The Interpretation of SARS-CoV-2 Diagnostic Tests

Cost effectiveness and decision analysis for national airport screening options to reduce risk of COVID-19 introduction in Uganda, 2020

INTRODUCTION

Early during the COVID-19 outbreak, various approaches were utilized to prevent COVID-19 introductions from incoming airport travellers. However, the costs and effectiveness of airport-specific interventions have not been evaluated.

METHODS

We evaluated policy options for COVID-19-specific interventions at Entebbe International Airport for costs and impact on COVID-19 case counts, we took the government payer perspective. Policy options included; (1)no screening, testing, or mandatory quarantine for any incoming traveller; (2)mandatory symptom screening for all incoming travellers with RT-PCR testing only for the symptomatic and isolation of positives; and (3)mandatory 14-day quarantine and one-time testing for all, with 10-day isolation of persons testing positive. We calculated incremental cost-effectiveness ratios (ICERs) in US$ per additional case averted.

RESULTS

Expected costs per incoming traveller were $0 (Option 1), $19 (Option 2), and $766 (Option 3). ICERs per case averted were $257 for Option 2 (which averted 4,948 cases), and $10,139 for Option 3 (which averted 5,097 cases) compared with Option I. Two-week costs were $0 for Option 1, $1,271,431 Option 2, and $51,684,999 Option 3. The per-case ICER decreased with increase in prevalence. The cost-effectiveness of our interventions was modestly sensitive to the prevalence of COVID-19, diagnostic test sensitivity, and testing costs.

CONCLUSION

Screening all incoming travellers, testing symptomatic persons, and isolating positives (Option 2) was the most cost-effective option. A higher COVID-19 prevalence among incoming travellers increased cost-effectiveness of airport-specific interventions. This model could be used to evaluate prevention options at the airport for COVID-19 and other infectious diseases with similar requirements for control.

Characterization of SARS-CoV-2 Distribution and Microbial Succession in a Clinical Microbiology Testing Facility during the SARS-CoV-2 Pandemic

The exchange of microbes between humans and the built environment is a dynamic process that has significant impact on health. Most studies exploring the microbiome of the built environment have been predicated on improving our understanding of pathogen emergence, persistence, and transmission. Previous studies have demonstrated that SARS-CoV-2 presence significantly correlates with the proportional abundance of specific bacteria on surfaces in the built environment. However, in these studies, SARS-CoV-2 originated from infected patients. Here, we perform a similar assessment for a clinical microbiology lab while staff were handling SARS-CoV-2 infected samples. The goal of this study was to understand the distribution and dynamics of microbial population on various surfaces within different sections of a clinical microbiology lab during a short period of 2020 Coronavirus disease (COVID-19) pandemic. We sampled floors, benches, and sinks in 3 sections (bacteriology, molecular microbiology, and COVID) of an active clinical microbiology lab over a 3-month period. Although floor samples harbored SARS-CoV-2, it was rarely identified on other surfaces, and bacterial diversity was significantly greater on floors than sinks and benches. The floors were primarily colonized by bacteria common to natural environments (e.g., soils), and benchtops harbored a greater proportion of human-associated microbes, including Staphylococcus and Streptococcus. Finally, we show that the microbial composition of these surfaces did not change over time and remained stable. Despite finding viruses on the floors, no lab-acquired infections were reported during the study period, which suggests that lab safety protocols and sanitation practices were sufficient to prevent pathogen exposures. IMPORTANCE For decades, diagnostic clinical laboratories have been an integral part of the health care systems that perform diagnostic tests on patient's specimens in bulk on a regular basis. Understanding their microbiota should assist in designing and implementing disinfection, and cleaning regime in more effective way. To our knowledge, there is a lack of information on the composition and dynamics of microbiota in the clinical laboratory environments, and, through this study, we have tried to fill that gap. This study has wider implications as understanding the makeup of microbes on various surfaces within clinical laboratories could help identify any pathogenic bacterial taxa that could have colonized these surfaces, and might act as a potential source of laboratory-acquired infections. Mapping the microbial community within these built environments may also be critical in assessing the reliability of laboratory safety and sanitation practices to lower any potential risk of exposures to health care workers.

