Aggressively find, test, trace and isolate to beat COVID-19

A Large Neighbourhood Search Metaheuristic for the Contagious Disease Testing Problem

In late 2019 a new coronavirus disease (COVID-19) emerged, causing a global pandemic within only a few weeks. A crucial factor in the public health response to pandemics is achieving a short turnaround time between a potential case becoming known, specimen collection and availability of a test result. In this article we address a logistics problem that arises in the context of testing potential cases. We assume that specimens can be collected in two ways: either by means of a mobile test-team or by means of a stationary test-team in a test-centre. After the specimens have been collected they must be delivered to a laboratory in order to be analysed. The problem we address aims at deciding how many test-centres to open and where, how many mobile test-teams to use, which suspected cases to assign to a test-centre and which to visit with a mobile test-team, which specimen to assign to which laboratory, and planning the routes of the mobile test-teams. The objective is to minimise the total cost of opening test-centres and routing mobile test-teams. We introduce this new problem, which we call the contagious disease testing problem (CDTP), and present a mixed-integer linear-programming formulation for it. We propose a large neighbourhood search metaheuristic for solving the CDTP and present an extensive computational study to illustrate its performance. Furthermore, we give managerial insights regarding COVID-19 test logistics, derived from problem instances based on real world data.

Socioeconomic and immigration status and COVID-19 testing in Toronto, Ontario: retrospective cross-sectional study

Background

Preliminary evidence suggests that individuals living in lower income neighbourhoods are at higher risk of COVID-19 infection. The relationship between sociodemographic characteristics and COVID-19 risk warrants further study.

Methods

We explored the association between COVID-19 test positivity and patients’ socio-demographic variables, using neighborhood sociodemographic data collected retrospectively from two COVID-19 Assessment Centres in Toronto, ON.

Results

Eighty-three thousand four hundred forty three COVID-19 tests completed between April 5–September 30, 2020, were analyzed. Individuals living in neighbourhoods with the lowest income or highest concentration of immigrants were 3.4 (95% CI: 2.7 to 4.9) and 2.5 (95% CI: 1.8 to 3.7) times more likely to test positive for COVID-19 than those in highest income or lowest immigrant neighbourhoods, respectively. Testing was higher among individuals from higher income neighbourhoods, at lowest COVID-19 risk, compared with those from low-income neighbourhoods.

Conclusions

Targeted efforts are needed to improve testing availability in high-risk regions. These same strategies may also ensure equitable COVID-19 vaccine delivery.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12889-022-13388-2.

Molecular and Serologic Diagnostic Technologies for SARS-CoV-2

The COVID-19 pandemic has presented many challenges that have spurred biotechnological research to address specific problems. Diagnostics is one area where biotechnology has been critical. Diagnostic tests play a vital role in managing a viral threat by facilitating the detection of infected and/or recovered individuals. From the perspective of what information is provided, these tests fall into two major categories, molecular and serological. Molecular diagnostic techniques assay whether a virus is present in a biological sample, thus making it possible to identify individuals who are currently infected. Additionally, when the immune system is exposed to a virus, it responds by producing antibodies specific to the virus. Serological tests make it possible to identify individuals who have mounted an immune response to a virus of interest and therefore facilitate the identification of individuals who have previously encountered the virus. These two categories of tests provide different perspectives valuable to understanding the spread of SARS-CoV-2. Within these categories, different biotechnological approaches offer specific advantages and disadvantages. Here we review the categories of tests developed for the detection of the SARS-CoV-2 virus or antibodies against SARS-CoV-2 and discuss the role of diagnostics in the COVID-19 pandemic.

Proposed framework for a national set of reporting measures in Canada in response to the COVID-19 pandemic

An effective strategy to control the ongoing coronavirus disease 2019 (COVID-19) pandemic takes into account inputs from many domains, including community epidemiology, surveillance and testing, contact tracing capacity, support for vulnerable populations, and health care system strain. Provincial and federal governments currently lack a universal approach to presenting relevant pandemic data from these domains to the general public in a way that engages them in decision making and promotes adherence to policies. We propose a framework to analyze COVID-19 pandemic data on an ongoing basis using inputs from these five domains, which can be scaled to the local public health unit, provincial, or national level. Data analysis was qualitative and semi-quantitative because there was a paucity of publicly available data on surveillance and testing, contact tracing, and health care system strain, which limited our ability to perform internal and external validation of our model. We urge the federal government to mandate a core set of reporting items across local, provincial, and federal jurisdictions that may then be used to perform validation and implementation of our proposed framework.

On the effect of the number of tests and their time of application in tracing policies against COVID-19

In this paper we explore the effect of the number of daily tests on an epidemics control policy purely based on testing and selective quarantine, and the impact of these actions depending on the time their application starts. We introduce a general model incorporating a stochastic disease evolution, a particular weighted graph representing the population, and an optimal contact tracing strategy to allocate available tests. Simulations on a community of 50'000 individuals show that the evolution of the epidemic produces a clear non-linear response to the variation of the number of tests used and to the starting time of their application. These results suggest that not only a minimum number of tests is necessary to obtain a positive outcome from the tracing strategy but also that there exists a saturation on the contribution of additional tests. The results also show that the timing in the application of the measures is as important as the measures themselves and that an excessive delay can be hardly overcome.

