Ecological, Genetic, and Phylogenetic Aspects of YFV 2017–2019 Spread in Rio de Janeiro State

Abstract

In Brazil, a yellow fever (YF) outbreak was reported in areas considered YF-free for decades. The low vaccination coverage and the increasing forest fragmentation, with the wide distribution of vector mosquitoes, have been related to yellow fever virus (YFV) transmission beyond endemic areas since 2016. Aiming to elucidate the molecular and phylogenetic aspects of YFV spread on a local scale, we generated 43 new YFV genomes sampled from humans, non-human primates (NHP), and primarily, mosquitoes from highly heterogenic areas in 15 localities from Rio de Janeiro (RJ) state during the YFV 2016–2019 outbreak in southeast Brazil. Our analysis revealed that the genetic diversity and spatial distribution of the sylvatic transmission of YFV in RJ originated from at least two introductions and followed two chains of dissemination, here named the YFV RJ-I and YFV RJ-II clades. They moved with similar dispersal speeds from the north to the south of the RJ state in parallel directions, separated by the Serra do Mar Mountain chain, with YFV RJ-I invading the north coast of São Paulo state. The YFV RJ-I clade showed a more significant heterogeneity across the entire polyprotein. The YFV RJ-II clade, with only two amino acid polymorphisms, mapped at NS1 (I1086V), present only in mosquitoes at the same locality and NS4A (I2176V), shared by all YFV clade RJ-II, suggests a recent clustering of YFV isolates collected from different hosts. Our analyses strengthen the role of surveillance, genomic analyses of YVF isolated from other hosts, and environmental studies into the strategies to forecast, control, and prevent yellow fever outbreaks.

Ecological Requirements for Abundance and Dispersion of Brazilian Yellow Fever Vectors in Tropical Areas

“…Recent studies have shown the importance of natural barriers, such as preserved native vegetation [17,24], mountain ranges like the Serra do Mar [29], and highly anthropized and modified areas such as agricultural areas and large urban centers [17,49], to limit virus propagation by restricting the movement of vector mosquitoes. The results obtained in this study corroborate these findings.…”

“…The largest and most recent outbreak of WYF recorded in Brazil occurred between 2016 and 2021 [9,15,27] in the southeast and south regions of the country [4,[27][28][29]. In these regions, Hg.…”

YELLOW ALERT: Persistent Yellow Fever Virus Circulation among Non-Human Primates in Urban Areas of Minas Gerais State, Brazil (2021–2023)

“…Several factors underpin the reemergence of YFV in Southern Brazil, including inadequate vaccination coverage; the abundance of sylvatic vectors and NHP hosts; favorable climatic conditions; the emergence of new virus lineages; and the movement of infected humans and NHPs into new areas sharing these conducive conditions [ 6 ]. In addition, during the recent YF outbreaks in Brazil, the observed temporal and geographical patterns of YFV dispersion indicated the important role of vectors in YFV movement [ 7 , 8 ]. From late 2016 to 2018, Brazil experienced a dramatic shift in YF epidemiology, with a major outbreak in the Southeast region of the country.…”