Understanding spatiotemporal symptom onset risk of Omicron BA.1, BA.2 and hamster-related Delta AY.127

Abstract

PurposeInvestigation of the community-level symptomatic onset risk regarding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern, is crucial to the pandemic control in the new normal.MethodsInvestigated in this study is the spatiotemporal symptom onset risk with Omicron BA.1, BA.2, and hamster-related Delta AY.127 by a joint analysis of community-based human mobility, virus genomes, and vaccinations in Hong Kong.ResultsThe spatial spread of Omicron BA.2 was found to be 2.91 times and 2.56 times faster than that of Omicron BA.1 and Delta AY.127. Identified has been an early spatial invasion process in which spatiotemporal symptom onset risk was associated with intercommunity and cross-community human mobility of a dominant source location, especially regarding enhancement of the effects of the increased intrinsic transmissibility of Omicron BA.2. Further explored is the spread of Omicron BA.1, BA.2, and Delta AY.127 under different full and booster vaccination rate levels. An increase in full vaccination rates has primarily contributed to the reduction in areas within lower onset risk. An increase in the booster vaccination rate can promote a reduction in those areas within higher onset risk.ConclusionsThis study has provided a comprehensive investigation concerning the spatiotemporal symptom onset risk of Omicron BA.1, BA.2, and hamster-related Delta AY.127, and as such can contribute some help to countries and regions regarding the prevention of the emergence of such as these variants, on a strategic basis. Moreover, this study provides scientifically derived findings on the impact of full and booster vaccination campaigns working in the area of the reduction of symptomatic infections.

How to control the spatiotemporal spread of Omicron in the region with low vaccination rates

“…As a further development of the original extended WKDE model (8,(20)(21)(22)(23), the district-level WKDE model, proposed in this study, includes the same three steps from the extended WKDE model (8,(20)(21)(22)(23). The main improvement is that i) V efficiency (S, t i ) denotes the vaccine efficiency against the infection of Omicron in the district with the location S on day t i (8) and ii) V P (S, t i ) is the proportion of the population that have been fully vaccinated and booster vaccinated in the district with the location S on day t i (8).…”

“…Considering the need for further exploration, based on the district-level weighted kernel density estimation (WKDE) model (20)(21)(22)(23), the prediction of the spatiotemporal COVID-19 symptom onset risk at the finer spatial scale is proposed in this study. In this research, we explored the spatiotemporal spread of Omicron in 52 districts (metropolitan or district municipalities) of South Africa during the first 90 days of the epidemic (i.e., the whole process from the outbreak to the slowdown of the epidemic).…”