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1.
Proc Natl Acad Sci U S A ; 119(26): e2202034119, 2022 06 28.
Article in English | MEDLINE | ID: covidwho-1900769

ABSTRACT

CRISPR diagnostics based on nucleic acid amplification faces barriers to its commercial use, such as contamination risks and insufficient sensitivity. Here, we propose a robust solution involving optochemical control of CRISPR RNA (crRNA) activation in CRISPR detection. Based on this strategy, recombinase polymerase amplification (RPA) and CRISPR-Cas12a detection systems can be integrated into a completely closed test tube. crRNA can be designed to be temporarily inactivated so that RPA is not affected by Cas12a cleavage. After the RPA reaction is completed, the CRISPR-Cas12a detection system is activated under rapid light irradiation. This photocontrolled, fully closed CRISPR diagnostic system avoids contamination risks and exhibits a more than two orders of magnitude improvement in sensitivity compared with the conventional one-pot assay. This photocontrolled CRISPR method was applied to the clinical detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA, achieving detection sensitivity and specificity comparable to those of PCR. Furthermore, a compact and automatic photocontrolled CRISPR detection device was constructed.


Subject(s)
Bacterial Proteins , CRISPR-Associated Proteins , CRISPR-Cas Systems , Clustered Regularly Interspaced Short Palindromic Repeats , Endodeoxyribonucleases , Reagent Kits, Diagnostic , Reverse Transcriptase Polymerase Chain Reaction , COVID-19/diagnosis , Clustered Regularly Interspaced Short Palindromic Repeats/radiation effects , Humans , RNA/radiation effects , Recombinases/genetics , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/isolation & purification , Sensitivity and Specificity
2.
Int J Mol Sci ; 23(6)2022 Mar 15.
Article in English | MEDLINE | ID: covidwho-1742492

ABSTRACT

SARS-CoV-2 variants surveillance is a worldwide task that has been approached with techniques such as Next Generation Sequencing (NGS); however, this technology is not widely available in developing countries because of the lack of equipment and limited funding in science. An option is to deploy a RT-qPCR screening test which aids in the analysis of a higher number of samples, in a shorter time and at a lower cost. In this study, variants present in samples positive for SARS-CoV-2 were identified with a RT-qPCR mutation screening kit and were later confirmed by NGS. A sample with an abnormal result was found with the screening test, suggesting the simultaneous presence of two viral populations with different mutations. The DRAGEN Lineage analysis identified the Delta variant, but there was no information about the other three mutations previously detected. When the sequenced data was deeply analyzed, there were reads with differential mutation patterns, that could be identified and classified in terms of relative abundance, whereas only the dominant population was reported by DRAGEN software. Since most of the software developed to analyze SARS-CoV-2 sequences was aimed at obtaining the consensus sequence quickly, the information about viral populations within a sample is scarce. Here, we present a faster and deeper SARS-CoV-2 surveillance method, from RT-qPCR screening to NGS analysis.


Subject(s)
COVID-19/diagnosis , DNA Mutational Analysis/methods , Genome, Viral/genetics , Mutation , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , COVID-19/epidemiology , COVID-19/virology , High-Throughput Nucleotide Sequencing/methods , Humans , Pandemics/prevention & control , Reproducibility of Results , SARS-CoV-2/physiology , Sensitivity and Specificity
3.
J Med Virol ; 94(4): 1450-1456, 2022 04.
Article in English | MEDLINE | ID: covidwho-1718389

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic is an overwhelming crisis across the world. Human Coronavirus OC43 (HCoV-OC43) is a Betacoronavirus responsible mostly for mild respiratory symptoms. Since the presentations of HCoV-OC43 and severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) are believed to resemble a lot, the aim of this study was to evaluate the frequency and characteristics of HCoV-OC43 in the current pandemic and the rate of coinfection for the two viruses. One hundred and seventeen patients referred to Children's Medical Center, Tehran, Iran with respiratory symptoms were included. Real-time reverse transcription-polymerase chain reaction (RT-PCR) methods were performed for the detection of HCoV-OC43 and SARS-COV-2. Totally, 23 (20%) had a positive RT-PCR for HCoV-OC43 and 25 (21%) were positive for SARS-COV-2. Two patients (2%) had a positive PCR for both HCoV-OC43 and SARS-COV-2. The two groups showed significant differences in having contact with family members with suspected or confirmed COVID-19 (p = 0.017), fever (p = 0.02), edema (p = 0.036), vomiting (p < 0.001), abdominal complaints (p = 0.005), and myalgia (p = 0.02). The median level of lymphocyte count in patients with HCoV-OC43 was significantly lower than patients with SARS-COV-2 infection (p = 0.039). The same frequency of SARS-COV-2 and HCoV-OC43 was found in children with respiratory symptoms during the COVID-19 pandemic. The rate of coinfection of SARS-COV-2 with HCoV-OC43 in our study was 0.08. Further research into the cocirculation of endemic coronaviruses, such as HCoV-OC43 and SARS-CoV2, in different regions, is highly recommended. Attempts to determine the geographic distribution and recruit more flexible test panel designs are also highly recommended.


