Validation of a Saliva-Based Test for the Molecular Diagnosis of SARS-CoV-2 Infection

Background. Since the beginning of the pandemic, clinicians and researchers have been searching for alternative tests to improve the screening and diagnosis of the SARS-CoV-2 infection. Currently, the gold standard for virus identification is the nasopharyngeal (NP) swab. Saliva samples, however, offer clear, practical, and logistical advantages but due to a lack of collection, transport, and storage solutions, high-throughput saliva-based laboratory tests are difficult to scale up as a screening or diagnostic tool. With this study, we aimed to validate an intralaboratory molecular detection method for SARS-CoV-2 on saliva samples collected in a new storage saline solution, comparing the results to NP swabs to determine the difference in sensitivity between the two tests. Methods. In this study, 156 patients (cases) and 1005 asymptomatic subjects (controls) were enrolled and tested simultaneously for the detection of the SARS-CoV-2 viral genome by RT-PCR on both NP swab and saliva samples. Saliva samples were collected in a preservative and inhibiting saline solution (Biofarma Srl). Internal method validation was performed to standardize the entire workflow for saliva samples. Results. The identification of SARS-CoV-2 conducted on saliva samples showed a clinical sensitivity of 95.1% and specificity of 97.8% compared to NP swabs. The positive predictive value (PPV) was 81% while the negative predictive value (NPV) was 99.5%. Test concordance was 97.6% (Cohen’s Kappa = 0.86 ; 95% CI 0.81-0.91). The LoD of the test was 5 viral copies for both samples. Conclusions. RT-PCR assays conducted on a stored saliva sample achieved similar performance to those on NP swabs, and this may provide a very effective tool for population screening and diagnosis. Collection of saliva in a stabilizing solution makes the test more convenient and widely available; furthermore, the denaturing properties of the solution reduce the infective risks belonging to sample manipulation.

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VALIDATION OF A SALIVA-BASED TEST FOR THE MOLECULAR DIAGNOSIS OF SARS-CoV-2 INFECTION

10.1101/2021.09.10.21263072 ◽

2021 ◽

Author(s):

Michela Bulfoni ◽

Emanuela Sozio ◽

Barbara Marcon ◽

Maria De Martino ◽

Daniela Cesselli ◽

...

Keyword(s):

Predictive Value ◽

Saliva Sample ◽

Scale Up ◽

Rt Pcr ◽

Clinical Sensitivity ◽

Virus Identification ◽

Stabilizing Solution ◽

The Difference ◽

Asymptomatic Subjects ◽

Screening And Diagnosis

Background: Since the beginning of the pandemic, clinicians and researchers have been searching for alternative tests to improve screening and diagnosis of SARS-CoV-2 infection. Currently, the gold standard for virus identification is the nasopharyngeal (NP) swab. Saliva samples, however, offer clear practical and logistical advantages but due to lack of collection, transport, and storage solutions, high-throughput saliva-based laboratory tests are difficult to scale up as a screening or diagnostic tool. With this study, we aimed to validate an intra-laboratory molecular detection method for SARS-CoV-2 on saliva samples collected in a new storage and inactivating solution, comparing the results to NP swabs to determine the difference in sensitivity between the two tests. Methods: In this study, 156 patients (cases) and 1005 asymptomatic subjects (controls) were enrolled and tested simultaneously for the detection of the SARS-CoV-2 viral genome by RT-PCR on both NP swab and saliva samples. Saliva samples were collected in a preservative and inhibiting saline solution (Biofarma Srl). Internal method validation was performed to standardize the entire workflow for saliva samples. Results: The identification of SARS-CoV-2 conducted on saliva samples showed a clinical sensitivity of 95.1% and specificity of 97.8% compared to NP swabs. The positive predictive value (PPV) was 81% while the negative predictive value (NPV) was 99.5%. Test concordance was 97.6% (Cohen's Kappa=0.86; 95% CI 0.81-0.91). The LoD of the test was 5 viral copies for both samples. Conclusions: RT-PCR assays conducted on a stored saliva sample achieved similar performance to those on NP swabs and this may provide a very effective tool for population screening and diagnosis. Collection of saliva in a stabilizing solution makes the test more convenient and widely available; furthermore, the denaturation properties of the solution reduces the infective risks belonging to sample manipulation.