Effective screening strategies for safe opening of universities under Omicron and Delta variants of COVID-19

As new COVID-19 variants emerge, and disease and population characteristics change, screening strategies may also need to change. We develop a decision-making model that can assist a college to determine an optimal screening strategy based on their characteristics and resources, considering COVID-19 infections/hospitalizations/deaths; peak daily hospitalizations; and the tests required. We also use this tool to generate screening guidelines for the safe opening of college campuses. Our compartmental model simulates disease spread on a hypothetical college campus under co-circulating variants with different disease dynamics, considering: (i) the heterogeneity in disease transmission and outcomes for faculty/staff and students based on vaccination status and level of natural immunity; and (ii) variant- and dose-dependent vaccine efficacy. Using the Spring 2022 academic semester as a case study, we study routine screening strategies, and find that screening the faculty/staff less frequently than the students, and/or the boosted and vaccinated less frequently than the unvaccinated, may avert a higher number of infections per test, compared to universal screening of the entire population at a common frequency. We also discuss key policy issues, including the need to revisit the mitigation objective over time, effective strategies that are informed by booster coverage, and if and when screening alone can compensate for low booster coverage.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulins using chemiluminescence immunoassay and its correlation with neutralizing antibodies

BACKGROUND

Neutralizing antibodies (NAbs) against SARS-CoV-2 infection have a pivotal role in protective immune response; however, their measurement requires specialized facilities. We evaluated the degree of correlation between NAbs and anti-SARS-CoV-2 IgG/total Ig antibodies detected by chemiluminescent immunoassay in asymptomatic and previously symptomatic SARS-CoV-2 patients.

METHODS

A total of 1241 participants (previously symptomatic patients and asymptomatic individuals), who were screened for SARS-CoV-2 infection by RT-PCR or serology, were enrolled in our study. Sera were analyzed for the presence of anti-spike-1(S1)-SARS-CoV-2 IgG/total Ig antibodies, using Ortho Clinical Diagnostics, USA. A signal/cut-off value (S/CO) ≥ 1 was considered reactive. NAbs were measured in 103 random samples from groups using microneutralization assay, with titer ≥ 1:10 being considered positive.

RESULTS

Asymptomatic (n = 229) and 261 previously symptomatic individuals with positive serology and negative RT-PCR were finally included. Significant higher anti-S1-IgG titers were seen in asymptomatic individuals (P < 0.0001). Conversely, anti-S1-total Ig titers were significantly higher in previously symptomatic (P < 0.0001). NAbs were detected in both groups, however, higher titers were seen in previously symptomatic patients. There is a correlation between NAbs and both IgG/total anti-S1-SARS-CoV-2 antibodies (r = 0.47, P < 0.0001 and r = 0.49, P < 0.0001, respectively). IgG and total Ig could predict a neutralization titer of ≥ 1:160 at S/CO >4.44 and >65 with AUC 0.69 and 0.67, respectively.

CONCLUSION

Asymptomatic SARS-CoV-2 infection can produce comparable antibodies response to previously symptomatic individuals, however higher neutralization activity was seen in the previously symptomatic. Anti-S1-SARS-CoV-2 IgG/total Ig antibodies showed a correlation with neutralization activity and can be used to estimate the presence of protective immunity.

COVID-19: A pluralistic and integrated approach for efficient management of the pandemic

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which triggered the ongoing pandemic, was first discovered in China in late 2019. SARS-CoV-2 is a respiratory virus responsible for coronavirus disease 2019 (COVID-19) that often manifests as a pneumonic syndrome. In the context of the pandemic, there are mixed views on the data provided by epidemiologists and the information collected by hospital clinicians about their patients. In addition, the literature reports a large proportion of patients free of pneumonia vs a small percentage of patients with severe pneumonia among confirmed COVID-19 cases. This raises the issue of the complexity of the work required to control or contain the pandemic. We believe that an integrative and pluralistic approach will help to put the analyses into perspective and reinforce collaboration and creativity in the fight against this major scourge. This paper proposes a comprehensive and integrative approach to COVID-19 research, prevention, control, and treatment to better address the pandemic. Thus, this literature review applies a pluralistic approach to fight the pandemic.

