Active testing of groups at increased risk of acquiring SARS-CoV-2 in Canada: costs and human resource needs

Bayesian hierarchical models incorporating study-level covariates for multivariate meta-analysis of diagnostic tests without a gold standard with application to COVID-19

When evaluating a diagnostic test, it is common that a gold standard may not be available. One example is the diagnosis of SARS-CoV-2 infection using saliva sampling or nasopharyngeal swabs. Without a gold standard, a pragmatic approach is to postulate a "reference standard," defined as positive if either test is positive, or negative if both are negative. However, this pragmatic approach may overestimate sensitivities because subjects infected with SARS-CoV-2 may still have double-negative test results even when both tests exhibit perfect specificity. To address this limitation, we propose a Bayesian hierarchical model for simultaneously estimating sensitivity, specificity, and disease prevalence in the absence of a gold standard. The proposed model allows adjusting for study-level covariates. We evaluate the model performance using an example based on a recently published meta-analysis on the diagnosis of SARS-CoV-2 infection and extensive simulations. Compared with the pragmatic reference standard approach, we demonstrate that the proposed Bayesian method provides a more accurate evaluation of prevalence, specificity, and sensitivity in a meta-analytic framework.

Determining optimal COVID-19 testing center locations and capacities

We study the problem of determining the locations and capacities of COVID-19 specimen collection centers to efficiently improve accessibility to polymerase chain reaction testing during surges in testing demand. We develop a two-echelon multi-period location and capacity allocation model that determines optimal number and locations of pop-up testing centers, capacities of the existing centers as well as assignments of demand regions to these centers, and centers to labs. The objective is to minimize the total number of delayed appointments and specimens subject to budget, capacity, and turnaround time constraints, which will in turn improve the accessibility to testing. We apply our model to a case study for locating COVID-19 testing centers in the Region of Waterloo, Canada using data from the Ontario Ministry of Health, public health databases, and medical literature. We also test the performance of the model under uncertain demand and analyze its outputs under various scenarios. Our analyses provide practical insights to the public health decision-makers on the timing of capacity expansions and the locations for the new pop-up centers. According to our results, the optimal strategy is to dynamically expand the existing specimen collection center capacities and prevent bottlenecks by locating pop-up facilities. The optimal locations of pop-ups are among the densely populated areas that are in proximity to the lab and a subset of those locations are selected with the changes in demand. A comparison with a static approach promises up to 39% cost savings under high demand using the developed multi-period model.

Salivary SARS-CoV-2 RNA for diagnosis of COVID-19 patients: a systematic revisew and meta-analysis of diagnostic accuracy

Accurate, self-collected, and non-invasive diagnostics are critical to perform mass-screening diagnostic tests for COVID-19. This systematic review with meta-analysis evaluated the accuracy, sensitivity, and specificity of salivary diagnostics for COVID-19 based on SARS-CoV-2 RNA compared with the current reference tests using a nasopharyngeal swab (NPS) and/or oropharyngeal swab (OPS). An electronic search was performed in seven databases to find COVID-19 diagnostic studies simultaneously using saliva and NPS/OPS tests to detect SARS-CoV-2 by RT-PCR. The search resulted in 10,902 records, of which 44 studies were considered eligible. The total sample consisted of 14,043 participants from 21 countries. The accuracy, specificity, and sensitivity for saliva compared with the NPS/OPS was 94.3% (95%CI= 92.1;95.9), 96.4% (95%CI= 96.1;96.7), and 89.2% (95%CI= 85.5;92.0), respectively. Besides, the sensitivity of NPS/OPS was 90.3% (95%CI= 86.4;93.2) and saliva was 86.4% (95%CI= 82.1;89.8) compared to the combination of saliva and NPS/OPS as the gold standard. These findings suggest a similarity in SARS-CoV-2 RNA detection between NPS/OPS swabs and saliva, and the association of both testing approaches as a reference standard can increase by 3.6% the SARS-CoV-2 detection compared with NPS/OPS alone. This study supports saliva as an attractive alternative for diagnostic platforms to provide a non-invasive detection of SARS-CoV-2.

Quantifying the economic gains associated with COVID-19 vaccination in the Canadian population: A cost-benefit analysis

Background

Vaccination has been a key part of Canada's coronavirus disease 2019 (COVID-19) pandemic response. Although the clinical benefits of vaccination are clear, an understanding of the population-level benefits of vaccination relative to the programmatic costs is of value. The objective of this article is to quantify the economic impact of COVID-19 vaccination in the Canadian population between December 2020 and March 2022.

Methods

We conducted a model-based cost-benefit analysis of Canada's COVID-19 vaccination program. We used an epidemiological model to estimate the number of COVID-19 symptomatic cases, hospitalizations, post-COVID condition (PCC) cases, and deaths in the presence and absence of vaccination. Median, lower and upper 95% credible interval (95% CrI) outcome values from 100 model simulations were used to estimate the direct and indirect costs of illness, including the value of health. We used a societal perspective and a 1.5% discount rate.

Results

We estimated that the costs of the vaccination program were far outweighed by the savings associated with averted infections and associated downstream consequences. Vaccination increased the net benefit by CAD $298.1 billion (95% CrI: 27.2-494.6) compared to the no vaccination counterfactual. The largest benefits were due to averted premature mortality, resulting in an estimated $222.0 billion (95% CrI: 31.2-379.0) benefit.

Conclusion

Our model-based economic evaluation provides a retrospective assessment of COVID-19 vaccination during the first 16 months of the program in Canada and suggests that it was welfare-improving, considering the decreased hospitalizations and use of healthcare resources, deaths averted and lower morbidity from conditions such as PCC.

Integrating tuberculosis and COVID-19 molecular testing in Lima, Peru: a cross-sectional, diagnostic accuracy study

BACKGROUND

Integrated molecular testing could be an opportunity to detect and provide care for both tuberculosis and COVID-19. Many high tuberculosis burden countries, such as Peru, have existing GeneXpert systems for tuberculosis testing with GeneXpert Xpert MTB/RIF Ultra (Xpert Ultra), and a GeneXpert SARS-CoV-2 assay, GeneXpert Xpert Xpress SARS-CoV-2 (Xpert Xpress), is also available. We aimed to assess the feasibility of integrating tuberculosis and COVID-19 testing using one sputum specimen with Xpert Ultra and Xpert Xpress in Lima, Peru.

