Now showing 1 - 10 of 10
  • Publication
    COVID-19 epidemiological parameters summary document
    In response to the coronavirus (COVID-19) outbreak, the Irish Epidemiological Modelling Advisory Group (IEMAG) for COVID-19 was established to assist the Irish National Public Health Emergency Team (NPHET) in their decision-making during the pandemic. A subcommittee from IEMAG (the epidemiological parameters team) was tasked with researching the various parameters, leading to the development of a series of synthesis documents relevant to the parameterisation of a COVID-19 transmission model for Ireland. These parameters include: • R0/R • Latent period & relative importance of pre-symptomatic period • Incubation period • Generation time & serial interval • Proportion of infected who are asymptomatic, by age • Length of infectious period in asymptomatic people and in symptomatic people who do not isolate • Time from onset of symptoms to diagnosis/test results and to hospitalisation • Length of hospital stay and admission to ICUs • Relative infectiousness of asymptomatic versus symptomatic infected people. The current document presents an up-to-date summary of these synthesis documents. A further synthesis document on age-related susceptibility and age-related infectiousness is in preparation.
  • Publication
    Cadmium exposure and consequences for the health and productivity of farmed ruminants
    This paper reviews Cd exposure and consequences for the health and productivity of farmed ruminants. In farmed ruminants, Cd exposure may be associated with a number of different activities, including industrial processing, mining, and agricultural practices, and is also higher in soils in some geographic regions. Cd kidney concentrations increase with age and Cd exposure. Although Cd toxicity in farmed ruminants has been demonstrated experimentally, there are no published reports of naturally occurring Cd toxicity in farmed ruminants. Clinical signs of Cd intoxication are unlikely with a daily dietary Cd intake of less than 5 mg/kg feed, which is 5–10 times higher than the maximum permitted Cd concentration in ruminant feed in the European Union. In farmed ruminants, Cd levels in tissue are largely dependent on the Cd content of diet. However, many factors affect Cd availability, relating to soils, plants and the presence of other trace elements including Ca, Cu, Fe, Mn, Mo, Se and Zn. Experimental studies have highlighted the ability of Cd to alter trace element status, and the protective effect of good mineral status, however, there remain gaps in knowledge of the impact of these interactions on the health and productivity of farmed animals.
      346Scopus© Citations 71
  • Publication
    Sampling Methodology to Maximize the Efficient Use of National Abattoir Surveillance: Using Archived Sera to Substantiate Freedom From Bluetongue Virus Infection in Ireland
    In recent years, there has been increasing recognition of the value of multiple data sources available to fulfill surveillance objectives, and the use of these has been applied to address many questions relating to animal health surveillance. In Ireland, we face a slightly different problem, namely, best use of an existing surveillance resource (serological samples collected over many years from cull cows at slaughter), which has been used to substantiate freedom from Brucella abortus following its successful eradication in 2009. In this study, we evaluate a sampling methodology to use this resource to substantiate freedom from bluetongue virus (BTV) infection. An examination of the degree to which cull cows were resident in the same herd throughout the midge biting season showed that, of 50,640 samples collected between 17 October and 23 December 2016, 80.2% were from animals resident in the same herd between 01 April 2016 and 2 months prior to their slaughter date, 74.1% for 1 month prior, 70.1% for 2 weeks prior, 66.4% for 1 week prior, and 56.4% up to 1 day prior to slaughter. An examination was made of the degree to which individual samples within the same 88-well frozen storage block came from geographically clustered herds, whether from a concentration of animals from the same herd in a single block, or from clustering around the slaughterhouse where the samples were taken. On the basis of these analyses, a sampling strategy was derived aimed at minimizing the number of storage blocks which needed to be thawed, whilst ensuring a large enough and representative sample, geographically stratified according to the bovine population of 51 squares, each 45 × 45 km, covering the entirety of Ireland. None of the 503 samples tested were positive for BTV, providing reassurance of national BTV freedom. More broadly, the study demonstrates the use of abattoir-based serological samples collected for one large scale surveillance programme in surveillance for other bovine infections.
      333Scopus© Citations 3
  • 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.
      219Scopus© Citations 21
  • Publication
    Incubation period of COVID-19: a rapid systematic review and meta-analysis of observational research
    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.
