A Comparative Study Between Nasopharyngeal/Oropharyngeal, Faecal and Saliva Viral Shedding In Ghanaian COVID-19 Patients attending KATH from October-December, 2020

ABSTRACT Background: Diagnostic testing for the current SARS CoV 2 infections involves the collection and testing of invasive pharyngeal specimens by qualified Health workers. Though fully clad in personal protective equipment, the concern is that sampling in close proximity to the patient poses as a major health hazard. The present study sought to verify if saliva or faeces could become a possible surrogate for pharyngeal samples for SARS CoV 2 testing in suspected Ghanaian COVID-19 patients. Objectives: To ascertain if there is SARS CoV 2 viral shedding in the saliva and faecal samples of Ghanaian COVID 19 patients, their sensitivity and specificity as compared to pharyngeal samples. Method: Fifty (50) recruited COVID 19 patients who have been confirmed via RT PCR using their nasopharyngeal/oropharyngeal samples and twenty (20) SARS CoV 2 negative suspected patients each provided some faecal and saliva sample for RT PCR analysis for SARS CoV 2. Results: Forty three (43) out of the fifty (50) COVID 19 patients recruited representing 86% tested positive for SARS CoV 2 via their saliva sample whiles all their faecal samples tested positive for SARS CoV 2 representing 100%. The sensitivity of saliva samples was 86% whiles the specificity was 100% but the sensitivity and specificity of the faecal samples were all 100%. Conclusion: There is indeed viral shedding of SARS CoV 2 in the saliva and faeces of Ghanaian COVID 19 patients just like their counterparts in other parts of the world. Saliva and faeces could possibly become an alternative sample to the current in place of the invasive pharyngeal samples for SARS CoV 2 testing in resource limited settings. Further research to explore this possibility at different testing sites with larger sample size is recommended. Keywords: Severe Acute Respiratory Syndrome Corona Virus 2 (SARS CoV2), Real Time Polymerase Chain Reaction (RT PCR), saliva, faeces, nasopharyngeal, oropharyngeal, sensitivity, specificity

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COMPARISON OF ARTIFICIAL INTELLIGENCE ENABLED METHODS IN THE COMPUTED TOMOGRAPHIC ASSESSMENT OF COVID-19 DISEASE.

10.1101/2020.09.02.20186650 ◽

2020 ◽

Author(s):

Atul Kapoor ◽

Goldaa Mahajan ◽

Aprajita Kapoor

Keyword(s):

Artificial Intelligence ◽

Sensitivity And Specificity ◽

Visual Analysis ◽

Test Results ◽

Friedman Test ◽

Rt Pcr ◽

Computed Tomographic ◽

Sensitivity Specificity ◽

Disease Parameters ◽

Higher Sensitivity

Objectives: Comparison of three different Artificial intelligence (AI) methods of assessment for patients undergoing Computed tomography (CT) for suspected Covid-19 disease. Parameters studied were probability of diagnosis, quantification of disease severity and the time to reach the diagnosis . Methods: 107 consecutive patients of suspected Covid-19 patients were evaluated using the three AI methods labeled as AI-I,II, III alongwith visual analysis labeled as VT for predicting probability of Covid-19, determining CT severity score (CTSS) and index (CTSI) , percentage opacification (PO) and high opacification (POHO). Sensitivity, specificity along with area under curves were estimated for each method and the CTSS and CTSI correlated using Friedman test. Results: Out of 107 patients 71 patients were Covid-19 positive and 20 negative by RT-PCR while 16 did not get RT-PCR done. AI-III method showed higher sensitivity and specificity of 93% and 88% respectively to predict probability of Covid 19. It had 2 false positive patients of interstitial lung disease. AI-II method had sensitivity and specificity of 66% and 83% respectively while visual (VT) analysis showed sensitivity and specificity of 59.7% and 62% respectively. Statistically significant differences were also seen in CTSI and PO estimation between AI-I and III methods (p<0.0001) with AI-III showing fastest time to calculate results. Conclusions: AI-III method gave better results to make an accurate and quick diagnosis of the Covid-19 with AUC of 0.85 to predict probability of Covid-19 alongwith quantification of Covid-19 lesions in the form of PO, POHO as compared to other AI methods and also by visual analysis.