METHODS

In this cross-sectional, diagnostic accuracy study, we recruited adults presenting with clinical symptoms or suggestive history of tuberculosis or COVID-19, or both. Participants were recruited from a total of 35 primary health facilities in Lima, Peru. Participants provided one nasopharyngeal swab and one sputum sample. For COVID-19, we tested nasopharyngeal swabs and sputum using Xpert Xpress; for tuberculosis, we tested sputum using culture and Xpert Ultra. We compared diagnostic accuracy of sputum testing using Xpert Xpress with nasopharyngeal swab testing using Xpert Xpress. Individuals with positive Xpert Xpress nasopharyngeal swab results were considered COVID-19 positive, and a positive culture indicated tuberculosis. To assess testing integration, the proportion of cases identified in sputum by Xpert Xpress was compared with Xpert Xpress on nasopharyngeal swabs, and sputum by Xpert Ultra was compared with culture.

FINDINGS

Between Jan 11, 2021, and April 26, 2022, we recruited 600 participants (312 [52%] women and 288 [48%] men). In-study prevalence of tuberculosis was 13% (80 participants, 95% CI 11-16) and of SARS-CoV-2 was 35% (212 participants, 32-39). Among tuberculosis cases, 13 (2·2%, 1·2-3·7) participants were concurrently positive for SARS-CoV-2. Regarding the diagnostic yield of integrated testing, Xpert Ultra detected 96% (89-99) of culture-confirmed tuberculosis cases (n=77), and Xpert Xpress-sputum detected 67% (60-73) of COVID-19 cases (n=134). All five study staff reported that integrated molecular testing was easy and acceptable.

INTERPRETATION

The diagnostic yield of Xpert Xpress on sputum was moderate, but integrated testing for tuberculosis and COVID-19 with GeneXpert was feasible. However, systematic testing for both diseases might not be the ideal approach for everyone presenting with presumptive tuberculosis or COVID-19, as concurrent positive cases were rare during the study period. Further research might help to identify when integrated testing is most worthwhile and its optimal implementation.

FUNDING

Canadian Institutes of Health Research and International Development Research Centre.

TRANSLATION

For the Spanish translation of the abstract see Supplementary Materials section.

Delivering COVID self-tests through GetaKit.ca: Creating testing access during a pandemic

OBJECTIVES

To determine the real-world outcomes associated with using the GetaKit.ca website to distribute COVID self-tests to persons with risk factors, with a focus on facilitating testing for persons who are Black, Indigenous, or of Colour (BIPOC).

METHODS

GetaKit was an open cohort observational study to distribute free self-tests, starting with HIV self-testings and then adding the Lucira Check-It® COVID self-test. Participants would register on our website and complete a risk assessment, which would calculate their need for each type of testing.

RESULTS

Focusing on the COVID self-tests, from September to December 2021 (with targeted outreach in winter 2022), we distributed 6474 COVID self-tests to 3653 persons through 4161 unique orders, of which 47% came from BIPOC participants. Compared to white participants, BIPOC participants were more likely to have been a contact of COVID but less likely to be vaccinated. As well, 69% of results were reported back via the GetaKit.ca website, with 5.3% of these being positive. The positivity rate for our 3653 participants was 9.6%.

CONCLUSIONS

Delivering COVID self-tests via our website provided tests to BIPOC communities and yielded positivity rates that matched local COVID testing centres. This highlights the utility of such systems for delivering testing during future pandemics.

Economic evaluation of COVID-19 rapid antigen screening programs in the workplace

BACKGROUND

Diagnostic testing has been pivotal in detecting SARS-CoV-2 infections and reducing transmission through the isolation of positive cases. We quantified the value of implementing frequent, rapid antigen (RA) testing in the workplace to identify screening programs that are cost-effective.

METHODS

To project the number of cases, hospitalizations, and deaths under alternative screening programs, we adapted an agent-based model of COVID-19 transmission and parameterized it with the demographics of Ontario, Canada, incorporating vaccination and waning of immunity. Taking into account healthcare costs and productivity losses associated with each program, we calculated the incremental cost-effectiveness ratio (ICER) with quality-adjusted life year (QALY) as the measure of effect. Considering RT-PCR testing of only severe cases as the baseline scenario, we estimated the incremental net monetary benefits (iNMB) of the screening programs with varying durations and initiation times, as well as different booster coverages of working adults.

RESULTS

Assuming a willingness-to-pay threshold of CDN$30,000 per QALY loss averted, twice weekly workplace screening was cost-effective only if the program started early during a surge. In most scenarios, the iNMB of RA screening without a confirmatory RT-PCR or RA test was comparable or higher than the iNMB for programs with a confirmatory test for RA-positive cases. When the program started early with a duration of at least 16 weeks and no confirmatory testing, the iNMB exceeded CDN$1.1 million per 100,000 population. Increasing booster coverage of working adults improved the iNMB of RA screening.

CONCLUSIONS

Our findings indicate that frequent RA testing starting very early in a surge, without a confirmatory test, is a preferred screening program for the detection of asymptomatic infections in workplaces.

Unintended consequences of measures implemented in the school setting to contain the COVID-19 pandemic: a scoping review

BACKGROUND

With the emergence of SARS-CoV-2 in late 2019, governments worldwide implemented a multitude of non-pharmaceutical interventions in order to control the spread of the virus. Most countries have implemented measures within the school setting in order to reopen schools or keep them open whilst aiming to contain the spread of SARS-CoV-2. For informed decision-making on implementation, adaptation, or suspension of such measures, it is not only crucial to evaluate their effectiveness with regard to SARS-CoV-2 transmission, but also to assess their unintended consequences.

OBJECTIVES

To comprehensively identify and map the evidence on the unintended health and societal consequences of school-based measures to prevent and control the spread of SARS-CoV-2. We aimed to generate a descriptive overview of the range of unintended (beneficial or harmful) consequences reported as well as the study designs that were employed to assess these outcomes. This review was designed to complement an existing Cochrane Review on the effectiveness of these measures by synthesising evidence on the implications of the broader system-level implications of school measures beyond their effects on SARS-CoV-2 transmission.

SEARCH METHODS

We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, Embase, four non-health databases, and two COVID-19 reference collections on 26 March 2021, together with reference checking, citation searching, and Google searches.

