Abstract

The largest outbreak of yellow fever of the 21st century in the Americas began in 2016, with intense circulation in the southeastern states of Brazil, particularly in sylvatic environments near densely populated areas including the metropolitan region of São Paulo city (MRSP) during 2017–2018. Herein, we describe the origin and molecular epidemiology of yellow fever virus (YFV) during this outbreak inferred from 36 full genome sequences taken from individuals who died following infection with zoonotic YFV. Our analysis revealed that these deaths were due to three genetic variants of sylvatic YFV that belong the South American I genotype and that were related to viruses previously isolated in 2017 from other locations in Brazil (Minas Gerais, Espírito Santo, Bahia and Rio de Janeiro states). Each variant represented an independent virus introduction into the MRSP. Phylogeographic and geopositioning analyses suggested that the virus moved around the peri-urban area without detectable human-to-human transmission, and towards the Atlantic rain forest causing human spill-over in nearby cities, yet in the absence of sustained viral transmission in the urban environment.

Details

Title
Origin of the São Paulo Yellow Fever epidemic of 2017–2018 revealed through molecular epidemiological analysis of fatal cases
Author
Marielton dos Passos Cunha 1   VIAFID ORCID Logo  ; Amaro Nunes Duarte-Neto 2   VIAFID ORCID Logo  ; Shahab Zaki Pour 1 ; Ortiz-Baez, Ayda Susana 3 ; Černý, Jiří 4 ; Bárbara Brito de Souza Pereira 1 ; Carla Torres Braconi 1 ; Yeh-Li, Ho 5   VIAFID ORCID Logo  ; Perondi, Beatriz 6 ; Jaques Sztajnbok 7 ; Venancio Avancini Ferreira Alves 2 ; Dolhnikoff, Marisa 2 ; Holmes, Edward C 8   VIAFID ORCID Logo  ; Paulo Hilário Nascimento Saldiva 2 ; Paolo Marinho de Andrade Zanotto 9   VIAFID ORCID Logo 

1  Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil 
2  Pathology Department, Clinical Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil 
3  Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil; Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life & Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia 
4  Faculty of Tropical AgriSciences, Czech University of Life Sciences in Prague, Prague, Czech Republic 
5  Intensive Care Unit, Division of Clinical Infectious and Parasitic Diseases, Clinical Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil 
6  Yellow Fever Crisis Committee, Clinical Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil 
7  Institute of Infectology Emílio Ribas, São Paulo, Brazil 
8  School of Life and Environmental Sciences & Sydney Medical School, The University of Sydney, Sydney, Australia 
9  Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil; Scientific Platform Pasteur - USP, São Paulo, Brazil 
Pages
1-10
Publication year
2019
Publication date
Dec 2019
Publisher
Nature Publishing Group
e-ISSN
20452322
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s41598-019-56650-1
ProQuest document ID
2331644381
Copyright
© 2019. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.