Analysis of COVID-19 rapid antigen and PCR detection policy

After the outbreak of COVID-19, Taiwan has implemented rigorous border control and taken specific measures such as virus detection, contact tracing, and quarantine since 2020. Its epidemic prevention performance has been quite outstanding. Even in May 2021, when the epidemic situation worsens, the people in Taiwan fully cooperate with the government's control measures so as to successfully alleviate and control the epidemic in less than three months. Among them, the detection policy has played a pivotal role. We analyze and discuss the false positive and false negative problems from rapid antigen and PCR detection in the screening policy as well as the timing of using these two instruments. This paper provides theoretical verification of the appropriateness of screening policy in Taiwan, offering a few feasible suggestions for related policies in other countries or regions at different stages of this and other potential epidemics. (c) 2022 by the authors;licensee Growing Science, Canada.

Presence of SARS-CoV-2 on surfaces and materials in supermarket social areas in Türkiye

The aim of this study was to monitor the presence of SARS-CoV-2, the virus that cause the coronavirus disease 2019 (COVID-19), particularly on certain foods and surfaces that come in contact with food in district supermarkets in Ankara, Türkiye, where the highest number of COVID-19 cases was reported based on data from the Ministry of Health. For this purpose, a total of 172 samples were taken from 5 supermarkets in 4 districts in Ankara. RNA was extracted from the samples and RdRp gene-targeting reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays were used to determine the presence of SARS-CoV-2. The results showed that all the supermarket samples collected during the period when there was a high number of COVID-19 cases in the district did not have SARS-CoV-2 except for one sample that was taken from a supermarket where COVID-19 had been detected among the staff. In this supermarket, COVID-19 RNA was detected with a high number of copies of 5 000, using Real-Time RT-PCR assay in pooled swab samples taken from salt shakers, pepper shakers, red pepper shakers, and vinegar and oil bottles in the social area that the staff used for lunchbreaks and other breaks. This finding shows that it is of great importance for public health agencies to monitor COVID-19 cases in food businesses in regions with a high number of cases and to take samples from these businesses at certain intervals, as a form of "early warning system.”. © 2023, Ankara University. All rights reserved.

RETRACTED ARTICLE: Deep learning system to screen coronavirus disease 2019 pneumonia

The Editor in Chief has retracted this article (1) because the data published here was previously presented by a different set of authors at arXiv pre-print server (2) and a large amount of text, some figures and tables have been re-used without appropriate citation or acknowledgment. The pre-print has been published (3). Author Benson Babu agrees to this retraction. Authors Charmine Butt, Jagpal Gill and David Chun did not respond to any correspondence regarding this retraction. © Springer Science+Business Media, LLC, part of Springer Nature 2020.

Rapid differential diagnosis of SARS-CoV-2, influenza A/B and respiratory syncytial viruses: Validation of a novel RT-PCR assay.

BACKGROUND: Influenza and respiratory syncytial (RSV) viruses are expected to co-circulate with SARS-CoV-2 in the upcoming seasons and clinical differential diagnosis between them is difficult. Laboratory-based RT-PCR is a gold standard diagnostic method for influenza, RSV and SARS-CoV-2. The objective of this study was to estimate the diagnostic performance of a novel point-of-care RT-PCR assay STANDARD M10 Flu/RSV/SARS-CoV-2 (SD Biosensor) in a large number of clinical specimens with diversified (co)-infection patterns and viral loads. METHODS: This was a retrospective study, in which all samples were tested in both STANDARD M10 Flu/RSV/SARS-CoV-2 index and Allplex SARS-CoV-2/Respiratory Panel 1 (Seegene) reference kits. Samples with discordant results were further processed in a third resolver test (Resp-4-Plex, Abbott). RESULTS: A total of 1,019 naso-/oropharyngeal samples (50.3% positive for at least one virus) were processed in both STANDARD M10 Flu/RSV/SARS-CoV-2 and Allplex assays and the overall between-assay agreement was as high as 94.6%. Positive percent agreement of the STANDARD M10 Flu/RSV/SARS-CoV-2 was 100%, 96.6%, 97.3% and 99.4% for influenza A, B, RSV and SARS-CoV-2, respectively. The corresponding negative percent agreement was 99.7%. 100%, 100% and 98.4%, respectively. The expected positive and negative predictive values for all viruses were constantly above 96% in a reasonable range of disease prevalence. CONCLUSIONS: STANDARD M10 Flu/RSV/SARS-CoV-2 is a reliable RT-PCR assay able to detect influenza A, influenza B, RSV and SARS-CoV-2 in one hour or less, fostering a rapid differential diagnosis of common respiratory viruses.