Testing Antigens, Antibodies, and Immune Cells in COVID-19 as a Public Health Topic—Experience and Outlines

The current COVID-19 pandemic has triggered an accelerated pace in all research domains, including reliable diagnostics methodology. Molecular diagnostics of the virus and its presence in biological samples relies on the RT-PCR method, the most used and validated worldwide. Nonconventional tests with improved parameters that are in the development stages will be presented, such as droplet digital PCR or CRISPR-based assays. These molecular tests were followed by rapid antigen testing along with the development of antibody tests, whether based on ELISA platform or on a chemiluminescent microparticle immunoassay. Less-conventional methods of testing antibodies (e.g., lateral flow immunoassay) are presented as well. Left somewhere in the backstage of COVID-19 research, immune cells and, furthermore, immune memory cells, are gaining the spotlight, more so in the vaccination context. Recently, methodologies using flow-cytometry evaluate circulating immune cells in infected/recovered patients. The appearance of new virus variants has triggered a surge for tests improvement. As the pandemic has entered an ongoing or postvaccination era, all methodologies that are used to monitor public health focus on diagnostic strategies and this review points out where gaps should be filled in both clinical and research settings.

SARS-CoV-2, Zika viruses and mycoplasma: Structure, pathogenesis and some treatment options in these emerging viral and bacterial infectious diseases

The molecular evolution of life on earth along with changing environmental, conditions has rendered mankind susceptible to endemic and pandemic emerging infectious diseases. The effects of certain systemic viral and bacterial infections on morbidity and mortality are considered as examples of recent emerging infections. Here we will focus on three examples of infections that are important in pregnancy and early childhood: SARS-CoV-2 virus, Zika virus, and Mycoplasma species. The basic structural characteristics of these infectious agents will be examined, along with their general pathogenic mechanisms. Coronavirus infections, such as caused by the SARS-CoV-2 virus, likely evolved from zoonotic bat viruses to infect humans and cause a pandemic that has been the biggest challenge for humanity since the Spanish Flu pandemic of the early 20th century. In contrast, Zika Virus infections represent an expanding infectious threat in the context of global climate change. The relationship of these infections to pregnancy, the vertical transmission and neurological sequels make these viruses highly relevant to the topics of this special issue. Finally, mycoplasmal infections have been present before mankind evolved, but they were rarely identified as human pathogens until recently, and they are now recognized as important coinfections that are able to modify the course and prognosis of various infectious diseases and other chronic illnesses. The infectious processes caused by these intracellular microorganisms are examined as well as some general aspects of their pathogeneses, clinical presentations, and diagnoses. We will finally consider examples of treatments that have been used to reduce morbidity and mortality of these infections and discuss briefly the current status of vaccines, in particular, against the SARS-CoV-2 virus. It is important to understand some of the basic features of these emerging infectious diseases and the pathogens involved in order to better appreciate the contributions of this special issue on how infectious diseases can affect human pregnancy, fetuses and neonates.

Unlocking SARS-CoV-2 detection in low- and middle-income countries

Low- and middle-income countries (LMICs) are significantly affected by SARS-CoV-2, partially due to their limited capacity for local production and implementation of molecular testing. Here, we provide detailed methods and validation of a molecular toolkit that can be readily produced and deployed using laboratory equipment available in LMICs. Our results show that lab-scale production of enzymes and nucleic acids can supply over 50,000 tests per production batch. The optimized one-step RT-PCR coupled to CRISPR-Cas12a-mediated detection showed a limit of detection of 102 ge/μL in a turnaround time of 2 h. The clinical validation indicated an overall sensitivity of 80%-88%, while for middle and high viral load samples (Cq ≤ 31) the sensitivity was 92%-100%. The specificity was 96%-100% regardless of viral load. Furthermore, we show that the toolkit can be used with the mobile laboratory Bento Lab, potentially enabling LMICs to implement detection services in unattended remote regions.

