Spatiotemporal transmission of SARS-CoV-2 lineages during 2020–2021 in Pernambuco—Brazil

• DOI: 10.1128/spectrum.04218-23
• Publication Date: 2024-04-23T13:01:38Z
• Authors: Lais Ceschini Mac...; Filipe Zimmer Dez...; Gustavo Barbosa d...; Raul Emídio de Lima; Lilian Caroliny A...; Leandro de Mattos...; Alexandre Freitas...; Antonio Marinho d...; André Luiz Sá de ...; Anderson da Costa...; Rômulo Pessoa-e-S...; Rodrigo Moraes Loyo; Barbara de Olivei...; Anderson Rodrigue...; Maira Galdino da ...; Francisco de Assi...; Marilda Mendonça ...; Paola Cristina Re...; Edson Delatorre; Felipe Gomes Naveca; Fabio Miyajima; Tiago Gräf; Rodrigo Feliciano...; Michelly Cristiny...; Tulio de Lima Campos; Matheus Filgueira...; Marcelo Henrique ...; Gabriel da Luz Wa...
• Keywords: Pandemic; Lineage (genetic)

SARS-CoV-2 virus emerged as a new threat to humans and spread around the world, leaving large death toll. As of January 2023, Brazil is among countries with highest number registered deaths. Nonpharmacological pharmacological interventions have been heterogeneously implemented in country, which, associated socioeconomic differences between country regions, has led distinct dynamics. Here, we investigate spatiotemporal dispersion lineages Pernambuco state (Northeast Brazil) throughout epidemiological scenarios that unfolded first 2 years pandemic. We generated total 1,389 genomes from June 2020 August 2021. This sampling captured arrival, communitary transmission, circulation B1.1, B.1.1.28, B.1.1.33 lineages; emergence former variant interest P.2; fast replacement all previous variants by more transmissible concern P.1 (Gamma). Based on incidence lineage pattern, observed an East-to-West inner pattern which agreement transmission populous metropolitan areas medium- small-size country-side cities state. Such patterns may be partially explained main routes traffic across municipalities Our results highlight fine-grained intrastate analysis can provide actionable insights for planning future nonpharmacological intervention air-borne human pathogens.IMPORTANCEDuring COVID-19 pandemic, was one most affected countries, mainly due its continental-size, heterogeneous implementation methods. In order dynamics Pernambuco, conducted study, covering period 2021, comprehend viral during Throughout this were able track three significant waves caused B.1.1.33, P.2, lineages. These analyses provided valuable into evolution landscape, contributing deeper understanding early pandemic Pernambuco.