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

SARS-CoV-2 clearance in term of Cycle Threshold (Ct) during first two waves of COVID-19 in Pakistan: a phenomenon of delayed viral clearance post-corticosteroid treatment

SARS-CoV-2 is recently emerged virus, which caused millions of deaths, all over the world. To tackle COVID-19 pandemic, there is an utmost need for in-depth analysis of viral replication. We aimed to examine viral load in SARS-CoV-2 patients during first two waves of COVID-19 in Pakistan. 225,615 suspected subjects from 75 different regions of Pakistan were selected in the study. SARS-CoV-2 RNAs were detected via real time PCR. During first wave (period of June-July, 2020) of COVID-19 the prevalence of SARS-CoV-2 was 20.38%. However, during second wave (period of November-December, 2020) of COVID-19, the rate of prevalence was 9.41%. During first wave of COVID-19 96.31% of participants remained PCR positive for 14 to 21 days, 3.39% of subjects showed positive results for 22 to 35 days, while delayed Ct values were observed among 0.26% of participants for 36 to 49 days. However, during second wave of COVID-19 89.31% of the subjects exhibited symptoms and showed real-time PCR positive results for 14 to 21 days, 9.42% showed positive results for 22 to 35 days, while significantly delayed Ct value results were observed among 1.026% of participants for 36 to 63 days (3.95 times higher than first wave). In contrast to first wave of COVID-19, the factors that were different in second wave were neither viral (different strains) nor host (same population). But treatment factors changed significantly. As during second wave besides azithromycin, corticosteroid dexamethasone consumption was increased consequently causing delayed Ct value negativity. This suggests that corticosteroid treatment might be linked with delayed Ct value or viral clearance. This study is crucial for re-considering effective therapeutic options against COVID-19.

Analytical assessment of clinical sensitivity and specificities of pharmaceutical rapid SARS-CoV-2 detection nasopharyngeal swab testing kits in Pakistan

Despite of the global unity against COVID-19 pandemic, the threat of SARS-CoV-2 variants on the lives of human being is still not over. SARS-CoV-2 pandemic has urged the need of rapid viral detection at earliest. To cope with gradually expanding scenario of SARS-CoV-2, accurate diagnosis is extremely crucial factor which should be noticed by international health organizations. Limited research followed by sporadic marketing of SARS-CoV-2 rapid pharmaceutical detection kits raises critical questions against quality assurance and quality control measures. Herein we aimed to interrogate effectivity and specificity analysis of SARS-CoV-2 pharmaceutical rapid detection kits (nasopharyngeal swab based) using conventional gold standard triple target real-time polymerase chain reaction (USFDA approved). A cross-sectional study was conducted over 1500 suspected SARS-CoV-2 patients. 100 real time-PCR confirmed patients were evaluated for pharmaceutical RDT kits based upon nasopharyngeal swab based kits. The SARS-CoV-2 nasopharyngeal swab based rapid diagnostic kit (NSP RDTs) analysis showed 78% reactivity. Among real time PCR confirmed negative subjects, 49.3% represented false positivity. The positive predictive analysis revealed 67.82%, while negative predictive values were 64.40%. The NSP RDTs showed limited sensitivities and specificities as compared to gold standard real time PCR. Valid and authentic detection of SARS-CoV-2 is deemed necessary for accurate COVID-19 surveillance across the globe. Current study highlights the potential consequences of inadequate detection of SARS-CoV-2 and emerging novel mutants, compromising vaccine preventable diseases. Current study emphasizes need to wake higher authorities including strategic organizations for designing adequate measures to prevent future SARS-CoV-2 epidemics.

Performance of different rapid antigen testing strategies for SARS-CoV-2: A living rapid review

BACKGROUND

Rapid antigen detection tests (RADTs) for SARS-CoV-2 testing offer several advantages over molecular tests, but there is little evidence supporting an ideal testing algorithm. We aimed to examine the diagnostic test accuracy (DTA) and the effectiveness of different RADT SARS-CoV-2 testing strategies.

METHODS

Following PRISMA DTA guidance, we carried out a living rapid review and meta-analysis. Searches were conducted in Ovid MEDLINE® ALL, Embase and Cochrane CENTRAL electronic databases until February 2022. Results were visualized using forest plots and included in random-effects univariate meta-analyses, where eligible.

RESULTS

After screening 8010 records, 18 studies were included. Only one study provided data on incidence outcomes. Seventeen studies were DTA reports with direct comparisons of RADT strategies, using RT-PCR as the reference standard. Testing settings varied, corresponding to original SARS-CoV-2 or early variants. Strategies included differences in serial testing, the individual collecting swabs and swab sample locations. Overall, specificity remained high (>98%) across strategies. Although results were heterogeneous, the sensitivity for healthcare worker-collected samples was greater than for self-collected samples. Nasal samples had comparable sensitivity when compared to paired RADTs with nasopharyngeal samples, but sensitivity was much lower for saliva samples. The limited evidence for serial testing suggested higher sensitivity if RADTs were administered every 3 days compared to less frequent testing.

CONCLUSIONS

Additional high-quality research is needed to confirm our findings; all studies were judged to be at risk of bias, with significant heterogeneity in sensitivity estimates. Evaluations of testing algorithms in real-world settings are recommended, especially for transmission and incidence outcomes.

