Potato virus X (PVX) occurs worldwide and causes an important potato disease. Complete PVX genomes were obtained from 326 new isolates from Peru, which is within the potato crop′s main domestication center, 10 from historical PVX isolates from the Andes (Bolivia, Peru) or Europe (UK), and three from Africa (Burundi). Concatenated open reading frames (ORFs) from these genomes plus 49 published genomic sequences were analyzed. Only 18 of them were recombinants, 17 of them Peruvian. A phylogeny of the non-recombinant sequences found two major (I, II) and five minor (I-1, I-2, II-1, II-2, II-3) phylogroups, which included 12 statistically supported clusters. Analysis of 488 coat protein (CP) gene sequences, including 128 published previously, gave a completely congruent phylogeny. Among the minor phylogroups, I-2 and II-3 only contained Andean isolates, I-1 and II-2 were of both Andean and...

Arracacha is a root crop cultivated in several countries of South America. The commercial product, which is the storage root, has multiple nutritional properties: its fine starch makes it easily digestible, and it contains high levels of calcium and vitamin A. High throughput sequencing (HTS) technology has been applied successfully for virus discovery in different agricultural crops, and it has been proposed to apply it in routine pathogen detection. Using HTS, novel sequences related to crinivirus and vitivirus were identified in apparently symptomeless arracacha, which were assembled into contigs located in different positions of the genome. Based on those sequences’ primers were designed to amplify corresponding sequences from further arracacha accessions and potato plant samples collected from farmers’ fields in Colombia and Peru. It was possible to determine the near complete g...