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Evaluation of accuracy, exclusivity, limit-of-detection and ease-of-use of LumiraDx™ - Antigen-detecting point-of-care device for SARS-CoV-2

10.1101/2021.03.02.21252430 ◽

2021 ◽

Author(s):

Lisa Johanna Krüger ◽

Julian A.F. Klein ◽

Frank Tobian ◽

Mary Gaeddert ◽

Federica Lainati ◽

...

Keyword(s):

Viral Load ◽

Limit Of Detection ◽

Point Of Care ◽

Scale Up ◽

Cross Reactivity ◽

Ease Of Use ◽

Analytical Sensitivity ◽

Rt Pcr ◽

Clinical Sensitivity ◽

Lateral Flow Assays

Background: Rapid antigen-detecting tests (Ag-RDTs) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can transform pandemic control. Thus far, sensitivity (≤85%) of lateral-flow assays has limited scale-up. Conceivably, microfluidic immunofluorescence Ag-RDTs could increase sensitivity for SARS-CoV-2 detection. Materials and Methods: This multi-centre diagnostic accuracy study investigated performance of the microfluidic immunofluorescence LumiraDx™ assay, enrolling symptomatic and asymptomatic participants with suspected SARS-CoV-2 infection. Participants collected a supervised nasal mid-turbinate (NMT) self-swab for Ag-RDT testing, in addition to a professionally-collected nasopharyngeal (NP) swab for routine testing with reverse transcriptase polymerase chain reaction (RT-PCR). Results were compared to calculate sensitivity and specificity. Sub-analyses investigated the results by viral load, symptom presence and duration. An analytical study assessed exclusivity and limit-of-detection (LOD). In addition, we evaluated ease-of-use. Results: Study conduct was between November 2nd 2020 and January 21st 2021. 761 participants were enrolled, with 486 participants reporting symptoms on testing day. 120 out of 146 RT-PCR positive cases were detected positive by LumiraDx™, resulting in a sensitivity of 82.2% (95% CI: 75.2%-87.5%). Specificity was 99.3% (CI: 98.3-99.7%). Sensitivity was increased in individuals with viral load ≥ 7 log10 SARS-CoV2 RNA copies/ml (93.8%; CI: 86.2%-97.3%). Testing against common respiratory commensals and pathogens showed no cross-reactivity and LOD was estimated to be 2-56 PFU/mL. The ease-of-use-assessment was favourable for lower throughput settings. Conclusion: The LumiraDx™ assay showed excellent analytical sensitivity, exclusivity and clinical specificity with good clinical sensitivity using supervised NMT self-sampling.

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Evaluation of accuracy, exclusivity, limit-of-detection and ease-of-use of LumiraDx™: An antigen-detecting point-of-care device for SARS-CoV-2

Infection ◽

10.1007/s15010-021-01681-y ◽

2021 ◽

Author(s):

Lisa J. Krüger ◽

Julian A. F. Klein ◽

Frank Tobian ◽

Mary Gaeddert ◽

Federica Lainati ◽

...

Keyword(s):

