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McAloon, Conor G.
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McAloon, Conor G.
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McAloon, Conor G.
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- PublicationEpidemiological analyses to support national control of SARS-CoV-2 in Ireland(University College Dublin. School of Public Health, Physiotherapy and Sports Science, 2022)
; 0000-0002-4984-4031Pathogen 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.257 - PublicationIncubation period of COVID-19: a rapid systematic review and meta-analysis of observational research(BMJ, 2020-08-16)
; ; ; ; ; ; ; ; ; ; ; ; ; Objectives: The aim of this study was to conduct a rapid systematic review and meta-analysis of estimates of the incubation period of COVID-19. Design: Rapid systematic review and meta-analysis of observational research. Setting: International studies on incubation period of COVID-19. Participants: Searches were carried out in PubMed, Google Scholar, Embase, Cochrane Library as well as the preprint servers MedRxiv and BioRxiv. Studies were selected for meta-analysis if they reported either the parameters and CIs of the distributions fit to the data, or sufficient information to facilitate calculation of those values. After initial eligibility screening, 24 studies were selected for initial review, nine of these were shortlisted for meta-analysis. Final estimates are from meta-analysis of eight studies. Primary outcome measures: Parameters of a lognormal distribution of incubation periods. Results: The incubation period distribution may be modelled with a lognormal distribution with pooled mu and sigma parameters (95% CIs) of 1.63 (95% CI 1.51 to 1.75) and 0.50 (95% CI 0.46 to 0.55), respectively. The corresponding mean (95% CIs) was 5.8 (95% CI 5.0 to 6.7) days. It should be noted that uncertainty increases towards the tail of the distribution: the pooled parameter estimates (95% CIs) resulted in a median incubation period of 5.1 (95% CI 4.5 to 5.8) days, whereas the 95th percentile was 11.7 (95% CI 9.7 to 14.2) days. Conclusions: The choice of which parameter values are adopted will depend on how the information is used, the associated risks and the perceived consequences of decisions to be taken. These recommendations will need to be revisited once further relevant information becomes available. Accordingly, we present an R Shiny app that facilitates updating these estimates as new data become available.412Scopus© Citations 302 - PublicationModeling of alternative testing strategies to demonstrate freedom from Mycobacterium avium ssp. paratuberculosis infection in test-negative dairy herds in the Republic of Ireland(Elsevier, 2019-03)
; ; ; ; In light of the various adverse effects of Johne's disease on animal productivity and the debate on the role of its causative organism, Mycobacterium avium ssp. paratuberculosis, in the etiology of Crohn's disease, major dairy-producing countries around the world have implemented national control programs aimed at reducing the prevalence of this infection in cattle. A pilot control program was initiated in Ireland in 2013, with a key objective to provide farmers with test-negative dairy herds with tools and knowledge to increase their confidence of freedom over time. The aim of this study was to estimate the confidence of freedom obtained in test-negative Irish dairy herds over time with various sampling scenarios and to evaluate the cost-effectiveness of alternative scenarios for achieving an acceptable level of confidence of freedom in herds with no evidence of infection. A stochastic model was developed to simulate repeated annual testing of individual animals using ELISA and confirmatory assays over a period of 20 yr. Two scenarios modeled the current herd-screening options, whereas 14 alternative scenarios explored the effect of varying parameters from the current testing strategies, such as the frequency of testing, the eligibility criteria for selecting animals, the type of assay, the probability of introduction, and the assay sensitivity. Results showed that the current testing strategy with milk twice a year or serum once a year in all animals over 2 yr old provided the highest annual herd sensitivity, with a median value of 55%. Although the median confidence of freedom increased over time for all scenarios, the time required to reach 90 and 95% confidence of freedom was highly variable between scenarios. Under the testing scenario where serum tests were used once a year, the confidence of freedom reached 90% after 4 yr and 95% after 7 yr of testing. Some of the alternative scenarios achieved an acceptable level of confidence of freedom in a reasonable timeframe and at lesser cost than the current testing strategies. The results of this work are used to provide recommendations for the next phases of the program.357Scopus© Citations 16 - PublicationDevelopment of a syndromic surveillance system for Irish dairy cattle using milk recording data(Elsevier, 2022-07)
