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, R(t), 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 R(t). Alert Level 4, New Zealand’s most stringent restriction setting which includes stay-at-home measures, was initially effective at reducing the median R(t)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, R(t) subsequently increased to a median 1.3 (1.2, 1.4). Increasing vaccination coverage along with regional restrictions were eventually sufficient to reduce R(t)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 R(t)estimates in real time as new case data become available to inform New Zealand’s ongoing pandemic response.