Early warning signal reliability varies with COVID-19 waves.

Early warning signals (EWSs) aim to predict changes in complex systems from phenomenological signals in time series data. These signals have recently been shown to precede the emergence of disease outbreaks, offering hope that policymakers can make predictive rather than reactive management decisions. Here, using a novel, sequential analysis in combination with daily COVID-19 case data across 24 countries, we suggest that composite EWSs consisting of variance, autocorrelation and skewness can predict nonlinear case increases, but that the predictive ability of these tools varies between waves based upon the degree of critical slowing down present. Our work suggests that in highly monitored disease time series such as COVID-19, EWSs offer the opportunity for policymakers to improve the accuracy of urgent intervention decisions but best characterize hypothesized critical transitions.

Challenges on the interaction of models and policy for pandemic control.

The COVID-19 pandemic has seen infectious disease modelling at the forefront of government decision-making. Models have been widely used throughout the pandemic to estimate pathogen spread and explore the potential impact of different intervention strategies. Infectious disease modellers and policymakers have worked effectively together, but there are many avenues for progress on this interface. In this paper, we identify and discuss seven broad challenges on the interaction of models and policy for pandemic control. We then conclude with suggestions and recommendations for the future.

Early warning signals predict emergence of COVID-19 waves (preprint)

Early warning signals (EWSs) aim to predict changes in complex systems from phenomenological signals in time series data. These signals have recently been shown to precede the initial emergence of disease outbreaks, offering hope that policy makers can make predictive rather than reactive management decisions. Here, using daily COVID-19 case data in combination with a novel, sequential analysis, we show that composite EWSs consisting of variance, autocorrelation, and return rate not only pre-empt the initial emergence of COVID-19 in the UK by 14 to 29 days, but also the following wave six months later. We also predict there is a high likelihood of a third wave as of the data available on 9th June 2021. Our work suggests that in highly monitored disease time series such as COVID-19, EWSs offer the opportunity for policy makers to improve the accuracy of time critical decisions based solely upon surveillance data.

Reproduction as a Means of Evaluating Policy Models: A Case Study of a COVID-19 Simulation (preprint)

This article proposes (and demonstrates the effectiveness of) a new strategy for assessing the results of epidemic models which we designate reproduction. The strategy is to build an independent model that uses (as far as possible) only the published information about the model to be assessed. In the example presented here, the independent model also follows a different modelling approach (agent-based modelling) to the model being assessed (the London School of Hygiene and Tropical Medicine compartmental model which has been influential in COVID lockdown policy). The argument runs that if the policy prescriptions of the two models match then this independently supports them (and reduces the chance that they are artefacts of assumptions, modelling approach or programming bugs). If, on the other hand, they do not match then either the model being assessed is not provided with sufficient information to be relied on or (perhaps) there is something wrong with it. In addition to justifying the approach, describing the two models and demonstrating the success of the approach, the article also discusses additional benefits of the reproduction strategy independent of whether match between policy prescriptions is actually achieved.

A Fast and Accessible Method for the Isolation of RNA, DNA, and Protein To Facilitate the Detection of SARS-CoV-2.

Management of the coronavirus disease 2019 (COVID-19) pandemic requires widespread testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A main limitation for widespread SARS-CoV-2 testing is the global shortage of essential supplies, among them RNA extraction kits. The need for commercial RNA extraction kits places a bottleneck on tests that detect SARS-CoV-2 genetic material, including PCR-based reference tests. Here, we propose an alternative method we call PEARL (precipitation-enhanced analyte retrieval) that addresses this limitation. PEARL uses a lysis solution that disrupts cell membranes and viral envelopes while simultaneously providing conditions suitable for alcohol-based precipitation of RNA, DNA, and proteins. PEARL is a fast, low-cost, and simple method that uses common laboratory reagents and offers performance comparable to that of commercial RNA extraction kits. PEARL offers an alternative method to isolate host and pathogen nucleic acids and proteins to streamline the detection of DNA and RNA viruses, including SARS-CoV-2.