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Parasite-derived circulating microRNAs as biomarkers for the detection of human Schistosoma japonicum infection

Parasitology ◽

10.1017/s0031182019001690 ◽

2019 ◽

Vol 147 (8) ◽

pp. 889-896 ◽

Cited By ~ 1

Author(s):

Yi Mu ◽

Pengfei Cai ◽

Remigio M. Olveda ◽

Allen G. Ross ◽

David U. Olveda ◽

...

Keyword(s):

Schistosoma Japonicum ◽

Diagnostic Performance ◽

Area Under The Curve ◽

Infection Intensity ◽

The Philippines ◽

Pcr Analysis ◽

Rt Pcr ◽

Serum Samples ◽

Sensitivity Specificity ◽

Pcr Targeting

AbstractNovel tools for early diagnosis and monitoring of schistosomiasis are urgently needed. This study aimed to validate parasite-derived miRNAs as potential novel biomarkers for the detection of human Schistosoma japonicum infection. A total of 21 miRNAs were initially validated by real-time-polymerase chain reaction (RT-PCR) using serum samples of S. japonicum-infected BALB/c mice. Of these, 6 miRNAs were further validated with a human cohort of individuals from a schistosomiasis-endemic area of the Philippines. RT-PCR analysis showed that two parasite-derived miRNAs (sja-miR-2b-5p and sja-miR-2c-5p) could detect infected individuals with low infection intensity with moderate sensitivity/specificity values of 66%/68% and 55%/80%, respectively. Analysis of the combined data for the two parasite miRNAs revealed a specificity of 77.4% and a sensitivity of 60.0% with an area under the curve (AUC) value of 0.6906 (P = 0.0069); however, a duplex RT-PCR targeting both sja-miR-2b-5p and sja-miR-2c-5p did not result in an increased diagnostic performance compared with the singleplex assays. Furthermore, the serum level of sja-miR-2c-5p correlated significantly with faecal egg counts, whereas the other five miRNAs did not. Targeting S. japonicum-derived miRNAs in serum resulted in a moderate diagnostic performance when applied to a low schistosome infection intensity setting.

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Comparative analysis of the diagnostic performance of five commercial COVID-19 qRT PCR kits used in India

Scientific Reports ◽

10.1038/s41598-021-00852-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

J. Singh ◽

A. K. Yadav ◽

A. Pakhare ◽

P. Kulkarni ◽

L. Lokhande ◽

...

Keyword(s):

Sensitivity And Specificity ◽

Diagnostic Performance ◽

Diagnostic Testing ◽

Rna Extraction ◽

Clinical Samples ◽

Diagnostic Process ◽

Control Group ◽

Rt Pcr ◽

Short Period ◽

Commercial Kits

AbstractTo meet the unprecedented requirement of diagnostic testing for SARS-CoV-2, a large number of diagnostic kits were authorized by concerned authorities for diagnostic use within a short period of time during the initial phases of the ongoing pandemic. We undertook this study to evaluate the inter-test agreement and other key operational features of 5 such commercial kits that have been extensively used in India for routine diagnostic testing for COVID-19. The five commercial kits were evaluated, using a panel of positive and negative respiratory samples, considering the kit provided by National Institute of Virology, Indian Council of Medical Research (2019-nCoV Kit) as the reference. The positive panel comprised of individuals who fulfilled the 3 criteria of being clinically symptomatic, having history of contact with diagnosed cases and testing positive in the reference kit. The negative panel included both healthy and disease controls, the latter being drawn from individuals diagnosed with other respiratory viral infections. The same protocol of sample collection, same RNA extraction kit and same RT-PCR instrument were used for all the kits. Clinical samples were collected from a panel of 92 cases and 60 control patients, who fulfilled our inclusion criteria. The control group included equal number of healthy individuals and patients infected with other respiratory viruses (n = 30, in each group). We observed varying sensitivity and specificity among the evaluated kits, with LabGun COVID-19 RT-PCR kit showing the highest sensitivity and specificity (94% and 100% respectively), followed by TaqPath COVID-19 Combo and Allplex 2019-nCoV assays. The extent of inter-test agreement was not associated with viral loads of the samples. Poor correlation was observed between Ct values of the same genes amplified using different kits. Our findings reveal the presence of wide heterogeneity and sub-optimal inter-test agreement in the diagnostic performance of the evaluated kits and hint at the need of adopting stringent standards for fulfilling the quality assurance requirements of the COVID-19 diagnostic process.

