Applying a pan-flavivirus RT-qPCR assay in Brazilian public health surveillance
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BRIEF REPORT
Applying a pan‑flavivirus RT‑qPCR assay in Brazilian public health surveillance Mariana Sequetin Cunha1 · Adriana Luchs2 · Fabiana Cristina Pereira dos Santos3 · Giovana Santos Caleiro1,4 · Maurício Lacerda Nogueira5 · Paulo César Maiorka6 Received: 13 February 2020 / Accepted: 24 April 2020 © Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract The aim of this study was to improve flavivirus field monitoring in Brazil using a reliable probe-based RT-qPCR assay. Standard flavivirus strains were employed to evaluate the performance of the assay, and its applicability was evaluated using 235 stored pools of Culicidae samples collected between 1993 and 1997 and in 2016. Flavivirus species were identified by sequencing. Sixteen (6.8%) samples tested positive: Ilheus virus, Iguape virus, and Saint Louis encephalitis virus were identified in historical specimens from 1993-1994, while insect-specific flaviviruses were detected in the samples from 2016. This approach was demonstrated to be accurate for flavivirus detection and characterization, and it can be successfully applied for vector surveillance and for monitoring and discovery of insect specific flaviviruses.
Introduction The genus Flavivirus (family Flaviviridae) consists of more than 70 virus species, and many members of this genus are arthropod-borne viruses that infect humans, livestock and captive animals [1]. Flaviviruses are enveloped positivestranded RNA viruses with genome of ~11 kb [2], and the Handling Editor: Tim Skern. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00705-020-04680-w) contains supplementary material, which is available to authorized users. * Mariana Sequetin Cunha [email protected] 1
Vector‑Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
2
Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
3
Respiratory Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
4
Virology Laboratory, São Paulo Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
5
Faculdade de Medicina de São Jose do Rio Preto (FAMERP), São Paulo, SP, Brazil
6
Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
genus includes pathogenic agents such as yellow fever virus (YFV), West Nile virus (WNV), Zika virus (ZIKV), Japanese encephalitis virus (JEV), and dengue virus (DENV), which can expand their geographic range and cause encephalitis or hemorrhagic fever, posing some of the most challenging public-health problems and causing emerging diseases in humans [3–5]. In addition, several mosquito-specific viruses have been discovered recently [6–8]. In addition to DENV, YFV and ZIKV, Brazil hosts other flaviviruses of medical importance, including Saint Louis encephalitis virus (SLEV), Ilheus virus (ILHV), Bussuquara virus (BUSV), Cacipacore virus (CPCV), Rocio virus (ROCV), and Iguap
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