Structural Insights of the SARS-CoV-2 Nucleocapsid Protein: Implications for the Inner-workings of Rapid Antigen Tests

The nucleocapsid (N) protein is an abundant component of SARS-CoV-2 and a key analyte for lateral-flow rapid antigen tests. Here, we present new structural insights for the SARS-CoV-2 N protein using cryo-electron microscopy (EM) and molecular modeling tools. Epitope mapping based on structural data supported host-immune interactions in the C-terminal portion of the protein, while other regions revealed protein-protein interaction sites. Complementary modeling results suggested that N protein structures from known variants of concern (VOC) are nearly 100% conserved at specific antibody-binding sites. Collectively, these results suggest that rapid tests that target the nucleocapsid C-terminal domain should have similar accuracy across all VOCs. In addition, our combined structural modeling workflow may guide the design of immune therapies to counter viral processes as we plan for future variants and pandemics.

Seroprevalence of anti-SARS-CoV-2 antibodies in high-risk occupational and low-risk groups in southwestern Iran

Background: Monitoring the spread of SARS-CoV-2 has been considered by the World Health Organization (WHO). We examined the prevalence of anti-SARS-CoV-2 immunoglobulin antibodies in southwestern Iran in spring 2020. The circulation of SARS-CoV-2 is high in the general population, especially among health care workers (HCWs) who are in close contact with patients. Objectives: The aim of this study was to determine the prevalence of anti-SARS-CoV-2 antigen in high-risk occupational and low-risk groups to investigate risk factors for serum positivity in Shiraz, southwestern Iran. Methods: A cross-sectional survey was performed on 366 participants (204 from high-risk and 162 from low-risk subjects). IgG and IgM antibodies were detected using Pishtaz Teb COVID-19 ELISA Kits to evaluate SARS-CoV-2-antigen in serum samples. After enzyme-linked immunosorbent assay (ELISA), serum prevalence, as well as IgG/IgM positive factors, was determined using logistic regression. Results: From July to September 2020 (a few months after reporting the first case of COVID-19 cases in Iran), out of 366 survived people, 72 (40.9%) were IgG positive, and 50 (27.5%) were IgM positive. The frequency of positive serology for IgG and IgM antibodies in individuals aged < 30 years was higher in the low-risk group than in the high-risk group. Multivariate logistic regression showed that headache (OR 0.312 [95% CI: 0.136 - 0.717]) and cough (OR 0.427 [95% CI: 0.182 - 1.004]) factors were associated with IgG or IgM positive serology. Conclusions: Between July and September 2020, the prevalence of anti-SARS-CoV-2 antigen was high in Shiraz. The prevalence of SARS-CoV-2 IgG/IgM antibodies in the high-risk group and their family as low risk was shown to increase viral infection due to close contact with COVID 19 patients than in the general population. Several factors were found to be related to the prevalence of anti-SARS-CoV-2 antigen that needs to be considered by policymakers to determine what to do about the SARS-CoV-2 pandemic.

Design and implementation of a digital site-less clinical study of serial rapid antigen testing to identify asymptomatic SARS-CoV-2 infection.

Background: Rapid antigen detection tests (Ag-RDT) for SARS-CoV-2 with emergency use authorization generally include a condition of authorization to evaluate the test's performance in asymptomatic individuals when used serially. We aim to describe a novel study design that was used to generate regulatory-quality data to evaluate the serial use of Ag-RDT in detecting SARS-CoV-2 virus among asymptomatic individuals. Methods: This prospective cohort study used a siteless, digital approach to assess longitudinal performance of Ag-RDT. Individuals over 2 years old from across the USA with no reported COVID-19 symptoms in the 14 days prior to study enrollment were eligible to enroll in this study. Participants throughout the mainland USA were enrolled through a digital platform between October 18, 2021 and February 15, 2022. Participants were asked to test using Ag-RDT and molecular comparators every 48 hours for 15 days. Enrollment demographics, geographic distribution, and SARS-CoV-2 infection rates are reported. Key Results: A total of 7361 participants enrolled in the study, and 492 participants tested positive for SARS-CoV-2, including 154 who were asymptomatic and tested negative to start the study. This exceeded the initial enrollment goals of 60 positive participants. We enrolled participants from 44 US states, and geographic distribution of participants shifted in accordance with the changing COVID-19 prevalence nationwide. Conclusions: The digital site-less approach employed in the "Test Us At Home" study enabled rapid, efficient, and rigorous evaluation of rapid diagnostics for COVID-19 and can be adapted across research disciplines to optimize study enrollment and accessibility.

