scholarly journals Spike vs nucleocapsid SARS-CoV-2 antigen detection: application in nasopharyngeal swab specimens

2021 ◽  
Author(s):  
Moria Barlev-Gross ◽  
Shay Weiss ◽  
Amir Ben-Shmuel ◽  
Assa Sittner ◽  
Keren Eden ◽  
...  
Keyword(s):  
Point Of Care ◽  
High Specificity ◽  
Antigen Detection ◽  
Screening Tools ◽  
Nasopharyngeal Swab ◽  
Lower Sensitivity ◽  
Sample Collection ◽  
Time Resolved ◽  
Qrt Pcr ◽  
Optimal Target

AbstractPublic health experts emphasize the need for quick, point-of-care SARS-CoV-2 detection as an effective strategy for controlling virus spread. To this end, many “antigen” detection devices were developed and commercialized. These devices are mostly based on detecting SARS-CoV-2’s nucleocapsid protein. Recently, alerts issued by both the FDA and the CDC raised concerns regarding the devices’ tendency to exhibit false positive results. In this work we developed a novel alternative spike-based antigen assay, comprised of four high-affinity, specific monoclonal antibodies, directed against different epitopes on the spike’s S1 subunit. The assay’s performance was evaluated for COVID-19 detection from nasopharyngeal swabs, compared to an in-house nucleocapsid-based assay, composed of antibodies directed against the nucleocapsid. Detection of COVID-19 was carried out in a cohort of 284 qRT-PCR positive and negative nasopharyngeal swab samples. The time resolved fluorescence (TRF) ELISA spike-assay displayed very high specificity (99%) accompanied with a somewhat lower sensitivity (66% for Ct<25), compared to the nucleocapsid ELISA assay which was more sensitive (85% for Ct<25) while less specific (87% specificity). Despite being out-performed by qRT-PCR, we suggest that there is room for such tests in the clinical setting, as cheap and rapid pre-screening tools. Our results further suggest that when applying antigen detection, one must consider its intended application (sensitivity vs specificity), taking into consideration that the nucleocapsid might not be the optimal target. In this regard, we propose that a combination of both antigens might contribute to the validity of the results.Abstract FigureGraphic abstractSchematic representation of sample collection and analysis. The figure was created using BioRender.com

scholarly journals Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis

Diagnostics ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 363
Author(s):  
Vânia M. Moreira ◽  
Paulo Mascarenhas ◽  
Vanessa Machado ◽  
João Botelho ◽  
José João Mendes ◽  
...  
Keyword(s):  
Systematic Review ◽  
Clinical Performance ◽  
Point Of Care ◽  
Meta Analysis ◽  
High Sensitivity ◽  
Nasopharyngeal Swab ◽  
Sample Collection ◽  
Rt Pcr ◽  
Oropharyngeal Swab ◽  
Nucleic Acid Assays

The rapid and accurate testing of SARS-CoV-2 infection is still crucial to mitigate, and eventually halt, the spread of this disease. Currently, nasopharyngeal swab (NPS) and oropharyngeal swab (OPS) are the recommended standard sampling techniques, yet, these have some limitations such as the complexity of collection. Hence, several other types of specimens that are easier to obtain are being tested as alternatives to nasal/throat swabs in nucleic acid assays for SARS-CoV-2 detection. This study aims to critically appraise and compare the clinical performance of RT-PCR tests using oral saliva, deep-throat saliva/posterior oropharyngeal saliva (DTS/POS), sputum, urine, feces, and tears/conjunctival swab (CS) against standard specimens (NPS, OPS, or a combination of both). In this systematic review and meta-analysis, five databases (PubMed, Scopus, Web of Science, ClinicalTrial.gov and NIPH Clinical Trial) were searched up to the 30th of December, 2020. Case-control and cohort studies on the detection of SARS-CoV-2 were included. The methodological quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS 2). We identified 1560 entries, 33 of which (1.1%) met all required criteria and were included for the quantitative data analysis. Saliva presented the higher accuracy, 92.1% (95% CI: 70.0–98.3), with an estimated sensitivity of 83.9% (95% CI: 77.4–88.8) and specificity of 96.4% (95% CI: 89.5–98.8). DTS/POS samples had an overall accuracy of 79.7% (95% CI: 43.3–95.3), with an estimated sensitivity of 90.1% (95% CI: 83.3–96.9) and specificity of 63.1% (95% CI: 36.8–89.3). The remaining index specimens could not be adequately assessed given the lack of studies available. Our meta-analysis shows that saliva samples from the oral region provide a high sensitivity and specificity; therefore, these appear to be the best candidates for alternative specimens to NPS/OPS in SARS-CoV-2 detection, with suitable protocols for swab-free sample collection to be determined and validated in the future. The distinction between oral and extra-oral salivary samples will be crucial, since DTS/POS samples may induce a higher rate of false positives. Urine, feces, tears/CS and sputum seem unreliable for diagnosis. Saliva testing may increase testing capacity, ultimately promoting the implementation of truly deployable COVID-19 tests, which could either work at the point-of-care (e.g. hospitals, clinics) or at outbreak control spots (e.g., schools, airports, and nursing homes).