Clinical Evaluation of Commercial HARDSON COVID-19 Antigen Rapid Test Kit for Routine COVID-19 Diagnosis

Objective

This study aimed to evaluate the sensitivity, specificity, and accuracy of the commercial HARDSON COVID-19 Antigen Rapid Test Kit for diagnosing COVID-19 among the Iranian population by compared with the results of commercial RT-PCR.

Materials and Methods

Two nasopharyngeal swabs were collected from each patient. One swab was tested with HARDSON COVID-19 Antigen Rapid Test Kit, and the second swab was placed in 3 mL of a virus-transmitted inactivated media for RT-PCR testing. Then, the results of both tests were compared to investigate the diagnostic accuracy of the rapid antigen test.

Results

A total of 275 suspected COVID-19 patients' samples were collected to investigate the diagnostic accuracy of HARDSON COVID-19 Antigen Rapid Test Kit. In this study, 162 positive and 113 negative samples were evaluated. As a result, the sensitivity, specificity, and accuracy of HARDSON COVID-19 Antigen Rapid Test Kit were 90%, 100%, and 94%, respectively.

Conclusion

The diagnostic kit analyzed in this study indicated excellent specificity and a relatively good overall sensitivity for the diagnosis of COVID-19 when compared with the RT-PCR detection kit. Based on the result of this study, COVID-19 Antigen Rapid Test Kit indicated a good sensitivity (96%) in low cycle threshold (Ct) value, and it would be recommended to be integrated into routine diagnostic laboratories and used as an at-home rapid antigen test.

A Metasynthesis and Meta-analysis of the Impact and Diagnostic Safety of COVID-19 Symptom Agnostic Rapid Testing in Low- and Middle-Income Countries: Protocol for a Systematic Review

BACKGROUND

Amid all public health measures to contain COVID-19, the most challenging has been how to break the transmission chain. This has been even more challenging in low- and middle-income countries (LMICs). A public health emergency warrants a public health perspective, which comes down to prevention. Rapid mass testing has been advocated throughout the pandemic as a way to promptly deal with asymptomatic infections, but its usefulness in LMICs is yet to be fully understood.

OBJECTIVE

The study objectives of this paper are to (1) investigate the impact of the different rapid mass testing options for SARS-CoV-2 that have been delivered at point of care in LMICs and (2) evaluate the diagnostic safety (accuracy) of rapid mass testing for SARS-CoV-2 in LMICs.

METHODS

This review will systematically search records in PubMed, EBSCOhost, Cochrane library, Global Index Medicus COVID-19 Register, and Scopus. Records will be managed using Mendeley reference manager and SWIFT-Review. Risk of bias for randomized controlled trials will be assessed using the RoB 2 assessment tool, while nonrandomized interventions will be assessed using the tool developed by the Evidence Project. A narrative approach will be used to synthesize data under the first objective, and either a meta-analysis or synthesis without meta-analysis for the second objective. Tables, figures, and textual descriptions will be used to present findings. The overall body of evidence for the first objective will be assessed using the Grading of Recommendations Assessment, Development, and Evaluation-Confidence in the Evidence from Reviews of Qualitative research (GRADE-CERQual) approach, and for the second objective using GRADE.

RESULTS

The screening of records has been finalized. We hope to finalize the synthesis by the end of February 2023 and to prepare the manuscript for publication by April 2023. The study will be reported in accordance with standard guidelines for the reporting of systematic reviews. Review results will be disseminated through conferences and their peer-reviewed publication in a relevant journal.

CONCLUSIONS

This review highlights the role of a preventive approach in infection control using rapid mass testing. It also flags the overriding need to involve users and providers in the evaluation of such tests in the settings for which they are intended. This will be the first review to the best of our knowledge to generate both qualitative and quantitative evidence regarding rapid mass testing specific to LMICs.

TRIAL REGISTRATION

PROSPERO CRD42022283776; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=283776.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

PRR1-10.2196/41132.

Direct Nasal Swab for Rapid Test and Saliva as an Alternative Biological Sample for RT-PCR in COVID-19 Diagnosis