Diagnosis of pediatric COVID-19

Accurate diagnosis of SARS-CoV-2 infection is critical for the management of individuals with suspected COVID-19 diseases, as well as instituting public health measures. The experience gained over twoyears of the pandemic has led to a better appreciation of the scope and utility of various diagnostic modalities. Laboratory tests to diagnose COVID-19 in human beings can be broadly categorized as direct and indirect tests. In children (as in adults), RT-PCR is the current gold standard for diagnosis. RT-PCR detects footprints of the virus and its variants. However, its sensitivity is still less than desired. Rapid antigen tests are less accurate than RT-PCR, but the quick availability of results helps in outbreak control. Antibody tests can be used for retrospective diagnosis of infection, but currently available tests do not correlate with protection conferred by vaccination. The initial hype around chest computed tomography scans for diagnosis has now settled, and it is no longer considered a primary diagnostic modality. There are nonspecific changes in many hematological and biochemical parameters, which are more useful for monitoring disease progression than diagnosis. © 2023 Elsevier Inc. All rights reserved.

Community pharmacy experience in SARS-CoV-2 antigen detection testing programs

BACKGROUND: SARS-CoV-2 infection was an unprecedented pandemic with unprecedented global health and socio-economic impact. More than 13 million cases had been confirmed in Spain by August 2022, and diagnostic testing to detect cases of infection in the country has helped to partially mitigate the spread of the virus. In 2021, the first self-testing antigen tests were marketed for dispensing in community pharmacies, and over-the-counter dispensing was allowed from July of that year. The network of community pharmacies played a key role, not only in the informed dispensing of these tests, but also in actively participating in the performance, supervision and reporting of results to the health authorities, and even in the issuing of digital certificates. A compilation has been made of all the available data on the subject, with a deadline of 13 February 2022, which is considered to be the end of the sixth wave of the epidemic in Spain. The results of the action taken by community pharmacies in twelve Autonomous Communities, which somehow participated in these initiatives by carrying out or supervising a total of 1,043,800 tests, from which 109,570 positive cases (10.5% of the total) were detected and reported to the National Health System, are presented in this article. Although the results are provisional, because many of the programmes are still ongoing, they are a clear demonstration of the potential that community pharmacies can play in Public Health work.

Rapid cassette test results in anti-SARS-CoV-2 antibody screening verification by electrochemiluminescence immunoassay method

