Supplemental Material

SARS-CoV-2 virus emerged as a new threat to humans and spread around the world, leaving a large death toll. As of January 2023, Brazil is among the countries with the highest number of registered deaths. Non-pharmacological and pharmacological interventions have been heterogeneously implemented in the country which, associated with large socioeconomic differences between the country regions, has led to distinct virus spread dynamics. Here we investigate the spatiotemporal dispersion of SARS-CoV-2 lineages in the Pernambuco state (Northeast Brazil) throughout the distinct epidemiological scenarios that unfolded in the first two years of the pandemics. We generated a total of 1389 new SARS-CoV-2 genomes from June 2020 to August 2021. This sampling captured the arrival, communitary transmission and the circulation of the B1.1, B.1.1.28 and B.1.1.33 lineages, the emergence of the former variant of interest P.2 and the emergence and fast replacement of all previous variants by the more transmissible variant of concern P.1 (Gamma). Based on the incidence and lineage spread pattern we observed an East-to-West to inner state pattern of transmission which is in agreement with the transmission of more populous metropolitan areas to medium and small size country-side cities in the state. Such transmission patterns may be partially explained by the main routes of traffic across municipalities in the state. Our results highlight that the fine grained intrastate analysis of lineages and incidence spread can provide actionable insights for planning future non-pharmacological intervention for air-borne transmissible human pathogens