Accurate and early diagnoses are prerequisites for prompt treatment. For coronavirus disease 2019 (COVID-19), it is even more crucial. Currently, choice of methods include rapid diagnostic tests and reverse transcription polymerase chain reaction (RT-PCR) using samples mostly of respiratory origin and sometimes saliva. We evaluated two rapid diagnostic tests with three specimen types using viral transport medium (VTM) containing naso-oropharyngeal (NOP) swabs, direct nasal and direct nasopharyngeal (NP) samples from 428 prospective patients. We also performed RT-PCR for 428 NOP VTM and 316 saliva samples to compare results. The sensitivity of the SD Biosensor Standard Q COVID-19 antigen (Ag) test kit drastically raised from an average of 65.55% (NOP VTM) to 85.25% (direct nasal samples), while RT-PCR was the gold standard. For the CareStart kit, the sensitivity was almost similar for direct NP swabs; the average was 84.57%. The specificities were ≥95% for both SD Biosensor Standard Q and CareStart COVID-19 Ag tests in all platforms. The kits were also able to detect patients with different variants as well. Alternatively, RT-PCR results from saliva and NOP VTM samples showed high sensitivities of 96.45% and 95.48% with respect to each other as standard. The overall results demonstrated high performance of the rapid tests, indicating the suitability for regular surveillance at clinical facilities when using direct nasal or direct NP samples rather than NOP VTM. Additionally, the analysis also signifies not showed that RT-PCR of saliva can be used as an choice of method to RT-PCR of NOP VTM, providing an easier, non-invasive sample collection method. IMPORTANCE There are several methods for the diagnosis of coronavirus disease 2019 (COVID-19), and the choice of methods depends mostly on the resources and level of sensitivity required by the user and health care providers. Still, reverse transcription polymerase chain reaction (RT-PCR) has been chosen as the best method using direct naso-oropharyngeal swabs. There are also other methods of fast detection, such as rapid diagnostic tests (RDTs), which offer result within 15 to 20 min and have become quite popular for self-testing and in the clinical setting. The major drawback of the currently used RT-PCR method is compliance, as it may cause irritation, and patients often refuse to test in such a way. RDTs, although inexpensive, suffer from low sensitivity due to technical issues. In this article, we propose saliva as a noninvasive source for RT-PCR samples and evaluate various specimen types at different times after infection for the best possible output from COVID-19 rapid tests.

Reinforced Sputnik-V Induced Spike Protein Antibody Levels in Pakistan: An Edge of Sputnik-V Over Sinopharm and SinoVac as Commercially Available COVID-19 Vaccines

Background: Despite several challenges, the SARS-CoV-2 pandemic is still not over. Rapid mass-scale immunization is critical to prevent further COVID-19-associated deaths. Objectives: Herein, we aimed to evaluate the rapid ramp-up effects of spike antibodies in response to Sputnik V, Sinopharm, and SinoVac first dose administration in the general public of Pakistan. Methods: A cross-sectional study was conducted on 2000 participants to examine Sputnik V, Sinopharm, and SinoVac first dose effects 21 days post-administration. From 1200 real-time PCR negative subjects, the samples were subjected to SARS-CoV-2 spike antibody levels using electro-chemiluminescence immunoassay (ECLIA) (Elecsys, # 09289267190 Roche, USA). Results: SARS-CoV-2 spike protein positivity was detected highest at 87% among participants receiving SputnikV with SARS-CoV-2 spike protein antibodies > 1.5 AU/mL compared to 47.6% and 25% in individuals receiving Sinopharm and SinoVac, respectively. Also, 36.04% of the Sputnik-administered individuals depicted antibody levels > 250 AU/mL. Of the participants, 55% had a previous history of COVID-19. Also, 14.86%, 4.76%, and 0% of the SputnikV, Sinopharm, and SinoVac administered subjects showed antibodies > 100 AU/mL, respectively, while > 25 AU/mL antibodies were found in 10.70% of SputnikV, 19.04% of Sinopharm and 10.71% of SinoVac administered individuals. Moreover, > 1.5 - 2.5 AU/mL antibodies levels were found in 25.10%, 23.80%, and 14.28% of participants with SputnikV, Sinopharm, and SinoVac administered vaccines, respectively. The antibody titers of < 1.5 AU/mL were detected among 13.30%, 52.38%, and 46.42% of subjects administered with SputnikV, Sinopharm, and SinoVac vaccines, respectively. Conclusions: Even before administrating the second booster dose of SputnikV, a significantly higher number of patients depicted rapid ramp-up of SARS-CoV-2 specific spike antibodies, which can significantly contribute to rapid mass-immunization. Despite all challenges, persistent antibody plateau monitoring is critical to attaining humoral immunity against SARS-CoV-2 infections.

SARS-CoV-2 induced hepatic injuries and liver complications

Background

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which is resilient, highly pathogenic, and rapidly transmissible. COVID-19 patients have been reported to have underlying chronic liver abnormalities linked to hepatic dysfunction.

Discussion

Viral RNAs are detectable in fecal samples by RT-PCR even after negative respiratory samples, which suggests that SARS-CoV-2 can affect the gastrointestinal tract and the liver. The case fatality rates are higher among the elderly and those with underlying comorbidities such as hypertension, diabetes, liver abnormality, and heart disease. There is insufficient research on signaling pathways. Identification of molecular mechanisms involved in SARS-CoV-2-induced damages to hepatocytes is challenging. Herein, we demonstrated the multifactorial effects of SARS-CoV-2 on liver injury such as psychological stress, immunopathogenesis, systemic inflammation, ischemia and hypoxia, drug toxicity, antibody-dependent enhancement (ADE) of infection, and several others which can significantly damage the liver.

Conclusion

During the COVID-19 pandemic, it is necessary for clinicians across the globe to pay attention to SARS-CoV-2-mediated liver injury to manage the rising burden of hepatocellular carcinoma. To face the challenges during the resumption of clinical services for patients with pre-existing liver abnormalities and HCC, the impact of SARS-CoV-2 on hepatocytes should be investigated both in vitro and in vivo.

