Evidence of multiple recombination events between two RNA sequence variants within a Citrus tristeza virus isolate

• Published in: Virology (New York, N.Y.) Vol. 331; no. 2; pp. 232 - 237
• Main Authors: Vives, María C., Rubio, Luis, Sambade, Adrián, Mirkov, T. Erik, Moreno, Pedro, Guerri, José
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 20.01.2005
• Subjects: Citrus - virology; Citrus tristeza virus; genetic recombination; Genetic Variation; Genome, Viral; homologous recombination; Molecular Sequence Data; nucleotide sequences; Polymorphism, Single-Stranded Conformational; Recombination, Genetic; RNA; RNA, Double-Stranded - genetics; RNA, Viral - analysis; RNA, Viral - genetics; Sequence Analysis, DNA; Virus; Virus; RNA; Citrus tristeza virus
• ISSN: 0042-6822; 1096-0341
• DOI: 10.1016/j.virol.2004.10.037

Analysis of sequence variants of a natural Citrus tristeza virus (CTV) isolate (SY568) revealed that its population was composed of three sequence types: (I) the most frequent type had ≥97.9% nucleotide identity with the sequence predominant in severe CTV isolates from different origins; (II) a second variant, genetically close to the major component of several mild isolates, had ≤85% identity with the first; and (III) several variants (less than 4%) resulted from homologous recombination at one or more sites between sequences I and II. Recombination sites had an AU-rich stretch of 8–89 nucleotides shared by both parental sequences, flanked by GC- and AU-rich regions upstream and downstream, respectively. This context has been suggested as a hot-spot for homologous recombination in other RNA viruses.