Browsing by Author "Jefferies S"

Now showing 1 - 4 of 4

COVID-19 vaccine strategies for Aotearoa New Zealand: a mathematical modelling study
(Elsevier Ltd, 2021-10) Nguyen T; Adnan M; Nguyen BP; de Ligt J; Geoghegan JL; Dean R; Jefferies S; Baker MG; Seah WKG; Sporle AA; French NP; Murdoch DR; Welch D; Simpson CR
Background: COVID-19 elimination measures, including border closures have been applied in New Zealand. We have modelled the potential effect of vaccination programmes for opening borders. Methods: We used a deterministic age-stratified Susceptible, Exposed, Infectious, Recovered (SEIR) model. We minimised spread by varying the age-stratified vaccine allocation to find the minimum herd immunity requirements (the effective reproduction number Reff<1 with closed borders) under various vaccine effectiveness (VE) scenarios and R0 values. We ran two-year open-border simulations for two vaccine strategies: minimising Reff and targeting high-risk groups. Findings: Targeting of high-risk groups will result in lower hospitalisations and deaths in most scenarios. Reaching the herd immunity threshold (HIT) with a vaccine of 90% VE against disease and 80% VE against infection requires at least 86•5% total population uptake for R0=4•5 (with high vaccination coverage for 30-49-year-olds) and 98•1% uptake for R0=6. In a two-year open-border scenario with 10 overseas cases daily and 90% total population vaccine uptake (including 0-15 year olds) with the same vaccine, the strategy of targeting high-risk groups is close to achieving HIT, with an estimated 11,400 total hospitalisations (peak 324 active and 36 new daily cases in hospitals), and 1,030 total deaths. Interpretation: Targeting high-risk groups for vaccination will result in fewer hospitalisations and deaths with open borders compared to targeting reduced transmission. With a highly effective vaccine and a high total uptake, opening borders will result in increasing cases, hospitalisations, and deaths. Other public health and social measures will still be required as part of an effective pandemic response. Funding: This project was funded by the Health Research Council [20/1018]. Research in context.
Creating symptom-based criteria for diagnostic testing: a case study based on a multivariate analysis of data collected during the first wave of the COVID-19 pandemic in New Zealand
(BioMed Central Ltd, 2021-12) French N; Jones G; Heuer C; Hope V; Jefferies S; Muellner P; McNeill A; Haslett S; Priest P
BACKGROUND: Diagnostic testing using PCR is a fundamental component of COVID-19 pandemic control. Criteria for determining who should be tested by PCR vary between countries, and ultimately depend on resource constraints and public health objectives. Decisions are often based on sets of symptoms in individuals presenting to health services, as well as demographic variables, such as age, and travel history. The objective of this study was to determine the sensitivity and specificity of sets of symptoms used for triaging individuals for confirmatory testing, with the aim of optimising public health decision making under different scenarios. METHODS: Data from the first wave of COVID-19 in New Zealand were analysed; comprising 1153 PCR-confirmed and 4750 symptomatic PCR negative individuals. Data were analysed using Multiple Correspondence Analysis (MCA), automated search algorithms, Bayesian Latent Class Analysis, Decision Tree Analysis and Random Forest (RF) machine learning. RESULTS: Clinical criteria used to guide who should be tested by PCR were based on a set of mostly respiratory symptoms: a new or worsening cough, sore throat, shortness of breath, coryza, anosmia, with or without fever. This set has relatively high sensitivity (> 90%) but low specificity (< 10%), using PCR as a quasi-gold standard. In contrast, a group of mostly non-respiratory symptoms, including weakness, muscle pain, joint pain, headache, anosmia and ageusia, explained more variance in the MCA and were associated with higher specificity, at the cost of reduced sensitivity. Using RF models, the incorporation of 15 common symptoms, age, sex and prioritised ethnicity provided algorithms that were both sensitive and specific (> 85% for both) for predicting PCR outcomes. CONCLUSIONS: If predominantly respiratory symptoms are used for test-triaging, a large proportion of the individuals being tested may not have COVID-19. This could overwhelm testing capacity and hinder attempts to trace and eliminate infection. Specificity can be increased using alternative rules based on sets of symptoms informed by multivariate analysis and automated search algorithms, albeit at the cost of sensitivity. Both sensitivity and specificity can be improved through machine learning algorithms, incorporating symptom and demographic data, and hence may provide an alternative approach to test-triaging that can be optimised according to prevailing conditions.
