Phylogeographic patterns of the yellow fever virus around the metropolitan region of Sao Paulo, Brazil, 2016-2019

From 2016 to 2019, the largest outbreak caused by the Yellow Fever virus (YFV) in the 21(st) century in the Americas occurred in southeastern Brazil. A sylvatic cycle of transmission was reported near densely populated areas, such as the large metropolitan area of the city of Sao Paulo. Here, we describe the origin, spread, and movement of the YFV throughout the state of Sao Paulo. Whole-genome sequences were obtained from tissues of two patients who died due to severe yellow fever, during 2018-2019. Molecular analysis indicated that all analyzed tissues were positive for YFV RNA, with the liver being the organ with the highest amount of viral RNA. Sequence analysis indicates that genomes belonged to the South American genotype I and were grouped in the epidemic clade II, which includes sequences from the states of Goias, Minas Gerais, and Sao Paulo of previous years. The analysis of viral dispersion indicates that the outbreak originated in Goias at the end of 2014 and reached the state of Sao Paulo through the state of Minas Gerais after 2016. When the virus reached near the urban area, it spread towards both the east and south regions of the state, not establishing an urban transmission cycle in the metropolitan region of Sao Paulo. The virus that moved towards the east met with YFV coming from the south of the state of Rio de Janeiro, and the YFV that was carried to the south reached the Brazilian states located in the south region of the country.

Automated summary

From 2016 to 2019, the largest outbreak of the Yellow Fever virus (YFV) in the Americas occurred in southeastern Brazil. The virus was transmitted through a sylvatic cycle near densely populated areas, such as the metropolitan region of Sao Paulo. The analysis of whole-genome sequences revealed that the outbreak originated in Goias in 2014 and spread through Minas Gerais before reaching Sao Paulo. The virus dispersed towards the east and south regions of Sao Paulo but did not establish an urban transmission cycle in the metropolitan region of Sao Paulo. The YFV from the south of Rio de Janeiro met with the virus moving east, while the virus carried to the south reached the southern states of Brazil.