Deciphering early-warning signals of SARS-CoV-2 elimination and resurgence from limited data at multiple scales

Abstract

Discriminating between second waves of community transmission, which necessitate broad-spectrum interventions, and multiple stuttering epidemic chains from repeated importations, which require targeted controls, is crucial for outbreak preparedness. However, necessarily scarce data available in the lull between potential epidemic waves cripples standard inference engines, blurring early-warning signals. We propose a novel framework for denoising inter-wave data, revealing how timely policy in New Zealand achieved local elimination and avoided dangerous resurgence.

Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence

“…4 In this context, the abrupt increase in the number of COVID-19 hospital admissions in Manaus during January, 2021 (3431 in Jan 1-19, 2021, vs 552 in Dec 1-19, 2020) is unexpected and of concern (figure). [5][6][7][8][9][10] After a large epidemic that peaked in late April, 2020, COVID-19 hospitalisations in Manaus remained stable and fairly low for 7 months from May to November, despite the relaxation of COVID-19 control measures during that period (figure ).…”

“…R t was calculated using the EpiFilter method. 10 Lines are median R t estimates; shaded areas are the 95% CIs. R t =Effective reproduction number.…”

“…The final NICE-SIGN-RCGP guideline, published on Dec 18, 2020, 10 should provide clear information on what is and is not known about the natural history of long COVID, provide guidance for healthcare workers to identify cases, and inform clinical practice for the correct management of people with symptoms. Accurate assessment, diagnosis, treatment, and rehabilitation are especially important given the increasing evidence of organ pathology Long COVID guidelines need to reflect lived experience…”

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

“…For example, Flaxman et al (2020) and Brauner et al (2020) fitted models of disease dynamics to case count and death data in different countries to estimate the effect of specific non-pharmaceutical interventions on the transmission rate of COVID-19. Modelling studies have indicated the importance of timely interventions for achieving local elimination and averting resurgent waves of COVID-19 in locations like New Zealand and the Australian state of Victoria (Parag et al, 2021).…”

“…On 8 June, after 17 consecutive days with no new reported cases, New Zealand officially declared elimination of community transmission following WHO guidelines (Baker et al, 2020c). This decision is supported by modelling work estimating the probability of elimination at this time (Binny et al, 2020c; Parag et al, 2021; Wilson et al, 2020). Between 22 May and 11 August, the only new cases detected were in international arrivals who were required to spend 14 days in government-managed isolation or quarantine facilities (Baker et al, 2020c).…”