Diagnostic Performance of RT-PCR-Based Sample Pooling Strategy for the Detection of SARS-CoV-2

Abstract Background: The rapid spread of SARS-CoV-2 has created a shortage of supplies of reagents for its detection throughout the world, especially in Latin America. The pooling of samples consists of combining individual patient samples in a block and analyzing the group as a particular sample. This strategy has been shown to reduce the burden of laboratory material and logistical resources by up to 80%. Therefore, we aimed to evaluate the diagnostic performance of the pool of samples analyzed by RT-PCR to detect SARS-CoV-2.Methods: A cross-sectional study of diagnostic tests was carried out. We individually evaluated 420 samples, and 42 clusters were formed, each one with ten samples. These clusters could contain 0, 1 or 2 positive samples to simulate a positivity of 0, 10 and 20%, respectively. RT-PCR analyzed the groups for the detection of SARS-CoV-2. The area under the ROC curve (AUC), the Youden index, the global and subgroup Sensitivity and specificity were calculated according to their Ct values that were classified as high (H: ≤25), moderate (M: 26-30) and low (L: 31-35) concentration of viral RNA.Results: From a total of 42 pools, 41 (97.6%) obtained the same result as the samples they contained (positive or negative). The AUC for pooling, Youden index, sensitivity, and specificity were 0.98 (95% CI, 0.95-1); 0.97 (95% CI, 0.90-1.03); 96.67% (95% CI; 88.58-100%) and 100% (95% CI; 95.83-100%) respectively. In the stratified analysis of the pools containing samples with CT <31, the Sensitivity was 100% (95% CI; 90-100%), while with the pools containing samples with Ct ≥31, the Sensitivity was 80% (95% CI, 34.94% - 100%). Finally, a median greater than 2.32 (IQR: 1.12 - 3.03) in the Ct was observed in the pools concerning the Ct of the individual samples (p <0.001).Conclusions: The strategy of pooling nasopharyngeal swab samples for analysis by SARS-CoV-2 RT-PCR showed high diagnostic performance.

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Evaluation of Pooled Sample Analysis Strategy for SARS-CoV-2 RT-PCR Tests in Diagnosis and Screening of COVID-19

Journal of Bangladesh College of Physicians and Surgeons ◽

10.3329/jbcps.v38i0.47349 ◽

2020 ◽

pp. 16-20

Author(s):

Susane Giti ◽

Md Monirul Hoque ◽

Arif Ahmed Khan ◽

Md Mehedhi Hasan Shourov

Keyword(s):

Armed Forces ◽

Cross Sectional Study ◽

Control Measures ◽

N Gene ◽

Rt Pcr ◽

Cross Sectional ◽

Infection Control Measures ◽

Sample Pooling ◽

The Individual ◽

Pcr Targeting

Introduction: The recent outbreak of COVID-19 is a serious global concern. The emergence of SARS-CoV-2 led to a current pandemic of unprecedented levels. Early detection of the infection and prompt isolation of the cases are fundamental for containment of such outbreak. By this time, healthcare systems are facing shortages of reagents for diagnosing this disease. In this context, sample pooling can be an effective strategy to overcome this situation. This study aimed to evaluate the effectiveness of sample pooling strategy for RT-PCR tests for diagnosing and screening of COVID- 19 in mass population. Methods: A cross-sectional study was performed at the COVID-19 laboratory of Armed Forces Institute of Pathology of Bangladesh to evaluate the efficacy of sample pooling technique for detecting SARS-CoV-2 infection. In this laboratory, nasopharyngeal and oropharyngeal swabs were taken for the RT-PCR test to diagnose COVID-19. For each patient, both nasopharyngeal and oropharyngeal samples were taken and then mixed to make a single sample. Pooling was performed from the samples collected from 1 April 2020 to 30 April 2020. Total 350 samples were distributed randomly in 70 pools, so that each pool contains 5 samples. Positive pools were deconvulated and each sample was tested separately. Screening was performed by using RT-PCR targeting the ORF-1ab Region and N-gene. Results: Out of 70 pools 16 (22.85%) were found positive. Eighty samples of these 16 pools were tested individually and 21 (21/80, 26.25%) samples were found positive. All the positive pools were reproducible with testing of the individual samples of that pool (100%). Conclusion: Strategies of using pooled samples for screening may facilitate detection of early community transmission of SARS-CoV-2 and enable timely implementation of appropriate infection control measures to reduce spread. J Bangladesh Coll Phys Surg 2020; 38(0): 16-20