SELECTION CRITERIA

We included quantitative (including mathematical modelling), qualitative, and mixed-methods studies of any design that provided evidence on any unintended consequences of measures implemented in the school setting to contain the SARS-CoV-2 pandemic. Studies had to report on at least one unintended consequence, whether beneficial or harmful, of one or more relevant measures, as conceptualised in a logic model.  DATA COLLECTION AND ANALYSIS: We screened the titles/abstracts and subsequently full texts in duplicate, with any discrepancies between review authors resolved through discussion. One review author extracted data for all included studies, with a second review author reviewing the data extraction for accuracy. The evidence was summarised narratively and graphically across four prespecified intervention categories and six prespecified categories of unintended consequences; findings were described as deriving from quantitative, qualitative, or mixed-method studies.

MAIN RESULTS

Eighteen studies met our inclusion criteria. Of these, 13 used quantitative methods (3 experimental/quasi-experimental; 5 observational; 5 modelling); four used qualitative methods; and one used mixed methods. Studies looked at effects in different population groups, mainly in children and teachers. The identified interventions were assigned to four broad categories: 14 studies assessed measures to make contacts safer; four studies looked at measures to reduce contacts; six studies assessed surveillance and response measures; and one study examined multiple measures combined. Studies addressed a wide range of unintended consequences, most of them considered harmful. Eleven studies investigated educational consequences. Seven studies reported on psychosocial outcomes. Three studies each provided information on physical health and health behaviour outcomes beyond COVID-19 and environmental consequences. Two studies reported on socio-economic consequences, and no studies reported on equity and equality consequences.

AUTHORS' CONCLUSIONS

We identified a heterogeneous evidence base on unintended consequences of measures implemented in the school setting to prevent and control the spread of SARS-CoV-2, and summarised the available study data narratively and graphically. Primary research better focused on specific measures and various unintended outcomes is needed to fill knowledge gaps and give a broader picture of the diverse unintended consequences of school-based measures before a more thorough evidence synthesis is warranted. The most notable lack of evidence we found was regarding psychosocial, equity, and equality outcomes. We also found a lack of research on interventions that aim to reduce the opportunity for contacts. Additionally, study investigators should provide sufficient data on contextual factors and demographics in order to ensure analyses of such are feasible, thus assisting stakeholders in making appropriate, informed decisions for their specific circumstances.

SARS-CoV-2 surveillance strategy in essential workers of the Madrid City Council during the first epidemic wave in Spain, March-July 2020

OBJECTIVES

To study prevalence of infection in essential workers of Madrid City Council by occupation, related characteristics, use of protective devices, risk perception, and main concerns about COVID-19 during lockdown.

METHODS

A total of 30 231 workers were PCR tested for SARS-CoV-2 infection. Information was collected on COVID-19-related symptoms, risk factors, preventive equipment, and risk perception. The crude prevalence was calculated for infection, use of protective devices, perceived risk and main concerns. Additionally, adjusted prevalence and prevalence ratios (PR) were estimated for these variables using logistic regression models with age, gender, occupation, epidemiological week and laboratory as confounding factors.

RESULTS

Overall prevalence of infection was 3.2% (95% CI 3.0% to 3.4%), being higher among policemen (4.4%) and bus drivers (4.2%), but lower among emergency healthcare personnel, firefighters, food market workers and burial services (<2%). Lower excess risk was observed in workers reporting occupational contact with COVID-19 cases only (PR=1.42; 95% CI 1.18 to 1.71) compared with household exposure only (PR=2.75; 95% CI 2.32 to 3.25). Infection was more frequent in symptomatic workers (PR=1.28; 95% CI 1.11 to 1.48), although 42% of detected infections were asymptomatic. Use of facial masks (78.7%) and disinfectants (86.3%) was common and associated with lower infection prevalence (PRmasks=0.68; 95% CI 0.58 to 0.79; PRdisinfectants=0.75; 95% CI 0.61 to 0.91). Over 50% of workers felt being at high risk of infection and worried about infecting others, yet only 2% considered quitting their work.

CONCLUSIONS

This surveillance system allowed for detecting and isolating SARS-CoV-2 cases among essential workers, identifying characteristics related to infection and use of protective devices, and revealing specific needs for work-safety information and psychological support.

Systematic on-site testing for SARS-CoV-2 infection among asymptomatic essential workers in Montréal, Canada: a prospective observational and cost-assessment study

BACKGROUND

Essential workers are at increased risk for SARS-CoV-2 infection. We aimed to estimate the yield, acceptability and cost of systematic workplace-based testing of asymptomatic essential workers for SARS-CoV-2 infection.

METHODS

From Jan. 27 to Mar. 12, 2021, we prospectively recruited non-health care essential businesses in Montréal, Canada, through email or telephone contact. Two trained mobile teams, each composed of 2 non-health care professionals, visited businesses. Consenting asymptomatic employees provided saline gargle samples under supervision. Samples were analyzed by means of reverse transcription polymerase chain reaction (RT-PCR). At businesses with outbreaks (≥ 2 participants with a positive result), we retested all participants with a negative result on initial testing. Our primary outcomes were yield (proportion of test results that were positive), acceptability (proportion of participants estimated to be present at the business who agreed to participate) and costs (including training, sample collection and analysis, and communicating results). Our secondary outcome was identification of factors associated with a positive test result on multivariable logistic regression.

RESULTS

Of the 366 businesses contacted, 69 (18.8%) agreed to participate. Nineteen businesses (28%) were manufacturers or suppliers, 12 (17%) were in auto sales or repair, and 11 (16%) were in childcare; the corresponding number of employees was 1225, 242 and 113. The median number of participants per business was 13 (interquartile range [IQR] 8-22). Of an estimated 2348 employees on site, 2128 (90.6%) participated (808 [38.0%] female, median age 48 [IQR 37-57] yr). Of the 2626 tests performed, 53 (2.0%) gave a positive result. Self-reported nonwhite ethnicity (adjusted odds ratio [OR] 3.7, 95% confidence interval [CI] 1.4-9.9) and a negative SARS-CoV-2 test result before the study (adjusted OR 0.4, 95% CI 0.2-0.8) were associated with a positive test result. Five businesses were experiencing an outbreak; at these businesses, 40/917 participants (4.4%) had a positive result on the initial test. We repeated testing for employees with initially negative results at 3 of these businesses over 2-3 weeks: 8/350 participants (2.3%) had a positive result on the second test, and none had a positive result on the third and fourth tests; no employer reported new positive results after our final visit (up to Mar. 26, 2021). At the remaining 64 businesses, 1211 participants were tested once, of whom 5 (0.4%) had a positive result. The per-person RT-PCR cost was $34, and all other costs, $8.67.