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Target Testing and Specificity of Nucleic Acid Based Diagnostics for COVID-19

RAS Medical Science ◽

10.51520/2766-5240-8 ◽

2021 ◽

Vol 1 (2) ◽

Author(s):

Ghazala Rubi ◽

Musbih ul Qayyum Zia ◽

Muhammad Yousaf Rana ◽

Ayaz Akbar ◽

Zainab Javiad

Keyword(s):

Nucleic Acid ◽

Diagnostic Testing ◽

Rt Pcr ◽

Likelihood Ratios ◽

International Importance ◽

Amplification Process ◽

Group 2 ◽

Novel Coronavirus ◽

Sensitivity Specificity

Objective: The seek of this study is to provide an indication on the features of diagnostic testing of SARS-CoV-2 by RT-PCR, including parameters of sensitivity, specificity, positive and negative likelihood ratios. Background: Coronavirus Disease is the fifth international emergency after 1918 Spanish flu pandemic, triggered by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2). On 30 January, the WHO acknowledged COVID-19 to be a global health disaster of international importance and a pandemic on 11 March 2020. In vitro analyses of the data shows that for SARS-CoV-2 the RT-PCR test is highly specific, as it is not counter react with nucleic acid of other viruses. Methods: Oropharyngeal and nasopharyngeal swabs were collected into a 3 ml viral transport media (VTM) and transported to Laboratory. Extraction of the viral RNA was done by Qiasymphony DSP Virus/ Pathogen mini kit (Qiagen GmbH, Germany). For amplification process of RT-PCR qualitative detection of SARS-CoV-2 RNA utilizing with SYSTAAQ 2019-Novel Coronavirus (COVID-19) Real time PCR kit using a BIORAD-CFX 96. Results: Out of 15,049, 3195 samples were positive for covid-19 qPCR. Ratio of the Males patients were greater than females. 63.7% males and 36.3% females were effected with Covid-19. Symptom wise analysis shows 62% patient were asymptomatic, 22.7% mild, 1.7% moderate, 12.7% stable, 0.6% severe and 0.2% were critical. Our analysis reveals age group 1 (4.9%), group 2 (55.5%), group 3 (27.5%), and group 4 (12.1%) were effected with SARS-nCoV-2. Our result shows 3.0 % patients were deceased and 97% were recovered. Conclusion: Our findings contribute to the evolving understanding of the sophisticated interaction between this emerging SARS-CoV-2 virus and nucleic acid based target testing of COVID-19.

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Analysis of bovine viral diarrhoea virus in Korea dairy farms

Indian Journal of Animal Research ◽

10.18805/ijar.9374 ◽

2016 ◽

Author(s):

Hong-Je Park ◽

Gyeong-Dong Kim ◽

Chi-Ho Lee ◽

Myung-Hwa Kang ◽

Kwan-Sik Min

Keyword(s):