Rapid, point-of-care antigen tests for diagnosis of SARS-CoV-2 infection

BACKGROUND

Accurate rapid diagnostic tests for SARS-CoV-2 infection would be a useful tool to help manage the COVID-19 pandemic. Testing strategies that use rapid antigen tests to detect current infection have the potential to increase access to testing, speed detection of infection, and inform clinical and public health management decisions to reduce transmission. This is the second update of this review, which was first published in 2020.

OBJECTIVES

To assess the diagnostic accuracy of rapid, point-of-care antigen tests for diagnosis of SARS-CoV-2 infection. We consider accuracy separately in symptomatic and asymptomatic population groups. Sources of heterogeneity investigated included setting and indication for testing, assay format, sample site, viral load, age, timing of test, and study design.

SEARCH METHODS

We searched the COVID-19 Open Access Project living evidence database from the University of Bern (which includes daily updates from PubMed and Embase and preprints from medRxiv and bioRxiv) on 08 March 2021. We included independent evaluations from national reference laboratories, FIND and the Diagnostics Global Health website. We did not apply language restrictions.

SELECTION CRITERIA

We included studies of people with either suspected SARS-CoV-2 infection, known SARS-CoV-2 infection or known absence of infection, or those who were being screened for infection. We included test accuracy studies of any design that evaluated commercially produced, rapid antigen tests. We included evaluations of single applications of a test (one test result reported per person) and evaluations of serial testing (repeated antigen testing over time). Reference standards for presence or absence of infection were any laboratory-based molecular test (primarily reverse transcription polymerase chain reaction (RT-PCR)) or pre-pandemic respiratory sample.

DATA COLLECTION AND ANALYSIS

We used standard screening procedures with three people. Two people independently carried out quality assessment (using the QUADAS-2 tool) and extracted study results. Other study characteristics were extracted by one review author and checked by a second. We present sensitivity and specificity with 95% confidence intervals (CIs) for each test, and pooled data using the bivariate model. We investigated heterogeneity by including indicator variables in the random-effects logistic regression models. We tabulated results by test manufacturer and compliance with manufacturer instructions for use and according to symptom status.

MAIN RESULTS

We included 155 study cohorts (described in 166 study reports, with 24 as preprints). The main results relate to 152 evaluations of single test applications including 100,462 unique samples (16,822 with confirmed SARS-CoV-2). Studies were mainly conducted in Europe (101/152, 66%), and evaluated 49 different commercial antigen assays. Only 23 studies compared two or more brands of test. Risk of bias was high because of participant selection (40, 26%); interpretation of the index test (6, 4%); weaknesses in the reference standard for absence of infection (119, 78%); and participant flow and timing 41 (27%). Characteristics of participants (45, 30%) and index test delivery (47, 31%) differed from the way in which and in whom the test was intended to be used. Nearly all studies (91%) used a single RT-PCR result to define presence or absence of infection. The 152 studies of single test applications reported 228 evaluations of antigen tests. Estimates of sensitivity varied considerably between studies, with consistently high specificities. Average sensitivity was higher in symptomatic (73.0%, 95% CI 69.3% to 76.4%; 109 evaluations; 50,574 samples, 11,662 cases) compared to asymptomatic participants (54.7%, 95% CI 47.7% to 61.6%; 50 evaluations; 40,956 samples, 2641 cases). Average sensitivity was higher in the first week after symptom onset (80.9%, 95% CI 76.9% to 84.4%; 30 evaluations, 2408 cases) than in the second week of symptoms (53.8%, 95% CI 48.0% to 59.6%; 40 evaluations, 1119 cases). For those who were asymptomatic at the time of testing, sensitivity was higher when an epidemiological exposure to SARS-CoV-2 was suspected (64.3%, 95% CI 54.6% to 73.0%; 16 evaluations; 7677 samples, 703 cases) compared to where COVID-19 testing was reported to be widely available to anyone on presentation for testing (49.6%, 95% CI 42.1% to 57.1%; 26 evaluations; 31,904 samples, 1758 cases). Average specificity was similarly high for symptomatic (99.1%) or asymptomatic (99.7%) participants. We observed a steady decline in summary sensitivities as measures of sample viral load decreased. Sensitivity varied between brands. When tests were used according to manufacturer instructions, average sensitivities by brand ranged from 34.3% to 91.3% in symptomatic participants (20 assays with eligible data) and from 28.6% to 77.8% for asymptomatic participants (12 assays). For symptomatic participants, summary sensitivities for seven assays were 80% or more (meeting acceptable criteria set by the World Health Organization (WHO)). The WHO acceptable performance criterion of 97% specificity was met by 17 of 20 assays when tests were used according to manufacturer instructions, 12 of which demonstrated specificities above 99%. For asymptomatic participants the sensitivities of only two assays approached but did not meet WHO acceptable performance standards in one study each; specificities for asymptomatic participants were in a similar range to those observed for symptomatic people. At 5% prevalence using summary data in symptomatic people during the first week after symptom onset, the positive predictive value (PPV) of 89% means that 1 in 10 positive results will be a false positive, and around 1 in 5 cases will be missed. At 0.5% prevalence using summary data for asymptomatic people, where testing was widely available and where epidemiological exposure to COVID-19 was suspected, resulting PPVs would be 38% to 52%, meaning that between 2 in 5 and 1 in 2 positive results will be false positives, and between 1 in 2 and 1 in 3 cases will be missed.

