Citrus tristeza virus (CTV) causes various syndromes of citrus and consists of diverse strains which may cause symptoms of differing severity. Lemon is the most important citrus crop produced in Tucumán province, Argentina, but the diversity of CTV strains within this region has been poorly studied. In this study we identified strains of CTV in lemons in 29 trees of five commonly planted lemon cultivars from this area using direct Sanger and next generation sequencing (NGS) of amplicons derived from the CTV p33 gene. The Kpg3/SP/T3 genotype was dominant in 28 of the 29 samples analysed, with one sample being dominant for a genotype of RB. This was confirmed with NGS in all but one instance. In addition, all thirteen samples tested by NGS were infected with RB, Kpg3/SP/T3 and HA 16-5 genotypes. One sample also had a minor VT component, while a further two samples also had a minor AT-1 component.

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Citrus tristeza virus (CTV) is endemic throughout the citrus production areas of South Africa and mild-strain cross-protection is employed to combat the negative effects of severe-strain infections. The country is among the world"s leading producers of grapefruit, however crossprotected trees often display severe stem grooving, regardless of the rootstock. Previously, cross-protection sources were evaluated empirically, through graft inoculations onto indicator hosts. Recent research has shown that cross-protection, possibly mediated by super-infection exclusion, is strain-specific. This, coupled with the varying affinities that cultivars display for different CTV strains, has shown the need to determine which CTV strains are associated with specific commercial cultivars. In this study, thirty-six Citrus paradisi (Macfad.) cv. "Marsh" plants were sampled in the South African grapefruit production areas of Malelane and Pongola. CTV populations from these samples were analysed through the amplification of the p33 gene and subsequent direct Sanger sequencing. A subset of twelve of these amplicons was selected for deep Illumina MiSeq sequencing. The resulting data showed high intra-and inter-orchard diversity of CTV, with populations showing similar genotype compositions to those found in recent studies on the "Star Ruby" cultivar. Populations were 2 composed of a clearly dominant component, in most cases RB or Kpg3/SP/T3-like sequences, with at least two minor sequence types. AT-1-like and VT-like sequences were found to be dominant in only four and one of the analysed populations respectively. HA16-5, Taiwan-Pum/M/T5, T30 and B165 were present as intermittent minor components (less than 10% of mapped reads) across the populations.

Citrus tristeza virus (CTV) is the most severe viral pathogen of citrus and is responsible for eliciting a wide range of devastating disease symptoms. Grapefruit cultivars (Citrus x paradisi) are the most sensitive among citrus to the effects of CTV infections. Grapefruit is an important crop within the north-western Argentine citrus industry; however, production has been affected by CTV stem-pitting. In general, CTV diversity within South America is poorly studied, with data on grapefruit CTV populations being particularly limited. In this study, 50 samples were collected from Star Ruby, Henninger's Ruby and Ruben Pink cultivars, within the provinces of Tucumán, Salta and Jujuy in north-western Argentina. The CTV p33 gene was PCR amplified and the resulting amplicons sequenced with Sanger sequencing. A subset of these amplicons was sequenced with Illumina MiSeq sequencing.AT-1-like sequences were dominant within the majority of populations, as determined by Sanger sequencing, followed by sequences clustering within the unresolved Kpg3/SP/T3 and RB clades. Sequencing by Illumina MiSeq confirmed this, as well as detecting minor sequence types within the HA 16-5, VT, B165 and A18 clades.