Objective: Since the resumption of face-to-face education in October 2020, which was suspended due to the COVID-19 pandemic, coincides with the period when SARS-CoV-2 infection rates in young adults are on the rise. This study focuses on the 2019 corona virus outbreak in young adults, the largest link in the chain of transmission, which can be defined as silent contagious agents. It is aimed to provide epidemiological data by detecting virus disease (COVID-19) seropositivity with two different serological methods, and to evaluate the symptom-test performance relationship of asymptomatic/mild symptom/symptomatic cases. Methods: A cross-sectional study was conducted with students studying at Cappadocia University health programs between December 2020 and February 2021 and who will attend practice courses face-to-face. Participants were surveyed about their COVID-19 symptoms and disease histories based on SARS-CoV-2 exposure. For SARS-CoV-2 antibody detection, blood samples were taken from the participants and investigated with a single lateral flow immunoAssay (LFIA, Novatech, Turkey) cassette test. The samples with positive test result were then SARS-CoV-2 Anti-N IgM+IgG;SARS-CoV-2 Anti-S IgM+IgG;SARS-CoV-2 Anti-RBD IgG;It was re-evaluated using the electrochemiluminescence immunoassay (ECLIA) method with the anti-SARS-CoV-2 kit (Roche, Germany). Results: Of the 239 samples participating in the study, 50 (20.9%) samples that were positive for SARS-CoV2 IgM/ IgG according to the LFIA method were then studied again with the ECLIA method. According to the ECLIA result, 72% (36/50) of individuals against both nucleocapsid (N) and spike (S) antigens, and 70% (35) against RBD antigen were seropositive. Based on the ECLIA test results, 239 samples were studied and 50 samples were found to be IgM/IgG positive, with a sensitivity of 64% and a specificity of 93%. Contingence history was reported in 46% (n=23) of patients who were seropositive by both methods, while 30% (n=15) showed a COVID-19 clinic. Fifty four percent (n=27) of the participants reported that they did not have a PCR (polymerase chain reaction) test, but antibody response was observed in all of them. Only 28% (n=14) of seropositive patients reported positive PCR results, and 4% of them stated that they had a chronic disease. It will be important to continue to observe the serological status of young people, particularly in the context of new COVID-19 variants and in the low interest in mass vaccination campaigns targeting young people. Conclusion: It is thought that the performance of ECLIA with rapid casette test does not have a good degree of agreement and confirmation with different immunoassay tests would be more useful for epidemiological surveillance. Especially the new COVID-19 in the context of the variants and targeting youth due to the lack of interest in vaccination champaigns continue to monitor the serological status of young people it will be important.

Current regulatory landscape for viral point-of-care testing in the United States.

Historically, the diagnosis of viral infections has been accomplished using a combination of laboratory-based methods, including culture, serology, antigen-based tests, and molecular (e.g., real-time PCR) assays. Although these methods provide an accurate way to detect viral pathogens, testing in a centralized laboratory may delay results, which could impact patient diagnosis and management. Point-of-care tests, including antigen- and molecular-based assays, have been developed to assist with the timely diagnosis of several viral infections, such as influenza, respiratory syncytial virus, and COVID-19. Despite the ability of point-of-care tests to provide rapid results (i.e., <30 min), there are issues to consider prior to their routine use, including test performance and specific regulatory requirements. This review will provide a summary of the regulatory landscape of point-of-care tests for viral infections in the United States, and address important considerations such as site certification, training and inspection readiness.

Evaluation of four laboratory-based high-throughput SARS-CoV-2 automated antigen tests compared to RT-PCR on nasal and oropharyngeal samples.

BACKGROUND: The demand for RT-PCR testing has been unprecedented during the SARS-CoV-2 pandemic. Fully automated antigen tests (AAT) are less cumbersome than RT-PCR, but data on performance compared to RT-PCR are scarce. METHODS: The study consists of two parts. A retrospective analytical part, comparing the performance of four different AAT on 100 negative and 204 RT-PCR positive deep oropharyngeal samples divided into four groups based on RT-PCR cycle of quantification levels. In the prospective clinical part, 206 individuals positive for and 199 individuals negative for SARS-CoV-2 were sampled from either the anterior nasal cavity (mid-turbinate) or by deep oropharyngeal swabs or both. The performance of AATs was compared to RT-PCR. RESULTS: The overall analytical sensitivity of the AATs differed significantly from 42% (95% CI 35-49) to 60% (95% CI 53-67) with 100% analytical specificity. Clinical sensitivity of the AATs differed significantly from 26% (95% CI 20-32) to 88% (95% CI 84-93) with significant higher sensitivity for mid-turbinate nasal swabs compared to deep oropharyngeal swabs. Clinical specificity varied from 97% to 100%. CONCLUSION: All AATs were highly specific for detection of SARS-CoV-2. Three of the four AATs were significantly more sensitive than the fourth AAT both in terms of analytical and clinical sensitivity. Anatomical test location significantly influenced the clinical sensitivity of AATs.