Viral Load ◽

Limit Of Detection ◽

Point Of Care ◽

Scale Up ◽

Cross Reactivity ◽

Ease Of Use ◽

Analytical Sensitivity ◽

Rt Pcr ◽

Clinical Sensitivity ◽

Lateral Flow Assays

Abstract Purpose Rapid antigen-detecting tests (Ag-RDTs) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can transform pandemic control. Thus far, sensitivity (≤ 85%) of lateral-flow assays has limited scale-up. Conceivably, microfluidic immunofluorescence Ag-RDTs could increase sensitivity for SARS-CoV-2 detection. Methods This multi-centre diagnostic accuracy study investigated performance of the microfluidic immunofluorescence LumiraDx™ assay, enrolling symptomatic and asymptomatic participants with suspected SARS-CoV-2 infection. Participants collected a supervised nasal mid-turbinate (NMT) self-swab for Ag-RDT testing, in addition to a professionally collected nasopharyngeal (NP) swab for routine testing with reverse transcriptase polymerase chain reaction (RT-PCR). Results were compared to calculate sensitivity and specificity. Sub-analyses investigated the results by viral load, symptom presence and duration. An analytical study assessed exclusivity and limit-of-detection (LOD). In addition, we evaluated ease-of-use. Results The study was conducted between November 2nd 2020 and 4th of December 2020. 761 participants were enrolled, with 486 participants reporting symptoms on testing day. 120 out of 146 RT-PCR positive cases were detected positive by LumiraDx™, resulting in a sensitivity of 82.2% (95% CI 75.2–87.5%). Specificity was 99.3% (CI 98.3–99.7%). Sensitivity was increased in individuals with viral load ≥ 7 log10 SARS-CoV2 RNA copies/ml (93.8%; CI 86.2–97.3%). Testing against common respiratory commensals and pathogens showed no cross-reactivity and LOD was estimated to be 2–56 PFU/mL. The ease-of-use-assessment was favourable for lower throughput settings. Conclusion The LumiraDx™ assay showed excellent analytical sensitivity, exclusivity and clinical specificity with good clinical sensitivity using supervised NMT self-sampling. Trial registration number and registration date DRKS00021220 and 01.04.2020

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Diagnosis of cerebral hemorrhage before the era of computed tomography

Orvosi Hetilap ◽

10.1556/oh.2013.29739 ◽

2013 ◽

Vol 154 (44) ◽

pp. 1743-1746

Author(s):

Gergely Hofgárt ◽

Rita Szepesi ◽

Bertalan Vámosi ◽

László Csiba

Keyword(s):

Computed Tomography ◽

Cerebrospinal Fluid ◽

Positive Predictive Value ◽

Predictive Value ◽

Hemorrhagic Stroke ◽

Cranial Computed Tomography ◽

Cerebral Stroke ◽

Daily Routine ◽

Stroke Patients ◽

The Difference

Introduction: During the past decades there has been a great progress in neuroimaging methods. Cranial computed tomography is part of the daily routine now and its use allows a fast diagnosis of parenchymal hemorrhage. However, before the availability of computed tomography the differentiation between ischemic and hemorrhagic stroke was based on patient history, physical examination, percutan angiography and cerebrospinal fluid sampling, and the clinical utility could be evaluated by autopsy of deceased patients. Aim: The authors explored the diagnostic performance of cerebrospinal fluid examination for the diagnosis of ischemic and hemorrhagic stroke. Method: Data of 200 deceased stroke patients were retrospectively evaluated. All patients had liquor sampling at admission and all of them had brain autopsy. Results: Bloody or yellowish cerebrospinal fluid at admission had a positive predictive value of 87.5% for hemorrhagic stroke confirmed by autopsy, while clear cerebrospinal fluid had positive predictive value of 90.7% for ischemic stroke. Patients who had clear liquor, but autopsy revealed hemorrhagic stroke had higher protein level in the cerebrospinal fluid, but the difference was not statistically significant (p = 0.09). Conclusions: The results confirm the importance of pathological evaluation of the brain in cases deceased from cerebral stroke. With this article the authors wanted to salute for those who contributed to the development of the Hungarian neuropathology. In this year we remember the 110th anniversary of the birth, and the 60th anniversary of the death of professor Kálmán Sántha. Professor László Molnár would be 90 years old in 2013. Orv. Hetil., 154 (44), 1743–1746.

