDLINE | ID: covidwho-1094345

ABSTRACT

BACKGROUND AND METHODS: 2019 Corona Virus Disease (COVID-19) caused by SARS-CoV-2 is still pandemic now. RT-qPCR detection was the most common method for the diagnosis of SARS-CoV-2 infection, facilitated by amounts of nucleic acid testing kits. However, the accuracy of nucleic acid detection is affected by various factors such as specimen collection, specimen preparation, reagents deficiency, and personnel quality. RESULTS: In this study, we found that unmatched virus preservation solution will inhibit N gene and OFR-1ab gene (two independent genes of SARS-CoV-2) amplification in one-step detection reagent. CONCLUSIONS: Despite just being a particular phenomenon we found in our work to fight 2019-nCoV, we concluded that unmatched virus preservation solution may have an inhibitory effect on SARS-CoV-2 nucleic acid detection which may lead to incorrect clinical diagnosis.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19 , Genes, Viral/drug effects , Organ Preservation Solutions/pharmacology , SARS-CoV-2 , Specimen Handling , COVID-19/diagnosis , COVID-19/virology , Diagnostic Errors/prevention & control , Humans , Reagent Kits, Diagnostic/standards , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Specimen Handling/adverse effects , Specimen Handling/methods
17.
PLoS One ; 16(2): e0246302, 2021.
Article in English | MEDLINE | ID: covidwho-1085153

ABSTRACT

BACKGROUND: Two automatable in-house protocols for high-troughput RNA extraction from nasopharyngeal swabs for SARS-CoV-2 detection have been evaluated. METHODS: One hundred forty one SARS-CoV-2 positive samples were collected during a period of 10-days. In-house protocols were based on extraction with magnetic beads and designed to be used with either the Opentrons OT-2 (OT-2in-house) liquid handling robot or the MagMAXTM Express-96 system (MMin-house). Both protocols were tested in parallel with a commercial kit that uses the MagMAXTM system (MMkit). Nucleic acid extraction efficiencies were calculated from a SARS-CoV-2 DNA positive control. RESULTS: No significant differences were found between both in-house protocols and the commercial kit in their performance to detect positive samples. The MMkit was the most efficient although the MMin-house presented, in average, lower Cts than the other two. In-house protocols allowed to save between 350€ and 400€ for every 96 extracted samples compared to the commercial kit. CONCLUSION: The protocols described harness the use of easily available reagents and an open-source liquid handling system and are suitable for SARS-CoV-2 detection in high throughput facilities.


Subject(s)
Automation, Laboratory/methods , COVID-19 Nucleic Acid Testing/methods , RNA, Viral/standards , Automation, Laboratory/economics , Automation, Laboratory/standards , COVID-19 Nucleic Acid Testing/economics , COVID-19 Nucleic Acid Testing/standards , Costs and Cost Analysis , Humans , RNA, Viral/chemistry , RNA, Viral/genetics , Reagent Kits, Diagnostic/economics , Reagent Kits, Diagnostic/standards , Sensitivity and Specificity
18.
J Clin Virol ; 134: 104712, 2021 01.
Article in English | MEDLINE | ID: covidwho-1082743

ABSTRACT

BACKGROUND: Currently, there are two rapid antigen detection (RAD) kits from the WHO Emergency Use List for detecting SARS-CoV-2. OBJECTIVE: The Panbio COVID-19 Ag Rapid Test Device was selected to evaluate the performance for detecting SARS-CoV-2. STUDY DESIGN: Analytical sensitivity for the detection of SARS-CoV-2 virus was determined by limit of detection (LOD) using RT-PCR as a reference method. Clinical sensitivity was evaluated by using respiratory specimens collected from confirmed COVID-19 patients. RESULTS: The LOD results showed that the RAD kit was 100 fold less sensitive than RT-PCR. Clinical sensitivity of the RAD kit was 68.6 % for detecting specimens from COVID-19 patients. CONCLUSIONS: The RAD kit evaluated in the present study shared similar performance with another kit from the WHO Emergency Use List, the Standard Q COVID-19 Ag. Understanding the clinical characteristics of RAD kits can guide us to decide different testing strategies in different settings.


Subject(s)
Antigens, Viral/analysis , COVID-19/diagnosis , Reagent Kits, Diagnostic/standards , SARS-CoV-2/immunology , COVID-19/pathology , COVID-19/virology , COVID-19 Testing/methods , Cross Reactions , Hong Kong , Humans , Limit of Detection , Nasopharynx/virology , Pharynx/virology , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2/pathogenicity , World Health Organization
19.
Ann Pharm Fr ; 79(5): 547-557, 2021 Sep.
Article in French | MEDLINE | ID: covidwho-1071846

ABSTRACT

OBJECTIVES: RDT and self-tests are sold in pharmacies. These are medical biology procedures that are currently reserved for biologists. Nevertheless, their use is now being reinforced by the COVID-19 pandemic. What role should the dispensing pharmacist have in relation to the patient? What role can the biologist have in this system? METHODS: A survey was carried out in pharmacies in the Auvergne-Rhône-Alpes region, as well as in Cameroon during the summer of 2020, to evaluate the use of RDT and self-tests. The answers obtained to the 10 questions were discussed after a simple statistical analysis. RESULTS: Two hundred and eighty-three pharmacies and 13 Cameroonian pharmacies participated in our survey. Pharmacists want to develop the use of RDT and self-test, but agree that training is necessary. Some tests are dispensed despite their unproven clinical usefulness. CONCLUSIONS: The delivery of TRODs and self-tests is acquired in pharmacies despite the reluctance of biologists. Pharmacists should be trained by biologists to use these tests in a relevant and appropriate manner.


Subject(s)
COVID-19/diagnosis , Pharmacists , Reagent Kits, Diagnostic/standards , Cameroon , Community Pharmacy Services , France , Humans , Pandemics , Pharmacies , Surveys and Questionnaires
20.
Int J Infect Dis ; 104: 303-305, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-1065186

ABSTRACT

BACKGROUND: Multiple molecular kits are available for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide, with many lacking proper clinical evaluation due to the emergency caused by the coronavirus disease 2019 (COVID-19) pandemic, particularly in developing countries. METHODS: This study was conducted to evaluate the clinical performance of the Isopollo COVID-19 detection kit (M Monitor, South Korea) for reverse transcription loop-mediated isothermal amplification (RT-LAMP) SARS-CoV-2 diagnosis, using the SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) protocol as the gold standard. RESULTS: A total of 220 clinical samples were included in the study; 168 samples were SARS-CoV-2-positive and 52 samples were SARS-CoV-2-negative according to the SARS-CoV-2 RT-PCR protocol. For the Isopollo COVID-19 detection kit, only 104 out of 168 samples were SARS-CoV-2-positive. This result shows a low clinical performance, with sensitivity of 61.9% for the evaluated RT-LAMP assay. CONCLUSIONS: Proper clinical performance evaluation studies by regulatory agencies in developing countries such as Ecuador should be mandatory prior to clinical use authorization of SARS-CoV-2 diagnosis kits, particularly when those kits lack either US Food and Drug Administration or country of origin clinical use authorization.


Subject(s)
COVID-19/diagnosis , Pandemics , Reagent Kits, Diagnostic/standards , SARS-CoV-2/isolation & purification , COVID-19/epidemiology , COVID-19/virology , COVID-19 Testing , Developing Countries , Ecuador/epidemiology , Humans , Molecular Diagnostic Techniques , Nucleic Acid Amplification Techniques , Reverse Transcription , SARS-CoV-2/genetics
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