Sensitivity of RT-PCR tests for SARS-CoV-2 through time.

Reverse transcriptase polymerase chain reaction (RT-PCR) tests are the gold standard for detecting recent infection with SARS-CoV-2. RT-PCR sensitivity varies over the course of an individual's infection, related to changes in viral load. Differences in testing methods, and individual-level variables such as age, may also affect sensitivity. Using data from New Zealand, we estimate the time-varying sensitivity of SARS-CoV-2 RT-PCR under varying temporal, biological and demographic factors. Sensitivity peaks 4-5 days post-infection at 92.7% [91.4%, 94.0%] and remains over 88% between 5 and 14 days post-infection. After the peak, sensitivity declined more rapidly in vaccinated cases compared to unvaccinated, females compared to males, those aged under 40 compared to over 40 s, and Pacific peoples compared to other ethnicities. RT-PCR remains a sensitive technique and has been an effective tool in New Zealand's border and post-border measures to control COVID-19. Our results inform model parameters and decisions concerning routine testing frequency.

Using mechanistic model-based inference to understand and project epidemic dynamics with time-varying contact and vaccination rates.

Epidemiological models range in complexity from relatively simple statistical models that make minimal assumptions about the variables driving epidemic dynamics to more mechanistic models that include effects such as vaccine-derived and infection-derived immunity, population structure and heterogeneity. The former are often fitted to data in real-time and used for short-term forecasting, while the latter are more suitable for comparing longer-term scenarios under differing assumptions about control measures or other factors. Here, we present a mechanistic model of intermediate complexity that can be fitted to data in real-time but is also suitable for investigating longer-term dynamics. Our approach provides a bridge between primarily empirical approaches to forecasting and assumption-driven scenario models. The model was developed as a policy advice tool for New Zealand's 2021 outbreak of the Delta variant of SARS-CoV-2 and includes the effects of age structure, non-pharmaceutical interventions, and the ongoing vaccine rollout occurring during the time period studied. We use an approximate Bayesian computation approach to infer the time-varying transmission coefficient from real-time data on reported cases. We then compare projections of the model with future, out-of-sample data. We find that this approach produces a good fit with in-sample data and reasonable forward projections given the inherent limitations of predicting epidemic dynamics during periods of rapidly changing policy and behaviour. Results from the model helped inform the New Zealand Government's policy response throughout the outbreak.

Modelling the dynamics of infection, waning of immunity and re-infection with the Omicron variant of SARS-CoV-2 in Aotearoa New Zealand.

Aotearoa New Zealand experienced a wave of the Omicron variant of SARS-CoV-2 in 2022 with around 200 confirmed cases per 1000 people between January and May. Waning of infection-derived immunity means people become increasingly susceptible to re-infection with SARS-CoV-2 over time. We investigated a model that included waning of vaccine-derived and infection-derived immunity under scenarios representing different levels of behavioural change relative to the first Omicron wave. Because the durability of infection-derived immunity is a key uncertainty in epidemiological models, we investigated outcomes under different assumptions about the speed of waning. The model was used to provide scenarios to the New Zealand Government, helping to inform policy response and healthcare system preparedness ahead of the winter respiratory illness season. In all scenarios investigated, a second Omicron wave was projected to occur in the second half of 2022. The timing of the peak depended primarily on the speed of waning and was typically between August and November. The peak number of daily infections in the second Omicron wave was smaller than in the first Omicron wave. Peak hospital occupancy was also generally lower than in the first wave but was sensitive to the age distribution of infections. A scenario with increased contact rates in older groups had higher peak hospital occupancy than the first wave. Scenarios with relatively high transmission, whether a result of relaxation of control measures or voluntary behaviour change, did not necessarily lead to higher peaks. However, they generally resulted in more sustained healthcare demand (>250 hospital beds throughout the winter period). The estimated health burden of Covid-19 in the medium term is sensitive to the strength and durability of infection-derived and hybrid immunity against reinfection and severe illness, which are uncertain.

Real-time estimation of the effective reproduction number of SARS-CoV-2 in Aotearoa New Zealand.

During an epidemic, real-time estimation of the effective reproduction number supports decision makers to introduce timely and effective public health measures. We estimate the time-varying effective reproduction number, Rt , during Aotearoa New Zealand's August 2021 outbreak of the Delta variant of SARS-CoV-2, by fitting the publicly available EpiNow2 model to New Zealand case data. While we do not explicitly model non-pharmaceutical interventions or vaccination coverage, these two factors were the leading drivers of variation in transmission in this period and we describe how changes in these factors coincided with changes in Rt . Alert Level 4, New Zealand's most stringent restriction setting which includes stay-at-home measures, was initially effective at reducing the median Rt to 0.6 (90% CrI 0.4, 0.8) on 29 August 2021. As New Zealand eased certain restrictions and switched from an elimination strategy to a suppression strategy, Rt subsequently increased to a median 1.3 (1.2, 1.4). Increasing vaccination coverage along with regional restrictions were eventually sufficient to reduce Rt below 1. The outbreak peaked at an estimated 198 (172, 229) new infected cases on 10 November, after which cases declined until January 2022. We continue to update Rt estimates in real time as new case data become available to inform New Zealand's ongoing pandemic response.