scholarly journals Head-to-head comparison of nasal and nasopharyngeal sampling using SARS-CoV-2 rapid antigen testing in Lesotho

2022 ◽  
Author(s):  
Niklaus Daniel Labhardt ◽  
Lucia Gonzalez Fernandez ◽  
Bulemba Katende ◽  
Josephine Muhairwe ◽  
Moniek Bresser ◽  
...  
Keyword(s):  
Point Of Care ◽  
High Specificity ◽  
Good Alternative ◽  
Nasopharyngeal Swab ◽  
Symptom Duration ◽  
High Agreement ◽  
Minimum Requirement ◽  
History Of ◽  
Antigen Testing ◽  
Or History

Objectives To assess the real-world diagnostic performance of nasal and nasopharyngeal swabs for SD Biosensor STANDARD Q COVID-19 Antigen Rapid Diagnostic Test (Ag-RDT). Methods Individuals ≥5 years with COVID-19 compatible symptoms or history of exposure to SARS-CoV-2 presenting at hospitals in Lesotho received two nasopharyngeal and one nasal swab. Ag-RDT from nasal and nasopharyngeal swabs were performed as point-of-care on site, the second nasopharyngeal swab used for polymerase chain reaction (PCR) as the reference standard. Results Out of 2198 participants enrolled, 2131 had a valid PCR result (61% female, median age 41 years, 8% children), 84.5% were symptomatic. Overall PCR positivity rate was 5.8%. The sensitivity for nasopharyngeal, nasal, and combined nasal and nasopharyngeal Ag-RDT result was 70.2% (95%CI: 61.3-78.0), 67.3% (57.3-76.3) and 74.4% (65.5-82.0), respectively. The respective specificity was 97.9% (97.1-98.4), 97.9% (97.2-98.5) and 97.5% (96.7-98.2). For both sampling modalities, sensitivity was higher in participants with symptom duration ≤ 3days versus ≤ 7days. Agreement between nasal and nasopharyngeal Ag-RDT was 99.4%. Conclusions The STANDARD Q Ag-RDT showed high specificity. Sensitivity was, however, below the WHO recommended minimum requirement of ≥ 80%. The high agreement between nasal and nasopharyngeal sampling suggests that for Ag-RDT nasal sampling is a good alternative to nasopharyngeal sampling.

scholarly journals A nanobody-functionalized organic electrochemical transistor for the rapid detection of SARS-CoV-2 and MERS antigens at the physical limit

2020 ◽  
Author(s):  
Keying Guo ◽  
Shofarul Wustoni ◽  
Anil Koklu ◽  
Escarlet Díaz-Galicia ◽  
Maximilian Moser ◽  
...  
Keyword(s):  
Single Molecule ◽  
Fluorescent Protein ◽  
Point Of Care ◽  
Protein Detection ◽  
High Specificity ◽  
Human Saliva ◽  
Nasopharyngeal Swab ◽  
Transistor Channel ◽  
Electrochemical Transistor ◽  
Detection And Quantification