Ethnic equity in Aotearoa New Zealand's COVID-19 response: A descriptive epidemiological study
(Elsevier Limited, United Kingdom, on behalf of The Royal Society for Public Health, 2025-07) Jefferies S; Gilkison C; Duff P; Grey C; French N; Carr H; Priest P; Crengle S
Objectives: Aotearoa New Zealand employed one of the most stringent public health pandemic responses internationally. We investigated whether ethnic health equity was achieved in the response and outcomes, from COVID-19 elimination in June 2020 through to Omicron-response easing, including international border reopening, in 2022. Study design: Descriptive epidemiology study. Methods: All COVID-19 cases, patients tested for SARS-CoV-2 and people vaccinated against COVID-19 between 9 June 2020 and 13 April 2022 were examined over three response periods: by demographic features and COVID-19 outcomes, transmission and vaccination patterns, time-to-vaccination and testing rates. Results: There were 15,693 cases per 100,000, 138·7 hospitalisations per 100,000, and 9·8 deaths per 100,000 people. Pacific peoples and Indigenous Māori had, respectively, 9·3 to 35-fold and 1·5 to 8·3-fold higher risk of COVID-19, 5·1-fold and 2·6-fold higher age-standardised risk of hospitalisation and 9-fold and 4-fold higher age-standardised risk of death, than European or Other. Māori and Pacific peoples had lower vaccination coverage at critical points in the response, and slower access to vaccination (Adjusted Time Ratios for two doses 1·32 (95% CI 1·31–1·32) and 1·14 (1·14–1·14), respectively), than European or Other. Testing rates remained high, especially among Māori and Pacific peoples. Conclusions: Despite achieving a low overall burden of disease by international comparisons, the multi-faceted New Zealand response did not prevent stark ethnic inequities in access to vaccination and COVID-19 outcomes. Policies which address disparities in upstream determinants, early vaccine programme planning and implementation with high-risk communities, and prioritisation that addresses systematic ethnic disadvantage and promotes health equity in response decisions is recommended.
Temporal reconstruction of a Salmonella Enteritidis ST11 outbreak in New Zealand
(Microbiology Society, 2025-10-30) Strydom H; Wright J; Bromhead C; Welch D; Williams E; Mulqueen K; de Ligt J; Biggs PJ; Paine S; Jefferies S; French N
Outbreaks caused by Salmonella Enteritidis are commonly linked to eggs and poultry meat internationally, but this serovar had never been detected in Aotearoa New Zealand (NZ) poultry prior to 2021. Locally designated genomic cluster Salmonella Enteritidis_2019_C_01, was implicated in a 2019 outbreak associated with a restaurant in Auckland. Four Enteritidis_2019_C_01 sub-clusters have since been identified, two retrospectively, in the Auckland region. Authorities initiated a formal outbreak investigation after genomically indistinguishable S. Enteritidis was isolated from the NZ poultry production environment. This study analysed 231 S. Enteritidis genomes obtained from the outbreak using Bayesian phylodynamic tools to gain insight into the outbreak's dynamics and origin. We used Bayesian integrated coalescent epoch plots to estimate the change of the Enteritidis ST11 population size over time and marginal structured coalescent approximation to estimate transmission between poultry producers. We investigated human and poultry isolates to elucidate the time and location of the most recent common ancestor of the outbreak and transmission pathways. The median most recent common ancestor was estimated to be February 2019. We found evidence of amplification and spread of strain Enteritidis_2019_C_01 within the poultry industry, as well as transmission events throughout the production chain. The intervention by the public health and food safety authorities coincided with a drop in the effective population size of the S. Enteritidis ST11 as well as notified human cases. This information is crucial for understanding and preventing the transmission of S. Enteritidis in NZ poultry to ensure poultry meat and eggs are safe for consumption.