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Evaluation of aseptic loosening of knee prostheses by quantitative bone scintigraphy

Nuklearmedizin ◽

10.3413/nukmed-0123 ◽

2008 ◽

Vol 47 (04) ◽

pp. 163-166 ◽

Cited By ~ 6

Author(s):

D. Steiner ◽

S. Laurich ◽

R. Bauer ◽

J. Kordelle ◽

R. Klett

Keyword(s):

Aseptic Loosening ◽

Bone Scintigraphy ◽

Revision Surgery ◽

Predictive Value ◽

Knee Prostheses ◽

Treatment Regimes ◽

Golden Standard ◽

The Difference ◽

Sensitivity Specificity ◽

Asymptomatic Control

SummaryIn not infected knee prostheses bone scintigraphy is a possible method to diagnose mechanical loosening, and therefore, to affect treatment regimes in symptomatic patients. However, hitherto studies showed controversial results for the reliability of bone scintigraphy in diagnosing loosened knee prostheses by using asymptomatic control groups. Therefore, the aim of our study was to optimize the interpretation procedure and to evaluate the accuracy using results from revision surgery as standard. Methods: Retrospectively, we were able to examine the tibial component in 31 cemented prostheses. In this prostheses infection was excluded by histological or bacteriological examination during revision surgery. To quantify bone scintigraphy, we used medial and lateral tibial regions with a reference region from the contralateral femur. Results: To differentiate between loosened and intact prostheses we found a threshold of 5.0 for the maximum tibia to femur ratio of the both tibial regions and a threshold of 18% for the difference of the ratio of both tibial regions. Using these thresholds, values of 0.9, 1, 0.85, 1, and 0.94 were calculated for sensitivity, specificity, negative predictive value, positive predictive value, and accuracy, respectively. To get a sensitivity of 1, we found a lower threshold of 3.3 for the maximum tibia to femur ratio. Conclusion: Quantitative bone scintigraphy appears to be a reliable diagnostic tool for aseptic loosening of knee prostheses with thresholds evaluated by revision surgery results being the golden standard.

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Antibiotic Susceptibility Evaluation of Bacterial Agents Causing Infection in Children with Acute Tonsillopharyngitis

Infectious Disorders - Drug Targets ◽

10.2174/1871526520666201116102441 ◽

2020 ◽

Vol 20 ◽

Author(s):

Hamidreza Sherkatolabbasieh ◽

Majid Firouzi ◽

Shiva Shafizadeh ◽

Iman Amiri

Keyword(s):

Sore Throat ◽

Predictive Value ◽

Positive Culture ◽

Clinical Score ◽

Streptococcal Pharyngitis ◽

Diffusion Method ◽

Disk Diffusion Method ◽

Cross Sectional ◽

Clinical Sensitivity ◽

Group A

Background: The aim of this study is to evaluate the prevalence of group A beta-hemolytic pharyngitis by assessing the outcome of the culture and the resistance and sensitivity of group A beta hemolytic streptococcus to antibiotics. Methods: This cross-sectional study was conducted on 170 patients, aged 3-15 years, referred to the clinic with complaints of sore throat. Patients’ history was collected and physical examination was performed and were score based on clinical findings. Patients with other underlying pathologies and those taking antibiotics prior to the study were excluded from our study. Antimicrobial susceptibility test was performed by disk diffusion method against cephalexin, cefazolin, erythromycin and amoxicillin. Results: A total of 170 patients were reported with sore throat. Patients with positive culture results were 60% male and 40% female. Amoxicillin resistance was the greatest (5%) in the culture. All isolated bacteria were sensitive to amoxicillin, cephalexin, cefazolin and erythromycin. Patients with McIssac score ≥ 6 showed clinical sensitivity 75% specificity 61% negative predictive value 94.8% and positive predictive value 20.3% for Group A beta-hemolytic streptococcal pharyngitis. Conclusion: The results showed the higher the clinical score, the greater the chance of positive throat culture.