AbstractThe COVID-19 pandemic highlights the need for rapid protein detection and quantification at the single-molecule level in a format that is simple and robust enough for widespread point-of-care applications. We here introduce a modular nanobody-organic electrochemical transistor architecture that enables the fast and specific detection and quantification of single-molecule to nanomolar protein antigen concentrations in complex bodily fluids. The sensor combines a new solution-processable organic semiconductor material in the transistor channel with the high-density and orientation-controlled bioconjugation of nanobody fusion proteins on disposable gate electrodes. It provides results after a 10 minutes exposure to 5 µL of unprocessed samples, maintains high specificity and single-molecule sensitivity in human saliva or serum, and is rapidly reprogrammed towards any protein target for which nanobodies exist. We demonstrate the use of this highly modular platform for the detection of green fluorescent protein, SARS-CoV-1/2, and MERS-CoV spike proteins and validate the sensor for COVID-19 screening in unprocessed clinical nasopharyngeal swab and saliva samples.

scholarly journals Leishmania infantum-Derived Glycoinositolphospholipids in the Immunodiagnosis of Subclinically Infected Dogs

2021 ◽  
Vol 8 ◽  
Author(s):  
Julia Ramos Sampaio ◽  
Rodrigo Pedro Soares ◽  
Thiago Doria Barral ◽  
Gabriela Porfirio Passos ◽  
Maisa Santos Fonseca ◽  
...  
Keyword(s):  
Leishmania Infantum ◽  
Point Of Care ◽  
High Specificity ◽  
Storage Conditions ◽  
Canine Leishmaniasis ◽  
Lower Sensitivity ◽  
Immune Recognition ◽  
Specificity And Sensitivity ◽  
Lower Specificity ◽  
Very High

Lipophosphoglycan (LPG), when used as an ELISA target, confers high specificity and sensitivity to the detection of Leishmania infantum antibodies in dogs. Glycoconjugates are economically viable because the yield is very high after extraction/purification. In addition, they are very stable, which allows their use in point-of-care testing without special storage conditions. During the glycoconjugate extraction, a glycoinositolphospholipid (GIPL)-enriched fraction is obtained in similar quantities as LPG. Since GIPLs can be extracted from the same parasite pellet as LPGs, this work aimed to evaluate the immune recognition of GIPLs by Leishmania infantum-infected dogs and its use for canine leishmaniasis (CanL) immunodiagnosis. Like LPG, GIPLs were recognized by sera from L. infantum-infected dogs, but with less sensitivity (83.8%). However, 80% (16/20) of subclinically infected dogs were detected as positive in the assay. Different from LPG, the GIPL-based assay achieved a lower specificity (73.7%) and cross-reactions occurred with T. cruzi and L. braziliensis-infected dogs. Although GIPLs exhibited a similar performance to LPG for subclinically L. infantum-infected dogs, the occurrence of cross-reactivities with other protozoa and a lower sensitivity hinders its use for an immunodiagnostic test. In places where those diseases do not co-exist such as in the Mediterranean region, its use for subclinically dogs could be an alternative.

scholarly journals Is the glass half full? Extraction-free RT-LAMP to detect SARS-CoV-2 is less sensitive but highly specific compared to standard RT-PCR in 101 samples

2020 ◽  
Author(s):  
John J. Schellenberg ◽  
Margaret Ormond ◽  
Yoav Keynan
Keyword(s):  
Point Of Care ◽  
N Gene ◽  
Nasopharyngeal Swab ◽  
Lower Sensitivity ◽  
Rt Pcr ◽  
Public And Private ◽  
Viral Loads ◽  
Negative Results ◽  
Viral Transport Medium ◽  
Point Of Care Tests

AbstractThe current scale of public and private testing cannot be expected to meet the emerging need for higher levels of community-level and repeated screening of asymptomatic Canadians for SARS-CoV-2. Rapid point-of-care techniques are increasingly being deployed to fill the gap in screening levels required to identify undiagnosed individuals with high viral loads. However, rapid, point-of-care tests often have lower sensitivity in practice. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for SARS-CoV-2 has proven sensitive and specific and provides visual results in minutes. Using a commercially available kit for RT-LAMP and primer set targetting nucleocapsid (N) gene, we tested a blinded set of 101 archived nasopharyngeal (NP) swab samples with known RT-PCR results. RT-LAMP reactions were incubated at 65°C for 30 minutes, using heat-inactivated nasopharyngeal swab sample in viral transport medium, diluted tenfold in water, as input. RT-LAMP agreed with all RT-PCR defined negatives (N=51), and all positives with Ct less than 20 (N=24), 65% of positives with Ct between 20-30 (N=17), and no positives with Ct greater than 30 (N=9). RT-LAMP requires fewer and different core components, so may not compete directly with the mainline testing workflow, preserving precious central laboratory resources and gold standard tests for those with the greatest need. Careful messaging must be provided when using less-sensitive tests, so that people are not falsely reassured by negative results – “glass half empty” – in exchange for reliable detection of those with high levels of virus within an hour, using <$10 worth of chemicals – “glass half full”.