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Evaluation of SARS-CoV-2 antigen-based rapid diagnostic kits in Pakistan: formulation of COVID-19 national testing strategy

Virology Journal ◽

10.1186/s12985-021-01505-3 ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Umar Saeed ◽

Sara Rizwan Uppal ◽

Zahra Zahid Piracha ◽

Azhar Rasheed ◽

Zubair Aftab ◽

...

Keyword(s):

Gold Standard ◽

Injection Drug Users ◽

Drug Users ◽

Diagnostic Testing ◽

False Negative ◽

Cross Sectional Study ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Cross Sectional ◽

Negative Results

AbstractRapid diagnosis of SARS-CoV-2 during pandemic enables timely treatment and prevention of COVID-19. Evaluating the accuracy and reliability of rapid diagnostic testing kits is crucial for surveillance and diagnosis of SARS-CoV-2 infections in general population, injection drug users, multi-transfused populations, healthcare workers, prisoners, barbers and other high risk populations. The aim of this study was to evaluate performance and effectiveness of nasopharyngeal swab (NSP) and saliva based rapid antigen detection testing kits in comparison with USFDA approved triple target gold standard real-time polymerase chain reaction. A cross-sectional study was conducted on 33,000 COVID-19 suspected patients. From RT-PCR positive patients, nasopharyngeal swab (NSP) and saliva samples were obtained for evaluation of rapid COVID-19 testing kits (RDT). 100/33,000 (0.3%) of specimens were RT-PCR positive for SARS-CoV-2. Among RT-PCR positive, 62% were males, 34% were females, and 4% were children. The NSP-RDT (Lepu Medical China) analysis revealed 53% reactivity among males, 58% reactivity among females, and 25% reactivity among children. However saliva based RDT (Lepu Medical China) analysis showed 21% reactivity among males and 23% among females, and no reactivity in children. False negative results were significantly more pronounced in saliva based RDT as compared to NSP-RDT. The sensitivity of these NSP-RDT and saliva based RDT were 52% and 21% respectively. The RDTs evaluated in this study showed limited sensitivities in comparison to gold standard RT-PCR, indicating that there is a dire need in Pakistan for development of suitable testing to improve accurate COVID-19 diagnosis in line with national demands.

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Effectivity Analysis of SARS-CoV-2 Nasopharyngeal Swab Rapid Testing Kits in Pakistan: A Scenario of Inadequate COVID-19 Diagnosis

10.21203/rs.3.rs-315851/v1 ◽

2021 ◽

Cited By ~ 1

Author(s):

Umar Saeed ◽

Sara Rizwan Uppal ◽

Zahra Zahid Piracha ◽

Aftab Ahmad Khan ◽

Azhar Rasheed ◽

...

Keyword(s):

Gold Standard ◽

Rapid Detection ◽

International Health ◽

Time Frame ◽

Cross Sectional Study ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Cross Sectional ◽