Subject(s)
COVID-19/diagnosis , Coronavirus OC43, Human/genetics , Respiratory Tract Infections/virology , SARS-CoV-2/genetics , Child , Child, Preschool , Female , Humans , Infant , Iran , Male , Reverse Transcriptase Polymerase Chain Reaction/methods
4.
Microbiol Spectr ; 10(1): e0251321, 2022 02 23.
Article in English | MEDLINE | ID: covidwho-1707792

ABSTRACT

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread worldwide. Many variants of SARS-CoV-2 have been reported, some of which have increased transmissibility and/or reduced susceptibility to vaccines. There is an urgent need for variant phenotyping for epidemiological surveillance of circulating lineages. Whole-genome sequencing is the gold standard for identifying SARS-CoV-2 variants, which constitutes a major bottleneck in developing countries. Methodological simplification could increase epidemiological surveillance feasibility and efficiency. We designed a novel multiplex real-time reverse transcriptase PCR (RT-PCR) to detect SARS-CoV-2 variants with S gene mutations. This multiplex PCR typing method was established to detect 9 mutations with specific primers and probes (ΔHV 69/70, K417T, K417N, L452R, E484K, E484Q, N501Y, P681H, and P681R) against the receptor-binding domain of the spike protein of SARS-CoV-2 variants. In silico analyses showed high specificity of the assays. Variants of concern (VOC) typing results were found to be highly specific for our intended targets, with no cross-reactivity observed with other upper respiratory viruses. The PCR-based typing methods were further validated using whole-genome sequencing and a commercial kit that was applied to clinical samples of 250 COVID-19 patients from Taiwan. The screening of these samples allowed the identification of epidemic trends by time intervals, including B.1.617.2 in the third Taiwan wave outbreak. This PCR typing strategy allowed the detection of five major variants of concern and also provided an open-source PCR assay which could rapidly be deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, P.1, and B.1.617.2 variants and of four Omicron mutations on the spike protein (ΔHV 69/70, K417N, N501Y, P681H). IMPORTANCE COVID-19 has spread globally. SARS-CoV-2 variants of concern (VOCs) are leading the next waves of the COVID-19 pandemic. Previous studies have pointed out that these VOCs may have increased infectivity, have reduced vaccine susceptibility, change treatment regimens, and increase the difficulty of epidemic prevention policy. Understanding SARS-CoV-2 variants remains an issue of concern for all local government authorities and is critical for establishing and implementing effective public health measures. A novel SARS-CoV-2 variant identification method based on a multiplex real-time RT-PCR was developed in this study. Five SARS-CoV-2 variants (Alpha, Beta, Gamma, Delta, and Omicron) were identified simultaneously using this method. PCR typing can provide rapid testing results with lower cost and higher feasibility, which is well within the capacity for any diagnostic laboratory. Characterizing these variants and their mutations is important for tracking SAR-CoV-2 evolution and is conducive to public infection control and policy formulation strategies.


Subject(s)
COVID-19/virology , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/classification , COVID-19/epidemiology , Epidemiological Monitoring , Humans , Mutation , Pandemics , Public Health , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Spike Glycoprotein, Coronavirus/genetics , Taiwan , Whole Genome Sequencing
5.
Sci Immunol ; 7(68): eabf2846, 2022 02 11.
Article in English | MEDLINE | ID: covidwho-1685480

ABSTRACT

Macrophages regulate protective immune responses to infectious microbes, but aberrant macrophage activation frequently drives pathological inflammation. To identify regulators of vigorous macrophage activation, we analyzed RNA-seq data from synovial macrophages and identified SLAMF7 as a receptor associated with a superactivated macrophage state in rheumatoid arthritis. We implicated IFN-γ as a key regulator of SLAMF7 expression and engaging SLAMF7 drove a strong wave of inflammatory cytokine expression. Induction of TNF-α after SLAMF7 engagement amplified inflammation through an autocrine signaling loop. We observed SLAMF7-induced gene programs not only in macrophages from rheumatoid arthritis patients but also in gut macrophages from patients with active Crohn's disease and in lung macrophages from patients with severe COVID-19. This suggests a central role for SLAMF7 in macrophage superactivation with broad implications in human disease pathology.