Cost-Benefit of Real-Time Multiplex PCR Testing of SARS-CoV-2 in German Hospitals.

BACKGROUND: The current Omicron COVID-19 pandemic has significant morbidity worldwide. OBJECTIVE: Assess the cost-benefit relation of implementing PCR point-of-care (POCT) COVID-19 testing in the emergency rooms (ERs) of German hospitals and in the case of inpatient admission due to other acute illnesses. METHODS: A deterministic decision-analytic model simulated the incremental costs of using the Savanna® Multiplex RT-PCR test compared to using clinical judgement alone to confirm or exclude COVID-19 in adult patients in German ERs prior to hospitalization or just prior to discharge. Direct and indirect costs were evaluated from the hospital perspective. Nasal or nasopharyngeal swabs of patients suspected to have COVID-19 by clinical judgement, but without POCT, were sent to external labs for RT-PCR testing. RESULTS: In probabilistic sensitivity analysis, assuming a COVID-19 prevalence ranging between 15.6-41.2% and a hospitalization rate between 4.3-64.3%, implementing the Savanna® test saved, on average, €107 as compared to applying the clinical-judgement-only strategy. A revenue loss of €735 can be avoided when SARS-CoV-2 infection in patients coming unplanned to the hospital due to other acute illnesses are excluded immediately by POCT. CONCLUSIONS: Using highly sensitive and specific PCR-POCT in patients suspected of COVID-19 infection at German ERs may significantly reduce hospital expenditures.

Simulation of SARS-CoV-2 epidemic trends in Tokyo considering vaccinations, virus mutations, government policies and PCR tests.

The eighth wave of COVID-19 infection in the Tokyo area has brought daily confirmed cases to a new higher level. This paper aims to explain the previous seven epidemic waves and forecast the eighth epidemic trend of the area using agent-based modeling and extended SEIR denotation. Four key considerations are investigated in this research, that are: 1. Vaccination, 2. Virus mutations, 3. Governmental policies and 4. PCR tests. Our study finds that the confirmed cases in the previous seven epidemic waves were only the tip of the iceberg. Using data prior to December 1 2022, the eighth wave is expected to hover high in December 2022 and January 2023. Our research pioneers in the simulation of antibody declination on an individual level. Comparing the simulated results, we find that the arrival of new epidemic waves are related to the decline in the number of antibody possessors, especially the sixth and the seventh epidemic waves. Our simulation also suggests that faced with low severe and death rates, PCR tests would not make much difference to reduce overall infections. In this case, maintaining PCR tests to a low level helps to reduce both social cost and public anxiety. However, if faced with the opposite case, PCR tests should be adjusted to a higher level to detect early infections. Such level of PCR tests should be compatible with available medical resources.

Evaluation of pooling strategy of SARS-CoV-2 RT-PCR in limited resources setting in Egypt at low prevalence.

Sample pooling testing for SARS-COV-2 can be an effective tool in COVID-19 screening when resources are limited, yet it is important to assess the performance before implementation as pooling has its limitations. Our objective was to assess the efficacy of pooling samples for coronavirus 2019 (COVID-19) compared to an individual analysis by using commercial platforms for nucleic acid testing. A total of 2200 nasopharyngeal swabs for SARS-COV-2 were tested individually and in pools of 4, 8, and 10. The cycle threshold (Ct) values of the positive pooled samples were compared to their corresponding individual positive samples. In pool size 10 samples, an estimated increase of 3-Ct was obtained, which led to false negative results in low viral load positive samples. Pooling SARS COV-2 samples is an effective strategy of screening to increase laboratories' capacity and reduce costs without affecting diagnostic performance. A pool size of 8 is recommended.

Duration of viable virus shedding and polymerase chain reaction positivity of the SARS-CoV-2 Omicron variant in the upper respiratory tract: a systematic review and meta-analysis.

