scholarly journals Detection of SARS-CoV-2 RNA in Urine by RT-LAMP: A Very Rare Finding

2021 ◽  
Vol 11 (1) ◽  
pp. 158
Author(s):  
Juan García-Bernalt Diego ◽  
Pedro Fernández-Soto ◽  
Juan Luis Muñoz-Bellido ◽  
Begoña Febrer-Sendra ◽  
Beatriz Crego-Vicente ◽  
...  
Keyword(s):  
Viral Particle ◽  
Colorimetric Method ◽  
High Sensitivity ◽  
Clinical Suspicion ◽  
Nasopharyngeal Swab ◽  
Rna Detection ◽  
Positive Group ◽  
Rare Finding ◽  
Viral Excretion ◽  
Respiratory Specimens

Detection of SARS-CoV-2 is routinely performed in naso/oropharyngeal swabs samples from patients via RT-qPCR. The RT-LAMP technology has also been used for viral RNA detection in respiratory specimens with both high sensitivity and specificity. Recently, we developed a novel RT-LAMP test for SARS-CoV-2 RNA detection in nasopharyngeal swab specimens (named, N15-RT-LAMP) that can be performed as a single-tube colorimetric method, in a real-time platform, and as dry-LAMP. To date, there has been very little success in detecting SARS-CoV-2 RNA in urine by RT-qPCR, and the information regarding urine viral excretion is still scarce and not comprehensive. Here, we tested our N15-RT-LAMP on the urine of 300 patients admitted to the Hospital of Salamanca, Spain with clinical suspicion of COVID-19, who had a nasopharyngeal swab RT-qPCR-positive (n = 100), negative (n = 100), and positive with disease recovery (n = 100) result. The positive group was also tested by RT-qPCR for comparison to N15-RT-LAMP. Only a 4% positivity rate was found in the positive group via colorimetric N15-RT-LAMP and 2% via RT-qPCR. Our results are consistent with those obtained in other studies that the presence of SARS-CoV-2 RNA in urine is a very rare finding. The absence of SARS-CoV-2 RNA in urine in the recovered patients might suggest that the urinary route is very rarely used for viral particle clearance.

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 Self-collected Saline Gargle Samples as an Alternative to Healthcare Worker Collected Nasopharyngeal Swabs for COVID-19 Diagnosis in Outpatients

2021 ◽  
Author(s):  
David M. Goldfarb ◽  
Peter Tilley ◽  
Ghada N. Al-Rawahi ◽  
Jocelyn A. Srigley ◽  
Geoffrey Ford ◽  
...  
Keyword(s):  
Room Temperature ◽  
Positive Sample ◽  
Nasopharyngeal Swab ◽  
Sample Type ◽  
Mouth Rinse ◽  
Rna Detection ◽  
School Aged Children ◽  
Primary Sample ◽  
User Acceptability ◽  
Temperature Storage

Background: We assessed the performance, stability, and user acceptability of swab-independent self-collected saliva and saline mouth rinse/gargle sample types for the molecular detection of SARS-CoV-2 in adults and school-aged children. Methods: Outpatients who had recently been diagnosed with COVID-19 or were presenting with suspected COVID-19 were asked to have a nasopharyngeal swab collected and provide at least one self-collected sample type. Participants were also asked about sample acceptability using a five point Likert scale. For those previously diagnosed with COVID-19, all samples underwent real-time PCR testing using a lab-developed assay, and the majority were also tested using an FDA-authorized assay. For those presenting with suspect COVID-19, only those with a positive nasopharyngeal swab sample went on to have other samples tested. Saline mouth rinse/gargle and saliva samples were tested daily at time zero, day one, and day 2 to assess nucleic acid stability at room temperature. Results: 50 participants (aged 4 to 71 years) were included; of these, 40 had at least one positive sample and were included in the primary sample yield analysis. Saline mouth rinse/gargle samples had a sensitivity of 98% (39/40) while saliva samples had a sensitivity of 79% (26/33). Both saline mouth rinse/gargle and saliva samples showed stable viral RNA detection after 2 days of room temperature storage. Mouth rinse/gargle samples had the highest (mean 4.9) and HCW-collected NP swabs had the lowest acceptability scores (mean 3.1). Conclusion: Saline mouth rinse/gargle samples demonstrated the highest combined user acceptability ratings and analytical performance when compared with saliva and HCW collected NP swabs. This sample type is a promising swab-independent option, particularly for outpatient self-collection in adults and school aged children.

