Genomic detection of a virus lineage replacement event of dengue virus serotype 2 in Brazil, 2019

Jaqueline Goes de Jesus, Karina Rocha Dutra, Flavia Cristina da Silva Sales, Ingra Morales Claro, Ana Carolina Terzian, Darlan da Silva Candido, Sarah C. Hill, Julien Thézé, Celeste Torres, Tatiana Lang D’agostini, Alvina Clara Felix, Andreia F. Negri Reis, Luiz Carlos Junior Alcantara, André L. de Abreu, Júlio H.R. Croda, Wanderson K. de Oliveira, Ana Maria Bispo de Filipis, Maria Do Carmo Rodrigues Dos Santos Camis, Camila Malta Romano, Nick J. LomanOliver G. Pybus, Ester Cerdeira Sabino, Mauricio L. Nogueira, Nuno Rodrigues Faria*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

8 Citations (Scopus)


BACKGROUND Despite efforts to mitigate the impact of dengue virus (DENV) epidemics, the virus remains a public health problem in tropical and subtropical regions around the world. Most DENV cases in the Americas between January and July 2019 were reported in Brazil. São Paulo State in the southeast of Brazil has reported nearly half of all DENV infections in the country. OBJECTIVES To understand the origin and dynamics of the 2019 DENV outbreak. METHODS Here using portable nanopore sequencing we generated20 new DENV genome sequences from viremic patients with suspected dengue infection residing in two of the most-affected municipalities of São Paulo State, Araraquara and São José do Rio Preto. We conducted a comprehensive phylogenetic analysis with 1,630 global DENV strains to better understand the evolutionary history of the DENV lineages that currently circulate in the region. FINDINGS The new outbreak strains were classified as DENV2 genotype III (American/Asian genotype). Our analysis shows that the 2019 outbreak is the result of a novel DENV lineage that was recently introduced to Brazil from the Caribbean region. Dating phylogeographic analysis suggests that DENV2-III BR-4 was introduced to Brazil in or around early 2014, possibly from the Caribbean region. MAIN CONCLUSIONS Our study describes the early detection of a newly introduced and rapidly-expanding DENV2 virus lineage in Brazil.

Original languageEnglish
Article numbere190423
JournalMemorias do Instituto Oswaldo Cruz
Issue number4
Publication statusPublished - Apr 2020
Externally publishedYes

Bibliographical note

Funding Information:
The research was supported by the FAPESP-MRC grant(CADDE, FAPESP 2018/14389-0), a Wellcome Trust and Royal Society Sir Henry Dale Fellowship (grant 204311/Z/16/Z), and by a CNPq # 400354/2016-0 and FAPESP # 2016/01735-2, and by the Oxford Martin School; Decit/SCTIE/MoH and CNPq (440685/2016-8 and 440856/2016-7); CAPES (88887.130716/2016-00, 88881.130825/2016-00 and 88887.130823/2016-00); EU?s Horizon 2020 Programme through ZIKAlliance (PRES-005-FEX-17-4-2-33). MLN is supported by FAPESP (grant # 13/21719-3); ACBT and KRD receive FAPESP Scholarships (grants #15/12295-0 and 15/14313-6, respectively); MLN and ECS are CNPq Research Fellows (PQ).

Publisher Copyright:
© 2020, Fundacao Oswaldo Cruz. All rights reserved.


  • Brazil
  • Dengue 2
  • Genomic surveillance
  • Lineage replacement
  • Outbreak


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