; ; ; ; ; ; ; In the last decade and a half, emerging vector-borne diseases have become a substantial threat to cattle across Europe. To mitigate the impact of the emergence of new diseases, outbreaks must be detected early. However, the clinical signs associated with many diseases may be nonspecific. Furthermore, there is often a delay in the development of new diagnostic tests for novel pathogens which limits the ability to detect emerging disease in the initial stages. Syndromic Surveillance has been proposed as an additional surveillance method that could augment traditional methods by detecting aberrations in non-specific disease indicators. The aim of this study was to develop a syndromic surveillance system for Irish dairy herds based on routinely collected milk recording and meteorological data. We sought to determine whether the system would have detected the 2012 Schmallenberg virus (SBV) incursion into Ireland earlier than conventional surveillance methods. Using 7,743,138 milk recordings from 730,724 cows in 7037 herds between 2007 and 2012, linear mixed-effects models were developed to predict milk yield and alarms generated with temporally clustered deviations from predicted values. Additionally, hotspot spatial analyses were conducted at corresponding time points. Using a range of thresholds, our model generated alarms throughout September 2012, between 4 and 6 weeks prior to the first laboratory confirmation of SBV in Ireland. This system for monitoring milk yield represents both a potentially useful tool for early detection of disease, and a valuable foundation for developing similar tools using other metrics.220Scopus© Citations 1 - PublicationNumbers of close contacts of individuals infected with SARS-CoV-2 and their association with government intervention strategies(Springer, 2021-12-09)
; ; ; ; ; ; ; 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.218Scopus© Citations 7 - PublicationJohne’s disease in Irish dairy herds: considerations for an effective national control programme(Springer, 2020-08-14)
; ; ; ; The Irish dairy industry has established a reputation for the production of safe and healthy dairy products and is seeking to further expand its export market for high value dairy products. To support its reputation, stakeholders aim to control Johne’s disease. To assist decision-makers determine the most appropriate design for an Irish programme, a narrative review of the scientific literature on the epidemiology of Johne’s disease, and selected control programmes throughout the world was undertaken. Two modelling studies specifically commissioned by Animal Health Ireland to assess testing methods used to demonstrate confidence of freedom in herds and to evaluate a range of possible surveillance strategies provided additional information. The majority of control programmes tend to be voluntary, because of the unique epidemiology of Johne’s disease and limited support for traditional regulatory approaches. While acknowledging that test performance and sub-clinical sero-negative shedders contributes to the spread of infection, a range of socio-political issues also exist that influence programme activities. The paper provides a rationale for the inclusion of a Veterinary Risk Assessment and Management Plan (VRAMP), including voluntary whole herd testing to identify infected herds and to support assurance-based trading through repeated rounds of negative testing, national surveillance for herd-level case-detection, and improved understanding of biosecurity management practices. Identification and promotion of drivers for industry and producer engagement in Ireland is likely to guide the future evolution of the Irish Johne’s Control Programme (IJCP) and further enhance its success. The provision of training, education and extension activities may encourage farmers to adopt relevant farm management practices and help them recognize that they are ultimately responsible for their herd’s health and biosecurity.199Scopus© Citations 5 - PublicationAn observational study of ear-tagged calf mortality (1 to 100 days) on Irish dairy farms and associations between biosecurity practices and calf mortality on farms participating in a Johne's disease control program(Elsevier, 2023-05-22)
; ; ; ; ; Postnatal mortality among replacement stock has a detrimental effect on the social, economic, and environmental sustainability of dairy production. Calf mortality rates vary between countries and show differences in temporal trends; most, however, are characterized by high levels of between-farm variability. Explaining this variation can be difficult because herd-level information on management practices relevant to calf health is often not available. The Irish Johne's Control Programme (IJCP) contains a substantial on-farm monitoring program called the Veterinary Risk Assessment and Management Plan (VRAMP). Although this risk assessment is largely focused on factors relevant to the transmission of paratuberculosis, many of its principles are good practice biocontainment policies that are also advocated for the protection of calf health. The objectives of this study were (1) to quantify mortality in ear-tagged Irish dairy calves between 2016 and 2020 using both survival and risk approaches, (2) to determine risk factors for 100-d cumulative mortality hazard in ear-tagged Irish dairy calves between 2016 and 2020, (3) to determine whether 100-d cumulative mortality hazard was higher in ear-tagged calves within herds registered in the IJCP versus those that were not registered in the IJCP and whether there were differences between these cohorts over time, and (4) within IJCP herds, to determine whether VRAMP score or changes in VRAMP score were associated with 100-d cumulative mortality hazard. Excluding perinatal mortality, the overall 100-d cumulative mortality hazard was 4.1%. Calf mortality was consistently underestimated using risk approaches that did not account for calf censoring. Cox proportional hazards models showed that cumulative mortality hazard was greater in male calves; particularly, calves born to Jersey breed dams and those with a beef breed sire. Mortality hazard increased with increasing herd size, was highest in