INTERPRETATION

On-site saline gargle sampling of essential workers for SARS-CoV-2 testing was acceptable and of modest cost, and appears most useful in the context of outbreaks. This sampling strategy should be evaluated further as a component of efforts to prevent SARS-CoV-2 transmission. PREPRINT: medRxiv - doi:10.1101/2021.05.12.21256956.

The University of Padua salivary-based SARS-CoV-2 surveillance program minimized viral transmission during the second and third pandemic wave

BACKGROUND

The active surveillance of students is proposed as an effective strategy to contain SARS-CoV-2 spread and prevent schools' closure. Saliva for molecular testing is as sensitive as naso-pharyngeal swab (NPS), self-collected and well accepted by participants. This prospective study aimed to verify whether the active surveillance of the Padua University employees by molecular testing of self-collected saliva is an effective and affordable strategy for limiting SARS-CoV-2 spread.

METHODS

A surveillance program based on self-collection of saliva every 2 weeks (October 2020-June 2021) was conducted. Among 8183 employees of the Padua University, a total of 6284 subjects voluntarily took part in the program. Eight collection points guaranteed the daily distribution and collection of barcoded salivary collection devices, which were delivered to the laboratory by a transport service for molecular testing. Quarantine of positive cases and contact tracing were promptly activated.

RESULTS

Among 6284 subjects, 206 individuals were SARS-CoV-2 positive (99 by salivary testing; 107 by NPS performed for contact tracing or symptoms). The cumulative SARS-CoV-2 incidence in this cohort was 3.1%, significantly lower than that of employees not in surveillance (8.0%), in Padua (7.1%) and in the Veneto region (7.2%). Employees with positive saliva results were asymptomatic or had mild symptoms. The levels of serum antibodies after 3 months from the infection were correlated with age and Ct values, being higher in older subjects with greater viral loads.

CONCLUSIONS

Salivary-based surveillance with contact tracing effectively allowed to limit SARS-CoV-2 contagion, also in a population with a high incidence.

Measures implemented in the school setting to contain the COVID-19 pandemic

BACKGROUND

In response to the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the impact of coronavirus disease 2019 (COVID-19), governments have implemented a variety of measures to control the spread of the virus and the associated disease. Among these, have been measures to control the pandemic in primary and secondary school settings.

OBJECTIVES

To assess the effectiveness of measures implemented in the school setting to safely reopen schools, or keep schools open, or both, during the COVID-19 pandemic, with particular focus on the different types of measures implemented in school settings and the outcomes used to measure their impacts on transmission-related outcomes, healthcare utilisation outcomes, other health outcomes as well as societal, economic, and ecological outcomes.  SEARCH METHODS: We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, Embase, and the Educational Resources Information Center, as well as COVID-19-specific databases, including the Cochrane COVID-19 Study Register and the WHO COVID-19 Global literature on coronavirus disease (indexing preprints) on 9 December 2020. We conducted backward-citation searches with existing reviews.

SELECTION CRITERIA

We considered experimental (i.e. randomised controlled trials; RCTs), quasi-experimental, observational and modelling studies assessing the effects of measures implemented in the school setting to safely reopen schools, or keep schools open, or both, during the COVID-19 pandemic. Outcome categories were (i) transmission-related outcomes (e.g. number or proportion of cases); (ii) healthcare utilisation outcomes (e.g. number or proportion of hospitalisations); (iii) other health outcomes (e.g. physical, social and mental health); and (iv) societal, economic and ecological outcomes (e.g. costs, human resources and education). We considered studies that included any population at risk of becoming infected with SARS-CoV-2 and/or developing COVID-19 disease including students, teachers, other school staff, or members of the wider community.  DATA COLLECTION AND ANALYSIS: Two review authors independently screened titles, abstracts and full texts. One review author extracted data and critically appraised each study. One additional review author validated the extracted data. To critically appraise included studies, we used the ROBINS-I tool for quasi-experimental and observational studies, the QUADAS-2 tool for observational screening studies, and a bespoke tool for modelling studies. We synthesised findings narratively. Three review authors made an initial assessment of the certainty of evidence with GRADE, and several review authors discussed and agreed on the ratings.

MAIN RESULTS

We included 38 unique studies in the analysis, comprising 33 modelling studies, three observational studies, one quasi-experimental and one experimental study with modelling components. Measures fell into four broad categories: (i) measures reducing the opportunity for contacts; (ii) measures making contacts safer; (iii) surveillance and response measures; and (iv) multicomponent measures. As comparators, we encountered the operation of schools with no measures in place, less intense measures in place, single versus multicomponent measures in place, or closure of schools. Across all intervention categories and all study designs, very low- to low-certainty evidence ratings limit our confidence in the findings. Concerns with the quality of modelling studies related to potentially inappropriate assumptions about the model structure and input parameters, and an inadequate assessment of model uncertainty. Concerns with risk of bias in observational studies related to deviations from intended interventions or missing data. Across all categories, few studies reported on implementation or described how measures were implemented. Where we describe effects as 'positive', the direction of the point estimate of the effect favours the intervention(s); 'negative' effects do not favour the intervention.  We found 23 modelling studies assessing measures reducing the opportunity for contacts (i.e. alternating attendance, reduced class size). Most of these studies assessed transmission and healthcare utilisation outcomes, and all of these studies showed a reduction in transmission (e.g. a reduction in the number or proportion of cases, reproduction number) and healthcare utilisation (i.e. fewer hospitalisations) and mixed or negative effects on societal, economic and ecological outcomes (i.e. fewer number of days spent in school). We identified 11 modelling studies and two observational studies assessing measures making contacts safer (i.e. mask wearing, cleaning, handwashing, ventilation). Five studies assessed the impact of combined measures to make contacts safer. They assessed transmission-related, healthcare utilisation, other health, and societal, economic and ecological outcomes. Most of these studies showed a reduction in transmission, and a reduction in hospitalisations; however, studies showed mixed or negative effects on societal, economic and ecological outcomes (i.e. fewer number of days spent in school). We identified 13 modelling studies and one observational study assessing surveillance and response measures, including testing and isolation, and symptomatic screening and isolation. Twelve studies focused on mass testing and isolation measures, while two looked specifically at symptom-based screening and isolation. Outcomes included transmission, healthcare utilisation, other health, and societal, economic and ecological outcomes. Most of these studies showed effects in favour of the intervention in terms of reductions in transmission and hospitalisations, however some showed mixed or negative effects on societal, economic and ecological outcomes (e.g. fewer number of days spent in school). We found three studies that reported outcomes relating to multicomponent measures, where it was not possible to disaggregate the effects of each individual intervention, including one modelling, one observational and one quasi-experimental study. These studies employed interventions, such as physical distancing, modification of school activities, testing, and exemption of high-risk students, using measures such as hand hygiene and mask wearing. Most of these studies showed a reduction in transmission, however some showed mixed or no effects.   As the majority of studies included in the review were modelling studies, there was a lack of empirical, real-world data, which meant that there were very little data on the actual implementation of interventions.