Performance of the PanbioTM COVID-19 Ag rapid test in a health care setting in Ouagadougou, Burkina Faso

This study aimed to evaluate the performance of the PanbioTM Covid-19 Ag Rapid Test (Abbott) in a medical center in Ouagadougou. The PanbioTM COVID-19 Ag test was evaluated from January 26 to March 31, 2021 in symptomatic and asymptomatic patients in the medical Centre of Kossodo. A total of 268 individuals were tested by both SARS-CoV-2 RT-PCR, and antigen RDT. Of these 268 individuals, 52 were positive and 216 were negative for COVID-19 RT-PCR. The performance parameters of the test and its Kappa agreement with the RT-PCR were calculated according to the presence or absence of symptoms in the patients on one hand, and according to the time onset of symptoms on the other hand. The sensitivity of the PanbioTM COVID-19 Ag Rapid Test ranged from 29.63% (95% CI: 13.75 to 50.18) among COVID-19 asymptomatic patients, to 87.5% (95% CI: 52.91 to97.76) among symptomatic patients with symptom onset time of 1-5 days. Similarly, the PanbioTM COVID-19 Ag Rapid Test specificity was 97.3% (95% CI: 90.58 to 99.67) and 96.4% (95% CI: 91.81 to 98.82) in symptomatic and asymptomatic RT PCR negative patients. The PanbioTM COVID-19 Ag Rapid Test shows good performance in detecting COVID-19 cases in patients with a symptom onset time of less than seven (7) days. This performance is even better when the symptom onset is reduced to five (5) days. The results show that the antigen RDT is not suitable for COVID-19 detection among asymptomatic patients.

New insights on malaria

Malaria is long known as a deadly vector borne infection, caused by five parasite species of the coccidian genus Plasmodia that are present in as many as 85 countries. Despite significant progresses have been achieved to control the infection by early diagnosis and artemisinin combination treatment, insecticide-treated nets and indoor residual spraying, malaria still represents a major public health issue in many endemic low-income countries. New diagnostic tools of higher sensitivity and specificity are now available for use in endemic countries to better guide diagnosis and treatment. In particular, highly sensitive rapid antigenic tests are now available and the loop-mediated isothermal amplification is a very promising and highly sensitive diagnostic tool. After 2015, decreasing morbidity and mortality trends have been stagnating because of limited funding, emergence of parasite and vector resistance to drugs and insecticides respectively and, recently, by the disrupting effect of COVID-19 pandemic. The incomplete knowledge of the complex immunity of malaria infection has slowed the development of an effective vaccine. However, in 2021, the RTS-S vaccine, however of suboptimal protective efficacy, has been made available for routine use in children above 5 months of age. Population movements has increased the chance of observing imported malaria in non-endemic areas, where malaria competent vectors may still exist.

Clinical profile of scrub typhus patients during COVID pandemic: a sub-Himalayan single center experience

Introduction: Scrub typhus is tropical zoonotic disease, commonly presented with multi organ dysfunction and high mortality rate in untreated patients. This study was done to identify clinical features commonly associated with scrub typhus during COVID pandemics, parameters associated with severe scrub typhus and mortality. Methods: This retrospective study was done in a tertiary care hospital with a total of 52 admitted scrub typhus positive patients in October 2020 to February 2022. Diagnosis was established by scrub IgM ELISA or Rapid antigen test. The clinical and laboratory data, duration of hospital stay and outcomes were collected. Common clinical and laboratory findings were of descriptive analysis. Factors associated with mortality were analysed using Chi-square test. Results: Fever was the most common presenting symptoms on admission (94.2%) followed by respiratory abnormalities (38.46%). Acute kidney injury was the most common organ failure on admission (67.3%), followed by acute liver injury (46.2%) and thrombocytopenia (32.7%). MODS was seen in 46.15%. Of the total, 30.8% were admitted in ICU. Mortality was seen in 7.7% of all patients. On Chi-square analysis, altered mental status and coagulopathy were associated with significant mortality with p value <0.05. Conclusion: Scrub typhus can manifest with potentially life-threatening complications such as acute kidney injury, acute liver injury, thrombocytopenia and MODS. The overall case-fatality rate was 7.7%, and presence of altered mental status and coagulopathy were associated with higher mortality. As per literature, COVID has changed few clinical profiles of scrub typhus compared to same center experience before.