Diagnostic Testing ◽

Bovine Viral Diarrhoea Virus ◽

Dairy Farms ◽

Rapid Screening ◽

Pcr Analysis ◽

Bovine Viral Diarrhoea ◽

Rt Pcr ◽

Bulk Milk ◽

Diarrhoea Virus ◽

Targeted Testing

A total of 2,194 bulk-tank milks from dairy farms were investigated, and of which 842 dairy farms (55,263 cattle) were assessed to detect persistently infected (PI) individual cattle by performing ELISA. Reverse transcription (RT)-PCR and immunohistochemistry (IHC) were used to develop a rapid screening test for detecting Bovine viral diarrhoea virus (BVDV) in ear tissues. Testing for the bulk-milk tank from dairy farms showed that 2,007 (91.5%) out of a total of 2,194 farms were determined to be positive for BVDV, while only 187 bulk-milk tanks (8.5%) were negative. A total of 55,263 cattle were tested for BVDV, of which 669 (1.2%) cattle from 387 farms (46%) were identified as PI. The distribution of PI was 178 (65.4%) of 272 herds under 14 months. A 220 (80.9%) herds were found in less than 23 month ages. Four infected herds were identified as PI based on RT-PCR analysis. BVDV protein was shown to be localized within epidermal hair bulb cells. This approach of targeted testing of dairy herds using ELISA and RT-PCR for pre-diagnostic testing proves to markedly reduce BVDV-infected herds in Korean dairy farms and in Korean Native Cows.

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Evaluation of the validity of Ag PANBIO-COVID19 in the diagnosis of SARS-CoV-2 infection in asymptomatic or mildly infected patients

Revista Española de Quimioterapia ◽

10.37201/req/054.2021 ◽

2021 ◽

Author(s):

Paula Gras-Valenti ◽

Inmaculada Vidal ◽

Inés Montiel-Higuero ◽

Isabel Escribano ◽

Natividad Algado-Selles ◽

...

Keyword(s):

Sensitivity And Specificity ◽

Diagnostic Tests ◽

Diagnostic Testing ◽

High Viral Load ◽

Reference Standard ◽

Rt Pcr ◽

Asymptomatic Group ◽

Symptomatic Group ◽

Asymptomatic Patients

Objective. To assess the validity of SARS-CoV-2 Antigen (Ag) detection for the diagnosis of SARS-CoV-2 infection in mildly infected or asymptomatic patients. Material and methods. Observational study to evaluate diagnostic tests. Non-hospitalized patients with indication for diagnostic testing for SARS-CoV-2 infection were included. The diagnostic test to be evaluated was the determination of Ag and as a reference standard to determine the presence of viral RNA the RT-PCR was used. Results. A total of 494 patients were included. Of these 71.5% (353/494) had symptoms and 28.5% (141/494) were asymptomatic (presurgery screening (35/494) and confirmed case-contact (106/494). The overall sensitivity of the Ag test was 61.1% and the specificity was 99.7%. The sensitivity and specificity in the asymptomatic group were 40% and 100% respectively, and in the symptomatic group 63.5% and 99.6% respectively. In turn, the sensitivity and specificity in the group of symptomatic patients varied according to the time of symptom evolution: in patients with recent symptoms, they were 71.4% and 99.6% respectively, while in patients with symptoms of more than 5 days of evolution, they were 26.7% and 100% respectively. In all groups studied, the presence of antigen is associated with a high viral load (Ct<30 cycles). Conclusions. The use of Ag detection test is not indicated for the diagnosis of SARS-CoV-2 infection in asymptomatic patients or with symptoms of more than 5 days of evolution, but it could be useful in patients with symptoms of 1-5 days of evolution.

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Rapid environmental monitoring, capture, and destruction activities of SARS-CoV-2 during the Covid-19 health emergency

10.1101/2020.11.24.20237040 ◽

2020 ◽

Author(s):

Roberto Marchetti ◽

Martina Stella ◽

Debjyoti Talukdar ◽

Rosaria Erika Pileci

Keyword(s):