Subject(s)
Inflammation/immunology , Macrophage Activation/immunology , Signaling Lymphocytic Activation Molecule Family/immunology , Transcriptome/immunology , Acute Disease , Adult , Arthritis, Rheumatoid/genetics , Arthritis, Rheumatoid/immunology , Arthritis, Rheumatoid/metabolism , COVID-19/genetics , COVID-19/immunology , COVID-19/metabolism , COVID-19/virology , Cells, Cultured , Chronic Disease , Crohn Disease/genetics , Crohn Disease/immunology , Crohn Disease/metabolism , Female , Humans , Inflammation/genetics , Inflammation/metabolism , Macrophage Activation/genetics , RNA-Seq/methods , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/immunology , SARS-CoV-2/physiology , Signaling Lymphocytic Activation Molecule Family/genetics , Signaling Lymphocytic Activation Molecule Family/metabolism , Single-Cell Analysis/methods , Synovial Membrane/immunology , Synovial Membrane/metabolism , Synovial Membrane/pathology , Transcriptome/genetics
6.
Viruses ; 14(2)2022 02 02.
Article in English | MEDLINE | ID: covidwho-1667351

ABSTRACT

Efficient, wide-scale testing for SARS-CoV-2 is crucial for monitoring the incidence of the infection in the community. The gold standard for COVID-19 diagnosis is the molecular analysis of epithelial secretions from the upper respiratory system captured by nasopharyngeal (NP) or oropharyngeal swabs. Given the ease of collection, saliva has been proposed as a possible substitute to support testing at the population level. Here, we used a novel saliva collection device designed to favour the safe and correct acquisition of the sample, as well as the processivity of the downstream molecular analysis. We tested 1003 nasopharyngeal swabs and paired saliva samples self-collected by individuals recruited at a public drive-through testing facility. An overall moderate concordance (68%) between the two tests was found, with evidence that neither system can diagnose the infection in 100% of the cases. While the two methods performed equally well in symptomatic individuals, their discordance was mainly restricted to samples from convalescent subjects. The saliva test was at least as effective as NP swabs in asymptomatic individuals recruited for contact tracing. Our study describes a testing strategy of self-collected saliva samples, which is reliable for wide-scale COVID-19 screening in the community and is particularly effective for contact tracing.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19 Nucleic Acid Testing/standards , RNA, Viral/analysis , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Saliva/virology , COVID-19/diagnosis , COVID-19/virology , Female , Humans , Male , Mass Screening , Nasopharynx/virology , RNA, Viral/genetics , SARS-CoV-2/isolation & purification , Specimen Handling/methods
7.
Sci Rep ; 12(1): 1614, 2022 01 31.
Article in English | MEDLINE | ID: covidwho-1661979

ABSTRACT

As the SARS-CoV-2 pandemic persists, methods that can quickly and reliably confirm infection and immune status is extremely urgently and critically needed. In this contribution we show that combining laser induced breakdown spectroscopy (LIBS) with machine learning can distinguish plasma of donors who previously tested positive for SARS-CoV-2 by RT-PCR from those who did not, with up to 95% accuracy. The samples were also analyzed by LIBS-ICP-MS in tandem mode, implicating a depletion of Zn and Ba in samples of SARS-CoV-2 positive subjects that inversely correlate with CN lines in the LIBS spectra.


Subject(s)
COVID-19/blood , COVID-19/diagnosis , Immunity , Lasers , Pandemics , SARS-CoV-2/immunology , Spectrophotometry, Atomic/methods , Barium/analysis , COVID-19/epidemiology , COVID-19/virology , Data Accuracy , Discriminant Analysis , False Negative Reactions , False Positive Reactions , Humans , Machine Learning , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Sensitivity and Specificity , Zinc/analysis
8.
Virchows Arch ; 480(3): 597-607, 2022 Mar.
Article in English | MEDLINE | ID: covidwho-1661693

ABSTRACT

Post-mortem examination plays a pivotal role in understanding the pathobiology of the SARS-CoV-2; thus, the optimization of virus detection on the post-mortem formalin-fixed paraffin-embedded (FFPE) tissue is needed. Different techniques are available for the identification of the SARS-CoV-2, including reverse transcription polymerase chain reaction (RT-PCR), immunohistochemistry (IHC), in situ hybridization (ISH), and electron microscopy. The main goal of this study is to compare ISH versus RT-PCR to detect SARS-CoV-2 on post-mortem lung samples of positive deceased subjects. A total of 27 samples were analyzed by RT-PCR targeting different viral RNA sequences of SARS-CoV-2, including envelope (E), nucleocapsid (N), spike (S), and open reading frame (ORF1ab) genes and ISH targeting S and Orf1ab. All 27 cases showed the N gene amplification, 22 out of 27 the E gene amplification, 26 out of 27 the S gene amplification, and only 6 the ORF1ab gene amplification. The S ISH was positive only in 12 out of 26 cases positive by RT-PCR. The S ISH positive cases with strong and diffuse staining showed a correlation with low values of the number of the amplification cycles by S RT-PCR suggesting that ISH is a sensitive assay mainly in cases carrying high levels of S RNA. In conclusion, our findings demonstrated that ISH assay has lower sensitivity to detect SARS-CoV-2 in FFPE compared to RT-PCR; however, it is able to localize the virus in the cellular context since it preserves the morphology.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , Humans , In Situ Hybridization/methods , Lung , RNA, Viral/genetics , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Sensitivity and Specificity
9.
Front Immunol ; 12: 785599, 2021.
Article in English | MEDLINE | ID: covidwho-1643498

