Now showing 1 - 5 of 5
  • Publication
    Potential Application of SARS-CoV-2 Rapid Antigen Diagnostic Tests for the Detection of Infectious Individuals Attending Mass Gatherings – A Simulation Study
    Rapid Antigen Diagnostic Tests (RADTs) for the detection of SARS-CoV-2 offer advantages in that they are cheaper and faster than currently used PCR tests but have reduced sensitivity and specificity. One potential application of RADTs is to facilitate gatherings of individuals, through testing of attendees at the point of, or immediately prior to entry at a venue. Understanding the baseline risk in the tested population is of particular importance when evaluating the utility of applying diagnostic tests for screening purposes. We used incidence data from January and from July-August 2021, periods of relatively high and low levels of infection, to estimate the prevalence of infectious individuals in the community at particular time points and simulated mass gatherings by sampling froma series of age cohorts. Nine different illustrative scenarios were simulated, small (n = 100), medium (n = 1,000) and large (n = 10,000) gatherings each with 3 possible age constructs: mostly younger, mostly older or a gathering with equal numbers from each age cohort. For each scenario, we estimated the prevalence of infectious attendees, then simulated the likely number of positive and negative test results, the proportion of cases detected and the corresponding positive and negative predictive values, and the cost per case identified. Our findings suggest that for each reported case on a given day, there are likely to be 13.8 additional infectious individuals also present in the community. Prevalence ranged from 0.26% for “mostly older” events in July-August, to 2.6% for “mostly younger” events in January. For small events (100 attendees) the expected number of infectious attendees ranged from <1 across all age constructs of attendees in July-August, to 2.6 for “mostly younger” events in January. For large events (10,000 attendees) the expected number of infectious attendees ranged from 27 (95% confidence intervals 12 to 45) for mostly older events in July-August, to 267 (95% confidence intervals 134 to 436) infectious attendees for mostly younger attendees in January. Given rapid changes in SARS-CoV-2 incidence over time, we developed an RShiny app to allow users to run updated simulations for specific events.
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  • Publication
    Epidemiological analyses to support national control of SARS-CoV-2 in Ireland
    (University College Dublin. School of Public Health, Physiotherapy and Sports Science, 2022) ;
    0000-0002-4984-4031
    Pathogen emergence has been increasing in recent decades. In December 2019, an outbreak of atypical pneumonia emerged in Wuhan, central China. The cause of the disease, was subsequently identified as a novel coronavirus (SARS-CoV-2) and the disease named COVID-19. Over a short period of time SARS-CoV-2 rapidly spread throughout mainland China and surrounding countries in the western pacific before cases appeared in Europe in February of 2020. The first case in Ireland was documented in Ireland on the 29th of February 2020. In response, a series of epidemiological analyses were conducted to support decision making in the national control of the disease. The objective of this thesis was to provide regions-specific estimates of region-specific epidemiological parameters of interest, to aid in the accurate modelling of the disease in the country. The ultimate goal was to improve models so that more accurate information could be provided to decision makers. Chapter one proposed the use of the number of close contacts of infected cases over time as a metric for monitoring behaviour of infected contacts. The study found that the distribution of contacts per case was overdispersed, with a small proportion of cases reporting very large numbers of contacts. The study also provided an evidence basis for mathematical age-cohort compartmental models, by providing data on the social contacts of the Irish population under different levels of restriction. Chapter two estimated the serial interval of SARS-CoV-2 in Ireland using contact tracing data. The median serial interval was 4.0 days which was lower than estimates previously used for the statistical approximation of the serial interval in Ireland. Furthermore, the study also suggested that up to two thirds of transmission events were likely to have occurred prior to the onset of symptoms in the primary case. Finally, chapter three evaluated the potential use of Rapid Antigen Diagnostic Tests in screening individuals attending mass gatherings. The baseline risk of infection in the tested population is of key importance when interpreting the results of any imperfect diagnostic tests. This study provided a mechanism for estimating the baseline risk, as well as the uncertainty around that risk, using incidence data. The studies presented in this thesis demonstrate that secondary analyses of contact tracing data can yield meaningful and useful pieces of information that may be used to more accurately reflect transmission in the population of interest. However, it is also worth pointing out that certain opportunities were underutilized in the collection and analysis of contact tracing data. Given the apparent acceleration of pathogen emergence, evidenced in particular by the temporal proximity of repeated coronavirus outbreaks in the past 20 years, it is vital that Ireland take steps to develop infrastructure to deal with the current pandemic as well as the threat of future endemic diseases. Similar to work in other countries, this thesis demonstrates the strength of a OneHealth approach to the management of emerging infectious diseases.