Evaluation of a COVID-19 rapid antigen testing program among student athletes in a public high school district.

PURPOSE: The purpose of this study is to evaluate a COVID-19 rapid antigen testing program among high school athletes through testing data and qualitative analysis from key stakeholders. METHODS: Testing data was obtained by the partnering school district. Testing staff, coaches, and parents participated in a focus group using a semi-structured focus group guide. Transcripts were analyzed using a grounded theory approach to produce the themes of the study. RESULTS: Rapid antigen tests quickly identified a COVID-19-positive student athlete, which allowed for quick isolation and zero transmission to teammates. Focus groups with parents, testing staff, and coaches indicated the testing program improved perceived safety and demonstrated the ability for school staff to implement a widespread COVID-19 screening program with minimal training. CONCLUSIONS: As schools continue to respond to various waves of COVID-19 infections, targeted testing for high-risk activities in school settings such as sports programs may help prevent school outbreaks during times of high community transmission rates. This evaluation adds to a body of literature that will aid schools and policy makers in their decision on how to best keep student athletes and school communities safe for future waves of COVID-19 infection and other pandemics.

Evaluation of the Diagnostic Performance of a SARS-CoV-2 and Influenza A/B Combo Rapid Antigen Test in Respiratory Samples.

This study aimed to evaluate the performance characteristics of a rapid antigen test developed to detect SARS-CoV-2 (COVID-19), influenza A virus (IAV), and influenza B virus (IBV) (flu) compared with those of the real-time reverse transcription-polymerase chain reaction (rRT-PCR) method. One hundred SARS-CoV-2, one hundred IAV, and twenty-four IBV patients whose diagnoses were confirmed by clinical and laboratory methods were included in the patient group. Seventy-six patients, who were negative for all respiratory tract viruses, were included as the control group. The Panbio™ COVID-19/Flu A&B Rapid Panel test kit was used in the assays. The sensitivity values of the kit were 97.5%, 97.9%, and 33.33% for SARS-CoV-2, IAV, and IBV, respectively, in samples with a viral load below 20 Ct values. The sensitivity values of the kit were 16.7%, 36.5%, and 11.11% for SARS-CoV-2, IAV, and IBV, respectively, in samples with a viral load above 20 Ct. The kit's specificity was 100%. In conclusion, this kit demonstrated high sensitivity to SARS-CoV-2 and IAV for viral loads below 20 Ct values, but the sensitivity values were not compatible with PCR positivity for lower viral loads over 20 Ct values. Rapid antigen tests may be preferred as a routine screening tool in communal environments, especially in symptomatic individuals, when diagnosing SARS-CoV-2, IAV, and IBV with high caution.

Diagnostic accuracy of SARS-CoV-2 rapid antigen self-tests in asymptomatic individuals in the omicron period: a cross-sectional study.