Optimizing direct RT-LAMP to detect transmissible SARS-CoV-2 from primary nasopharyngeal swab and saliva patient samples

2020 ◽  
Author(s):  
Dawn M Dudley ◽  
Christina M. Newman ◽  
Andrea M Weiler ◽  
Mitchell D. Ramuta ◽  
Ceclia G. Shortreed ◽  
...  
Keyword(s):  
Infectious Virus ◽  
Limit Of Detection ◽  
Rna Extraction ◽  
Nasopharyngeal Swab ◽  
Lower Sensitivity ◽  
Acid Extraction ◽  
Short Supply ◽  
Screening Programs ◽  
Qrt Pcr ◽  
The Us

SARS-CoV-2 testing is crucial to controlling the spread of this virus, yet shortages of nucleic acid extraction supplies and other key reagents have hindered the response to COVID-19 in the US. Several groups have described loop-mediated isothermal amplification (LAMP) assays for SARS-CoV-2, including testing directly from nasopharyngeal swabs and eliminating the need for reagents in short supply. Here we describe a fluorescence-based RT-LAMP test using direct nasopharyngeal swab samples and show consistent detection in clinically confirmed samples, albeit with approximately 100-fold lower sensitivity than qRT-PCR. We demonstrate that adding lysis buffer directly into the RT-LAMP reaction improves the sensitivity of some samples by approximately 10-fold. Overall, the limit of detection (LOD) of RT-LAMP using direct nasopharyngeal swab or saliva samples without RNA extraction is 1x105-1x106 copies/ml. This LOD is sufficient to detect samples from which infectious virus can be cultured. Therefore, samples that test positive in this assay contain levels of virus that are most likely to perpetuate transmission. Furthermore, purified RNA in this assay achieves a similar LOD to qRT-PCR and we provide a revised method to work directly with saliva as starting material. These results indicate that high-throughput RT-LAMP testing could augment qRT-PCR in SARS-CoV-2 screening programs, especially while the availability of qRT-PCR testing and RNA extraction reagents is constrained.

scholarly journals Performance of SARS-CoV-2 antigen testing in symptomatic and asymptomatic adults: a single-center evaluation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Stephanie L. Mitchell ◽  
Steven Orris ◽  
Tanner Freeman ◽  
Megan C. Freeman ◽  
Michelle Adam ◽  
...  
Keyword(s):  
Symptom Onset ◽  
Point Of Care ◽  
False Negative ◽  
Poor Performance ◽  
Nasopharyngeal Swab ◽  
Lower Sensitivity ◽  
Negative Results ◽  
Asymptomatic Patients ◽  
False Negative Results ◽  
Antigen Testing

Abstract Background Antigen testing offers rapid and inexpensive testing for SARS-CoV-2 but concerns regarding performance, especially sensitivity, remain. Limited data exists for use of antigen testing in asymptomatic patients; thus, performance and reliability of antigen testing remains unclear. Methods 148 symptomatic and 144 asymptomatic adults were included. A nasal swab was collected for testing by Quidel Sofia SARS IFA (Sofia) as point of care. A nasopharyngeal swab was also collected and transported to the laboratory for testing by Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV RT-PCR (Cepheid). Results Overall, Sofia had good agreement with Cepheid (> 95%) in adults, however was less sensitive. Sofia had a sensitivity of 87.8% and 33.3% for symptomatic and asymptomatic patients, respectively. Among symptomatic patients, testing > 5 days post symptom onset resulted in lower sensitivity (82%) when compared with testing within 5 days of symptom onset (90%). Of the four Sofia false-negative results in the asymptomatic cohort, 50% went on to develop COVID-19 disease within 5 days of testing. Specificity in both symptomatic and asymptomatic cohorts was 100%. Conclusions Sofia has acceptable performance in symptomatic adults when tested < 5 days of symptom onset. Caution should be taken when testing patients with ≥ 5 days of symptoms. The combination of low prevalence and reduced sensitivity results in relatively poor performance of in asymptomatic patients. NAAT-based diagnostic assays should be considered in when antigen testing is unreliable, particularly in symptomatic patients with > 5 days of symptom onset and asymptomatic patients.