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Triage of Patients Suspected of COVID-19 in Chronic Hemodialysis: Eosinophil Count Differentiates Low and High Suspicion of COVID-19

Journal of Clinical Medicine ◽

10.3390/jcm10010004 ◽

2020 ◽

Vol 10 (1) ◽

pp. 4

Author(s):

Romain Vial ◽

Marion Gully ◽

Mickael Bobot ◽

Violaine Scarfoglière ◽

Philippe Brunet ◽

...

Keyword(s):

Predictive Value ◽

Eosinophil Count ◽

Characteristic Curve ◽

Final Analysis ◽

Hemodialysis Patients ◽

Chronic Hemodialysis ◽

Screening Methods ◽

Dialysis Session ◽

Diagnostic Study ◽

Rt Pcr

Background: Daily management to shield chronic dialysis patients from SARS-CoV-2 contamination makes patient care cumbersome. There are no screening methods to date and a molecular biology platform is essential to perform RT-PCR for SARS-CoV-2; however, accessibility remains poor. Our goal was to assess whether the tools routinely used to monitor our hemodialysis patients could represent reliable and quickly accessible diagnostic indicators to improve the management of our hemodialysis patients in this pandemic environment. Methods: In this prospective observational diagnostic study, we recruited patients from La Conception hospital. Patients were eligible for inclusion if suspected of SARS-CoV-2 infection when arriving at our center for a dialysis session between March 12th and April 24th 2020. They were included if both RT-PCR result for SARS-CoV-2 and cell blood count on the day that infection was suspected were available. We calculated the area under the curve (AUC) of the receiver operating characteristic curve. Results: 37 patients were included in the final analysis, of which 16 (43.2%) were COVID-19 positive. For the day of suspected COVID-19, total leukocytes were significantly lower in the COVID-19 positive group (4.1 vs. 7.4 G/L, p = 0.0072) and were characterized by lower neutrophils (2.7 vs. 5.1 G/L, p = 0.021) and eosinophils (0.01 vs. 0.15 G/L, p = 0.0003). Eosinophil count below 0.045 G/L identified SARS-CoV-2 infection with AUC of 0.9 [95% CI 0.81—1] (p < 0.0001), sensitivity of 82%, specificity of 86%, a positive predictive value of 82%, a negative predictive value of 86% and a likelihood ratio of 6.04. Conclusions: Eosinophil count enables rapid routine screening of symptomatic chronic hemodialysis patients suspected of being COVID-19 within a range of low or high probability.

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A meta-analysis of accuracy and sensitivity of chest CT and RT-PCR in COVID-19 diagnosis

Scientific Reports ◽

10.1038/s41598-020-80061-2 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Fatemeh Khatami ◽

Mohammad Saatchi ◽

Seyed Saeed Tamehri Zadeh ◽

Zahra Sadat Aghamir ◽

Alireza Namazi Shabestari ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Reverse Transcriptase ◽

Ct Scan ◽

Predictive Value ◽

Meta Analysis ◽

Chest Ct ◽

Rt Pcr ◽

Chain Reaction ◽

Polymerase Chain ◽

Chest Ct Scan

AbstractNowadays there is an ongoing acute respiratory outbreak caused by the novel highly contagious coronavirus (COVID-19). The diagnostic protocol is based on quantitative reverse-transcription polymerase chain reaction (RT-PCR) and chests CT scan, with uncertain accuracy. This meta-analysis study determines the diagnostic value of an initial chest CT scan in patients with COVID-19 infection in comparison with RT-PCR. Three main databases; PubMed (MEDLINE), Scopus, and EMBASE were systematically searched for all published literature from January 1st, 2019, to the 21st May 2020 with the keywords "COVID19 virus", "2019 novel coronavirus", "Wuhan coronavirus", "2019-nCoV", "X-Ray Computed Tomography", "Polymerase Chain Reaction", "Reverse Transcriptase PCR", and "PCR Reverse Transcriptase". All relevant case-series, cross-sectional, and cohort studies were selected. Data extraction and analysis were performed using STATA v.14.0SE (College Station, TX, USA) and RevMan 5. Among 1022 articles, 60 studies were eligible for totalizing 5744 patients. The overall sensitivity, specificity, positive predictive value, and negative predictive value of chest CT scan compared to RT-PCR were 87% (95% CI 85–90%), 46% (95% CI 29–63%), 69% (95% CI 56–72%), and 89% (95% CI 82–96%), respectively. It is important to rely on the repeated RT-PCR three times to give 99% accuracy, especially in negative samples. Regarding the overall diagnostic sensitivity of 87% for chest CT, the RT-PCR testing is essential and should be repeated to escape misdiagnosis.