ABSTRACT

Zinc ion as an enzyme cofactor exhibits antiviral and anti-inflammatory activity during infection, but circulating zinc ion level during Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is unclear. This study aimed to evaluate serum zinc ion level in Coronavirus Disease 2019 (COVID-19) patients and healthy subjects, as well as its correlation with antibodies against SARS-CoV-2. 114 COVID-19 patients and 48 healthy subjects (38 healthy volunteers and 10 close contacts of patients with COVID-19) were included. Zinc ion concentration and levels of antibodies against SARS-CoV-2 Spike 1 + Spike 2 proteins, nucleocapsid protein, and receptor-binding domain in serum were measured. Results showed that the concentration of zinc ion in serum from COVID-19 patients [median: 6.4 nmol/mL (IQR 1.5 - 12.0 nmol/mL)] were significantly lower than that from the healthy subjects [median: 15.0 nmol/mL (IQR 11.9 - 18.8 nmol/mL)] (p < 0.001) and the difference remained significant after age stratification (p < 0.001) or when the patients were at the recovery stage (p < 0.001). Furthermore, COVID-19 patients with more severe hypozincemia showed higher levels of IgG against the receptor-binding domain of SARS-CoV-2 spike protein. Further studies to confirm the effect of zinc supplementation on improving the outcomes of COVID-19, including antibody response against SARS-CoV-2, are warranted.


Subject(s)
Antibodies, Viral/blood , COVID-19/blood , COVID-19/immunology , Immunity , SARS-CoV-2/immunology , Zinc/blood , Adult , Antibodies, Viral/immunology , COVID-19/virology , Case-Control Studies , Cations, Divalent/blood , Coronavirus Nucleocapsid Proteins/immunology , Female , Humans , Immunoglobulin G/blood , Immunoglobulin G/immunology , Male , Middle Aged , Phosphoproteins/immunology , Protein Domains/immunology , Real-Time Polymerase Chain Reaction/methods , Retrospective Studies , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/immunology
10.
PLoS One ; 17(1): e0262656, 2022.
Article in English | MEDLINE | ID: covidwho-1638777

ABSTRACT

SARS-CoV-2, the cause of COVID-19, requires reliable diagnostic methods to track the circulation of this virus. Following the development of RT-qPCR methods to meet this diagnostic need in January 2020, it became clear from interlaboratory studies that the reported Ct values obtained for the different laboratories showed high variability. Despite this the Ct values were explored as a quantitative cut off to aid clinical decisions based on viral load. Consequently, there was a need to introduce standards to support estimation of SARS-CoV-2 viral load in diagnostic specimens. In a collaborative study, INSTAND established two reference materials (RMs) containing heat-inactivated SARS-CoV-2 with SARS-CoV-2 RNA loads of ~107 copies/mL (RM 1) and ~106 copies/mL (RM 2), respectively. Quantification was performed by RT-qPCR using synthetic SARS-CoV-2 RNA standards and digital PCR. Between November 2020 and February 2021, German laboratories were invited to use the two RMs to anchor their Ct values measured in routine diagnostic specimens, with the Ct values of the two RMs. A total of 305 laboratories in Germany were supplied with RM 1 and RM 2. The laboratories were requested to report their measured Ct values together with details on the PCR method they used to INSTAND. This resultant 1,109 data sets were differentiated by test system and targeted gene region. Our findings demonstrate that an indispensable prerequisite for linking Ct values to SARS-CoV-2 viral loads is that they are treated as being unique to an individual laboratory. For this reason, clinical guidance based on viral loads should not cite Ct values. The RMs described were a suitable tool to determine the specific laboratory Ct for a given viral load. Furthermore, as Ct values can also vary between runs when using the same instrument, such RMs could be used as run controls to ensure reproducibility of the quantitative measurements.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Diagnostic Tests, Routine/methods , RNA, Viral/genetics , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Viral Load/methods , COVID-19/epidemiology , COVID-19/virology , Genes, Viral , Germany/epidemiology , Humans , Reproducibility of Results
11.
PLoS One ; 17(1): e0262178, 2022.
Article in English | MEDLINE | ID: covidwho-1637832