OBJECTIVES: To assess the performances of three commonly used antigen rapid diagnostic tests used as self-tests in asymptomatic individuals in the Omicron period. METHODS: We performed a cross-sectional diagnostic test accuracy study in the Omicron period in three public health service COVID-19 test sites in the Netherlands, including 3600 asymptomatic individuals aged ≥ 16 years presenting for SARS-CoV-2 testing for any reason except confirmatory testing after a positive self-test. Participants were sampled for RT-PCR (reference test) and received one self-test (either Acon Flowflex [Flowflex], MP Biomedicals (MPBio), or Siemens-Healthineers CLINITEST [CLINITEST]) to perform unsupervised at home. Diagnostic accuracies of each self-test were calculated. RESULTS: Overall sensitivities were 27.5% (95% CI, 21.3-34.3%) for Flowflex, 20.9% (13.9-29.4%) for MPBio, and 25.6% (19.1-33.1%) for CLINITEST. After applying a viral load cut-off (≥5.2 log10 SARS-CoV-2 E-gene copies/mL), sensitivities increased to 48.3% (37.6-59.2%), 37.8% (22.5-55.2%), and 40.0% (29.5-51.2%), respectively. Specificities were >99% for all tests in most analyses. DISCUSSION: The sensitivities of three commonly used SARS-CoV-2 antigen rapid diagnostic tests when used as self-tests in asymptomatic individuals in the Omicron period were very low. Antigen rapid diagnostic test self-testing in asymptomatic individuals may only detect a minority of infections at that point in time. Repeated self-testing in case of a negative self-test is advocated to improve the diagnostic yield, and individuals should be advised to re-test when symptoms develop.

Rapid antigen testing in COVID-19 management for school-aged children: an observational study in Cheshire and Merseyside, UK.

BACKGROUND: Twice weekly lateral flow tests (LFTs) for secondary school children was UK Government policy from 8 March 2021. We evaluate use of LFTs (both supervised at test centres, and home test kits) in school-aged children in Cheshire and Merseyside. METHODS: We report (i) number of LFT positives (ii) proportion of LFT positive with confirmatory reverse transcription polymerase chain reaction (PCR) test within 2 days, and (iii) agreement between LFT-positive and confirmatory PCR, and dependence of (i-iii) on COVID-19 prevalence. FINDINGS: 1 248 468 LFTs were taken by 211 255 12-18 years old, and 163 914 by 52 116 5-11 years old between 6 November 2020 and 31 July 2021. Five thousand three hundred and fourteen (2.5%) 12-18 years old and 1996 (3.8%) 5-11 years old returned LFT positives, with 3829 (72.1%) and 1535 (76.9%) confirmatory PCRs, and 3357 (87.7%) and 1383 (90.1%) confirmatory PCR-positives, respectively.Monthly proportions of LFT positive with PCR negative varied between 4.7% and 35.3% in 12-18 years old (corresponding proportion of all tests positive: 9.7% and 0.3%).Deprivation and non-White ethnicity were associated with reduced uptake of confirmatory PCR. INTERPRETATION: Substantial inequalities in confirmatory testing need more attention to avoid further disadvantage through education loss. When prevalence is low additional measures, including confirmatory testing, are needed. Local Directors of Public Health taking more control over schools testing may be needed. FUNDING: DHSC, MRC, NIHR, EPSRC.

Can we trust in Sars-CoV-2 rapid antigen testing? Preliminary results from a paediatric cohort in the emergency department.

BACKGROUND: Rapid identification of Covid-19 in the paediatric emergency department is critical; Antigen tests are fast but poorly investigated in children. AIMS: To investigate Sars-CoV-2 antigen rapid test in children. METHODS: We compare the performance of LumiraDx with molecular tests in a paediatric emergency department. RESULTS: A retrospective cohort of 191 patients with AT and PCR tests performed in the same episode was analysed; 16% resulted positive for Sars-CoV-2. Using the PCR test as the gold standard, we calculated antigen testing overall sensitivity of 94.1%, specificity of 91.9%, and NPV of 99.4%. Only one false-negative test was found. CONCLUSIONS: AT may be helpful in the initial screening of patients at PED.

Evaluation of Four Strategies for SARS-CoV-2 Detection: Characteristics and Prospects.