calves born in herds that contract-reared heifers, and lowest in those born in mixed dairy-beef enterprises. Mortality hazard decreased over time with the mortality hazard in 2020 being 0.83 times that of 2016. Mortality hazard was higher in IJCP-registered herds than nonregistered herds (hazard ratio 1.06, 95% CI 1.01–1.12), likely reflecting differences in herds that enrolled in the national program. However, we detected a significant interaction between IJCP status (enrolled vs. not enrolled) and year (hazard ratio 0.96, 95% CI 0.92–1.00), indicating that the decrease in mortality hazard between 2016 and 2020 was greater in IJCP herds versus non-IJCP herds. Finally, increasing VRAMP scores (indicating higher risk for paratuberculosis transmission) were positively associated with increased calf mortality hazard. Postnatal calf mortality rates in Irish dairy herds declined between 2016 and 2020. Our study suggests that implementation of recommended biocontainment practices to control paratuberculosis in IJCP herds was associated with a reduction in calf mortality hazard.25 - PublicationInferred duration of infectious period of SARS-CoV-2: rapid scoping review and analysis of available evidence for asymptomatic and symptomatic COVID-19 cases(BMJ Journals, 2020-08-01)
; ; ; ; ; ; ; ; ; ; ; Objectives. Our objective was to review the literature on the inferred duration of the infectious period of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, and provide an overview of the variation depending on the methodological approach. Design. Rapid scoping review. Literature review with fixed search terms, up to 1 April 2020. Central tendency and variation of the parameter estimates for infectious period in (A) asymptomatic and (B) symptomatic cases from (1) virological studies (repeated testing), (2) tracing studies and (3) modelling studies were gathered. Narrative review of viral dynamics. Information sources. Search strategies developed and the following searched: PubMed, Google Scholar, MedRxiv and BioRxiv. Additionally, the Health Information Quality Authority (Ireland) viral load synthesis was used, which screened literature from PubMed, Embase, ScienceDirect, NHS evidence, Cochrane, medRxiv and bioRxiv, and HRB open databases. Results. There was substantial variation in the estimates, and how infectious period was inferred. One study provided approximate median infectious period for asymptomatic cases of 6.5–9.5 days. Median presymptomatic infectious period across studies varied over <1–4 days. Estimated mean time from symptom onset to two negative RT-PCR tests was 13.4 days (95% CI 10.9 to 15.8) but was shorter when studies included children or less severe cases. Estimated mean duration from symptom onset to hospital discharge or death (potential maximal infectious period) was 18.1 days (95% CI 15.1 to 21.0); time to discharge was on average 4 days shorter than time to death. Viral dynamic data and model infectious parameters were often shorter than repeated diagnostic data. Conclusions. There are limitations of inferring infectiousness from repeated diagnosis, viral loads and viral replication data alone and also potential patient recall bias relevant to estimating exposure and symptom onset times. Despite this, available data provide a preliminary evidence base to inform models of central tendency for key parameters and variation for exploring parameter space and sensitivity analysis.373Scopus© Citations 195 - PublicationThe prevalence, temporal and spatial trends in bulk tank equivalent milk fat depression in Irish milk recorded herds.(Springer, 2017-05-18)
; ; ; ; ; ; ; Milk fat is important in terms of economic value and in its potential to provide information concerning cow diet and health. Under current milk payment schemes in Ireland farmer income is directly linked to milk fat production.461Scopus© Citations 9 - PublicationPresymptomatic transmission of SARS-CoV-2 infection: a secondary analysis using published data(BMJ, 2021-06-28)
; ; ; ; ; ; ; ; ; ; ; ; ; ; Objective To estimate the proportion of presymptomatic transmission of SARS-CoV-2 infection that can occur, and the timing of transmission relative to symptom onset.Setting/design Secondary analysis of international published data.Data sources Meta-analysis of COVID-19 incubation period and a rapid review of serial interval and generation time, which are published separately.Participants Data from China, the Islamic Republic of Iran, Italy, Republic of Korea, Singapore and Vietnam from December 2019 to May 2020.Methods Simulations were generated of incubation period and of serial interval or generation time. From these, transmission times relative to symptom onset, and the proportion of presymptomatic transmission, were estimated.Outcome measures Transmission time of SARS-CoV-2 relative to symptom onset and proportion of presymptomatic transmission.Results Based on 18 serial interval/generation time estimates from 15 papers, mean transmission time relative to symptom onset ranged from −2.6 (95% CI −3.0 to –2.1) days before infector symptom onset to 1.4 (95% CI 1.0 to 1.8) days after symptom onset. The proportion of presymptomatic transmission ranged from 45.9% (95% CI 42.9% to 49.0%) to 69.1% (95% CI 66.2% to 71.9%).Conclusions There is substantial potential for presymptomatic transmission of SARS-CoV-2 across a range of different contexts. This highlights the need for rapid case detection, contact tracing and quarantine. The transmission patterns that we report reflect the combination of biological infectiousness and transmission opportunities which vary according to context.341Scopus© Citations 27