First genome sequence of an isolate of hibiscus chlorotic ringspot virus from the Western hemisphere

Abstract

For the first time, the near-complete genome sequence of the betacarmovirus, hibiscus chlorotic ringspot virus (HCRSV) isolated from the Americas is disclosed. High throughput sequencing of the total RNA extract from a Hibiscus-rosa sinensis (L.) plant collected in São Paulo state, Brazil, revealed the genome sequence of HCRSV isolate SBO1, which is 3945 nucleotides long and shows 93.1% nucleotide sequence identity with HCRSV_Singapore (X86448), considered the type member of the species. These two viruses display a similar genomic organization and potentially encode seven open reading frames (ORFs). In addition, a phylogenetic analysis based on a fragment with 557 nts of p38, the coat protein gene, from a cohort of 14 samples collected in Brazil revealed a no clearly defined segregation of South American isolates from those previously detected in geographical areas outside this continent. The practical consequences of the use of p38 ORF-derived amplicons for detection and variability studies of HCRSV are concisely discussed.