Association between new-onset anosmia and positive SARS-CoV-2 tests among people accessing outpatient testing in Toronto, Ontario: a retrospective cross-sectional study

BACKGROUND

Reports have suggested that anosmia is strongly associated with SARS-CoV-2 infection, but patients were often asked about this symptom after their diagnosis. This study assessed associations between prospectively reported anosmia and other symptoms related to SARS-CoV-2 infection, and SARS-CoV-2 positivity in community testing centres in Toronto, Ontario.

METHODS

We conducted a retrospective cross-sectional study in which data were collected from 2 COVID-19 assessment centres affiliated with 2 hospitals in Toronto, Ontario, from Apr. 5 to Sept. 30, 2020. We included symptomatic profiles of all people who underwent a SARS-CoV-2 test at either clinic within the study period. We used generalized estimating equations to account for repeat visits and to assess associations between anosmia and other symptoms and SARS-CoV-2 positivity.

RESULTS

A total of 83 443 SARS-CoV-2 tests were conducted across the 2 sites for 72 692 participants during the study period. Of all tests, 1640 (2.0%) were positive; 837 (51.0%) of people who tested positive were asymptomatic. The adjusted odds ratio for the association between anosmia and test positivity was 5.29 (95% confidence interval [CI] 4.50-6.22), with sensitivity of 0.138 (95% CI 0.121-0.154), specificity of 0.980 (95% CI 0.979-0.981), a positive predictive value of 0.120 (95% CI 0.106-0.135) and a negative predictive value of 0.983 (95% CI 0.982-0.984).

INTERPRETATION

Anosmia had high specificity and a positive predictive value of 12% for SARS-CoV-2 infection in this community population with low prevalence of SARS-CoV-2 positivity. The presence of anosmia should increase clinical suspicion of SARS-CoV-2 infection, and our findings suggest that people presenting with this symptom should be tested.

Is My Cough a Cold or Covid? A Qualitative Study of COVID-19 Symptom Recognition and Attitudes Toward Testing in the UK

Objective: Key to reducing the spread of COVID-19 in the UK is increased use of the NHS Test and Trace (NHSTT) system. This study explored one of the main issues that determine whether people engage with NHSTT, how people understand symptoms that may indicate the presence of COVID-19 and that should trigger a request for a test.

Methods: In this qualitative study, a series of semi-structured telephone interviews were conducted with 40 people (21 members of the general population, 19 students). There was nearly an equal split between male and female participants in both samples. Data were collected between 30 November and 11 December 2020 and explored using thematic analysis. There was substantial similarity in responses for both populations so we combined our results and highlighted where differences were present.

Results: Participants generally had good knowledge of the main symptoms of COVID-19 (high temperature, new, persistent cough, anosmia) but had low confidence in their ability to differentiate them from symptoms of other illnesses. Attribution of symptoms to COVID-19 was most likely where the symptoms were severe, many symptoms were present, symptoms had lasted for some time and when perceived risk of exposure to infection was high due to previous contact with others. Participants felt encouraged to engage in testing where symptoms were present and had persisted for several days, though, many had concerns about the safety of testing centres and the accuracy of test results. Students had mixed feelings about mass asymptomatic testing, seeing it as a way to access a more normal student experience, but also a potential waste of resources.

Conclusions: This study offers novel insights into how people attribute symptoms to COVID-19 and barriers and facilitators to engaging with NHSTT. Participants had positive views of testing, but there is a need to improve not just recognition of each main symptom, but also understanding that even single, mild symptoms may necessitate a test rather than a “wait and see” approach, and to address concerns around test accuracy to increase testing uptake.

Exploring Changes to the Actionability of COVID-19 Dashboards Over the Course of 2020 in the Canadian Context: Descriptive Assessment and Expert Appraisal Study

BACKGROUND

Public web-based COVID-19 dashboards are in use worldwide to communicate pandemic-related information. Actionability of dashboards, as a predictor of their potential use for data-driven decision-making, was assessed in a global study during the early stages of the pandemic. It revealed a widespread lack of features needed to support actionability. In view of the inherently dynamic nature of dashboards and their unprecedented speed of creation, the evolution of dashboards and changes to their actionability merit exploration.

OBJECTIVE

We aimed to explore how COVID-19 dashboards evolved in the Canadian context during 2020 and whether the presence of actionability features changed over time.

METHODS

We conducted a descriptive assessment of a pan-Canadian sample of COVID-19 dashboards (N=26), followed by an appraisal of changes to their actionability by a panel of expert scorers (N=8). Scorers assessed the dashboards at two points in time, July and November 2020, using an assessment tool informed by communication theory and health care performance intelligence. Applying the nominal group technique, scorers were grouped in panels of three, and evaluated the presence of the seven defined features of highly actionable dashboards at each time point.

RESULTS

Improvements had been made to the dashboards over time. These predominantly involved data provision (specificity of geographic breakdowns, range of indicators reported, and explanations of data sources or calculations) and advancements enabled by the technologies employed (customization of time trends and interactive or visual chart elements). Further improvements in actionability were noted especially in features involving local-level data provision, time-trend reporting, and indicator management. No improvements were found in communicative elements (clarity of purpose and audience), while the use of storytelling techniques to narrate trends remained largely absent from the dashboards.

CONCLUSIONS

Improvements to COVID-19 dashboards in the Canadian context during 2020 were seen mostly in data availability and dashboard technology. Further improving the actionability of dashboards for public reporting will require attention to both technical and organizational aspects of dashboard development. Such efforts would include better skill-mixing across disciplines, continued investment in data standards, and clearer mandates for their developers to ensure accountability and the development of purpose-driven dashboards.