A smart and rapid colorimetric method for the detection of codeine sulphate, using unmodified gold nanoprobe

RSC Advances ◽  
2014 ◽  
Vol 4 (92) ◽  
pp. 50443-50448 ◽  
Author(s):  
Anand Lodha ◽  
Alok Pandya ◽  
Pinkesh G. Sutariya ◽  
Shobhana K. Menon
Keyword(s):  
Gold Nanoparticles ◽  
Electrochemical Properties ◽  
Colorimetric Method ◽  
High Sensitivity ◽  
Toxicological Screening ◽  
Spot Detection ◽  
Gold Nanoprobe

Herein, we reported unique optical and electrochemical properties of citrate-stabilized gold nanoparticles (AuNPs) as a probe for smartphone-assisted, on-spot detection of codeine sulphate in toxicological screening with high sensitivity (0.9 μM).

scholarly journals Confirmed or unconfirmed cases of 2019 novel coronavirus pneumonia in Italian patients: a retrospective analysis of clinical features

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Giulia De Angelis ◽  
Brunella Posteraro ◽  
Federico Biscetti ◽  
Gianluca Ianiro ◽  
Lorenzo Zileri Dal Verme ◽  
...  
Keyword(s):  
Clinical Features ◽  
Multivariable Analysis ◽  
Etiologic Agent ◽  
Nasopharyngeal Swab ◽  
Imaging Features ◽  
Rt Pcr ◽  
Rna Detection ◽  
Incubation Periods ◽  
Novel Coronavirus ◽  
To Receive

Abstract Background Since December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged as a novel etiologic agent of viral pneumonia. We aimed to compare clinical features of 165 Italian patients with laboratory confirmed or unconfirmed 2019-nCoV pneumonia. Methods On March 31, 2020, hospitalized patients who presented with fever and/or respiratory symptoms, exposures, and presence of lung imaging features consistent with 2019-nCoV pneumonia were included. Before admission to a hospital ward, patients underwent RT-PCR based SARS-CoV-2 RNA detection in their nasopharyngeal swab samples. Results Of 165 patients studied, 119 had positive RT-PCR results and 46 were RT-PCR negative for 2 days or longer (i.e., when the last swab sample was obtained). The median age was 70 years (IQR, 58–78), and 123 (74.6%) of 165 patients had at least one comorbidity. The majority of patients (101/165, 61.2%) had a mild pneumonia, and the remaining patients (64/165, 38.8%) a severe/critical pneumonia. We did not find any substantial difference in symptoms, incubation periods, and radiographic/CT abnormalities as well as in many of the biological abnormalities recorded. However, at multivariable analysis, higher concentrations of hemoglobin (OR, 1.34; 95% CI, 1.11–1.65; P = 0.003) and lower counts of leukocytes (OR, 0.81; 95% CI, 0.72–0.90; P < 0.001) were statistically associated with confirmed COVID-19 diagnosis. While mortality rates were similar, patients with confirmed diagnosis were more likely to receive antivirals (95% vs 19.6%, P < 0.001) and to develop ARDS (63% vs 37%, P = 0.003) than those with unconfirmed COVID-19 diagnosis. Conclusions Our findings suggest that unconfirmed 2019-nCoV pneumonia cases may be actually COVID-19 cases and that clinicians should be cautious when managing patients with presentations compatible with COVID-19.

scholarly journals Posterior Oropharyngeal Saliva for the Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

2020 ◽  
Vol 71 (11) ◽  
pp. 2939-2946 ◽  
Author(s):  
Sally Cheuk Ying Wong ◽  
Herman Tse ◽  
Hon Kei Siu ◽  
Tsz Shan Kwong ◽  
Man Yee Chu ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Diagnostic Testing ◽  
Limiting Factors ◽  
Rna Detection ◽  
Acceptable Alternative ◽  
Percent Agreement ◽  
Pearson Coefficient ◽  
The Mean ◽  
Alternative Specimen ◽  
Respiratory Specimens