AUTHORS' CONCLUSIONS

Our review suggests that a broad range of measures implemented in the school setting can have positive impacts on the transmission of SARS-CoV-2, and on healthcare utilisation outcomes related to COVID-19. The certainty of the evidence for most intervention-outcome combinations is very low, and the true effects of these measures are likely to be substantially different from those reported here. Measures implemented in the school setting may limit the number or proportion of cases and deaths, and may delay the progression of the pandemic. However, they may also lead to negative unintended consequences, such as fewer days spent in school (beyond those intended by the intervention). Further, most studies assessed the effects of a combination of interventions, which could not be disentangled to estimate their specific effects. Studies assessing measures to reduce contacts and to make contacts safer consistently predicted positive effects on transmission and healthcare utilisation, but may reduce the number of days students spent at school. Studies assessing surveillance and response measures predicted reductions in hospitalisations and school days missed due to infection or quarantine, however, there was mixed evidence on resources needed for surveillance. Evidence on multicomponent measures was mixed, mostly due to comparators. The magnitude of effects depends on multiple factors. New studies published since the original search date might heavily influence the overall conclusions and interpretation of findings for this review.

Validation of a Saliva-Based Test for the Molecular Diagnosis of SARS-CoV-2 Infection

BACKGROUND

Since the beginning of the pandemic, clinicians and researchers have been searching for alternative tests to improve the screening and diagnosis of the SARS-CoV-2 infection. Currently, the gold standard for virus identification is the nasopharyngeal (NP) swab. Saliva samples, however, offer clear, practical, and logistical advantages but due to a lack of collection, transport, and storage solutions, high-throughput saliva-based laboratory tests are difficult to scale up as a screening or diagnostic tool. With this study, we aimed to validate an intralaboratory molecular detection method for SARS-CoV-2 on saliva samples collected in a new storage saline solution, comparing the results to NP swabs to determine the difference in sensitivity between the two tests.

METHODS

In this study, 156 patients (cases) and 1005 asymptomatic subjects (controls) were enrolled and tested simultaneously for the detection of the SARS-CoV-2 viral genome by RT-PCR on both NP swab and saliva samples. Saliva samples were collected in a preservative and inhibiting saline solution (Biofarma Srl). Internal method validation was performed to standardize the entire workflow for saliva samples.

RESULTS

The identification of SARS-CoV-2 conducted on saliva samples showed a clinical sensitivity of 95.1% and specificity of 97.8% compared to NP swabs. The positive predictive value (PPV) was 81% while the negative predictive value (NPV) was 99.5%. Test concordance was 97.6% (Cohen's Kappa = 0.86; 95% CI 0.81-0.91). The LoD of the test was 5 viral copies for both samples.

CONCLUSIONS

RT-PCR assays conducted on a stored saliva sample achieved similar performance to those on NP swabs, and this may provide a very effective tool for population screening and diagnosis. Collection of saliva in a stabilizing solution makes the test more convenient and widely available; furthermore, the denaturing properties of the solution reduce the infective risks belonging to sample manipulation.

The psychological impact of the COVID-19 pandemic and a SARS-CoV-2 testing programme on obstetric patients and healthcare workers

Objectives:

The aim of this study was to describe the psychological impact of the COVID-19 pandemic and the specific impact of a universal SARS-CoV-2 testing programme on obstetric patients and healthcare workers at The Ottawa Hospital.

Methods:

This was a follow-up survey study of obstetric healthcare workers and then-pregnant patients who participated in a SARS-CoV-2 testing programme conducted in The Ottawa Hospital obstetrical triage units from 19 October to 17 November 2020. Surveys explored the effects of the COVID-19 pandemic and the testing programme on participants’ psychological well-being. Responses were collected from April to September 2021. Descriptive summary statistics were calculated for both groups.

Results:

During hospitalization for delivery, obstetric patients (n = 143) worried about giving COVID-19 to their new baby (88.11%), catching COVID-19 (83.22%), and giving COVID-19 to their partner (76.22%). Patients felt relief at being tested for COVID-19 during the universal testing programme (24.65%) and at getting their results (28.87%). Patients also believed that universal SARS-CoV-2 testing was a good way to slow COVID-19 spread (79.72%), reduce anxiety (75.52%), and increase relief (76.22%). In addition, patients felt good about participating in research that could help others (91.61%). Among obstetric healthcare workers (n = 94), job satisfaction decreased and job stress increased during the COVID-19 pandemic. The universal testing programme led to minor increases in healthcare worker job stress and burden, particularly among nurses, but the majority (85.23%) believed it was a valuable research initiative.

Conclusion:

The COVID-19 pandemic has had a negative psychological impact on obstetric patients and healthcare workers. Universal SARS-CoV-2 testing was generally viewed favourably and may serve as an effective strategy for estimating COVID-19 prevalence without adding undue stress onto patients and healthcare workers during the pandemic.

Protecting Nursing Homes and Long-Term Care Facilities From COVID-19: A Rapid Review of International Evidence

OBJECTIVES

The COVID-19 pandemic has highlighted the extreme vulnerability of older people and other individuals who reside in long-term care, creating an urgent need for evidence-based policy that can adequately protect these community members. This study aimed to provide synthesized evidence to support policy decision making.

DESIGN

Rapid narrative review investigating strategies that have prevented or mitigated SARS-CoV-2 transmission in long-term care.

