Phylogenetic analysis
TA Talita Émile Ribeiro Adelino MG Marta Giovanetti VF Vagner Fonseca JX Joilson Xavier ÁA Álvaro Salgado de Abreu VN Valdinete Alves do Nascimento LD Luiz Henrique Ferraz Demarchi MO Marluce Aparecida Assunção Oliveira VS Vinícius Lemes da Silva AM Arabela Leal e. Silva de Mello GC Gabriel Muricy Cunha RS Roselene Hans Santos EO Elaine Cristina de Oliveira JJ Jorge Antônio Chamon Júnior FI Felipe Campos de Melo Iani AF Ana Maria Bispo de Filippis AA André Luiz de Abreu RJ Ronaldo de Jesus CA Carlos Frederico Campelo de Albuquerque JR Jairo Mendez Rico RS Rodrigo Fabiano do Carmo Said JS Joscélio Aguiar Silva NM Noely Fabiana Oliveira de Moura PL Priscila Leite LF Lívia Carla Vinhal Frutuoso SH Simone Kashima Haddad AM Alexander Martínez FB Fernanda Khouri Barreto CV Cynthia Carolina Vazquez RC Rivaldo Venâncio da Cunha EA Emerson Luiz Lima Araújo ST Stephane Fraga de Oliveira Tosta AF Allison de Araújo Fabri FC Flávia Löwen Levy Chalhoub PL Poliana da Silva Lemos FB Fernanda de Bruycker-Nogueira GL Gislene Garcia de Castro Lichs MZ Marina Castilhos Souza Umaki Zardin FS Fátima María Cardozo Segovia CG Crhistinne Cavalheiro Maymone Gonçalves ZG Zoraida Del Carmen Fernandez Grillo SS Svetoslav Nanev Slavov LP Luiz Augusto Pereira AM Ana Flávia Mendonça FP Felicidade Mota Pereira JM Jurandy Júnior Ferraz de Magalhães AJ Agenor de Castro Moreira dos Santos Júnior ML Maricélia Maia de Lima RN Rita Maria Ribeiro Nogueira AG Aristóteles Góes-Neto

DENV genotyping was performed using the Dengue Virus Typing Tool (https://www.genomedetective.com/app/typingtool/dengue/)6. To investigate the evolution and population dynamics of DENV1-2 in different Brazilian regions, the DENV1 (n = 57) and DENV2 (n = 170) complete genome sequences generated in this study were combined with globally sampled and publicly available complete genome sequences from DENV1 genotype V (DENV1-V = 444) and DENV2 genotype III (DENV2-III = 450) as these represent the dominant genotypes in the Americas. The latter were retrieved from NCBI up to November 2019. We also included 17 recently published of the outbreaks in the Brazilian Southeast region25. Sequences without sampling date and location were excluded, as were sequences covering less than 50% of the viral genome.

Sequence alignment was performed using MAFFT41 and manually curated to remove artifacts using Aliview42. Maximum Likelihood (ML) phylogenetic trees were estimated using IQ-TREE43 under the GTR nucleotide substitution model, which was inferred as the best-fit model by the ModelFinder application implemented in IQ-TREE44. The robustness of the tree topology was determined using 1,000 bootstrap replicates, and the presence of temporal signal was evaluated in TempEst45 through a regression of root-to-tip genetic distances against sampling time. Time-scaled phylogenetic trees were inferred using the BEAST package46. We employed a stringent model selection analysis using both path-sampling (PS) and stepping stone (SS) procedures to estimate the most appropriate molecular clock model for the Bayesian phylogenetic analysis47. The uncorrelated relaxed molecular clock model was chosen as indicated by estimating marginal likelihoods, also employing the codon based SRD06 model of nucleotide substitution and the non-parametric Bayesian Skyline coalescent model. A discrete phylogeographic model48 was used to reconstruct the virus spatial diffusion across the sampling locations. Discrete locations were initially defined as the country of sampling. However, a different resolution was applied according to sampling availability. Phylogeographic analyses were then performed by applying an asymmetric model of location transitioning coupled with the Bayesian Stochastic Search Variable Selection (BSSVS) procedure. Markov Chain Monte Carlo (MCMC) were run in duplicate for 100 million iterations to ensure stationarity and an adequate effective sample size (ESS) of >200. Maximum clade trees were summarized using TreeAnnotator after discarding 10% as burn-in and visualized using FigTree v1.4.4.

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