ABSTRACT

BACKGROUND: COVID-19 is an ongoing public health pandemic regardless of the countless efforts made by various actors. Quality diagnostic tests are important for early detection and control. Notably, several commercially available one step RT-PCR based assays have been recommended by the WHO. Yet, their analytic and diagnostic performances have not been well documented in resource-limited settings. Hence, this study aimed to evaluate the diagnostic sensitivities and specificities of three commercially available one step reverse transcriptase-polymerase chain reaction (RT-PCR) assays in Ethiopia in clinical setting. METHODS: A cross-sectional study was conducted from April to June, 2021 on 279 respiratory swabs originating from community surveillance, contact cases and suspect cases. RNA was extracted using manual extraction method. Master-mix preparation, amplification and result interpretation was done as per the respective manufacturer. Agreements between RT-PCRs were analyzed using kappa values. Bayesian latent class models (BLCM) were fitted to obtain reliable estimates of diagnostic sensitivities, specificities of the three assays and prevalence in the absence of a true gold standard. RESULTS: Among the 279 respiratory samples, 50(18%), 59(21.2%), and 69(24.7%) were tested positive by TIB, Da An, and BGI assays, respectively. Moderate to substantial level of agreement was reported among the three assays with kappa value between 0 .55 and 0.72. Based on the BLCM relatively high specificities (95% CI) of 0.991(0.973-1.000), 0.961(0.930-0.991) and 0.916(0.875-0.952) and considerably lower sensitivities with 0.813(0.658-0.938), 0.836(0.712-0.940) and 0.810(0.687-0.920) for TIB MOLBIOL, Da An and BGI respectively were found. CONCLUSIONS: While all the three RT-PCR assays displayed comparable sensitivities, the specificities of TIB MOLBIOL and Da An were considerably higher than BGI. These results help adjust the apparent prevalence determined by the three RT-PCRs and thus support public health decisions in resource limited settings and consider alternatives as per their prioritization matrix.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , COVID-19/epidemiology , Diagnostic Tests, Routine/methods , Pandemics/prevention & control , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Adolescent , Adult , Aged , Aged, 80 and over , Bayes Theorem , COVID-19/virology , Child , Cross-Sectional Studies , Ethiopia/epidemiology , False Positive Reactions , Female , Humans , Male , Middle Aged , Molecular Diagnostic Techniques/methods , RNA, Viral/genetics , RNA, Viral/isolation & purification , Sensitivity and Specificity , Young Adult
12.
PLoS One ; 17(1): e0262170, 2022.
Article in English | MEDLINE | ID: covidwho-1637228

ABSTRACT

The SARS-CoV-2 responsible for the ongoing COVID pandemic reveals particular evolutionary dynamics and an extensive polymorphism, mainly in Spike gene. Monitoring the S gene mutations is crucial for successful controlling measures and detecting variants that can evade vaccine immunity. Even after the costs reduction resulting from the pandemic, the new generation sequencing methodologies remain unavailable to a large number of scientific groups. Therefore, to support the urgent surveillance of SARS-CoV-2 S gene, this work describes a new feasible protocol for complete nucleotide sequencing of the S gene using the Sanger technique. Such a methodology could be easily adopted by any laboratory with experience in sequencing, adding to effective surveillance of SARS-CoV-2 spreading and evolution.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , COVID-19/epidemiology , Genes, Viral , Pandemics/prevention & control , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Sequence Analysis, RNA/methods , Spike Glycoprotein, Coronavirus/genetics , Base Sequence , Brazil/epidemiology , COVID-19/virology , Diagnostic Tests, Routine/methods , Electrophoresis, Agar Gel/methods , Epidemiological Monitoring , Humans , Mutation , RNA, Viral/genetics , RNA, Viral/isolation & purification
13.
PLoS One ; 17(1): e0262820, 2022.
Article in English | MEDLINE | ID: covidwho-1628968

ABSTRACT

BACKGROUND: Early and accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to prevent spread of the infection. Understanding of the antibody response to SARS-CoV-2 in patients with coronavirus disease 2019 (COVID-19) is insufficient, particularly in relation to those whose responses persist for more than 1 month after the onset of symptoms. We conducted a SARS-CoV-2 antibody test to identify factors affecting the serological response and to evaluate its diagnostic utility in patients with COVID-19. METHODS AND FINDING: We collected 1,048 residual serum samples from 396 patients with COVID-19 confirmed by real-time reverse transcription polymerase chain reaction (RT-PCR) for SARS-CoV-2. The samples had been used for routine admission tests in six healthcare institutions in Daegu. Antibody to SARS-CoV-2 was analyzed and the cutoff index (COI) was calculated for quantitative analysis. The patients' information was reviewed to evaluate the relationship between antibody positivity and clinical characteristics. The anti-SARS-CoV-2 antibody positivity rate was 85% and the average COI was 24·3. The positivity rate and COI increased with time elapsed since symptom onset. Anti-SARS-CoV-2 antibody persisted for at least 13 weeks after symptom onset at a high COI. There was a significant difference in anti-SARS-CoV-2 antibody positivity rate between patients with and without symptoms, but not according to sex or disease course. The descending COI pattern at weeks 1 to 5 after symptom onset was significantly more frequent in patients who died than in those who recovered. CONCLUSIONS: Anti-SARS-CoV-2 antibody persisted for at least 13 weeks at a high COI in patients with COVID-19. A decreasing COI pattern up to fifth week may be associated with a poor prognosis of COVID-19. As new treatments and vaccines are introduced, it is important to monitor continuously the usefulness of anti-SARS-CoV-2 antibody assays.