OBJECTIVES: To assess the duration of viable virus shedding and polymerase chain reaction (PCR) positivity of the SARS-CoV-2 Omicron variant in the upper respiratory tract. METHODS: We systematically searched PubMed, Cochrane, and Web of Science for original articles reporting the duration of viable virus shedding and PCR positivity of the SARS-CoV-2 Omicron variant in the upper respiratory tract from November 11, 2021 to December 11, 2022. This meta-analysis was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and was registered with PROSPERO (CRD42022357349). We used the DerSimonian-Laird random-effects meta-analyses to obtain the pooled value and the 95% confidence intervals. RESULTS: We included 29 studies and 230,227 patients. The pooled duration of viable virus shedding of the SARS-CoV-2 Omicron variant in the upper respiratory tract was 5.16 days (95% CI: 4.18-6.14), and the average duration of PCR positivity was 10.82 days (95% CI: 10.23-11.42). The duration of viable virus shedding and PCR positivity of the SARS-CoV-2 Omicron variant in symptomatic patients was slightly higher than that in asymptomatic patients, but the difference was not significant (P >0.05). CONCLUSION: The current study improves our understanding of the status of the literature on the duration of viable virus shedding and PCR positivity of Omicron in the upper respiratory tract. Our findings have implications for pandemic control strategies and infection control measures.

Occurrence of Bovine Coronavirus and other Major Respiratory Viruses in Cattle in Poland.

Introduction: Bovine coronavirus (BCoV) is a causative agent of enteric and respiratory diseases in cattle. Despite its importance for animal health, no data is available on its prevalence in Poland. The aim of the study was to determine the virus' seroprevalence, identify risk factors of BCoV exposure in selected cattle farms and investigate the genetic variability of circulating strains. Material and Methods: Serum and nasal swab samples were collected from 296 individuals from 51 cattle herds. Serum samples were tested with ELISA for the presence of BCoV-, bovine herpesvirus-1 (BoHV-1)- and bovine viral diarrhoea virus (BVDV)-specific antibodies. The presence of those viruses in nasal swabs was tested by real-time PCR assays. Phylogenetic analysis was performed using fragments of the BCoV S gene. Results: Antibodies specific to BCoV were found in 215 (72.6%) animals. Seropositivity for BCoV was more frequent (P>0.05) in calves under 6 months of age, animals with respiratory signs coinfected with BoHV-1 and BVDV and increased with herd size. In the final model, age and herd size were established as risk factors for BCoV-seropositivity. Genetic material of BCoV was found in 31 (10.5%) animals. The probability of BCoV detection was the highest in medium-sized herds. Polish BCoVs showed high genetic homology (98.3-100%) and close relatedness to European strains. Conclusion: Infections with BCoV were more common than infections with BoHV-1 and BVDV. Bovine coronavirus exposure and shedding show age- and herd density-dependence.

Detection Methods for H1N1 Virus.

Influenza A virus H1N1, a respiratory virus transmitted via droplets and responsible for the global pandemic in 2009, belongs to the Orthomyxoviridae family, a single-negative-stranded RNA. It possesses glycoprotein spikes neuraminidase (NA), hemagglutinin (HA), and a matrix protein named M2. The Covid-19 pandemic affected the world population belongs to the respiratory virus category is currently mutating, this can also be observed in the case of H1N1 influenza A virus. Mutations in H1N1 can enhance the viral capacity which can lead to another pandemic. This virus affects children below 5 years, pregnant women, old age people, and immunocompromised individuals due to its high viral capacity. Its early detection is necessary for the patient's recovery time. In this book chapter, we mainly focus on the detection methods for H1N1, from traditional ones to the most advance including biosensors, RT-LAMP, multi-fluorescent PCR.

Cytomegalovirus pneumonitis in infants: The challenge in diagnosis among pediatricians.

Cytomegalovirus (CMV) pneumonitis infections might present mild or severe illnesses and need sophisticated diagnostic tools, so it remains a diagnostic challenge. We reported five infants diagnosed with CMV pneumonitis who were initially and undiagnosed by the pediatrician in secondary private or public health hospitals with no improvement with standard and escalation of antibiotics treatment for bronchopneumonia as the initial diagnoses. As all cases occurred during the COVID-19 pandemic, they proved negative COVID-19 identified by polymerase chain reaction (PCR) SARS-CoV-2. We diagnosed acquired perinatal pneumonitis CMV in all claims based on clinical criteria, imaging studies, CMV serology, and PCR-CMV urinary tests as diagnostic tools. They showed clinical improvement after two weeks of valganciclovir therapy. Other organs' involvement was considered to be evaluated, including brain-evoked response audiometry (BERA) and eye examination. The physician should consider the possibility of CMV pneumonitis, who did not respond to standard and escalation of antibiotics treatment after initial diagnoses of bronchopneumonia.

A multiplex-NGS approach to identifying respiratory RNA viruses during the COVID-19 pandemic.