SETTING AND PARTICIPANTS

Residents and staff in care settings such as nursing homes and long-term care facilities.

METHODS

PubMed/Medline, Cochrane Library, and Scopus were systematically searched, with studies describing potentially effective strategies included. Studies were excluded if they did not report empirical evidence (eg, commentaries and consensus guidelines). Study quality was appraised on the basis of study design; data were extracted from published reports and synthesized narratively using tabulated data extracts and summary tables.

RESULTS

Searches yielded 713 articles; 80 papers describing 77 studies were included. Most studies were observational, with no randomized controlled trials identified. Intervention studies provided strong support for widespread surveillance, early identification and response, and rigorous infection prevention and control measures. Symptom- or temperature-based screening and single point-prevalence testing were found to be ineffective, and serial universal testing of residents and staff was considered crucial. Attention to ventilation and environmental management, digital health applications, and acute sector support were also considered beneficial although evidence for effectiveness was lacking. In observational studies, staff represented substantial transmission risk and workforce management strategies were important components of pandemic response. Higher-performing facilities with less crowding and higher nurse staffing ratios had reduced transmission rates. Outbreak investigations suggested that facility-level leadership, intersectoral collaboration, and policy that facilitated access to critical resources were all significant enablers of success.

CONCLUSIONS AND IMPLICATIONS

High-quality evidence of effectiveness in protecting LTCFs from COVID-19 was limited at the time of this study, though it continues to emerge. Despite widespread COVID-19 vaccination programs in many countries, continuing prevention and mitigation measures may be required to protect vulnerable long-term care residents from COVID-19 and other infectious diseases. This rapid review summarizes current evidence regarding strategies that may be effective.

Implementation of a pooled surveillance testing program for asymptomatic SARS-CoV-2 infections in K-12 schools and universities

BACKGROUND

The negative impact of continued school closures during the height of the COVID-19 pandemic warrants the establishment of cost-effective strategies for surveillance and screening to safely reopen and monitor for potential in-school transmission. Here, we present a novel approach to increase the availability of repetitive and routine COVID-19 testing that may ultimately reduce the overall viral burden in the community.

METHODS

We implemented a testing program using the SalivaClear࣪ pooled surveillance method that included students, faculty and staff from K-12 schools (student age range 5-18 years) and universities (student age range >18 years) across the country (Mirimus Clinical Labs, Brooklyn, NY). The data analysis was performed using descriptive statistics, kappa agreement, and outlier detection analysis.

FINDINGS

From August 27, 2020 until January 13, 2021, 253,406 saliva specimens were self-collected from students, faculty and staff from 93 K-12 schools and 18 universities. Pool sizes of up to 24 samples were tested over a 20-week period. Pooled testing did not significantly alter the sensitivity of the molecular assay in terms of both qualitative (100% detection rate on both pooled and individual samples) and quantitative (comparable cycle threshold (Ct) values between pooled and individual samples) measures. The detection of SARS-CoV-2 in saliva was comparable to the nasopharyngeal swab. Pooling samples substantially reduced the costs associated with PCR testing and allowed schools to rapidly assess transmission and adjust prevention protocols as necessary. In one instance, in-school transmission of the virus was determined within the main office and led to review and revision of heating, ventilating and air-conditioning systems.

INTERPRETATION

By establishing low-cost, weekly testing of students and faculty, pooled saliva analysis for the presence of SARS-CoV-2 enabled schools to determine whether transmission had occurred, make data-driven decisions, and adjust safety protocols. We provide strong evidence that pooled testing may be a fundamental component to the reopening of schools by minimizing the risk of in-school transmission among students and faculty.

FUNDING

Skoll Foundation generously provided funding to Mobilizing Foundation and Mirimus for these studies.

Implementation of a pooled surveillance testing program for asymptomatic SARS-CoV-2 infections in K-12 schools and universities

BACKGROUND

The negative impact of continued school closures during the height of the COVID-19 pandemic warrants the establishment of cost-effective strategies for surveillance and screening to safely reopen and monitor for potential in-school transmission. Here, we present a novel approach to increase the availability of repetitive and routine COVID-19 testing that may ultimately reduce the overall viral burden in the community.

METHODS

We implemented a testing program using the SalivaClear࣪ pooled surveillance method that included students, faculty and staff from K-12 schools (student age range 5-18 years) and universities (student age range >18 years) across the country (Mirimus Clinical Labs, Brooklyn, NY). The data analysis was performed using descriptive statistics, kappa agreement, and outlier detection analysis.

FINDINGS

From August 27, 2020 until January 13, 2021, 253,406 saliva specimens were self-collected from students, faculty and staff from 93 K-12 schools and 18 universities. Pool sizes of up to 24 samples were tested over a 20-week period. Pooled testing did not significantly alter the sensitivity of the molecular assay in terms of both qualitative (100% detection rate on both pooled and individual samples) and quantitative (comparable cycle threshold (Ct) values between pooled and individual samples) measures. The detection of SARS-CoV-2 in saliva was comparable to the nasopharyngeal swab. Pooling samples substantially reduced the costs associated with PCR testing and allowed schools to rapidly assess transmission and adjust prevention protocols as necessary. In one instance, in-school transmission of the virus was determined within the main office and led to review and revision of heating, ventilating and air-conditioning systems.

INTERPRETATION

By establishing low-cost, weekly testing of students and faculty, pooled saliva analysis for the presence of SARS-CoV-2 enabled schools to determine whether transmission had occurred, make data-driven decisions, and adjust safety protocols. We provide strong evidence that pooled testing may be a fundamental component to the reopening of schools by minimizing the risk of in-school transmission among students and faculty.

FUNDING

Skoll Foundation generously provided funding to Mobilizing Foundation and Mirimus for these studies.

Mass Testing With Contact Tracing Compared to Test and Trace for the Effective Suppression of COVID-19 in the United Kingdom: Systematic Review

BACKGROUND

Making testing available to everyone and tracing contacts might be the gold standard to control COVID-19. Many countries including the United Kingdom have relied on the symptom-based test and trace strategy in bringing the COVID-19 pandemic under control. The effectiveness of a test and trace strategy based on symptoms has been questionable and has failed to meet testing and tracing needs. This is further exacerbated by it not being delivered at the point of care, leading to rising cases and deaths. Increases in COVID-19 cases and deaths in the United Kingdom despite performing the highest number of tests in Europe suggest that symptom-based testing and contact tracing might not be effective as a control strategy. An alternative strategy is making testing available to all.

