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

Abstract

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. Nonpharmacological 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 2 years of the pandemic. We generated a total of 1,389 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 nonpharmacological intervention for air-borne transmissible human pathogens.IMPORTANCEDuring the COVID-19 pandemic, Brazil was one of the most affected countries, mainly due its continental-size, socioeconomic differences among regions, and heterogeneous implementation of intervention methods. In order to investigate SARS-CoV-2 dynamics in the state of Pernambuco, we conducted a spatiotemporal dispersion study, covering the period from June 2020 to August 2021, to comprehend the dynamics of viral transmission during the first 2 years of the pandemic. Throughout this study, we were able to track three significant epidemiological waves of transmission caused by B1.1, B.1.1.28, B.1.1.33, P.2, and P.1 lineages. These analyses provided valuable insights into the evolution of the epidemiological landscape, contributing to a deeper understanding of the dynamics of virus transmission during the early years of the pandemic in the state of Pernambuco.

Keywords: COVID-19; genomic surveillance; lineage replacement; state level.

Fig 1

Brazilian map and federal states highlighting the Pernambuco state and maximum likelihood phylogenetic reconstruction of the SARS-CoV-2 global data set including 7,228 sequences; genomes generated from the Pernambuco state are marked with circles in the tip labels, and colors branches denote lineages.

Fig 2

(A) Number of SARS-CoV-2 new cases per 100,000 habitants (gray bars) and percentage of Pernambuco population vaccinated based on the Pernambuco population (9,674,793) estimated in 2021 by the Instituto Brasileiro de Geografia e Estatística (IBGE), X axis: number of cases per 100,000 habitants, Y axis: From Jan 2020 to Aug 2021. ; (B) Case-fatality ratio (gray bars) and mean ICU occupancy (red line) in Pernambuco by period, X axis: mean ICU occupancy, Y axis: months Jan 2020 and Aug 2021; (C) SARS-CoV-2 lineage frequencies and number of genomes (black line) by period; (D) monthly incidence of SARS-CoV-2 infections across Pernambuco state.

Fig 3

Temporal analysis of SARS-CoV-2 clades detected in the Pernambuco state. The number above the node shows the posterior probability support. The pink bars are the HPD 95% credible interval of the estimated tMRCA estimated on BEAST analysis. The gray rectangle represents the estimated origin of the Gamma lineage in the Amazonas state (32).

Fig 4

Origin and density of vehicle mobility in the state of Pernambuco. (A) shows the origin/destination intensity of vehicles departing from elsewhere in Brazil to the state of Pernambuco in 2018. (B) shows the destination from vehicles with both origin and destination within the state of Pernambuco. (C) shows the modeling of the average 2020 vehicle flux intensity on the roads according to the automated vehicle counters distributed throughout the region. Capital letters denotes Brazilian state acronyms as follows: AP: Amapá; PA: Pará; MA: Maranhão; PI: Piauí; CE: Ceará; RN: Rio Grande do Norte; TO: Tocantins; PB: Paraíba; PE: Pernambuco; BA: Bahia; MT: Mato Grosso; AL: Alagoas; SE: Sergipe; GO: Goiás; DF: Distrito Federal; MG: Minas Gerais; ES: Espírito Santo; MS: Mato Grosso do Sul; SP: São Paulo; RJ: Rio de Janeiro; PR: Paraná; SC: Santa Catarina; and RS: Rio Grande do Sul.