AUTHORS' CONCLUSIONS

Antigen tests vary in sensitivity. In people with signs and symptoms of COVID-19, sensitivities are highest in the first week of illness when viral loads are higher. Assays that meet appropriate performance standards, such as those set by WHO, could replace laboratory-based RT-PCR when immediate decisions about patient care must be made, or where RT-PCR cannot be delivered in a timely manner. However, they are more suitable for use as triage to RT-PCR testing. The variable sensitivity of antigen tests means that people who test negative may still be infected. Many commercially available rapid antigen tests have not been evaluated in independent validation studies. Evidence for testing in asymptomatic cohorts has increased, however sensitivity is lower and there is a paucity of evidence for testing in different settings. Questions remain about the use of antigen test-based repeat testing strategies. Further research is needed to evaluate the effectiveness of screening programmes at reducing transmission of infection, whether mass screening or targeted approaches including schools, healthcare setting and traveller screening.

Recent Advances in Clustered Regularly Interspaced Short Palindromic Repeats-Based Biosensors for Point-of-Care Pathogen Detection

Infectious pathogens are pressing concerns due to their heavy toll on global health and socioeconomic infrastructure. Rapid, sensitive, and specific pathogen detection methods are needed more than ever to control disease spreading. The fast evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics (CRISPR-Dx) has opened a new horizon in the field of molecular diagnostics. This review highlights recent efforts in configuring CRISPR technology as an efficient diagnostic tool for pathogen detection. It starts with a brief introduction of different CRISPR-Cas effectors and their working principles for disease diagnosis. It then focuses on the evolution of laboratory-based CRISPR technology toward a potential point-of-care test, including the development of new signaling mechanisms, elimination of preamplification and sample pretreatment steps, and miniaturization of CRISPR reactions on digital assay chips and lateral flow devices. In addition, promising examples of CRISPR-Dx for pathogen detection in various real samples, such as blood, saliva, nasal swab, plant, and food samples, are highlighted. Finally, the challenges and perspectives of future development of CRISPR-Dx for infectious disease monitoring are discussed.

Saliva as a diagnostic specimen for SARS-CoV-2 detection: a scoping review

Objectives

This scoping review aims to summarize the diagnostic value of saliva assessed from current studies that (1) compare its performance in reverse transcriptase‐polymerase chain reaction testing to nasopharyngeal swabs, (2) evaluate its performance in rapid and point‐of‐care COVID‐19 diagnostic tests, and (3) explore its use as a specimen for detecting anti‐SARS‐CoV‐2 antibodies.

Materials and Methods

A systematic search was performed on the following databases: Medline and Embase (Ovid), World Health Organization, Centers for Disease Control and Prevention, and Global Health (Ovid) from January 2019 to September 2021. Of the 657 publications identified from the searches, n = 146 articles were included in the final scoping review.

Results

Our findings showcase that salivary samples exceed nasopharyngeal swabs in detecting SARS‐CoV‐2 using reverse transcriptase‐polymerase chain reaction testing in several studies. A select number of rapid antigen and point‐of‐care tests from the literature were also identified capable of high detection rates using saliva. Moreover, anti‐SARS‐CoV‐2 antibodies have been shown to be detectable in saliva through biochemical assays.

Conclusion

We highlight the potential of saliva as an all‐rounded specimen in detecting SARS‐CoV‐2. However, future large‐scale clinical studies will be needed to support its widespread use as a non‐invasive clinical specimen for COVID‐19 testing.

Assessment of the Quality of COVID-19 Antigen Rapid Diagnostic Testing in the Testing Sites of Ekiti State, Nigeria: A Quality Improvement Cross-Sectional Study

Background Antigen rapid diagnostic testing (Ag-RDT) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important testing technique used for the control and containment of COVID-19. This study aims to assess the quality of COVID-19 Ag-RDT in the testing sites in Ekiti State, Nigeria. Methods A validated World Health Organization (WHO) questionnaire was used to collect data from 138 testing sites located in 138 health facilities in Ekiti State. The assessment was based on the activities carried out in the last three months before the study. Results A total of 138 testing sites participated in the study out of which 121 (87.7%) were primary health facility testing sites. The mean number of samples tested in these sites was 26 samples, and 97 (70.3%) testing sites were tested below this. The average quality performance of the secondary/tertiary health facility testing sites (64.46 ± 10.47) was significantly higher than that of the primary health facility testing sites (53.13 ± 13.54) (p = 0.002). Additionally, the average quality performance of testing sites that tested 26 samples or more (61.61 ± 9.84) was significantly higher than that of the testing sites that tested below this mean cut-off (51.53 ± 13.97) (p < 0.001). Conclusion The majority of the testing sites that tested below the mean 26 samples, secondary/tertiary health facility testing sites, and sites that tested above the mean cut-off had higher average quality performance scores. Therefore, encouraging clinicians to refer for more testing of suspected cases and supportive supervision of COVID-19 Ag-RDT, especially in primary health facilities, is recommended.

