Detection of a new yellow fever virus lineage within the South American genotype I in Brazil

Abstract

Nucleotide sequences of two regions of the genomes of 11 yellow fever virus (YFV) samples isolated from monkeys or humans with symptomatic yellow fever (YF) in Brazil in 2000, 2004, and 2008 were determined with the objective of establishing the genotypes and studying the genetic variation. Results of the Bayesian phylogenetic analysis showed that sequences generated from strains from 2004 and 2008 formed a new subclade within the clade 1 of the South American genotype I. The new subgroup is here designated as 1E. Sequences of YFV strains recovered in 2000 belong to the subclade 1D, which comprises previously characterized YFV strains from Brazil. Molecular dating analyses suggested that the new subclade 1E started diversifying from 1D about 1975 and that the most recent 2004-2008 isolates arose about 1985.

Yellow fever in Brazil: thoughts and hypotheses on the emergence in previously free areas

“…1,10,19 More recently, during the 2008 and 2009 outbreaks, it was commonly captured infected in the municipalities of Rio Grande do Sul and São Paulo, where human cases and epizootic cases in monkeys (Alouatta caraya) were reported. 2,12 These fi ndings support the hypothesis that this species plays a role in yellow fever transmission in Brazilian southern areas, especially due to absence of Hg. janthinomys.…”

“…23 Lineage 1D, which has emerged and circulated in Brazil since 1998 in the state of Pará (Northern Brazil), caused yellow fever epidemics until 2007. 15,16,19,20 It later gave rise to lineage 1E, which replaced it, as reported by Sousa et al 12 and Cardoso et al 2 …”

“…In the 2008-2009 epidemic in Rio Grande do Sul 2 and São Paulo, 12 a new viral lineage (genotype 1E) emerged from the previously described lineage genotype 1D. 20 Molecular evidence indicates that the emergence of this new genetic lineage follows a pattern described for several viruses with a "boom-and-bust cycle," where the current lineage originates from the previous lineage and replaces it.…”

“…Once the virus is established in the area, an explosive viral transmission via vectors occurs among non-human primates without natural immunity, resulting in an almost total elimination of these monkey populations, which has been demonstrated in a molecular study with more than 70 strains of yellow fever virus isolated in Brazil 20 and in the recent epidemic registered in the states of Rio Grande do Sul and São Paulo. 12 Indeed, molecular analysis showed that yellow fever virus isolates from Marajó island in the Northern state of Pará 16 were identical to yellow fever viral strains found in Goiás and Bahia. 15 Since these two areas where infection probably occurred were more than 2,000 km apart ( Figure), viral spread through monkeys is not possible, and only viremic humans with oligosymptomatic or even asymptomatic infections could have carried these yellow fever virus strains.…”

The Yellow Fever Outbreak in Global Perspective is Serious and of Great Concern

“…During this boundary expansion, five viral sub-lineages (1A to 1E) successively arose within the genotype I. They were distinguished by analysis of partial nucleotide sequencing of the YFV genome particularly the pre-membrane and envelope (prM/E) gene junction [9,10,13]. Most recently, South America genotype I has been divided into two major lineages named as old lineages (enclosing Old Para, and 1A, 1B, and 1C sub-lineages) and Modern lineage (enclosing Trinidad and Tobago, and 1D and 1E sub-lineages) ( Figure 1 and The Phylogenetic records validate that the vector of YF might ultimately have reached Asian subcontinent from the West African trade route, and thus Asian countries possibly became infected with A. aegypti later than the Americas [6,17,18].…”