The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed an enormous burden on the global public health system and has had disastrous socioeconomic consequences. Currently, single sampling tests, 20-in-1 pooling tests, nucleic acid point-of-care tests (POCTs), and rapid antigen tests are implemented in different scenarios to detect SARS-CoV-2, but a comprehensive evaluation of them is scarce and remains to be explored. In this study, 3 SARS-CoV-2 inactivated cell culture supernatants were used to evaluate the analytical performance of these strategies. Additionally, 5 recombinant SARS-CoV-2 nucleocapsid (N) proteins were also used for rapid antigen tests. For the wild-type (WT), Delta, and Omicron strains, the lowest inactivated virus concentrations to achieve 100% detection rates of single sampling tests ranged between 1.28 × 102 to 1.02 × 103, 1.28 × 102 to 4.10 × 103, and 1.28 × 102 to 2.05 × 103 copies/mL. The 20-in-1 pooling tests ranged between 1.30 × 102 to 1.04 × 103, 5.19 × 102 to 2.07 × 103, and 2.59 × 102 to 1.04 × 103 copies/mL. The nucleic acid POCTs were all 1.42 × 103 copies/mL. The rapid antigen tests ranged between 2.84 × 105 to 7.14 × 106, 8.68 × 104 to 7.14 × 106, and 1.12 × 105 to 3.57 × 106 copies/mL. For the WT, Delta AY.2, Delta AY.1/AY.3, Omicron BA.1, and Omicron BA.2 recombinant N proteins, the lowest concentrations to achieve 100% detection rates of rapid antigen tests ranged between 3.47 to 142.86, 1.74 to 142.86, 3.47 to 142.86, 3.47 to 142.86, and 5.68-142.86 ng/mL, respectively. This study provided helpful insights into the scientific deployment of tests and recommended the full-scale consideration of the testing purpose, resource availability, cost performance, result rapidity, and accuracy to facilitate a profound pathway toward the long-term surveillance of coronavirus disease 2019 (COVID-19). IMPORTANCE In the study, we reported an evaluation of 4 detection strategies implemented in different scenarios for SARS-CoV-2 detection: single sampling tests, 20-in-1 pooling tests, nucleic acid point-of-care tests, and rapid antigen tests. 3 SARS-CoV-2-inactivated SARS-CoV-2 cell culture supernatants and 5 recombinant SARS-CoV-2 nucleocapsid proteins were used for evaluation. In this analysis, we found that for the WT, Delta, and Omicron supernatants, the lowest concentrations to achieve 100% detection rates of single sampling tests ranged between 1.28 × 102 to 1.02 × 103, 1.28 × 102 to 4.10 × 103, and 1.28 × 102 to 2.05 × 103 copies/mL. The 20-in-1 pooling tests ranged between 1.30 × 102 to 1.04 × 103, 5.19 × 102 to 2.07 × 103, and 2.59 × 102 to 1.04 × 103 copies/mL. The nucleic acid POCTs were all 1.42 × 103 copies/mL. The rapid antigen tests ranged between 2.84 × 105 to 7.14 × 106, 8.68 × 104 to 7.14 × 106, and 1.12 × 105 to 3.57 × 106 copies/mL. For the WT, Delta AY.2, Delta AY.1/AY.3, Omicron BA.1, and Omicron BA.2 recombinant N proteins, the lowest concentrations to achieve 100% detection rates of rapid antigen tests ranged between 3.47 to 142.86, 1.74 to 142.86, 3.47 to 142.86, 3.47 to 142.86, and 5.68 to 142.86 ng/mL, respectively.

COI vs Ct: comparing automated antigen tests cut-off index (COI) to PCR cycle threshold (Ct)

Introduction: The objective of this study was to compare the numeric cut-off index (COI) of automated antigen tests with the cycle-threshold (Ct) value. Materials and methods: COI values of all samples processed with the Elecsys® SARS-CoV-2 Antigen (Roche, Switzerland) from January to February 2022 were retrieved and the positive were compared to RdRP Cts of Allplex Variants I (Seegene, Korea). COI between 0.6 and 1 were considered indeterminate and overproved by RT-PCR. Results: From 13,937 samples 7944(57%) were positive and 189(1.35%) indeterminate. There was a strong correlation between Cts and COI values at the positive samples, but that was not the case for indeterminates. Conclusions: COI values of the positive samples (COI >1) are comparable to Ct values and may therefore be used as proxy viral loads, however this is not the case for indeterminate samples. © 2022 Elsevier Inc.