Health Care ◽

Health Care Workers ◽

Healthcare Workers ◽

Health Workers ◽

Pcr Analysis ◽

List Type ◽

Rt Pcr ◽

Care Workers ◽

Polymerase Chain ◽

Hospital Wards

ABSTRACTObjectivesSARS-CoV-2 pandemic is a health emergency for occupational healthcare workers at COVID19 hospital wards in Italy. The objective of the study was to investigate if U-Earth AIRcel bioreactors were effective in monitoring and improving air quality via detection, capture, and destruction of the SARS-CoV-2 virus, reducing the risk of transmission among healthcare workers.MethodsU-Earth AIRcel bioreactors are a demonstrated effective biomonitoring system. We implemented a methodological approach wherein they were placed at various hospitals treating COVID-19 patients in Italy. The detection of the SARS-CoV-2 virus was achieved through rapid biomonitoring testing of the solutes from the AIRcel bioreactors via SARS-CoV-2 rapid test antigen and consecutive reverse transcription-polymerase chain reaction (RT-PCR) analysis with the multiplex platform (XABT) and the Real-Time PCR Rotor-Gene.ResultsThe marked presence of the SARS-CoV-2 virus was found in multiple water samples via the detection of ORF1ab + N and/or E gene involved in gene expression and cellular signaling of the SARS-CoV virus. The AIRcel bioreactors were able to neutralize the virus effectively as traces of the viruses were no longer found in multiple solute samples after an overnight period.ConclusionsTransmission of COVID-19 via bio-aerosols, transmitted by infected patients, remains a viable threat for health workers. AIRcel bioreactors allow for rapid biomonitoring testing for early virus detection within the environment, reducing the risk of exponential contagion exposure and maintaining good air quality without endangering health workers. This same protocol can also be extended to public spaces as a bio-monitoring tool for hotpots early detection.Key messagesWhat is already known about this subject?Transmission of SARS-CoV-2 virus via bio-aerosols is a threat to health care workers. Only few studies have conducted investigations on how to limit the spread of the virus via air purifiers.Existing studies show a higher risk to health care workers serving at COVID-19 wards with a higher risk of viral transmission.What are the new findings?In this study, SARS-CoV-2 virus traces were captured by U-Earth air purifier bioreactor units placed at several hospitals in Italy.AIRcel bioreactors achieved early detection of the SARS-CoV-2 virus within the environment via rapid biomonitoring testing.AIRcel bioreactors have proved effective in biomonitoring via the detection, capture, and destruction of SARS-CoV-2 virus through reverse transcription-polymerase chain reaction (RT-PCR) analysis with the multiplex platform (XABT) Multiple Real-Time PCR Rotor-Gene.How might this impact on policy or clinical practice in the foreseeable future?This study shows the need for effective surveillance and biomonitoring to contain the spread of the SARS-CoV-2 virus. AIRcel bioreactors, an effective occupational surveillance system, can reduce the transmission of the virus to health care workers serving COVID-19 infected patients at hospital wards.AIRcel bioreactors can also be used in public spaces and other settings, such as schools, to increase the speed of detection of the SARS-CoV-2 virus and improve control of the environment, thereby decreasing the exponential growth of the pandemic.

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Detection of SARS-CoV-2 infection by rapid antigen test in comparison with RT-PCR in a public setting

10.1101/2021.01.22.21250042 ◽

2021 ◽

Cited By ~ 1

Author(s):

Kathrine Kronberg Jakobsen ◽

Jakob Schmidt Jensen ◽

Tobias Todsen ◽

Freddy Lippert ◽

Cyril Jean-Marie Martel ◽

...

Keyword(s):

False Negative ◽

Pcr Analysis ◽

Nasopharyngeal Swab ◽

Test Results ◽

Antigen Test ◽

Rt Pcr ◽

Predictive Values ◽

Public Setting ◽

Antigen Tests ◽

Sensitivity Specificity

AbstractBackgroundRapid and accurate detection of SARS-CoV-2 infection is essential in limiting the spread of infection during the ongoing COVID-19 pandemic. The aim of this study was to determine the accuracy of the STANDARD Q COVID-19 Ag test (SD BIOSENSOR) by comparison with RT-PCR in a public setting.MethodIndividuals aged 18 years or older who had booked an appointment for a RT-PCR test on December 26-31, 2020 at a public test center in Copenhagen, Denmark, were invited to participate. An oropharyngeal swab was collected for RT-PCR analysis, immediately followed by a nasopharyngeal swab examined by the STANDARD Q COVID-19 Ag test (SD BIOSENSOR). Sensitivity, specificity, positive and negative predictive values of the antigen test were calculated with test results from RT-PCR as reference.ResultsOverall, 4697 individuals were included (female n=2456, 53.3%; mean age: 44.7 years, SD: 16.9 years); 196 individuals were tested twice or more. Among 4811 paired conclusive test results from the RT-PCR and antigen tests, 221 (4.6%) RT-PCR tests were positive. The overall sensitivity and specificity of the antigen test were 69.7% and 99.5%, the positive and negative predictive values were 87.0% and 98.5%. Ct values were significantly higher among individuals with false negative antigen tests compared to true positives.ConclusionThe sensitivity, specificity, and predictive values found indicate that the STANDARD Q COVID-19 Ag is a good supplement to RT-PCR testing.