Abstract Background The coronavirus disease 2019 (COVID-19) pandemic has put tremendous pressure on the healthcare system worldwide. Diagnostic testing remained one of the limiting factors for early identification and isolation of infected patients. This study aimed to evaluate posterior oropharyngeal saliva (POPS) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection among patients with confirmed or suspected COVID-19. Methods The laboratory information system was searched retrospectively for all respiratory specimens and POPS requested for SARS-CoV-2 RNA detection between 1 February 2020 and 15 April 2020. The agreement and diagnostic performance of POPS against NPsp were evaluated. Results A total of 13772 specimens were identified during the study period, including 2130 POPS and 8438 nasopharyngeal specimens (NPsp). Two hundred and twenty-nine same-day POPS-NPsp paired were identified with POPS and NPsp positivity of 61.5% (95% confidence interval [CI] 55.1–67.6%) and 53.3% (95% CI 46.8–59.6%). The overall, negative and positive percent agreement were 76.0% (95% CI 70.2–80.9%), 65.4% (95% CI 55.5–74.2%), 85.2% (95% CI 77.4–90.8%). Better positive percent agreement was observed in POPS-NPsp obtained within 7 days (96.6%, 95% CI 87.3–99.4%) compared with after 7 days of symptom onset (75.0%, 95% CI 61.4–85.2%). Among the 104 positive pairs, the mean difference in Cp value was 0.26 (range: 12.63 to −14.74), with an overall higher Cp value in NPsp (Pearson coefficient 0.579). No significant temporal variation was noted between the 2 specimen types. Conclusions POPS is an acceptable alternative specimen to nasopharyngeal specimen for the detection of SARS-CoV-2.

scholarly journals Performance of a PCR Assay for Detection of Pneumocystis carinii from Respiratory Specimens

1998 ◽  
Vol 36 (4) ◽  
pp. 979-982 ◽  
Author(s):  
Angela M. Caliendo ◽  
Peter L. Hewitt ◽  
Jessica M. Allega ◽  
Anne Keen ◽  
Kathryn L. Ruoff ◽  
...  
Keyword(s):  
Internal Control ◽  
Fluorescent Antibody ◽  
Pneumocystis Carinii ◽  
High Sensitivity ◽  
Clinical Microbiology Laboratory ◽  
Hybridization Technique ◽  
Acid Extraction ◽  
Pcr Assay ◽  
Simple Method ◽  
Respiratory Specimens

This study evaluates the performance of a PCR assay for the detection of Pneumocystis carinii from respiratory specimens that has been designed for use in the clinical microbiology laboratory. The test includes a simple method for nucleic acid extraction and amplification, a colorimetric probe hybridization technique for detection of amplicons, and an internal control to evaluate for the presence of inhibitors of amplification. Two hundred thirty-two clinical specimens (120 induced-sputum [IS] and 112 bronchoalveolar lavage [BAL] specimens) from 168 patients were tested by both immunofluorescent (direct fluorescent-antibody [DFA]) staining and PCR. Of the 112 BAL specimens, 17 were positive for P. carinii by DFA staining and PCR. An additional two specimens were DFA negative and PCR positive. For BAL specimens, the sensitivity and specificity of PCR compared to DFA were 100 and 98%, respectively. Eighteen IS specimens were positive for P. carinii by DFA, and 27 were positive by PCR. One of the 18 DFA-positive IS specimens was negative by PCR; this patient had just completed therapy for P. cariniipneumonia. Of the 10 specimens that were PCR positive and DFA negative, 4 were from patients who had a subsequent BAL specimen that was positive by DFA and PCR. For IS specimens, the sensitivity of DFA and PCR was 82 and 95%, respectively. The specificity of PCR for IS specimens was 94%. Due to the high sensitivity of PCR for the detection of P. carinii from IS specimens, a PCR-based diagnostic test may be a useful screening test and may alleviate the need for bronchoscopy in some patients.

scholarly journals SARS-CoV-2 Detection in Different Respiratory Sites: A Systematic Review and Meta-Analysis

2020 ◽  
Author(s):  
Abbas Mohammadi ◽  
Elmira Esmaeilzadeh ◽  
Yijia Li ◽  
Ronald J Bosch ◽  
Jonathan Li
Keyword(s):  
Systematic Review ◽  
Symptom Onset ◽  
Meta Analysis ◽  
Nasopharyngeal Swab ◽  
Inclusion Criteria ◽  
Rna Detection ◽  
Timely Initiation ◽  
Detection Rates ◽  
Diverse Range ◽  
Oropharyngeal Swab