SARS-CoV-2-Associated CRP, DD, FER, HBA1c, IL6, LDH, PBNP, and PCT Biomarkers and High-Resolution Computed Tomography During the First Three Waves of COVID-19 in Pakistan (2019-2021)

Collapse

Field evaluation of seven SARS-COV-2 antigen assays

There is a global demand for rapid diagnostic tests (RDTs) for Coronavirus disease 2019 (COVID-19), and the interest in their clinical compliance is growing. In this study, we evaluated the clinical compliance of seven different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen RDTs. Nasopharyngeal/oropharyngeal swab specimens from COVID-19-confirmed cases and reverse-transcription PCR (RT-PCR) screening were used to evaluate the performance of seven RDTs. Using the RT-PCR and RDT results, we predicted the cycle threshold (Ct) of each target gene (E, RdRP, and N genes) which 50% (Ct₅₀) and 95% (Ct₉₅) detection rates were achieved in the RDTs. A total of 482 specimens were enrolled in our study: 316 specimens from COVID-19-confirmed cases and 166 RT-PCR-negative specimens. The median values of Ct₅₀ and Ct₉₅ for the seven RDTs were in the ranges of ranged 24.3-30.9 and 19.3-22.6 for E, 25.5-31.5 and 20.9-24.0 for RdRP, and 26.8-32.3 and 22.7-25.7 for N, respectively. The RDTs showed acceptable compliance only for specimens with high viral burdens (Ct < 20). However, the false-negative rate increased by more than 50% for most of the RDTs in low-viral burden specimens (Ct> 30). These results suggest that RDTs should not be used without molecular assays for COVID-19 screening for asymptomatic patients because of their high false-negative rates.

Clinical Evaluation of a New Antigen-Based COVID-19 Rapid Diagnostic Test from Symptomatic Patients

Accurate diagnosis at the right moment is the prerequisite for treatment of any disease. Failure to correctly diagnose a disease can result in highly detrimental effects, unmistakably a crucial factor during the COVID-19 pandemic. RT-PCR is the gold standard for COVID-19 detection while there are other test procedures available, such as LAMP, X-Ray, and ELISA. However, these tests are expensive, require sophisticated equipment and a highly trained workforce, and multiple hours or even days are often required to obtain the test results. A rapid and cheap detection system can thus render a solution to the screening system on a larger scale and be added as an aid to the current detection processes. Recently, some rapid antigen-based COVID-19 tests devices have been developed and commercialized. In this study, we evaluated the clinical performance of a new rapid detection device (OnSite^® COVID-19 Ag Rapid Test by CTK Biotech Inc., Poway, CA, USA) on COVID-19 symptomatic patients (n = 380). The overall sensitivity and specificity were 91.0% (95% CI: 84.8–95.3%) and 99.2% (95% CI: 97.1–99.9), against gold standard RT-PCR. The kit was capable of detecting patients even after 06 days of onset of symptoms and the sensitivity can be maximized to 98% in samples with an average RT-PCR Ct ≤ 26.48, demonstrating a high potential of the kit for clinical diagnosis of symptomatic patients in healthcare facilities.

Clinical evaluation of SARS-CoV-2 antigen-based rapid diagnostic test kit for detection of COVID-19 cases in Bangladesh

The rapid and early detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is key to control the current Coronavirus disease 2019 (COVID-19) pandemic. The present study was conducted to clinically evaluate a rapid diagnostic test (RDT) kit, Standard Q COVID-19 Ag Test (SD Biosensor®, Republic of Korea), with reference to the standard real-time RT-PCR for detection of COVID-19 cases in Bangladesh. Nasopharyngeal swabs were taken from 900 COVID-19 suspected patients. Among them, 34.11% (n = 307) were diagnosed as COVID-19 cases by RT-PCR assay, of which 85% (n = 261) were also detectable using the RDT. The overall sensitivity and specificity of the RDT compared to RT-PCR were 85.02% and 100%, respectively, regardless of age, sex, and type of SARS-CoV-2 variants. Most of the RT-PCR positive cases (94%) were found within the first five days of disease onset, and the sensitivity of RDT was 85.91% for the same samples. The positive predictive value (PPV) of the RDT was 100%, and the negative predictive value (NPV) was 92.8%. The Cohen's kappa value of 0.882 indicated excellent agreement between the RDT and RT-PCR assays. The findings of this study showed the potential use of SARS-CoV-2 antigen-based RDT to expedite the diagnostic process and onward COVID-19 management in Bangladesh.

Evaluation of Epidemic Prevention Abilities for Severe Acute Respiratory Syndrome Coronavirus-2 and Middle East Respiratory Syndrome Coronavirus in South Korea

: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) preferentially infects respiratory tract cells, but it has organotropism. Middle East respiratory syndrome coronavirus (MERS-CoV) is significantly distinct from common cold and SARS coronavirus. In past few years, the SARS-CoV-2 and MERS-CoV caused several deaths in South Korea. The aim of current study was to assess SARS-CoV-2 and MERS-CoV awareness and epidemic prevention ability in South Koreans.According to our results, out of 1500 participants, 98.8% and 64.3% were aware of SARS-CoV-2 and MERS-CoV, respectively. Moreover, 97% of the participants used masks for prevention of airborne diseases, while 65.3% of the participants reused the same mask for several days. In addition, 50% of the participants were not satisfied with the government support. Future viral epidemics can be prevented by disseminating advanced knowledge and awareness among general public.