A methodological approach based on reverse transcription (RT)-multiplex PCR followed by next-generation sequencing (NGS) was implemented to identify multiple respiratory RNA viruses simultaneously. A convenience sampling from respiratory surveillance and SARS-CoV-2 diagnosis in 2020 and 2021 in Montevideo, Uruguay, was analyzed. The results revealed the cocirculation of SARS-CoV-2 with human rhinovirus (hRV) A, B and C, human respiratory syncytial virus (hRSV) B, influenza A virus, and metapneumovirus B1. SARS-CoV-2 coinfections with hRV or hRSV B and influenza A virus coinfections with hRV C were identified in adults and/or children. This methodology combines the benefits of multiplex genomic amplification with the sensitivity and information provided by NGS. An advantage is that additional viral targets can be incorporated, making it a helpful tool to investigate the cocirculation and coinfections of respiratory viruses in pandemic and post-pandemic contexts.

Clinical performance of rapid antigen tests in comparison to RT-PCR for SARS-COV-2 diagnosis in Omicron variant: A systematic review and meta-analysis.

The Omicron variant of concern has a high level of mutations in different genes that has raised awareness about the performance of immunological products such as vaccines and antigen detection kits. In this systematic review and meta-analysis, we investigated whether Omicron had a significant influence on rapid antigen test (RAT) performance in comparison to PCR. We registered this systematic review and meta-analysis in PROSPERO with the registration number CRD42022355510. We searched PubMed, Scopus, Embase, and Web of Science databases systematically to 1 August 2022. After article screening, we assessed the quality of the included studies based on the JBI checklist. Following data extraction, we performed a meta-analysis using R software. We included 18 qualified articles presenting sufficient data about RATs performance in comparison to RT-PCR in Omicron infections. The pooled specificity and sensitivity of RATs were 1.000 (0.997-1.000) and 0.671 (0.595-0.721), respectively. The FDA-approved kits showed a better performance than WHO-approved ones with a sensitivity of 0.728 (0.620-0.815). The use of RATs with nasal swabs showed a higher sensitivity compared with nasopharyngeal swabs. The sensitivity for samples with a CT-value >25 was 0.108 (0.048-0.227). Rapid antigen tests show impaired performance for COVID-19 diagnosis when the Omicron variant is circulating, particularly in samples with low viral loads.

Oral lesions with immunohistochemical evidence of Sars-CoV-2 in swab-negative post-COVID syndrome.

OBJECTIVES: Growing evidence exists about post-COVID condition/syndrome as sequelae of Sars-CoV-2 infection in healed patients, possibly involving the lungs, brain, kidney, cardiovascular and neuromuscular system, as well the persistency of taste dysfunction. Such symptoms develop during or after infection and continue for more than 12 weeks with pathogenesis related to virus persistency but variable by organs or systems. MATERIALS AND METHODS: We recently observed six patients recovered from COVID-19 and with negative RT-PCR testing, showing oral mucosa lesions (mainly ulcers) overlapping those occurring in the acute phase, persisting up to 20 days and thus needing a biopsy with histological investigation and spike protein evaluation by immunohistochemistry. RESULTS: We found epithelial ulceration, inflammatory infiltrate, vessels with increased diameter and flattened endothelium but no thrombi formation; also, we found a weak epithelial SARS-CoV-2 positivity limited to the basal/spinosum layers, progressively decreasing toward the periphery, and the intraepithelial lymphomonocytes, endothelium, and perivascular pericytes too. CONCLUSIONS: Our findings provide evidence that SARS-CoV-2 can persist, as for other organs/systems, also in the oral epithelium/mucosa after the acute phase and can be responsible for lesions, although by a pathogenetic mechanism that should be better defined but certainly referable as the oral mucosa counterpart of post-COVID syndrome.

A Laboratory-Based Study on Multiple Biomarker Testing in the Diagnosis of COVID-19-Associated Pulmonary Aspergillosis (CAPA): Real-Life Data.