Managing cancer care during the covid-19 pandemic-experience at a cancer department in a tertiary hospital in antigua and Barbuda

The emergence of corona virus disease 2019 (COVID-19) has caused a global public health emergency and the pandemic has forced the healthcare givers to organise their work differently to provide the same level of care to their patients. Meticulous planning and implementation of robust infection control, proper triage of patients, patient education and awareness and establishment of good command structure has become the norm. In this article we illustrate how the COVID-19 pandemic has affected the oncology department in a tertiary centre in the Caribbean country of Antigua & Barbuda. We describe the changes in treatment decisions for outpatient and inpatient services along with a look at the ethical considerations and the well-being of the oncology team.

A Fast and Accessible Method for the Isolation of RNA, DNA, and Protein to Facilitate the Detection of SARS-CoV-2 (preprint)

Management of the COVID-19 pandemic requires widespread SARS-CoV-2 testing. A main limitation for widespread SARS-CoV-2 testing is the global shortage of essential supplies, among these, RNA extraction kits. The need for commercial RNA extraction kits places a bottleneck on tests that detect SARS-CoV-2 genetic material, including PCR-based reference tests. Here we propose an alternative method we call PEARL (Precipitation Enhanced Analyte RetrievaL) that addresses this limitation. PEARL uses a lysis solution that disrupts cell membranes and viral envelopes while simultaneously providing conditions suitable for alcohol-based precipitation of RNA, DNA, and proteins. PEARL is a fast, low-cost, and simple method that uses common laboratory reagents and offers comparable performance to commercial RNA extraction kits. PEARL offers an alternative method to isolate host and pathogen nucleic acids and proteins to streamline the detection of DNA and RNA viruses, including SARS-CoV-2.

Geographical Accessibility to Glucose-6-Phosphate Dioxygenase Deficiency Point-of-Care Testing for Antenatal Care in Ghana.

BACKGROUND: Glucose-6-Phosphate Dehydrogenase (G6PD) deficiency screening test is essential for malaria treatment, control, and elimination programs. G6PD deficient individuals are at high risk of severe hemolysis when given anti-malarial drugs such as primaquine, quinine, other sulphonamide-containing medicines, and chloroquine, which has recently been shown to be potent for the treatment of coronavirus disease (COVID-19). We evaluated the geographical accessibility to POC testing for G6PD deficiency in Ghana, a malaria-endemic country. METHODS: We obtained the geographic information of 100 randomly sampled clinics previously included in a cross-sectional survey. We also obtained the geolocated data of all public hospitals providing G6PD deficiency testing services in the region. Using ArcGIS 10.5, we quantified geographical access to G6PD deficiency screening test and identified clinics as well as visualize locations with poor access for targeted improvement. The travel time was estimated using an assumed speed of 20 km per hour. FINDINGS: Of the 100 clinics, 58% were Community-based Health Planning and Services facilities, and 42% were sub-district health centers. The majority (92%) were Ghana Health Service facilities, and the remaining 8% were Christian Health Association of Ghana facilities. Access to G6PD deficiency screening test was varied across the districts, and G6PD deficiency screening test was available in all eight public hospitals. This implies that the health facility-to-population ratio for G6PD deficiency testing service was approximately 1:159,210 (8/1,273,677) population. The spatial analysis quantified the current mean distance to a G6PD deficiency testing service from all locations in the region to be 34 ± 14 km, and travel time (68 ± 27 min). The estimated mean distance from a clinic to a district hospital for G6PD deficiency testing services was 15 ± 11 km, and travel time (46 ± 33 min). CONCLUSION: Access to POC testing for G6PD deficiency in Ghana was poor. Given the challenges associated with G6PD deficiency, it would be essential to improve access to G6PD deficiency POC testing to facilitate administration of sulphadoxine-pyrimethamine to pregnant women, full implementation of the malaria control program in Ghana, and treatment of COVID-19 patients with chloroquine in malaria-endemic countries. To enable the World Health Organization include appropriate G6PD POC diagnostic tests in its list of essential in-vitro diagnostics for use in resource-limited settings, we recommend a wider evaluation of available POC diagnostic tests for G6PD deficiency, particularly in malaria-endemic countries.