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Origin of the São Paulo Yellow Fever epidemic of 2017-2018 revealed through molecular epidemiological analysis of fatal cases.

Marielton Dos Passos Cunha1 Amaro Nunes Duarte-Neto2 Shahab Zaki Pour3 Ayda Susana Ortiz-Baez3,4 Jiří Černý5 Bárbara Brito de Souza Pereira3 Carla Torres Braconi3 Yeh-Li Ho6 Beatriz Perondi7 Jaques Sztajnbok8 Venancio Avancini Ferreira Alves2 Marisa Dolhnikoff2 Edward C Holmes9 Paulo Hilário Nascimento Saldiva2 Paolo Marinho de Andrade Zanotto10,11
Affiliations 11 institutions
  1. Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil. [email protected].
  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.
  4. 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, NSW 2006, Australia.
  5. Faculty of Tropical AgriSciences, Czech University of Life Sciences in Prague, Prague, Czech Republic.
  6. Intensive Care Unit, Division of Clinical Infectious and Parasitic Diseases, Clinical Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.
  7. Yellow Fever Crisis Committee, Clinical Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.
  8. Institute of Infectology Emílio Ribas, São Paulo, Brazil.
  9. School of Life and Environmental Sciences & Sydney Medical School, The University of Sydney, Sydney, Australia.
  10. Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil. [email protected].
  11. Scientific Platform Pasteur - USP, São Paulo, Brazil. [email protected].
PMID 31892699 2019 Sci Rep eng epublish
PubMed DOI Browse context

Article

Publication summary

The largest outbreak of yellow fever of the 21<sup>st</sup> 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.

Epidemics Brazil Cities Humans Molecular Epidemiology RNA, Viral Yellow Fever Yellow fever virus

Structured evidence records

Evidence records

3 total
Genomic Evolution 1 records
Genomic Evolution Extraction confidence 0.95
Key finding

Full-genome and phylogenetic analyses of yellow fever virus from fatal human cases in São Paulo revealed three genetic variants of the sylvatic South American I genotype, each representing independent introductions related to viruses from other Brazilian states.

Virus
YFV
Location
Not specified
Supporting text

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.

Genes or proteins
whole genome
Analysis methods
molecular epidemiology; full genome sequencing; phylogeographic analysis
Spillover Event 1 records
Spillover Event Extraction confidence 0.90
Key finding

Sylvatic yellow fever virus caused spillover infections in humans near the Atlantic rainforest during the 2017–2018 São Paulo outbreak.

Virus
YFV
Location
Brazil São Paulo, Brazil Atlantic rain forest Brazil
Supporting text

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.

Method
phylogeographic analysis; geopositioning analysis; full genome sequencing
Study design
molecular epidemiological analysis
Transmission direction
animal-to-human
Geographic raw
São Paulo; Atlantic rain forest; Brazil
Country inferred
Brazil
Zoonotic Surveillance 1 records
Zoonotic Surveillance Extraction confidence 0.70
Key finding

Molecular surveillance identified three sylvatic yellow fever virus variants of the South American I genotype responsible for fatal human infections during the 2017–2018 São Paulo outbreak.

Virus
YFV
Location
Brazil São Paulo, Brazil Minas Gerais, Brazil Espírito Santo Bahia, Brazil Rio de Janeiro, Brazil
Supporting text

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.

Method
molecular epidemiology; genome sequencing; phylogeographic analysis
Sample type
fatal cases
Geographic raw
São Paulo; Minas Gerais; Espírito Santo; Bahia; Rio de Janeiro
Country inferred
Brazil