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  • Publication
    Estimation of the serial interval and proportion of pre-symptomatic transmission events of COVID-19 in Ireland using contact tracing data
    The serial interval is the period of time between the onset of symptoms in an infector and an infectee and is an important parameter which can impact on the estimation of the reproduction number. Whilst several parameters influencing infection transmission are expected to be consistent across populations, the serial interval can vary across and within populations over time. Therefore, local estimates are preferable for use in epidemiological models developed at a regional level. We used data collected as part of the national contact tracing process in Ireland to estimate the serial interval of SARS-CoV-2 infection in the Irish population, and to estimate the proportion of transmission events that occurred prior to the onset of symptoms. Results After data cleaning, the final dataset consisted of 471 infected close contacts from 471 primary cases. The median serial interval was 4 days, mean serial interval was 4.0 (95% confidence intervals 3.7, 4.3) days, whilst the 25th and 75th percentiles were 2 and 6 days respectively. We found that intervals were lower when the primary or secondary case were in the older age cohort (greater than 64 years). Simulating from an incubation period distribution from international literature, we estimated that 67% of transmission events had greater than 50% probability of occurring prior to the onset of symptoms in the infector. Conclusions Whilst our analysis was based on a large sample size, data were collected for the primary purpose of interrupting transmission chains. Similar to other studies estimating the serial interval, our analysis is restricted to transmission pairs where the infector is known with some degree of certainty. Such pairs may represent more intense contacts with infected individuals than might occur in the overall population. It is therefore possible that our analysis is biased towards shorter serial intervals than the overall population.
    Scopus© Citations 8  165
  • Publication
    Numbers of close contacts of individuals infected with SARS-CoV-2 and their association with government intervention strategies
    Background: Contact tracing is conducted with the primary purpose of interrupting transmission from individuals who are likely to be infectious to others. Secondary analyses of data on the numbers of close contacts of confirmed cases could also: provide an early signal of increases in contact patterns that might precede larger than expected case numbers; evaluate the impact of government interventions on the number of contacts of confirmed cases; or provide data information on contact rates between age cohorts for the purpose of epidemiological modelling. We analysed data from 140,204 close contacts of 39,861 cases in Ireland from 1st May to 1st December 2020. Results: Negative binomial regression models highlighted greater numbers of contacts within specific population demographics, after correcting for temporal associations. Separate segmented regression models of the number of cases over time and the average number of contacts per case indicated that a breakpoint indicating a rapid decrease in the number of contacts per case in October 2020 preceded a breakpoint indicating a reduction in the number of cases by 11 days. Conclusions: We found that the number of contacts per infected case was overdispersed, the mean varied considerable over time and was temporally associated with government interventions. Analysis of the reported number of contacts per individual in contact tracing data may be a useful early indicator of changes in behaviour in response to, or indeed despite, government restrictions. This study provides useful information for triangulating assumptions regarding the contact mixing rates between different age cohorts for epidemiological modelling.
    Scopus© Citations 7  210
  • Publication
    Relative infectiousness of asymptomatic SARS-CoV-2 infected persons compared with symptomatic individuals: a rapid scoping review
    Objectives The aim of this study was to determine the relative infectiousness of asymptomatic SARS-CoV-2 infected persons compared with symptomatic individuals based on a scoping review of available literature. Design Rapid scoping review of peer-reviewed literature from 1 January to 5 December 2020 using the LitCovid database and the Cochrane library. Setting International studies on the infectiousness of individuals infected with SARS-CoV-2. Participants Studies were selected for inclusion if they defined asymptomatics as a separate cohort distinct from presymptomatics and if they provided a quantitative measure of the infectiousness of asymptomatics relative to symptomatics. Primary outcome measures PCR result (PCR studies), the rate of infection (mathematical modelling studies) and secondary attack rate (contact tracing studies) - in each case from asymptomatic in comparison with symptomatic individuals. Results There are only a limited number of published studies that report estimates of relative infectiousness of asymptomatic compared with symptomatic individuals. 12 studies were included after the screening process. Significant differences exist in the definition of infectiousness. PCR studies in general show no difference in shedding levels between symptomatic and asymptomatic individuals; however, the number of study subjects is generally limited. Two modelling studies estimate relative infectiousness to be 0.43 and 0.57, but both of these were more reflective of the infectiousness of undocumented rather than asymptomatic cases. The results from contact tracing studies include estimates of relative infectiousness of 0, but with insufficient evidence to conclude that it is significantly different from 1. Conclusions There is considerable heterogeneity in estimates of relative infectiousness highlighting the need for further investigation of this important parameter. It is not possible to provide any conclusive estimate of relative infectiousness, as the estimates from the reviewed studies varied between 0 and 1.
    Scopus© Citations 29  286