scholarly journals Evaluation of saliva molecular point of care for detection of SARS-CoV-2 in ambulatory care

2021 ◽  
Author(s):  
Jerome Le Goff ◽  
Solen Kerneis ◽  
Caroline Elie ◽  
Severine Mercier Delarue ◽  
Nabil Gastli ◽  
...  
Keyword(s):  
Point Of Care ◽  
False Negative ◽  
Lamp Assay ◽  
Rapid Identification ◽  
Ambulatory Setting ◽  
Nasopharyngeal Swab ◽  
Lower Sensitivity ◽  
Rt Pcr ◽  
A Prospective Study ◽  
Antigen Testing

Background: The rapid identification of SARS-CoV-2 infected individuals is a cornerstone in strategies for the control of virus spread. The sensitivity of SARS-CoV-2 RNA detection by RT-PCR is similar in saliva and nasopharyngeal swab. Rapid molecular point-of-care tests in saliva could facilitate, broaden and speed up the diagnosis. Objectives and methods: We conducted a prospective study in two community COVID-19 screening centers to evaluate the performances of a CE-marked RT-LAMP assay (EasyCoV) specifically designed for the detection of SARS-CoV-2 RNA from fresh saliva samples, compared to nasopharyngeal RT-PCR as reference test, saliva RT-PCR and nasopharyngeal antigen testing. Results: Overall, 117 of the 1718 participants (7%) were tested positive with nasopharyngeal RT-PCR. Sensitivities of saliva RT-PCR and nasopharyngeal antigen test were 93% (95% Confidence Interval (95%CI): 86-97) and 85% (95%CI: 77-91), respectively. The sensitivity and specificity of the RT-LAMP assay in saliva were 34% (95%CI: 26-44) and 97% (95%CI: 96-98). The performance was similar in symptomatic and asymptomatic participants and whatever the reference standard considered. Ct values of nasopharyngeal RT-PCR were significantly lower in the 40 true positive subjects with saliva RT-LAMP (Ct 25.9) than in the 48 false negative subjects with saliva RT-LAMP (Ct 28.4) (p=0.028). Conclusion: In the ambulatory setting, the detection of SARS-CoV-2 from crude saliva samples with the RT-LAMP assay had a lower sensitivity than nasopharyngeal RT-PCR, saliva RT-PCR and nasopharyngeal antigen testing.

scholarly journals Exploring salivary diagnostics in COVID-19: a scoping review and research suggestions

BDJ Open ◽  
2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Priyanka Kapoor ◽  
Aman Chowdhry ◽  
Om Prakash Kharbanda ◽  
Deepika Bablani Popli ◽  
Kamini Gautam ◽  
...  
Keyword(s):  
Scoping Review ◽  
Point Of Care ◽  
Data Extraction ◽  
Nasopharyngeal Swab ◽  
Free Text ◽  
Sample Collection ◽  
Mesh Terms ◽  
Study Characteristics ◽  
Set Up ◽  
Salivary Diagnostics

Abstract Introduction Molecular diagnostics for SARS-CoV-2 infection characteristically involves the sampling of the throat or nasopharyngeal swab (NPS). However, these procedures are invasive, require necessary skills for sample collection, cause patient discomfort, and are non-conducive for extensive scale testing. Saliva is increasingly being suggested as an alternate diagnostic sample in SARS‐CoV‐2 infection. Objectives This scoping review was done with the objective of exploring the evidence on the role of saliva as an alternate diagnostic sample in SARS‐CoV‐2 condition. Methods Thorough search of the literature in major databases was undertaken in June 2020 using free text and MESH terms, followed by PRISMA to identify 17 studies for data extraction. Results and conclusions Evidence was summarised for study characteristics, salivary sampling characteristics, viral load, and longevity of virus in saliva. The literature supports that saliva offers a simple sample collection method compared to technique-sensitive NPS and has the advantage of point-of-care testing for initial screening in community or hospital-based set-up. The additional highlights of this review are heterogeneity in the current literature and the gaps in methodology. Therefore, a robust study design to generate higher levels of evidence has been proposed.

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