International Health Organizations ◽

Polymerase Chain

Abstract COVID-19 pandemic has urged the need of rapid detection of SARS-CoV-2 in limited time frame. To cope with current, COVID-19 expanding scenario, accurate diagnosis of SARS-CoV-2 should be ensured by both national and international health organizations. Sporadic marketing of SARS-CoV-2 rapid detection kits raises questions regarding quality control and assurance. To aim of this study was to examine the effectiveness of SARS-CoV-2 nasopharyngeal swab based rapid detection kits, in comparison to gold standard USFDA approved triple target real-time polymerase chain reaction. A cross-sectional study of 1500 suspected COVID-19 patients was conducted. 100 RT-PCR confirmed patients nasopharyngeal swabs were evaluated for RDT. The COVID-19/SARS-CoV-2 NSP based RDT analysis showed 78% reactivity. Among RT-PCR confirmed negative subjects, 49.3% showed false positivity. The positive predictive analysis revealed 67.82% values, while the negative predictive vales of were 64.40%. The NSP RDTs showed limited sensitivities and specificities compared to gold standard RT-PCR. Accurate surveillance of COVID-19 is dependent upon authentic and validated SARS-CoV-2 detection nation-wide, which needs to be monitored by higher authorities. This study is critical for designing adequate measures by several COVID-19 strategic organizations to prevent future viral epidemics.

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Is the COVID-19 disease associated with de novo nephritic syndrome?

Revista da Associação Médica Brasileira ◽

10.1590/1806-9282.66.9.1258 ◽

2020 ◽

Vol 66 (9) ◽

pp. 1258-1263

Author(s):

Hamad Dheir ◽

Savas Sipahi ◽

Selcuk Yaylaci ◽

Ahmed Cihad Genc ◽

Fevziye Turkoglu Genc ◽

...

Keyword(s):

De Novo ◽

Spontaneous Remission ◽

Cross Sectional Study ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Dipstick Test ◽

Cross Sectional ◽

Nephritic Syndrome ◽

The Mean

SUMMARY INTRODUCTION: This study aims to determine the incidence of de novo nephritic syndrome (NS) in COVID-19 patients and identify its associated factors. METHODS: All ward patients with COVID-19 pneumonia were investigated. After determining the inclusion and exclusion criteria, the study population was identified. The urine dipstick test and urine protein creatinine ratio (UPCR) measurements were performed. Patients with de novo NS findings, nasopharyngeal swab, and urine RT-PCR tests were performed simultaneously RESULTS: This descriptive cross-sectional study was conducted with 21 patients with COVID-19. The mean age of the patients was 42.2±8.8 years, and 71.4% of them were male. The mean duration of follow-up was 28.4±9.3 days. The urine RT-PCR test was positive in one patient (4.8%). Improvements were observed in hematuria by 71.4%, and proteinuria by 85.7% at the end of the follow-up. A significant decrease in the measured UPCR was found in comparison to the baseline(P=0.000). Also, improvements were recorded in the complete blood counts, inflammatory parameters, ferritin, and coagulation tests, compared to the baseline. There was a positive correlation between baseline UPCR and ferritin, and a negative correlation between baseline UPCR and sodium values CONCLUSION: COVID-19-induced de novo nephritic syndrome may occur mainly due to tubulointerstitial involvement and often results in spontaneous remission. However, why these findings were not present in all patients who had no comorbidities is not clear.

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Xpert Ultra Assay on Stool to Diagnose Pulmonary Tuberculosis in Children

Clinical Infectious Diseases ◽

10.1093/cid/ciaa583 ◽

2020 ◽

Cited By ~ 3

Author(s):

Senjuti Kabir ◽

S M Mazidur Rahman ◽

Shakil Ahmed ◽

Md Shamiul Islam ◽

Rupali Sisir Banu ◽

...

Keyword(s):