Subject(s)
Antibodies, Viral/blood , COVID-19 Serological Testing/methods , COVID-19/blood , COVID-19/epidemiology , SARS-CoV-2/immunology , Aged , Antibodies, Viral/immunology , COVID-19/diagnosis , COVID-19/immunology , COVID-19 Nucleic Acid Testing/methods , Enzyme-Linked Immunosorbent Assay/methods , Female , Humans , Immunoglobulin G/blood , Immunoglobulin G/immunology , Immunoglobulin M/blood , Immunoglobulin M/immunology , Male , Middle Aged , Real-Time Polymerase Chain Reaction/methods , Republic of Korea/epidemiology , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Sensitivity and Specificity
14.
Vopr Virusol ; 66(6): 417-424, 2022 01 08.
Article in Russian | MEDLINE | ID: covidwho-1623043

ABSTRACT

INTRODUCTION: Currently, the basis for molecular diagnostics of most infections is the use of reverse transcription polymerase chain reaction (RT-PCR). Technologies based on reverse transcription isothermal loop amplification (RT-LAMP) can be used as an alternative to RT-PCR for diagnostic purposes. In this study, we compared the RTLAMP and RT-PCR methods in order to analyze both the advantages and disadvantages of the two approaches. MATERIAL AND METHODS: For the study, we used reagent kits based on RT-PCR and RT-LAMP. The biological material obtained by taking swabs from the mucous membrane of the oropharynx and nasopharynx in patients with symptoms of a new coronavirus infection was used. RESULTS: We tested 381 RNA samples of the SARS-CoV-2 virus (Coronaviridae: Coronavirinae: Betacoronavirus; Sarbecovirus) from various patients. The obtained values of the threshold cycle (Ct) for RT-PCR averaged 20.0 ± 3.7 s (1530 ± 300 s), and for RT-LAMP 12.8 ± 3.7 s (550 ± 160 s). Proceeding from the theoretical assumptions, a linear relationship between values obtained in two kits was proposed as a hypothesis; the correlation coefficient was approximately 0.827. At the same time, for samples with a low viral load (VL), the higher Ct values in RT-LAMP did not always correlated with those obtained in RT-PCR. DISCUSSION: We noted a significant gain in time for analysis using RT-LAMP compared to RT-PCR, which can be important in the context of testing a large number of samples. Being easy to use and boasting short turnaround time, RT-LAMP-based test systems can be used for mass screening in order to identify persons with medium and high VLs who pose the greatest threat of the spread of SARS-CoV-2, while RT-PCR-based diagnostic methods are also suitable for estimation of VL and its dynamics in patients with COVID-19.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Mass Screening/methods , Nucleic Acid Amplification Techniques/methods , SARS-CoV-2/genetics , Humans , Molecular Diagnostic Techniques , Polymerase Chain Reaction , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/isolation & purification , Sensitivity and Specificity
15.
Front Immunol ; 12: 732756, 2021.
Article in English | MEDLINE | ID: covidwho-1597480

ABSTRACT

Coronavirus disease 2019 (COVID-19), which started out as an outbreak of pneumonia, has now turned into a pandemic due to its rapid transmission. Besides developing a vaccine, rapid, accurate, and cost-effective diagnosis is essential for monitoring and combating the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its related variants on time with precision and accuracy. Currently, the gold standard for detection of SARS-CoV-2 is Reverse Transcription Polymerase Chain Reaction (RT-PCR), but it lacks accuracy, is time-consuming and cumbersome, and fails to detect multi-variant forms of the virus. Herein, we have summarized conventional diagnostic methods such as Chest-CT (Computed Tomography), RT-PCR, Loop Mediated Isothermal Amplification (LAMP), Reverse Transcription-LAMP (RT-LAMP), as well new modern diagnostics such as CRISPR-Cas-based assays, Surface Enhanced Raman Spectroscopy (SERS), Lateral Flow Assays (LFA), Graphene-Field Effect Transistor (GraFET), electrochemical sensors, immunosensors, antisense oligonucleotides (ASOs)-based assays, and microarrays for SARS-CoV-2 detection. This review will also provide an insight into an ongoing research and the possibility of developing more economical tools to tackle the COVID-19 pandemic.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Clinical Laboratory Techniques/methods , Molecular Diagnostic Techniques/methods , SARS-CoV-2/genetics , COVID-19/epidemiology , COVID-19/virology , Humans , Immunoassay/methods , Nucleic Acid Amplification Techniques/methods , Oligonucleotide Probes/genetics , Pandemics , RNA, Viral/genetics , Reproducibility of Results , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/physiology , Sensitivity and Specificity
16.
Eur J Med Res ; 26(1): 147, 2021 Dec 17.
Article in English | MEDLINE | ID: covidwho-1582004