Background: The accurate detection of SARS-CoV-2 through respiratory sampling is critical for the prevention of further transmission and the timely initiation of treatment for COVID-19. There is a diverse range of SARS-CoV-2 detection rates in reported studies, with uncertainty as to the optimal sampling strategy for COVID-19 diagnosis and monitoring. Methods: We performed a systematic review and meta-analysis of studies comparing respiratory sampling strategies for the detection of SARS-CoV-2 RNA. The inclusion criteria were studies that assessed at least two respiratory sampling sites (oropharyngeal swab, nasopharyngeal swab, and sputum) in participants with COVID-19. The percentage positive tests were compared between sampling modalities by constructing a Z-test assuming independence and using the standard errors obtained from the random effects meta-analysis. Findings: From 1039 total studies, we identified 11 studies that met our inclusion criteria, with SARS-CoV-2 testing results from a total of 3442 respiratory tract specimens. Compared to nasopharyngeal swab sampling, sputum testing resulted in significantly higher rates of SARS-CoV-2 RNA detection while oropharyngeal swab testing had lower rates of viral RNA detection. Earlier sampling after symptom onset was associated with improved detection rates, but the differences in SARS-CoV-2 RNA detection by sampling method was consistent regardless of the duration of symptoms. Interpretation: The results support sputum sampling as a primary method of COVID-19 diagnosis and monitoring, and highlight the importance of early testing after symptom onset to increase the rates of COVID-19 diagnosis.

scholarly journals COVID-19 pneumonia: Significance of diagnostic approaches other than PCR testing

2020 ◽  
Vol 4 (7) ◽  
pp. 25-28
Author(s):  
Jovan Javorac ◽  
Dejan Živanović ◽  
Ana Milenković ◽  
Zvonko Dimoski
Keyword(s):  
False Negative ◽  
Fatal Outcome ◽  
High Sensitivity ◽  
Lung Parenchyma ◽  
Diagnostic Methods ◽  
Pcr Analysis ◽  
Nasopharyngeal Swab ◽  
Test Results ◽  
Radiological Findings ◽  
Diagnostic Approaches

The infection by SARS-CoV-2 virus leads to the development of COVID-19 disease, which can manifest asymptomatically, or cause pneumonia caracterised by mild to severe symptoms, with potential fatal outcome. The gold diagnostic standard for COVID-19 disease is the PCR analysis of biological materials sampled by nasopharyngeal swab. However, despite the high sensitivity of this diagnostic method, our clinical experience has shown that in some cases, false-negative PCR test results can be obtained. This paper reports a case of a patient with developed pneumonia that could be related to COVID-19 disease based on the clinical picture, laboratory and radiological findings, but two nasopharyngeal swabs were negative for SARS-CoV-2 after PCR analysis. The patient was treated with the therapy recommended for COVID-19, achieving both clinical and radiological improvement, which indicates that the infection by SARS-CoV-2 virus was probably the UN-derlying factor of of the inflammatory process in the lung parenchyma. Therefore, the aim of this paper is to highlight the importance of other diagnostic methods in diagnosing COVID-19, not only PCR testing.

scholarly journals Colorimetric Test for Fast Detection of SARS-CoV-2 in Nasal and Throat Swabs

2020 ◽  
Author(s):  
Bartolomeo Della Ventura ◽  
Michele Cennamo ◽  
Antonio Minopoli ◽  
Raffaele Campanile ◽  
Sergio Bolletti Censi ◽  
...  
Keyword(s):  
Viral Particle ◽  
Extinction Spectrum ◽  
Colorimetric Method ◽  
Surface Proteins ◽  
Mixed Solution ◽  
Colorimetric Test ◽  
The People ◽  
Viral Particles ◽  
New Perspective ◽  
Viral Target

Mass testing is fundamental to face the pandemic caused by the coronavirus SARS-CoV-2 discovered at the end of 2019. To this aim, it is necessary to establish reliable, fast and cheap tools to detect viral particles in biological material so to identify the people capable to spread the infection. We demonstrate that a colorimetric biosensor based on gold nanoparticle (AuNP) interaction induced by SARS-CoV-2 lends itself as an outstanding tool for detecting viral particles in nasal and throat swabs. The extinction spectrum of a colloidal solution of multiple viral-target gold nanoparticles - AuNPs functionalized with antibodies targeting three surface proteins of SARS-CoV-2 (spike, envelope and membrane) - is redshifted in few minutes when mixed to a solution containing the viral particle. The optical density of the mixed solution measured at 560 nm was compared to the threshold cycle (Ct) of a Real Time-PCR (gold standard for detecting the presence of viruses) finding that the colorimetric method is able to detect very low viral load with a detection limit approaching that of RT-PCR. Since the method is sensitive to the infecting viral particle rather than to its RNA, the achievements reported here open new perspective not only in the context of the current and possible future pandemics, but also in microbiology as the biosensor proves itself to be a powerful though simple tool for measuring the viral particle concentration.

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