Pulmonary Tuberculosis ◽

Sensitivity And Specificity ◽

Diagnostic Performance ◽

Tertiary Care ◽

Cross Sectional Study ◽

Induced Sputum ◽

World Health ◽

Cross Sectional ◽

Health Organization ◽

Tuberculosis In Children

Abstract Background The World Health Organization recommends the Xpert MTB/RIF Ultra assay for diagnosing pulmonary tuberculosis (PTB) in children. Though stool is a potential alternative to respiratory specimens among children, the diagnostic performance of Xpert Ultra on stool is unknown. Thus, we assessed the diagnostic performance of Xpert Ultra on stool to diagnose PTB in children. Methods We conducted a cross-sectional study among consecutively recruited children (< 15 years of age) with presumptive PTB admitted in 4 tertiary care hospitals in Dhaka, Bangladesh, between January 2018 and April 2019. Single induced sputum and stool specimens were subjected to culture, Xpert, and Xpert Ultra. We considered children as bacteriologically confirmed on induced sputum if any test performed on induced sputum was positive for Mycobacterium tuberculosis and bacteriologically confirmed if M. tuberculosis was detected on either induced sputum or stool. Results Of 447 children, 29 (6.5%) were bacteriologically confirmed on induced sputum and 72 (16.1%) were bacteriologically confirmed. With “bacteriologically confirmed on induced sputum” as a reference, the sensitivity and specificity of Xpert Ultra on stool were 58.6% and 88.1%, respectively. Xpert on stool had sensitivity and specificity of 37.9% and 100.0%, respectively. Among bacteriologically confirmed children, Xpert Ultra on stool was positive in 60 (83.3%), of whom 48 (80.0%) had “trace call.” Conclusions In children, Xpert Ultra on stool has better sensitivity but lesser specificity than Xpert. A high proportion of Xpert Ultra assays positive on stool had trace call. Future longitudinal studies on clinical evolution are required to provide insight on the management of children with trace call.

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Diagnostic performance of midupper arm circumference for detecting severe wasting among infants aged 1–6 months in Ethiopia

American Journal of Clinical Nutrition ◽

10.1093/ajcn/nqaa294 ◽

2020 ◽

Vol 113 (1) ◽

pp. 55-62

Author(s):

Beshada R Jima ◽

Hamid Y Hassen ◽

Yalemwork Getnet ◽

Paluku Bahwere ◽

Seifu H Gebreyesus

Keyword(s):

Predictive Value ◽

Diagnostic Performance ◽

Operating Characteristic ◽

Cross Sectional Study ◽

Child Growth ◽

Youden Index ◽

Cross Sectional ◽

Growth Standards ◽

Arm Circumference ◽

Sensitivity Specificity

ABSTRACT Background Midupper arm circumference (MUAC) is used as an independent diagnostic tool to detect wasting in children aged 6–59 mo. However, little is known about the diagnostic performance of MUAC for detecting wasting among infants aged 1–6 mo. Objective The objective of this study was to evaluate the diagnostic performance of MUAC in detecting severe wasting in infants aged 1–6 mo. Methods We conducted a facility-based cross-sectional study among 467 hospitalized infants aged 1–6 mo in Ethiopia. Severe wasting was defined as having a weight for length z score (WLZ) below the cutoff value of −3 SDs from the median as per the WHO 2006 child growth standards. Receiver operating characteristic (ROC) analysis along with the calibration test was used to test the discriminatory performance of MUAC. Furthermore, we calculated the sensitivity, specificity, positive predictive value, and negative predictive value for the proposed optimal cutoffs. Results The median age, MUAC, and WLZ were 100 d (IQR: 69–145 d), 119 mm (IQR: 103–130 mm), and −1.27 (IQR: −2.66 to 0.34), respectively. The prevalence of severe and moderate wasting was n = 101 (21.6%) and n = 61 (13.0%), respectively. The MUAC area under the ROC curve accuracy level in identifying severe wasting was 0.86 (95% CI: 0.82, 0.89). The optimal MUAC cutoff of ≤112 mm yielded the highest Youden index of 0.61, with a sensitivity of 85.1% (95% CI: 76.7%, 91.4%) and a specificity of 76.0% (95% CI: 71.2%, 80.2%). Conclusions A MUAC cutoff of ≤112 mm performed well in detecting severe wasting among infants aged 1–6 mo. Further research is needed to evaluate the performance of MUAC for detecting wasting at community level and for predicting mortality among infants aged <6 mo.