ABSTRACT

BACKGROUND: The outbreak of novel coronavirus disease 2019 (COVID-19) has become a public health emergency of international concern. Quantitative testing of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) virus is demanded in evaluating the efficacy of antiviral drugs and vaccines and RT-PCR can be widely deployed in the clinical assay of viral loads. Here, we developed a quantitative RT-PCR method for SARS-CoV-2 virus detection in this study. METHODS: RT-PCR kits targeting E (envelope) gene, N (nucleocapsid) gene and RdRP (RNA-dependent RNA polymerase) gene of SARS-CoV-2 from Roche Diagnostics were evaluated and E gene kit was employed for quantitative detection of COVID-19 virus using Cobas Z480. Viral load was calculated according to the standard curve established by series dilution of an E-gene RNA standard provided by Tib-Molbiol (a division of Roche Diagnostics). Assay performance was evaluated. RESULTS: The performance of the assay is acceptable with limit of detection (LOD) below 10E1 copies/µL and lower limit of quantification (LLOQ) as 10E2 copies/µL. CONCLUSION: A quantitative detection of the COVID-19 virus based on RT-PCR was established.


Subject(s)
COVID-19/diagnosis , Coronavirus Envelope Proteins/genetics , Coronavirus Nucleocapsid Proteins/genetics , Coronavirus RNA-Dependent RNA Polymerase/genetics , Reverse Transcriptase Polymerase Chain Reaction/methods , Humans , Limit of Detection , Phosphoproteins/genetics , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Viral Load/methods
17.
Lab Med ; 52(6): e147-e153, 2021 Nov 02.
Article in English | MEDLINE | ID: covidwho-1574316

ABSTRACT

OBJECTIVE: In this study, the performance of 2 commercially available SARS-CoV-2 antibody assays is evaluated. METHODS: The Siemens SARS-CoV-2 Total (COV2T) and IgG (COV2G) antibody tests were evaluated on a Siemens Atellica IM1300 analyzer. Imprecision was assessed with the CLSI EP15 protocol using positive controls. Ninety control group specimens were analyzed for specificity, and 175 specimens from 58 patients with polymerase chain reaction-confirmed SARS-CoV-2 were measured for the sensitivity and kinetics of the antibody response. RESULTS: Within-run and total imprecision were acceptable for both assays. Both tests showed a specificity of 100%. Sensitivity earlier in the disease state was greater for the COV2T assay than for the COV2G assay, but sensitivity >14 days after onset of symptoms approached 100% for both. For all patients, antibody titers remained above the seroconversion cutoff for all follow-up specimens. CONCLUSION: This study shows acceptable performance for both the Siemens COV2T and COV2G test, although seroconversion occurs earlier with the COV2T test.


Subject(s)
Antibodies, Viral/blood , COVID-19 Serological Testing/standards , COVID-19/diagnosis , Immunoglobulin G/blood , SARS-CoV-2/immunology , Aged , Aged, 80 and over , Automation, Laboratory , COVID-19/blood , COVID-19/immunology , COVID-19/virology , COVID-19 Serological Testing/methods , Enzyme-Linked Immunosorbent Assay/methods , Female , Humans , Male , Reagent Kits, Diagnostic , Retrospective Studies , Reverse Transcriptase Polymerase Chain Reaction/methods , Sensitivity and Specificity
18.
J Clin Lab Anal ; 36(1): e24161, 2022 Jan.
Article in English | MEDLINE | ID: covidwho-1560639