Current diagnostic approaches to detect two important betacoronaviruses: Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are two common betacoronaviruses, which are still causing transmission among the human population worldwide. The major difference between the two coronaviruses is that MERS-CoV is now causing sporadic transmission worldwide, whereas SARS-CoV-2 is causing a pandemic outbreak globally. Currently, different guidelines and reports have highlighted several diagnostic methods and approaches which could be used to screen and confirm MERS-CoV and SARS-CoV-2 infections. These methods include clinical evaluation, laboratory diagnosis (nucleic acid-based test, protein-based test, or viral culture), and radiological diagnosis. With the presence of these different diagnostic approaches, it could cause a dilemma to the clinicians and diagnostic laboratories in selecting the best diagnostic strategies to confirm MERS-CoV and SARS-CoV-2 infections. Therefore, this review aims to provide an up-to-date comparison of the advantages and limitations of different diagnostic approaches in detecting MERS-CoV and SARS-CoV-2 infections. This review could provide insights for clinicians and scientists in detecting MERS-CoV and SARS-CoV-2 infections to help combat the transmission of these coronaviruses.

Comparison of SARS-CoV-2 antigen electrochemiluminescence immunoassay to RT-PCR assay for laboratory diagnosis of COVID-19 in Peshawar

OBJECTIVES

Antigen based rapid diagnostic tests possesses a potential to be utilized along with Gold standard methods to detect Covid-19 infection to cope with the demand of testing. The aim of this study was to determine diagnostic accuracy of electrochemiluminescence based automated antigen detection immunoassay comparing with molecular based test RT-PCR (Covid-19).

METHODS

It was a cross-sectional study conducted in RMI Peshawar, from 1st April 2021 till 30th April 2021. The study comprised 170 individuals who were suspected of having Covid-19. Nasopharyngeal samples taken from suspected individuals were analyzed by RT-PCR and automated antigen test (Elecsys SARS-CoV-2 Antigen) simultaneously. The correlation of SARS-CoV-2 antigen with PCR positive and negative cases was analyzed for specificity, sensitivity respectively.

RESULTS

The ECLIA based Elecsys antigen test (Roche) revealed overall sensitivity 72%, specificity 95% and accuracy of 94.9%. Sensitivity of antigen test progressively declined from 94.3% in Ct <25 to 70.8% in Ct 26-29 and then to 47.2% in Ct 30-35.

CONCLUSIONS

Based on the findings of our study we conclude that automated antigen testing (Elecsys SARS-CoV-2 Antigen) cannot replace molecular based testing like RT PCR. Elecsys SARS-CoV-2 Ag test should be used complementary to RT-PCR in testing algorithms. Frequent testing strategy should be adopted while using automated antigen testing to overcome its limitation in individuals with low viral loads.

IFCC interim guidelines on rapid point-of-care antigen testing for SARS-CoV-2 detection in asymptomatic and symptomatic individuals

With an almost unremittent progression of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections all around the world, there is a compelling need to introduce rapid, reliable, and high-throughput testing to allow appropriate clinical management and/or timely isolation of infected individuals. Although nucleic acid amplification testing (NAAT) remains the gold standard for detecting and theoretically quantifying SARS-CoV-2 mRNA in various specimen types, antigen assays may be considered a suitable alternative, under specific circumstances. Rapid antigen tests are meant to detect viral antigen proteins in biological specimens (e.g. nasal, nasopharyngeal, saliva), to indicate current SARS-CoV-2 infection. The available assay methodology includes rapid chromatographic immunoassays, used at the point-of-care, which carries some advantages and drawbacks compared to more conventional, instrumentation-based, laboratory immunoassays. Therefore, this document by the International Federation for Clinical Chemistry and Laboratory Medicine (IFCC) Taskforce on COVID-19 aims to summarize available data on the performance of currently available SARS-CoV-2 antigen rapid detection tests (Ag-RDTs), providing interim guidance on clinical indications and target populations, assay selection, and evaluation, test interpretation and limitations, as well as on pre-analytical considerations. This document is hence mainly aimed to assist laboratory and regulated health professionals in selecting, validating, and implementing regulatory approved Ag-RDTs.

Accuracy of novel antigen rapid diagnostics for SARS-CoV-2: A living systematic review and meta-analysis

BACKGROUND

SARS-CoV-2 antigen rapid diagnostic tests (Ag-RDTs) are increasingly being integrated in testing strategies around the world. Studies of the Ag-RDTs have shown variable performance. In this systematic review and meta-analysis, we assessed the clinical accuracy (sensitivity and specificity) of commercially available Ag-RDTs.