Assessing the capacity of symptom scores to predict COVID-19 positivity in Nigeria: a national derivation and validation cohort study

OBJECTIVES

This study aimed to develop and validate a symptom prediction tool for COVID-19 test positivity in Nigeria.

DESIGN

Predictive modelling study.

SETTING

All Nigeria States and the Federal Capital Territory.

PARTICIPANTS

A cohort of 43 221 individuals within the national COVID-19 surveillance dataset from 27 February to 27 August 2020. Complete dataset was randomly split into two equal halves: derivation and validation datasets. Using the derivation dataset (n=21 477), backward multivariable logistic regression approach was used to identify symptoms positively associated with COVID-19 positivity (by real-time PCR) in children (≤17 years), adults (18-64 years) and elderly (≥65 years) patients separately.

OUTCOME MEASURES

Weighted statistical and clinical scores based on beta regression coefficients and clinicians' judgements, respectively. Using the validation dataset (n=21 744), area under the receiver operating characteristic curve (AUROC) values were used to assess the predictive capacity of individual symptoms, unweighted score and the two weighted scores.

RESULTS

Overall, 27.6% of children (4415/15 988), 34.6% of adults (9154/26 441) and 40.0% of elderly (317/792) that had been tested were positive for COVID-19. Best individual symptom predictor of COVID-19 positivity was loss of smell in children (AUROC 0.56, 95% CI 0.55 to 0.56), either fever or cough in adults (AUROC 0.57, 95% CI 0.56 to 0.58) and difficulty in breathing in the elderly (AUROC 0.53, 95% CI 0.48 to 0.58) patients. In children, adults and the elderly patients, all scoring approaches showed similar predictive performance.

CONCLUSIONS

The predictive capacity of various symptom scores for COVID-19 positivity was poor overall. However, the findings could serve as an advocacy tool for more investments in resources for capacity strengthening of molecular testing for COVID-19 in Nigeria.

Testing at scale during the COVID-19 pandemic

Assembly and publication of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome in January 2020 enabled the immediate development of tests to detect the new virus. This began the largest global testing programme in history, in which hundreds of millions of individuals have been tested to date. The unprecedented scale of testing has driven innovation in the strategies, technologies and concepts that govern testing in public health. This Review describes the changing role of testing during the COVID-19 pandemic, including the use of genomic surveillance to track SARS-CoV-2 transmission around the world, the use of contact tracing to contain disease outbreaks and testing for the presence of the virus circulating in the environment. Despite these efforts, widespread community transmission has become entrenched in many countries and has required the testing of populations to identify and isolate infected individuals, many of whom are asymptomatic. The diagnostic and epidemiological principles that underpin such population-scale testing are also considered, as are the high-throughput and point-of-care technologies that make testing feasible on a massive scale.

The use of pediatric flexible bronchoscopy in the COVID-19 pandemic era

On March 11, 2020, the World Health Organization (WHO) declared the pandemic because of a novel coronavirus, called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In January 2020, the first transmission to healthcare workers (HCWs) was described. SARS-CoV-2 is transmitted between people because of contact, droplets, and airborne. Airborne transmission is caused by aerosols that remain infectious when suspended in air over long distances and time. In the clinical setting, airborne transmission may occur during aerosol generating procedures like flexible bronchoscopy. To date, although the role of children in the transmission of SARS-CoV-2 is not clear the execution of bronchoscopy is associated with a considerably increased risk of SARS-CoV-2 transmission to HCWs. The aim of this overview is to summarize available recommendations and to apply them to pediatric bronchoscopy. We performed systematic literature searches using the MEDLINE (accessed via PubMed) and Scopus databases. We reviewed major recommendations and position statements published at the moment by the American Association for Bronchology and Interventional Pulmonology, WHO, European Center for Disease Prevention and Control and expert groups on the management of patients with COVID-19 to limit transmission among HCWs. To date there is a lack of recommendations for safe bronchoscopy during the pandemic period. The main indications concern adults and little has been said about children. We have summarized available recommendations and we have applied them to pediatric bronchoscopy.