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The long-quarantined case of COVID-19 with prolonged viral shedding and intermittent fever for more than 70 days

Future Virology ◽

10.2217/fvl-2020-0423 ◽

2021 ◽

Vol 16 (2) ◽

pp. 79-84

Author(s):

Eijiro Yamada ◽

Emi Ishida ◽

Yasuyo Nakajima ◽

Kazuhiko Horiguchi ◽

Shunichi Matsumoto ◽

...

Keyword(s):

Japanese Woman ◽

Pcr Analysis ◽

Rt Pcr ◽

Intermittent Fever ◽

Laboratory Findings ◽

Inflammatory Reactions ◽

Mild Disease ◽

Viral Shedding ◽

Reverse Transcription Pcr ◽

Pcr Test

A 79-year old Japanese woman was diagnosed with coronavirus disease (COVID-19), caused by SARS coronavirus 2 (SARS-CoV-2), based on a positive reverse transcription-PCR (RT-PCR) test result. Chest computed tomography revealed mild interstitial pneumonia. She had intermittent persistent inflammatory reactions with fever. Laboratory findings and RT-PCR test results showed SARS-CoV-2 positivity for more than 70 days. To the best of our knowledge, this relatively mild case has the longest duration of viral shedding recorded, as confirmed by RT-PCR analysis. This case demonstrates that the viral shedding in COVID-19 can be prolonged, even in mild disease, and highlights the difficulties in distinguishing viral shedding from SARS-CoV-2 infectivity.

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Improving the Diagnostic Accuracy of the PD-L1 Test with Image Analysis and Multiplex Hybridization

Cancers ◽

10.3390/cancers12051114 ◽

2020 ◽

Vol 12 (5) ◽

pp. 1114 ◽

Cited By ~ 3

Author(s):

Matthew P. Humphries ◽

Victoria Bingham ◽

Fatima Abdullahi Sidi ◽

Stephanie G. Craig ◽

Stephen McQuaid ◽

...

Keyword(s):

Image Analysis ◽

Sensitivity And Specificity ◽

Digital Image Analysis ◽

Checkpoint Inhibitors ◽

Diagnostic Testing ◽

Programmed Death ◽

Sensitivity Specificity ◽

Nsclc Patients ◽

Assessment Sensitivity ◽

Cell Death Protein

Targeting of the programmed cell death protein (PD-1)/programmed death-ligand 1 (PD-L1) axis with checkpoint inhibitors has changed clinical practice in non-small cell lung cancer (NSCLC). However, clinical assessment remains complex and ambiguous. We aim to assess whether digital image analysis (DIA) and multiplex immunofluorescence can improve the accuracy of PD-L1 diagnostic testing. A clinical cohort of routine NSCLC patients reflex tested for PD-L1 (SP263) immunohistochemistry (IHC), was assessed using DIA. Samples of varying assessment difficulty were assessed by multiplex immunofluorescence. Sensitivity, specificity, and concordance was evaluated between manual diagnostic evaluation and DIA for chromogenic and multiplex IHC. PD-L1 expression by DIA showed significant concordance (R² = 0.8248) to manual assessment. Sensitivity and specificity was 86.8% and 91.4%, respectively. Evaluation of DIA scores revealed 96.8% concordance to manual assessment. Multiplexing enabled PD-L1+/CD68+ macrophages to be readily identified within PD-L1+/cytokeratin+ or PD-L1-/cytokeratin+ tumor nests. Assessment of multiplex vs. chromogenic IHC had a sensitivity and specificity of 97.8% and 91.8%, respectively. Deployment of DIA for PD-L1 diagnostic assessment is an accurate process of case triage. Multiplex immunofluorescence provided higher confidence in PD-L1 assessment and could be offered for challenging cases by centers with appropriate expertise and specialist equipment.

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