OBJECTIVE

The primary objective of this review was to compare mass testing and contact tracing with the conventional test and trace method in the suppression of SARS-CoV-2 infections. The secondary objective was to determine the proportion of asymptomatic COVID-19 cases reported during mass testing interventions.

METHODS

Literature in English was searched from September through December 2020 in Google Scholar, ScienceDirect, Mendeley, and PubMed. Search terms included "mass testing," "test and trace," "contact tracing," "COVID-19," "SARS-CoV-2," "effectiveness," "asymptomatic," "symptomatic," "community screening," "UK," and "2020." Search results were synthesized without meta-analysis using the direction of effect as the standardized metric and vote counting as the synthesis metric. A statistical synthesis was performed using Stata 14.2. Tabular and graphical methods were used to present findings.

RESULTS

The literature search yielded 286 articles from Google Scholar, 20 from ScienceDirect, 14 from Mendeley, 27 from PubMed, and 15 through manual search. A total of 35 articles were included in the review, with a sample size of nearly 1 million participants. We found a 76.9% (10/13, 95% CI 46.2%-95.0%; P=.09) majority vote in favor of the intervention under the primary objective. The overall proportion of asymptomatic cases among those who tested positive and in the tested sample populations under the secondary objective was 40.7% (1084/2661, 95% CI 38.9%-42.6%) and 0.0% (1084/9,942,878, 95% CI 0.0%-0.0%), respectively.

CONCLUSIONS

There was low-level but promising evidence that mass testing and contact tracing could be more effective in bringing the virus under control and even more effective if combined with social distancing and face coverings. The conventional test and trace method should be superseded by decentralized and regular mass rapid testing and contact tracing, championed by general practitioner surgeries and low-cost community services.

The Sensitivity and Costs of Testing for SARS-CoV-2 Infection With Saliva Versus Nasopharyngeal Swabs : A Systematic Review and Meta-analysis

BACKGROUND

Nasopharyngeal swabs are the primary sampling method used for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but they require a trained health care professional and extensive personal protective equipment.

PURPOSE

To determine the difference in sensitivity for SARS-CoV-2 detection between nasopharyngeal swabs and saliva and estimate the incremental cost per additional SARS-CoV-2 infection detected with nasopharyngeal swabs.

DATA SOURCES

Embase, Medline, medRxiv, and bioRxiv were searched from 1 January to 1 November 2020. Cost inputs were from nationally representative sources in Canada and were converted to 2020 U.S. dollars.

STUDY SELECTION

Studies including at least 5 paired nasopharyngeal swab and saliva samples and reporting diagnostic accuracy for SARS-CoV-2 detection.

DATA EXTRACTION

Data were independently extracted using standardized forms, and study quality was assessed using QUADAS-2 (Quality Assessment of Diagnostic Accuracy Studies 2).

DATA SYNTHESIS

Thirty-seven studies with 7332 paired samples were included. Against a reference standard of a positive result on either sample, the sensitivity of saliva was 3.4 percentage points lower (95% CI, 9.9 percentage points lower to 3.1 percentage points higher) than that of nasopharyngeal swabs. Among persons with previously confirmed SARS-CoV-2 infection, saliva's sensitivity was 1.5 percentage points higher (CI, 7.3 percentage points lower to 10.3 percentage points higher) than that of nasopharyngeal swabs. Among persons without a previous SARS-CoV-2 diagnosis, saliva was 7.9 percentage points less (CI, 14.7 percentage points less to 0.8 percentage point more) sensitive. In this subgroup, if testing 100 000 persons with a SARS-CoV-2 prevalence of 1%, nasopharyngeal swabs would detect 79 more (95% uncertainty interval, 5 fewer to 166 more) persons with SARS-CoV-2 than saliva, but with an incremental cost per additional infection detected of $8093.

LIMITATION

The reference standard was imperfect, and saliva collection procedures varied.

CONCLUSION

Saliva sampling seems to be a similarly sensitive and less costly alternative that could replace nasopharyngeal swabs for collection of clinical samples for SARS-CoV-2 testing.

PRIMARY FUNDING SOURCE

McGill Interdisciplinary Initiative in Infection and Immunity. (PROSPERO: CRD42020203415).

Comparison of Saliva and Nasopharyngeal Swab Nucleic Acid Amplification Testing for Detection of SARS-CoV-2: A Systematic Review and Meta-analysis

Importance

Nasopharyngeal swab nucleic acid amplification testing (NAAT) is the noninvasive criterion standard for diagnosis of coronavirus disease 2019 (COVID-19). However, it requires trained personnel, limiting its availability. Saliva NAAT represents an attractive alternative, but its diagnostic performance is unclear.

Objective

To assess the diagnostic accuracy of saliva NAAT for COVID-19.

Data Sources

In this systematic review, a search of the MEDLINE and medRxiv databases was conducted on August 29, 2020, to find studies of diagnostic test accuracy. The final meta-analysis was performed on November 17, 2020.

Study Selection

Studies needed to provide enough data to measure salivary NAAT sensitivity and specificity compared with imperfect nasopharyngeal swab NAAT as a reference test. An imperfect reference test does not perfectly reflect the truth (ie, it can give false results). Studies were excluded if the sample contained fewer than 20 participants or was neither random nor consecutive. The Quality Assessment of Diagnostic Accuracy Studies 2 tool was used to assess the risk of bias.

Data Extraction and Synthesis

Preferred Reporting Items for Systematic Reviews and Meta-analyses reporting guideline was followed for the systematic review, with multiple authors involved at each stage of the review. To account for the imperfect reference test sensitivity, we used a bayesian latent class bivariate model for the meta-analysis.

Main Outcomes and Measures

The primary outcome was pooled sensitivity and specificity. Two secondary analyses were performed: one restricted to peer-reviewed studies, and a post hoc analysis limited to ambulatory settings.