(1) Background: Coronavirus disease 2019 (COVID-19)-associated pulmonary aspergillosis (CAPA) raises concerns to contribute to an increased mortality. The incidence of CAPA varies widely within hospitals and countries, partly because of difficulties in obtaining a reliable diagnosis. (2) Methods: Here, we assessed Aspergillus culture-positive and culture-negative respiratory tract specimens via direct fungal microscopy (gold standard) and compared the results with galactomannan enzyme immunoassay (GM-EIA) and Aspergillus PCR. (3) Results: 241 respiratory samples from patients suffering from SARS-CoV-2 pneumonia were evaluated. Results showed both diagnostic tools, Aspergillus PCR and GM-EIA, to be positive or negative displaying a sensitivity of 0.90, a specificity of 0.77, a negative predictive value (NPV) of 0.95, and a positive predictive value (PPV) of 0.58 in Aspergillus sp. culture and microscopic-positive specimens. Non-bronchoalveolar lavage (BAL) samples, obtained within a few days from the same patient, showed a high frequency of intermittent positive or negative GM-EIA or Aspergillus PCR results. Positivity of a single biomarker is insufficient for a proper diagnosis. A broad spectrum of Aspergillus species was detected. (4) Conclusions: Our study highlights the challenges of combined biomarker testing as part of diagnosing CAPA. From the results presented, we highly recommend the additional performance of direct microscopy in respiratory specimens to avoid overestimation of fungal infections by applying biomarkers.

Analysis of COVID-19 Infection Chains in a School Setting: Data From a School-Based rRT-PCR-Gargle Pool Test System.

BACKGROUND: School testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was implemented in some countries to monitor and prevent SARS-CoV-2 transmissions. Here, we analyze infection chains in primary schools and household members of infected students based on systematic real-time reverse-transcriptase polymerase-chain-reaction (rRT-PCR)-gargle pool testing. METHODS: Students and school staff (N = 4300) of all 38 primary schools in the rural county of Cham, Germany, were tested twice per week with a gargle pool rRT-PCR system from April to July of 2021. Infection chains of all 8 positive cases identified by school testing were followed up. RESULTS: In total, 8 positive cases were found by gargle pool PCR testing based on 96,764 school tests. While no transmissions occurred in the school setting, 20 of 27 household members of the 8 cases tested positive. The overall attack rate was 74.1% in families. CONCLUSIONS: No school outbreaks occurred during the study period. All cases but 1 were initially picked up by school testing. No transmission from school to families was observed.

Evaluation of loop-mediated isothermal amplification for detecting COVID-19.

The emergence of SARS-CoV-2 has caused worldwide pandemic of COVID-19. Infection is difficult to diagnose early as some patients remain asymptomatic and may carry this virus to other people. Currently, qRT-PCR is the widely accepted mode for detection. However, the need for sophisticated instrument and trained personnel may hinder its application, especially in remote and facility-lacking areas. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) may serve as a potential approach for detection of SARS-CoV-2 as the resources needed in its application is far less complex than those of qRT-PCR. Herein, we evaluated RT-LAMP based analytical method (COVIDNow), relative to qRT-PCR, in detecting SARS-CoV-2 by using 63 clinical respiratory samples. Based on our finding, COVIDNow exhibited sensitivity and specificity values of 87.5% and 80.6%, respectively. Taken together, RT-LAMP based detection of SARS-CoV-2 by utilizing COVIDNow might serves as a valuable diagnostic tool in the management of global COVID-19 pandemic condition.

Acute Appendicitis in COVID-19-Positive Children: Report of 4 Cases from an Endemic Area in Northeastern Romania.

Acute appendicitis (AA) is one of the most common surgical emergencies in children. Some reports have suggested that the COVID-19 pandemic was responsible for delays in the diagnostic and proper treatment of AA in pediatric patients. The aim of our study was to perform a retrospective study of cases of AA in children with SARS-CoV-2 infection treated in a highly endemic area for COVID-19 in Romania during a 2-year time interval. The SARS-CoV-2 infection had no unfavorable impact on children who presented with AA. Further data analysis should clarify the overall influence of COVID-19 on the management of surgical pediatric patients in such endemic areas.

Evaluation of sample pooling for the detection of SARS-CoV-2 in a resource-limited setting, Dominican Republic.

INTRODUCTION: COVID-19 is a worldwide public health threat. Diagnosis by RT-PCR has been employed as the standard method to confirm viral infection. Sample pooling testing can optimize the resources by reducing the workload and reagents shortage, and be useful in laboratories and countries with limited resources. This study aims to evaluate SARS-CoV-2 detection by sample pooling testing in comparison with individual sample testing. MATERIALS AND METHODS: We created 210 pools out of 245 samples, varying from 4 to 10 samples per pool, each containing a positive sample. We conducted detection of SARS-CoV-2-specific RdRp/E target sites. RESULTS: Pooling of three samples for SARS-CoV-2 detection might be an efficient strategy to perform without losing RT-PCR sensitivity. CONCLUSIONS: Considering the positivity rate in Dominican Republic and that larger sample pools have higher probabilities of obtaining false negative results, the optimal sample size to perform a pooling strategy shall be three samples.