Performance of the EUROIMMUN Anti-SARS-CoV-2 ELISA Assay for detection of IgA and IgG antibodies in South Africa

Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) has been identified as the causative agent for causing the clinical syndrome of COVID -19. Accurate detection of SARS-CoV-2 infection is not only important for management of infected individuals but also to break the chain of transmission. South Africa is the current epicenter of SARS-CoV-2 infection in Africa. To optimize the diagnostic algorithm for SARS-CoV-2 in the South African setting, the study aims to evaluate the diagnostic performance of the EUROIMMUN Anti-SARS-CoV-2 assays. This study reported the performance of EUROIMMUN enzyme-linked immunosorbent assay (ELISA) for semi-quantitative detection of IgA and IgG antibodies in serum and plasma samples targeting the recombinant S1 domain of the SARS-CoV-2 spike protein as antigen. Samples were collected from 391 individuals who had tested positive for SARS-CoV-2 and 139 SARS CoV-2 negative controls. Samples were stratified by number of days’ post-PCR diagnosis and symptoms. The sensitivity of EUROIMMUN IgG was 64.1% (95% CI: 59.1–69.0%) and 74.3% (95% CI: 69.6–78.6%) for IgA and the specificity was lower for IgA [84.2% (95% CI: 77–89.2%)] than IgG [95.2% (95% CI: 90.8–98.4%)]. The EUROIMMUN Anti-SARS-CoV-2 ELISA Assay sensitivity was higher for IgA but low for IgG and improved for both assays in symptomatic individuals and at later timepoints post PCR diagnosis.

An overview of basic molecular biology of SARS-CoV-2 and current COVID-19 prevention strategies

Coronavirus Disease 2019 (COVID-19) manifests as extreme acute respiratory conditions caused by a novel beta coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) which is reported to be the seventh coronavirus to infect humans. Like other SARS-CoVs it has a large positive-stranded RNA genome. But, specific furin site in the spike protein, mutation prone and phylogenetically mess open reading frame1ab (Orf1ab) separates SARS-CoV-2 from other RNA viruses. Since the outbreak (February-March 2020), researchers, scientists, and medical professionals are inspecting all possible facts and aspects including its replication, detection, and prevention strategies. This led to the prompt identification of its basic biology, genome characterization, structural and expression based functional information of proteins, and utilization of this information in optimizing strategies to prevent its spread. This review summarizes the recent updates on the basic molecular biology of SARS-CoV-2 and prevention strategies undertaken worldwide to tackle COVID-19. This recent information can be implemented for the development and designing of therapeutics against SARS-CoV-2.

Possible correlation of electrochemiluminescence based numerical cut off index value with concentration of anti-SARS-CoV-2 antibody: Is it worth reporting?

Background: Many laboratories are reporting a numerical cutoff index value (COI) value for most anti-SARS-CoV-2 qualitative tests. These numerical values in patients' report ultimately created great confusion in the public and physicians, therefore this study was designed to evaluate the correlation of electrochemiluminescence (ECLIA) based numerical COI values with quantitative ELISA of anti-SARS-CoV-2 antibody. Design and Methods: Two hundred and twenty-eight (228) recovered COVID-19 patients were included; their serum samples were analyzed by quantitative ELISA and ECLIA for anti-SARSCOV- 2 antibodies. Results: One hundred and seventy-three (75.8%) patients tested positive by ECLIA and ELISA assay and thirty-seven (6.2%) were tested negative by both methods. A weak positive correlation (r=0.37) was found between numerical COI value of ECLIA with ELISA concentration, which was statistically significant with p<0.001. All values were dispersed on scatter plot and there was no significant linear relationship between ECLIA and ELISA assay. Conclusions: As both testing techniques are base upon the same immunological phenomena of detecting antibodies against nucleocapsid protein. We suggest that COI values are not meant to describe the immunity level of the individuals thus the physicians should not consider it as a quantitative value for antibody levels in COVID-19 patients.