An isolate of sweet potato chlorotic stunt virus from Brazil with a distinct genome organization

• Published in: Archives of virology Vol. 164; no. 8; pp. 2175 - 2178
• Main Authors: Rossato, Maurício, Souza, Caroline Amaral, Melo, Fernando Lucas, Orilio, Anelise Franco, Resende, Renato Oliveira, Ribeiro, Simone Graça, Naito, Fernanda Yuri Borges, Ribeiro, Gilvan Pio, Andrade, Genira Pereira, Pereira-Carvalho, Rita Cássia
• Format: Journal Article
• Language: English
• Published: Vienna Springer Vienna 01-08-2019; Springer Nature B.V
• Subjects: Annotated Sequence Record; Biomedical and Life Sciences; Biomedicine; Coat protein; Comparative analysis; Genetic distance; Genomes; Infectious Diseases; Ipomoea batatas; Medical Microbiology; Nucleotide sequence; Open reading frames; Phylogeny; Potatoes; Primers; Recombination; Ribonucleic acid; RNA; Virology; Brazil
• ISSN: 0304-8608; 1432-8798
• DOI: 10.1007/s00705-019-04281-2

Sweet potato chlorotic stunt virus (SPCSV; genus
Crinivirus,
family
Closteroviridae
), is an economically important pathogen of sweet potato. In the present work, the nucleotide sequences of two RNA segments of SPCSV (isolate SPCSV-UNB-01) were determined by MiSeq Illumina sequencing of samples of sweet potato plants grafted onto
Ipomoea setosa
. A comparative analysis of the genome organization of SPCSV-UNB-01 and other SPCSV sequences showed that RNA1 was lacking p22, and p5.1 and that p5.2. was absent in RNA2, indicating a unique genomic pattern. SPCSV-UNB-01 contained longer p6 and p5 regions, with little similarity to orthologous sequences. Sequence comparison did not reveal any previously identified functional domains within these open reading frames (ORFs). No recombination or rearrangement events were detected. Phylogenetic analysis suggested the possibility of separate entries of SPCSV into South America based on the genetic distance between SPCSV-UNB-01 and the Peruvian isolate m2-47. Samples from northeastern Brazil (State of Pernambuco) were positive for SPCSV when tested using specific primers for the major coat protein (CP) gene. This is the first full-length genome sequence of SPCSV-UNB-01 from Brazil.