Complete genome characterization of Rocio virus (Flavivirus: Flaviviridae), a Brazilian flavivirus isolated from a fatal case of encephalitis during an epidemic in São Paulo state

Abstract

The flaviviruses of major medical importance in South American countries are yellow fever, dengue, Saint Louis encephalitis, West Nile and Rocio viruses. Rocio virus (ROCV) has been responsible for epidemics of severe encephalitis in Brazil with a case-fatality rate of 10 % and development of sequelae in 20 % of the survivors. We have sequenced and characterized the entire genome of ROCV for the first time, by determining the general traits of the open reading frame and the characteristics of viral genes including the potential cleavage sites, conserved or unique motifs, cysteine residues and potential glycosylation sites. The conserved sequences in the 39-non-coding region were identified, and the predicted secondary structures during cyclization between 59-and 39-non-coding regions were studied. Multiple protein and phylogenetic analyses based on antigenically important and phylogenetically informative genes confirmed a close relationship between ROCV and Ilheus virus (ILHV), together constituting a unique and distinct phylogenetic subgroup as well as the genetic relationship of ROCV with several members of the Japanese encephalitis group. Although ROCV is phylogenetically related to ILHV, our study shows that it is still a virus distinct from the latter virus. This is the first flavivirus uniquely indigenous to Brazil that has been sequenced completely and the genome characterized. The data should be useful for further studies at the molecular level, including construction of infectious clone, identification of gene function, improved disease surveillance based on molecular diagnostic tools and vaccine development. INTRODUCTIONIn South America, until the mid-1970s, the two neurotropic flaviviruses had been Saint Louis encephalitis virus (SLEV) and Ilheus virus (ILHV). However, in contrast to North America, an epidemic of encephalitis in humans by SLEV in South America was not recorded for many years until the first outbreak in Argentina in 2005(Diaz et al., 2006, despite accumulated records of virus isolation from mosquitoes and vertebrate hosts throughout the continent (Spence, 1980). As for the other virus, ILHV, human infection was sporadic and development of neurotropic manifestations has been even more infrequent. Thus, the sudden emergence of an outbreak of encephalitis caused by a flavivirus in 1974-75 in Brazil was unexpected.Rocio virus (ROCV) belongs to the genus Flavivirus in the family Flaviviridae. Its prototype (strain SPH 34675) was isolated in Ribeira Valley in the south-eastern São Paulo state of Brazil in 1975 from the cerebellum of a fatal human case during an epidemic of encephalitis that could not be readily diagnosed with the reagents then available for known encephalitic viruses. The epidemic, which began in 1974, spread to more than 20 municipalities over the following 2 years causing approximately 1000 diagnosed cases.Members of the genus Flavivirus (hereafter called flaviviruses) are positive-sense, single-stranded RNA viruses that infect humans and other vertebrates. They are mainly...

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