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Bacterial and Fungal Co-Infections among ICU COVID-19 Hospitalized Patients in a Palestinian Hospital: Incidence and Antimicrobial Stewardship

10.1101/2021.09.12.21263463 ◽

2021 ◽

Author(s):

Hani A. Naseef ◽

Ula Mohammad ◽

Nimeh Al-Shami ◽

Yousef Sahoury ◽

Abdallah D. Abukhalil ◽

...

Keyword(s):

Cross Sectional Study ◽

Hospitalized Patients ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Cross Sectional ◽

Appropriate Treatment ◽

Enterobacter Species ◽

Medical Reports ◽

Patient’S Information ◽

Multiple Pathogens

AbstractDiagnosis of co-infections with multiple pathogens among hospitalized COVID-19 patients can be jointly challenging and very essential for appropriate treatment, shortening hospital stay and preventing antimicrobial resistance. This study proposes to investigate the burden of bacterial and fungal co-infections outcomes on COVID-19 patients. It is a single centre cross-sectional study of hospitalized COVID-19 patients at Beit-Jala hospital in Palestine. The study included 321 hospitalized patients admitted to the ICU between June 2020 and March 2021 aged ≥ 20 years, with a confirmed diagnosis of COVID-19 via RT-PCR conducted on a nasopharyngeal swab. The patient’s information was gathered using graded data forms from electronic medical reports. The diagnosis of bacterial and fungal infection was proved through the patient’s clinical presentation and positive blood or sputum culture results. All cases had received empirical antimicrobial therapy before the ICU admission, and different regimens during the ICU stay. The rate of bacterial co-infection was 51.1%, mainly from gram-negative isolates (Enterobacter species and K.pneumoniae). The rate of fungal co-infection caused by A.fumigatus was 48.9%, and the mortality rate was 8.1%. However, it is unclear if it had been attributed to SARS-CoV-2 or coincidental.

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The Role of Elastography in Fibroadenoma of the Breast and Differentiating it from its Mimics

QJM ◽

10.1093/qjmed/hcab106.038 ◽

2021 ◽

Vol 114 (Supplement_1) ◽

Author(s):

Marina Essam Fares Massak ◽

Sahar M. El Fiky ◽

Asmaa M Salama

Keyword(s):

Sensitivity And Specificity ◽

Diagnostic Performance ◽

High Sensitivity ◽

Strain Ratio ◽

Cross Sectional Study ◽

Ultrasound Elastography ◽

University Hospitals ◽

Cross Sectional ◽

Strain Elastography ◽

Imaging Characteristics

Abstract Background Fibroadenomas are one of the most common benign diseases of the breast varying in number and size in all quadrants of the breast. Less than 2% of lesions with the typical ultrasound features of a fibroadenoma, are found to be malignant on biopsy. Aim of the Work To evaluate the diagnostic performance of combined ultrasonography and strain elastography and to compare the imaging characteristics of fibroadenomas with other benign and malignant mimics and assess the results by histopathological characteristics. Patients and Methods Type of Study: Cross-sectional study. Study Setting: The study was conducted at Ain Shams University Hospitals, Radiodiagnosis department. Study Period: 6 months (From March 2020 till September 2020). Study Population: Female Patients with breast lumps. Results Ultrasound elastography combined with B-mode ultrasonography had shown variable degrees of sensitivity and specificity. However, in our study it showed high sensitivity and specificity as compared to other studies. The most reliable tool in our study was the strain ratio having the highest sensitivity and specificity. Conclusion Strain elastography combined to B-mode sonography improves the diagnostic performance of differentiating benign from malignant well circumscribed breast lesions with an additional benefit of preventing unnecessary biopsies and speeding up the diagnosis of malignant lesions instead of follow up of the patient for early diagnosis of malignancies.

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Evaluation of SARS-CoV-2 antigen-based rapid diagnostic kits in Pakistan: formulation of COVID-19 national testing strategy.