METHODS AND FINDINGS

We registered the review on PROSPERO (registration number: CRD42020225140). We systematically searched multiple databases (PubMed, Web of Science Core Collection, medRvix, bioRvix, and FIND) for publications evaluating the accuracy of Ag-RDTs for SARS-CoV-2 up until 30 April 2021. Descriptive analyses of all studies were performed, and when more than 4 studies were available, a random-effects meta-analysis was used to estimate pooled sensitivity and specificity in comparison to reverse transcription polymerase chain reaction (RT-PCR) testing. We assessed heterogeneity by subgroup analyses, and rated study quality and risk of bias using the QUADAS-2 assessment tool. From a total of 14,254 articles, we included 133 analytical and clinical studies resulting in 214 clinical accuracy datasets with 112,323 samples. Across all meta-analyzed samples, the pooled Ag-RDT sensitivity and specificity were 71.2% (95% CI 68.2% to 74.0%) and 98.9% (95% CI 98.6% to 99.1%), respectively. Sensitivity increased to 76.3% (95% CI 73.1% to 79.2%) if analysis was restricted to studies that followed the Ag-RDT manufacturers' instructions. LumiraDx showed the highest sensitivity, with 88.2% (95% CI 59.0% to 97.5%). Of instrument-free Ag-RDTs, Standard Q nasal performed best, with 80.2% sensitivity (95% CI 70.3% to 87.4%). Across all Ag-RDTs, sensitivity was markedly better on samples with lower RT-PCR cycle threshold (Ct) values, i.e., <20 (96.5%, 95% CI 92.6% to 98.4%) and <25 (95.8%, 95% CI 92.3% to 97.8%), in comparison to those with Ct ≥ 25 (50.7%, 95% CI 35.6% to 65.8%) and ≥30 (20.9%, 95% CI 12.5% to 32.8%). Testing in the first week from symptom onset resulted in substantially higher sensitivity (83.8%, 95% CI 76.3% to 89.2%) compared to testing after 1 week (61.5%, 95% CI 52.2% to 70.0%). The best Ag-RDT sensitivity was found with anterior nasal sampling (75.5%, 95% CI 70.4% to 79.9%), in comparison to other sample types (e.g., nasopharyngeal, 71.6%, 95% CI 68.1% to 74.9%), although CIs were overlapping. Concerns of bias were raised across all datasets, and financial support from the manufacturer was reported in 24.1% of datasets. Our analysis was limited by the included studies' heterogeneity in design and reporting.

CONCLUSIONS

In this study we found that Ag-RDTs detect the vast majority of SARS-CoV-2-infected persons within the first week of symptom onset and those with high viral load. Thus, they can have high utility for diagnostic purposes in the early phase of disease, making them a valuable tool to fight the spread of SARS-CoV-2. Standardization in conduct and reporting of clinical accuracy studies would improve comparability and use of data.

Comparison of SARS-CoV-2 Detection by Rapid Antigen and by Three Commercial RT-qPCR Tests: A Study from Martin University Hospital in Slovakia

The global pandemic of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is having a tremendous impact on the global economy, health care systems and the lives of almost all people in the world. The Central European country of Slovakia reached one of the highest daily mortality rates per 100,000 inhabitants in the first 3 months of 2021, despite implementing strong prophylactic measures, lockdowns and repeated nationwide antigen testing. The present study reports a comparison of the performance of the Standard Q COVID-19 antigen test (SD Biosensor) with three commercial RT-qPCR kits (vDetect COVID-19-MultiplexDX, gb SARS-CoV-2 Multiplex-GENERI BIOTECH Ltd. and Genvinset COVID-19 [E]-BDR Diagnostics) in the detection of infected individuals among employees of the Martin University Hospital in Slovakia. Health care providers, such as doctors and nurses, are classified as “critical infrastructure”, and there is no doubt about the huge impact that incorrect results could have on patients. Out of 1231 samples, 14 were evaluated as positive for SARS-CoV-2 antigen presence, and all of them were confirmed by RT-qPCR kit 1 and kit 2. As another 26 samples had a signal in the E gene, these 40 samples were re-isolated and subsequently re-analysed using the three kits, which detected the virus in 22, 23 and 12 cases, respectively. The results point to a divergence not only between antigen and RT-qPCR tests, but also within the “gold standard” RT-qPCR testing. Performance analysis of the diagnostic antigen test showed the positive predictive value (PPV) to be 100% and negative predictive value (NPV) to be 98.10%, indicating that 1.90% of individuals with a negative result were, in fact, positive. If these data are extrapolated to the national level, where the mean daily number of antigen tests was 250,000 in April 2021, it points to over 4700 people per day being misinterpreted and posing a risk of virus shedding. While mean Ct values of the samples that were both antigen and RT-qPCR positive were about 20 (kit 1: 20.47 and 20.16 for Sarbeco E and RdRP, kit 2: 19.37 and 19.99 for Sarbeco E and RdRP and kit 3: 17.47 for ORF1b/RdRP), mean Ct values of the samples that were antigen-negative but RT-qPCR-positive were about 30 (kit 1: 30.67 and 30.00 for Sarbeco E and RdRP, kit 2: 29.86 and 31.01 for Sarbeco E and RdRP and kit 3: 27.47 for ORF1b/RdRP). It confirms the advantage of antigen test in detecting the most infectious individuals with a higher viral load. However, the reporting of Ct values is still a matter of ongoing debates and should not be conducted without normalisation to standardised controls of known concentration.

Azithromycin Treatment for SARS-CoV-2-related COVID-19 Pandemic Could Worsen Extensively Drug Resistant (XDR) Typhoid: A Risk of Losing the Last Bullet Against Salmonella enterica Serovar Typhi

Collapse