      319Scopus© Citations 261
  • Publication
    Inferred duration of infectious period of SARS-CoV-2: rapid scoping review and analysis of available evidence for asymptomatic and symptomatic COVID-19 cases
    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.
      291Scopus© Citations 157
  • Publication
    The Irish Programme to Eradicate Bovine Viral Diarrhoea Virus—Organization, Challenges, and Progress
    A mandatory national Irish bovine viral diarrhoea (BVD) eradication programme, coordinated by Animal Health Ireland, commenced in 2013. Key decisions and programme review are undertaken by a cross-industry Implementation Group (BVDIG) supported by a Technical Working Group. Ear notch tissue is collected from all new-born calves using modified official identity tags, supplemented by additional blood sampling, including for confirmatory testing of calves with initial positive results and testing of their dams. Testing is delivered by private laboratories in conjunction with the National Reference Laboratory, with all results reported to a central database. This database manages key elements of the programme, issuing results to herdowners by short message service messaging supplemented by letters; assigning and exchanging animal-level statuses with government databases of the Department of Agriculture, Food and the Marine to enable legislated restrictions on animal movements; assigning negative herd status based on test results; generating regular reports for programme management and evaluation and providing herd-specific dashboards for a range of users. Legislation supporting the programme has been in place throughout but has not thus far mandated the slaughter of persistently infected (PI) calves. A key challenge in the early years, highlighted by modeling, was the retention of PI animals by some herd owners. This has largely been resolved by measures including graduated financial supports to encourage their early removal, herd-level movement restrictions, ongoing programme communications and the input of private veterinary practitioners (PVPs). A framework for funded investigations by PVPs in positive herds was developed to identify plausible sources of infection, to resolve the status of all animals in the herd and to agree up to three measures to prevent re-introduction of the virus. The prevalence of PI calves in 2013 was 0.66%, within 11.3% of herds, reducing in each subsequent year, to 0.03 and 0.55%, respectively, at the end of 2020. Recent regulatory changes within the European Union for the first time make provision for official approval of national eradication programmes, or recognition of BVD freedom, and planning is underway to seek approval and, in due course, recognition of freedom within this framework by 2023.
      170Scopus© Citations 7
  • Publication
    Presymptomatic transmission of SARS-CoV-2 infection: a secondary analysis using published data
    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.
      236Scopus© Citations 21
  • Publication
    Cadmium and other heavy metal concentrations in bovine kidneys in the Republic of Ireland
    In Ireland, an estimated 15% of Irish soils exceed the EU threshold limit for soil Cd of 1 mg/kg. The aim was to determine the concentrations of Cd and other heavy metals (As, Hg and Pb) in kidneys collected from cattle at slaughter. Systematic sampling of eligible animals (animals that were born and reared until slaughter in the same Irish county) at the time of slaughter was conducted, until a threshold number of animals from all 26 counties and 6 age categories was reached. A predictive surface of soil Cd was generated, by kriging the Cd values of 1310 previously reported soil samples. A linear regression weighted model was developed to model kidney Cd concentration, using the risk factors of age, sex, breed, province and estimated soil Cd concentration. Kidney Cd (n = 393) concentrations varied between 0.040 and 8.630 mg/kg wet weight; while concentrations of As, Hg and Pb were low. The estimated weighted proportion of animals with a high (≥ 1 mg/kg) kidney Cd concentration was 11.25% (95% CI: 8.63–14.53%). Key predictors for high kidney Cd concentration were soil Cd, animal age and province. At a soil Cd concentration of 1.5 mg/kg, it was predicted that an age threshold to avoid exceeding a kidney Cd concentration of 1 mg/kg in most animals would be ~ 3 y in Connacht, > 4 y in Ulster, and > 5 y in Leinster and Munster. In naturally occurring areas of high Cd levels in soils in Ireland, the Cd level in bovine kidneys can exceed the current EU ML of 1 mg/kg in older animals. Kidneys of most cattle under three years of age will conform with EU requirements.
      267Scopus© Citations 25
  • Publication
    Rapid review of available evidence on the serial interval and generation time of COVID-19
    The serial interval is the time between symptom onsets in an infector–infectee pair. The generation time, also known as the generation interval, is the time between infection events in an infector–infectee pair. The serial interval and the generation time are key parameters for assessing the dynamics of a disease. A number of scientific papers reported information pertaining to the serial interval and/or generation time for COVID-19.
      200Scopus© Citations 53