10.21203/rs.3.rs-113852/v2 ◽

2021 ◽

Author(s):

Umar Saeed ◽

Sara Rizwan Uppal ◽

Zahra Zahid Piracha ◽

Azhar Rasheed ◽

Zubair Aftab ◽

...

Keyword(s):

Gold Standard ◽

Injection Drug Users ◽

Drug Users ◽

Diagnostic Testing ◽

False Negative ◽

Cross Sectional Study ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Cross Sectional ◽

Negative Results

Abstract Rapid diagnosis of SARS-CoV-2 during pandemic enables timely treatment and prevention of COVID-19. Evaluating the accuracy and reliability of rapid diagnostic testing kits is crucial for surveillance and diagnosis of SARS-CoV-2 infections in general population, injection drug users, multi-transfused populations, healthcare workers, prisoners, barbers and other high risk populations. The aim of this study was to evaluate performance and effectiveness of nasopharyngeal swab (NSP) and saliva based rapid antigen detection testing kits in comparison with USFDA approved triple target gold standard real-time polymerase chain reaction. A cross-sectional study was conducted on 33,000 COVID-19 suspected patients. From RT-PCR positive patients, nasopharyngeal swab (NSP) and saliva samples were obtained for evaluation of rapid COVID-19 testing kits (RDT). 100/33000 (0.3%) of specimens were RT-PCR positive for SARS-CoV-2. Among RT-PCR positive, 62% were males, 34% were females, and 4% were children. The NSP-RDT (Lepu Medical China) analysis revealed 53% reactivity among males, 58% reactivity among females, and 25% reactivity among children. However saliva based RDT (Lepu Medical China) analysis showed 21% reactivity among males and 23% among females, and no reactivity in children. False negative results were significantly more pronounced in saliva based RDT as compared to NSP-RDT. The sensitivity of these NSP-RDT and saliva based RDT were 52% and 21% respectively. The RDTs evaluated in this study showed limited sensitivities in comparison to gold standard RT-PCR, indicating that there is a dire need in Pakistan for development of suitable testing to improve accurate COVID-19 diagnosis in line with national demands.

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Performance assessment of four HIV self-test devices in South Africa: A cross-sectional study

South African Journal of Science ◽

10.17159/sajs.2021/7738 ◽

2021 ◽

Vol 117 (1/2) ◽

Author(s):

Mohammed Majam ◽

Alex E. Fischer ◽

Naleni Rhagnath ◽

Vanessa Msolomba ◽

Willem D.F. Venter ◽

...

Keyword(s):

Sensitivity And Specificity ◽

Cross Sectional Study ◽

World Health ◽

Fourth Generation ◽

Sectional Study ◽

Cross Sectional ◽

Health Device ◽

And Performance ◽

Health Organization ◽

Index Sensitivity

HIV self-testing (HIVST) has been introduced to supplement existing HIV testing methods to increase the number of people knowing their HIV status. Various HIVST kits have been developed; however, in many countries, their entry into the market is contingent on either being listed as World Health Organization (WHO) prequalified diagnostics/products or being approved by that country’s health device regulator or both. In this cross-sectional study, we evaluated the usability, sensitivity and specificity of HIVSTs, as directed by the WHO prequalification literature. A boxed, sealed HIVST kit was provided to enrolled lay users with no further instruction, who then performed the test under observation. For each HIVST, a product-specific semi-structured checklist was used to calculate a usability index, while the sensitivity and specificity of each HIVST were calculated by comparing the HIVST results to the ‘gold standard’ – fourth-generation ELISA laboratory blood test. The average usability index was 97.1% (95.9–97.8%), while the average sensitivity and specificity were 98.2% (96.8–99.3%) and 99.8% (99.4–100.0%), respectively. We also diagnosed 507 (15.1%) HIV-positive participants from the general population. The average usability index, sensitivity and specificity were all comparatively high, and these results corroborate previous usability and performance studies from other regions. These results suggest HIVSTs are appropriate for the South African market and can assist manufacturers with readying their devices for final WHO prequalification evaluation.

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