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Estimative of the intra and inter genic and genetic diversity from the populations of the baculovirus Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) in field isolates from South America

Grant number: 14/06090-4
Support type:Scholarships in Brazil - Post-Doctorate
Effective date (Start): January 01, 2015
Effective date (End): January 20, 2016
Field of knowledge:Biological Sciences - Genetics - Molecular Genetics and Genetics of Microorganisms
Principal researcher:Paolo Marinho de Andrade Zanotto
Grantee:Caio César de Melo Freire
Home Institution: Instituto de Ciências Biomédicas (ICB). Universidade de São Paulo (USP). São Paulo , SP, Brazil

Abstract

The Baculoviridae family comprises a huge and diverse group of viruses, which genomes are formed by a double strand DNA molecule with 95 to 130 thousands base pairs. They infect a lot of insect orders, e. g., Lepidoptera, Diptera, Hymenoptera, Siphonaptera, Coleoptera etc. The viruses of this family have a significant host specificity that permits their employment as a tool of biological control. Since 1978, the baculovirus AgMNPV is used to control the caterpillar Anticarsia gemmatalis in more than 2 million hectares of planting soybeans at Brazil. In our group, the genome from viral prototype (AgMNPV-2D) was sequenced in 2006, the transcriptome was quantified in 2013 and the proteome was elucidated in 2014. Preliminary studies, using RFLP, revealed that natural populations of AgMNPV are diverse and have several viral lineages, which polymorphisms were not well characterized. To understand the genomic diversity, we started the study of 17 AgMNPV sylvatic isolates, collected from 1980 to 1990 in Brazil, Argentina and Uruguay. The samples are from viral populations genetically distinct with natural occurrence in soybean plantations without previous applications of AgMNPV as bio-pesticide. In this moment, we have a preliminary master sequence of each isolate, from Roche 454 sequencing platform. These sequences are the most representative genotype of each population, without a more curate analysis about genetic linkage and allelic frequency. This post-doctoral proposal aims study in a fine grain, using ultra-deep-sequencing by Illumina, the genetic diversity of the 17 sylvatic isolates and reveal the linkage and, thus, identify variants into a population. Moreover, we also pretend investigate the heterogeneity and the partitioning of variation in coding, non-coding and regulatory regions of different genomes. (AU)

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Scientific publications
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
DE MELO FREIRE, CAIO CESAR; PALMISANO, GIUSEPPE; BRACONI, CARLA T.; CUGOLA, FERNANDA R.; RUSSO, FABIELE B.; BELTRAO-BRAGES, PATRICIA C. B.; LAMARINO, ATILA; DE LIMA NETO, DANIEL FERREIRA; SALL, AMADOU ALPHA; ROSA-FERNANDES, LIVIA; LARSEN, MARTIN R.; DE ANDRADE ZANOTTO, PAOLO MARINHO. NS1 codon usage adaptation to humans in pandemic Zika virus. Memórias do Instituto Oswaldo Cruz, v. 113, n. 5, p. -, 2018. Web of Science Citations: 2.
FREIRE, CAIO C. M.; IAMARINO, ATILA; LY SOUMARE, PEINDA O.; FAYE, OUSMANE; SALL, AMADOU A.; ZANOTTO, PAOLO M. A. Reassortment and distinct evolutionary dynamics of Rift Valley Fever virus genomic segments. SCIENTIFIC REPORTS, v. 5, JUN 23 2015. Web of Science Citations: 9.

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