Analytical sensitivity of six lateral flow antigen test kits for variant strains of SARS-CoV-2.

INTRODUCTION: The lateral flow antigen test is a useful tool for rapid diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The analytical sensitivity of six lateral flow antigen test kits was compared. METHODS: The limit of detection (LoD) and time to positive results were evaluated for six lateral flow tests including ImmunoArrow®, ESPLINE® SARS-CoV-2, QuickNavi™ COVID19 Ag, ImmunoAce® SARS-CoV-2, Panbio™ COVID-19 Ag Rapid Test Device, and SARS-CoV-2 Rapid Antigen Test using the heat-inactivated virus. The LoD of ImmunoArrow® against the Omicron variants was compared with that against the wild-type using recombinant proteins. RESULTS: ImmunoArrow® and ESPLINE® showed the lowest LoD. The time to positive results of all tests except for ESPLINE® was within 200 s in the evaluation at high dose of antigens (2.5 × 105 TCID50/mL) and 500 s in the evaluation at low dose of antigens (2.5 × 104 TCID50/mL). The LoD of ImmunoArrow® against the Omicron variants was the same concentration against the wild-type antigen. CONCLUSIONS: ImmunoArrow® detected SARS-CoV-2 antigens including the Omicron variants with good sensitivity among the six lateral flow antigen tests. These finding support that it can support the rapid diagnosis of COVID-19 with the good sensitivity.

Comparative Evaluation of Different SARS-CoV-2 Rapid Point-of-Care Antigen Tests with SARS-CoV-2 PCR for Diagnosis of COVID-19

BACKGROUND: Detection of positive 2019-nCoV nucleic acids by real-time reverse transcriptase-polymerase chain reaction (rRT-PCR)-based assays performed on the upper and lower respiratory samples remains the gold standard for the diagnosis of COVID-19. However, antigen-detecting rapid diagnostic tests can offer a faster (15-30 min) and less expensive way to diagnose active severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection than nucleic acid amplification tests. AIM: Hence, the present study aimed to compare and evaluate the results of different SARS-CoV-2 rapid point-of-care antigen tests with SARS-CoV-2 PCR as a reference method. METHOD(S): Sixty-five nasopharyngeal swab specimens were collected from attendees of the Reference Laboratory of Egyptian university hospitals. The samples were placed in viral transport medium for RNA extraction. The remaining part of the suspension was stored at -70degreeC until use for COVID-19 antigen testing. All samples were processed for the COVID-19 Ag rapid test and RT-PCR simultaneously. RESULT(S): RT-PCR assay revealed 46 (70.8%) positive samples and 19 (29.2%) negative samples for COVID-19. All eight rapid antigen assays indicated specificity and positive predictive value of 100% each. As for the other parameters, the sensitivity, negative predictive value (NPV), and accuracy ranged from 43.8 to 93.8, 33.3 to 90, and 60 to 96, respectively. Biozak exhibited the best performance with the highest sensitivities 91.3, 81.8, and 93.75, respectively, while Viro and Standard Q were the worst among the tested kits with sensitivity, NPV, and accuracy of 50, 33.3, and 60 each. Regarding the relationship between the viral load of COVID-19 detected by RT-PCR and the results of the eight rapid antigen tests (RAT), we deduced that the higher the viral load, the better the sensitivity observed. CONCLUSION(S): The RATs used, in our study, exhibited heterogeneous diagnostic performance, where some of them showed very promising results in comparison to the reference RT-PCR assay. Copyright © 2022 Ghada Ismail, Dalia H. Abdelhamid, Rania Abdel Halim, Marwa Salah Mostafa, Hossam Abdelghaffar, Noha Alaa Eldin Fahim, Ahmed Elshafei, Menna Asker, Nashwa Naguib Omar.