Results

The search strategy yielded 385 references, and 16 unique studies were identified for quantitative synthesis. Eight peer-reviewed studies and 8 preprints were included in the meta-analyses (5922 unique patients). There was significant variability in patient selection, study design, and stage of illness at which patients were enrolled. Fifteen studies included ambulatory patients, and 9 exclusively enrolled from an outpatient population with mild or no symptoms. In the primary analysis, the saliva NAAT pooled sensitivity was 83.2% (95% credible interval [CrI], 74.7%-91.4%) and the pooled specificity was 99.2% (95% CrI, 98.2%-99.8%). The nasopharyngeal swab NAAT had a sensitivity of 84.8% (95% CrI, 76.8%-92.4%) and a specificity of 98.9% (95% CrI, 97.4%-99.8%). Results were similar in secondary analyses.

Conclusions and Relevance

These results suggest that saliva NAAT diagnostic accuracy is similar to that of nasopharyngeal swab NAAT, especially in the ambulatory setting. These findings support larger-scale research on the use of saliva NAAT as an alternative to nasopharyngeal swabs.

Cost effective reproduction number based strategies for reducing deaths from COVID-19

In epidemiology, the effective reproduction number R e is used to characterize the growth rate of an epidemic outbreak. If R e > 1 , the epidemic worsens, and if R e < 1 , then it subsides and eventually dies out. In this paper, we investigate properties of R e for a modified SEIR model of COVID-19 in the city of Houston, TX USA, in which the population is divided into low-risk and high-risk subpopulations. The response of R e to two types of control measures (testing and distancing) applied to the two different subpopulations is characterized. A nonlinear cost model is used for control measures, to include the effects of diminishing returns. Lowest-cost control combinations for reducing instantaneous R e to a given value are computed. We propose three types of heuristic strategies for mitigating COVID-19 that are targeted at reducing R e , and we exhibit the tradeoffs between strategy implementation costs and number of deaths. We also consider two variants of each type of strategy: basic strategies, which consider only the effects of controls on R e , without regard to subpopulation; and high-risk prioritizing strategies, which maximize control of the high-risk subpopulation. Results showed that of the three heuristic strategy types, the most cost-effective involved setting a target value for R e and applying sufficient controls to attain that target value. This heuristic led to strategies that begin with strict distancing of the entire population, later followed by increased testing. Strategies that maximize control on high-risk individuals were less cost-effective than basic strategies that emphasize reduction of the rate of spreading of the disease. The model shows that delaying the start of control measures past a certain point greatly worsens strategy outcomes. We conclude that the effective reproduction can be a valuable real-time indicator in determining cost-effective control strategies.

Measures implemented in the school setting to contain the COVID-19 pandemic: a scoping review

BACKGROUND

In response to the spread of SARS-CoV-2 and the impact of COVID-19, national and subnational governments implemented a variety of measures in order to control the spread of the virus and the associated disease. While these measures were imposed with the intention of controlling the pandemic, they were also associated with severe psychosocial, societal, and economic implications on a societal level. One setting affected heavily by these measures is the school setting. By mid-April 2020, 192 countries had closed schools, affecting more than 90% of the world's student population. In consideration of the adverse consequences of school closures, many countries around the world reopened their schools in the months after the initial closures. To safely reopen schools and keep them open, governments implemented a broad range of measures. The evidence with regards to these measures, however, is heterogeneous, with a multitude of study designs, populations, settings, interventions and outcomes being assessed. To make sense of this heterogeneity, we conducted a rapid scoping review (8 October to 5 November 2020). This rapid scoping review is intended to serve as a precursor to a systematic review of effectiveness, which will inform guidelines issued by the World Health Organization (WHO). This review is reported in line with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) checklist and was registered with the Open Science Framework.

OBJECTIVES

To identify and comprehensively map the evidence assessing the impacts of measures implemented in the school setting to reopen schools, or keep schools open, or both, during the SARS-CoV-2/COVID-19 pandemic, with particular focus on the types of measures implemented in different school settings, the outcomes used to measure their impacts and the study types used to assess these.

SEARCH METHODS

We searched the Cochrane COVID-19 Study Register, MEDLINE, Embase, the CDC COVID-19 Research Articles Downloadable Database for preprints, and the WHO COVID-19 Global literature on coronavirus disease on 8 October 2020.

SELECTION CRITERIA

We included studies that assessed the impact of measures implemented in the school setting. Eligible populations were populations at risk of becoming infected with SARS-CoV-2, or developing COVID-19 disease, or both, and included people both directly and indirectly impacted by interventions, including students, teachers, other school staff, and contacts of these groups, as well as the broader community. We considered all types of empirical studies, which quantitatively assessed impact including epidemiological studies, modelling studies, mixed-methods studies, and diagnostic studies that assessed the impact of relevant interventions beyond diagnostic test accuracy. Broad outcome categories of interest included infectious disease transmission-related outcomes, other harmful or beneficial health-related outcomes, and societal, economic, and ecological implications.

DATA COLLECTION AND ANALYSIS

We extracted data from included studies in a standardized manner, and mapped them to categories within our a priori logic model where possible. Where not possible, we inductively developed new categories. In line with standard expectations for scoping reviews, the review provides an overview of the existing evidence regardless of methodological quality or risk of bias, and was not designed to synthesize effectiveness data, assess risk of bias, or characterize strength of evidence (GRADE).

MAIN RESULTS

We included 42 studies that assessed measures implemented in the school setting. The majority of studies used mathematical modelling designs (n = 31), while nine studies used observational designs, and two studies used experimental or quasi-experimental designs. Studies conducted in real-world contexts or using real data focused on the WHO European region (EUR; n = 20), the WHO region of the Americas (AMR; n = 13), the West Pacific region (WPR; n = 6), and the WHO Eastern Mediterranean Region (EMR; n = 1). One study conducted a global assessment and one did not report on data from, or that were applicable to, a specific country. Three broad intervention categories emerged from the included studies: organizational measures to reduce transmission of SARS-CoV-2 (n = 36), structural/environmental measures to reduce transmission of SARS-CoV-2 (n = 11), and surveillance and response measures to detect SARS-CoV-2 infections (n = 19). Most studies assessed SARS-CoV-2 transmission-related outcomes (n = 29), while others assessed healthcare utilization (n = 8), other health outcomes (n = 3), and societal, economic, and ecological outcomes (n = 5). Studies assessed both harmful and beneficial outcomes across all outcome categories.

AUTHORS' CONCLUSIONS

We identified a heterogeneous and complex evidence base of measures implemented in the school setting. This review is an important first step in understanding the available evidence and will inform the development of rapid reviews on this topic.