Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants

During the first semester of 2021, all of Brazil has suffered an intense wave of COVID-19 associated with the Gamma variant. In July, the first cases of Delta variant were detected in the state of Rio de Janeiro. In this work, we have employed phylodynamic methods to analyze more than 1,600 genomic sequences of Delta variant collected until September in Rio de Janeiro to reconstruct how this variant has surpassed Gamma and dispersed throughout the state. After the introduction of Delta, it has initially spread mostly in the homonymous city of Rio de Janeiro, the most populous of the state. In a second stage, dispersal occurred to mid- and long-range cities, which acted as new close-range hubs for spread. We observed that the substitution of Gamma by Delta was possibly caused by its higher viral load, a proxy for transmissibility. This variant turnover prompted a new surge in cases, but with lower lethality than was observed during the peak caused by Gamma. We reason that high vaccination rates in the state of Rio de Janeiro were possibly what prevented a higher number of deaths. Impact statement Understanding how SARS-CoV-2 spreads is vital to propose efficient containment strategies, especially when under the perspective of new variants emerging in the next year. Still, models of SARS-CoV-2 dispersal are still largely based in large cities from high-income countries, resulting in an incomplete view of the possible scenarios consequent of a new variant introduction. The work improves this discussion by reconstructing the spatio-temporal dispersal of Delta variant since its introduction in Rio de Janeiro, a densely populated region in South America. We also analyzed the epidemiological outcome of this spread, with a decrease in lethality rate uncommon to the observed in other countries. Data summary Four supplementary figures, one supplementary table and one supplementary file are available with the online version of this article. Raw short reads of the newly sequenced genomes are available at SRA-NCBI database ( https://www.ncbi.nlm.nih.gov/sra ) under the BioProject PRJNA774631 and the assembled genomes are deposited at GISAID database ( https://www.gisaid.org/ ) under the accession numbers listed in Table S1. Other genomic sequences used in the analyses are listed in Table S2. Epidemiological data for the state of Rio de Janeiro was obtained from https://www.saude.rj.gov.br/informacao-sus/dados-sus/2020/11/covid-19 .