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.

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.

Early intervention is the key to success in COVID-19 control.

New Zealand responded to the COVID-19 pandemic with a combination of border restrictions and an Alert Level (AL) system that included strict stay-at-home orders. These interventions were successful in containing an outbreak and ultimately eliminating community transmission of COVID-19 in June 2020. The timing of interventions is crucial to their success. Delaying interventions may reduce their effectiveness and mean that they need to be maintained for a longer period. We use a stochastic branching process model of COVID-19 transmission and control to simulate the epidemic trajectory in New Zealand's March-April 2020 outbreak and the effect of its interventions. We calculate key measures, including the number of reported cases and deaths, and the probability of elimination within a specified time frame. By comparing these measures under alternative timings of interventions, we show that changing the timing of AL4 (the strictest level of restrictions) has a far greater impact than the timing of border measures. Delaying AL4 restrictions results in considerably worse outcomes. Implementing border measures alone, without AL4 restrictions, is insufficient to control the outbreak. We conclude that the early introduction of stay-at-home orders was crucial in reducing the number of cases and deaths, enabling elimination.