ABSTRACT

BACKGROUND: Various nucleic acid amplification assays for the diagnosis of SARS-CoV-2 infection have been developed, and there is a need to assess their test performance relative to one another. The aim of this study was to compare the performance characteristics of the Biosewoom Real-Q 2019-nCoV assay targeting the E and RdRP genes to DaAn Gene 2019-nCoV kit targeting the N gene and ORF1ab in the diagnosis of SARS-CoV-2. METHODS: We performed a diagnostic comparison study by testing nasopharyngeal samples for SARS-CoV-2 using the two reverse transcription polymerase chain reaction (RT-PCR) assays. Assay agreement was assessed by overall percent agreement, negative percent agreement, positive percent agreement, and Cohen's kappa coefficient. RESULTS: A total of 48 nasopharyngeal samples were tested using the two assays. One sample was invalid, and three showed inconclusive results with Real-Q; hence, 44 were included for the comparative analysis. Overall, percent agreement between the assays was 93.2% (95% CI 81.3%-98.6%), Positive percent agreement (PPA) was 86.4% (95% CI 65.1%-97.1%) and negative percent agreement (NPA) was 100% (95% CI 84.6%-100%). The kappa coefficient was 0.86 (95% CI 0.72-1.01). Three samples (6.8%) were positive with DaAn gene kit and negative with Real-Q. The fluorescence intensity for Real-Q reporter dyes was low. CONCLUSION: The two kits showed high levels of concordance in their detection of SARS-CoV-2 despite having different gene targets. The Biosewoom kit can be improved through addressing the fluorescence intensity of the target dyes, and feedback was given to the manufacturer.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Coronavirus Nucleocapsid Proteins/genetics , Humans , Nasopharynx/virology , Phosphoproteins/genetics , Reagent Kits, Diagnostic
19.
Lab Med ; 52(6): e154-e158, 2021 Nov 02.
Article in English | MEDLINE | ID: covidwho-1559980

ABSTRACT

OBJECTIVE: This study aims to evaluate the performance of an antigen-based rapid diagnostic test (RDT) for the detection of the SARS-CoV-2 virus. METHODS: A cross-sectional study was conducted on 677 patients. Two nasopharyngeal swabs and 1 oropharyngeal swab were collected from patients. The RDT was performed onsite by a commercially available immune-chromatographic assay on the nasopharyngeal swab. The nasopharyngeal and oropharyngeal swabs were examined for SARS-CoV-2 RNA by real-time reverse-transcription quantitative polymerase chain reaction (RT-qPCR) assay. RESULTS: The overall sensitivity of the SARS-CoV-2 RDT was 34.5% and the specificity was 99.8%. The positive predictive value and negative predictive value of the test were 96.6% and 91.5%, respectively. The detection rate of RDT in RT-qPCR positive results was high (45%) for cycle threshold values <25. CONCLUSION: The utility of RDT is in diagnosing symptomatic patients and may not be particularly suited as a screening tool for patients with low viral load. The low sensitivity of RDT does not qualify its use as a single test in patients who test negative; RT-qPCR continues to be the gold standard test.


Subject(s)
Antigens, Viral/genetics , COVID-19 Serological Testing/standards , COVID-19/diagnosis , Chromatography, Affinity/methods , RNA, Viral/genetics , SARS-CoV-2/genetics , Adolescent , Aged , Aged, 80 and over , Automation, Laboratory , COVID-19/immunology , COVID-19/virology , COVID-19 Serological Testing/methods , Cross-Sectional Studies , Female , Humans , Male , Middle Aged , Nasopharynx/virology , Oropharynx/virology , Reagent Kits, Diagnostic , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/immunology , Sensitivity and Specificity , Viral Load/genetics
20.
J Clin Lab Anal ; 36(1): e24137, 2022 Jan.
Article in English | MEDLINE | ID: covidwho-1549207

ABSTRACT

BACKGROUND: Coronavirus disease 2019 (COVID-19) has had a devastating impact on public health services worldwide. Currently, there are no standard remedies or therapies for COVID-19. it is important to identify and diagnose COVID-19 to control the spread. But clinical symptoms of COVID-19 are very similar to those of other respiratory viruses. RESULTS: As a result, the diagnosis of COVID-19 relies heavily on detecting pathogens. We established a bunch of triplex new TaqMan real-time PCR assays. Three sets of primers and probes (targeting the ORF1ab, N, and E genes, respectively) are poorly consistent with other human coronaviruses and the human influenza virus. The sensitivity of established PCR assays notices as few as 100 copies per PCR of the ORF1ab, N, and E genes. Meanwhile, standard curves concluded from constant PCR reaction all showed glorious linear correlations between Ct values and the polymer loading copy variety (correlation coefficient (R2 ) of ORF1ab, N, and E genes is 0.996, 0.991, and 0.998, respectively). Surveillance of RNA-based pseudovirus demonstrated that they were identified to be positive with respect to SARS-CoV-2 and that established PCR assays are achievable. CONCLUSION: The assays established provide a smaller reaction volume for diagnosing COVID-19.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , Real-Time Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , DNA Primers , Humans , RNA, Viral , Reproducibility of Results , Reverse Transcriptase Polymerase Chain Reaction/methods , Sensitivity and Specificity
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