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The role of CT imaging for management of COVID-19 in epidemic area: early experience from a University Hospital

Insights into Imaging ◽

10.1186/s13244-020-00957-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Vikram rao Bollineni ◽

Koenraad Hans Nieboer ◽

Seema Döring ◽

Nico Buls ◽

Johan de Mey

Keyword(s):

Ct Scan ◽

Predictive Value ◽

Ct Imaging ◽

Chest Ct ◽

University Hospital ◽

Rt Pcr ◽

Ct Findings ◽

Epidemic Area ◽

Chest Ct Scan ◽

Pcr Test

Abstract Background To evaluate the clinical value of the chest CT scan compared to the reference standard real-time polymerase chain reaction (RT-PCR) in COVID-19 patients. Methods From March 29th to April 15th of 2020, a total of 240 patients with respiratory distress underwent both a low-dose chest CT scan and RT-PCR tests. The performance of chest CT in diagnosing COVID-19 was assessed with reference to the RT-PCR result. Two board-certified radiologists (mean 24 years of experience chest CT), blinded for the RT-PCR result, reviewed all scans and decided positive or negative chest CT findings by consensus. Results Out of 240 patients, 60% (144/240) had positive RT-PCR results and 89% (213/240) had a positive chest CT scans. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of chest CT in suggesting COVID-19 were 100% (95% CI: 97–100%, 144/240), 28% (95% CI: 19–38%, 27/240), 68% (95% CI: 65–70%) and 100%, respectively. The diagnostic accuracy of the chest CT suggesting COVID-19 was 71% (95% CI: 65–77%). Thirty-three patients with positive chest CT scan and negative RT-PCR test at baseline underwent repeat RT-PCR assay. In this subgroup, 21.2% (7/33) cases became RT-PCR positive. Conclusion Chest CT imaging has high sensitivity and high NPV for diagnosing COVID-19 and can be considered as an alternative primary screening tool for COVID-19 in epidemic areas. In addition, a negative RT-PCR test, but positive CT findings can still be suggestive of COVID-19 infection.

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Quantitative Analysis of Fluorescence Detection Using a Smartphone Camera for a PCR Chip

Sensors ◽

10.3390/s21113917 ◽

2021 ◽

Vol 21 (11) ◽

pp. 3917

Author(s):

Jong-Dae Kim ◽

Chan-Young Park ◽

Yu-Seop Kim ◽

Ji-Soo Hwang

Keyword(s):

Quantitative Analysis ◽

Fluorescence Detection ◽

High Performance ◽

Low Cost ◽

Dna Amplification ◽

Fluorescent Detection ◽

Rt Pcr ◽

Commercial System ◽

Intensity Changes ◽

The Difference

Most existing commercial real-time polymerase chain reaction (RT-PCR) instruments are bulky because they contain expensive fluorescent detection sensors or complex optical structures. In this paper, we propose an RT-PCR system using a camera module for smartphones that is an ultra small, high-performance and low-cost sensor for fluorescence detection. The proposed system provides stable DNA amplification. A quantitative analysis of fluorescence intensity changes shows the camera’s performance compared with that of commercial instruments. Changes in the performance between the experiments and the sets were also observed based on the threshold cycle values in a commercial RT-PCR system. The overall difference in the measured threshold cycles between the commercial system and the proposed camera was only 0.76 cycles, verifying the performance of the proposed system. The set calibration even reduced the difference to 0.41 cycles, which was less than the experimental variation in the commercial system, and there was no difference in performance.

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