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Potato virus A isolates from three continents: Their biological properties, phylogenetics, and prehistory


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Fuentes, S, Gibbs, AJ, Adams, IP, Wilson, C ORCID: 0000-0001-5434-3816, Botermans, M, Fox, A, Kreuze, J, Boonham, N, Kehoe, MA and Jones, RAC 2021 , 'Potato virus A isolates from three continents: Their biological properties, phylogenetics, and prehistory' , Phytopathology, vol. 111, no. 1 , pp. 217-226 , doi: 10.1094/PHYTO-08-20-0354-FI.

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Forty-seven potato virus A (PVA) isolates from Europe, Australia, and South America’s Andean region were subjected to high-throughput sequencing, and 46 complete genomes from Europe (n = 9), Australia (n = 2), and the Andes (n = 35) obtained. These and 17 other genomes gave alignments of 63 open reading frames 9,180 nucleotides long; 9 were recombinants. The nonrecombinants formed three tightly clustered, almost equidistant phylogroups; A comprised 14 Peruvian potato isolates; W comprised 37 from potato in Peru, Argentina, and elsewhere in the world; and T contained three from tamarillo in New Zealand. When five isolates were inoculated to a potato cultivar differential, three strain groups (= pathotypes) unrelated to phylogenetic groupings were recognized. No temporal signal was detected among the dated nonrecombinant sequences, but PVA and potato virus Y (PVY) are from related lineages and ecologically similar; therefore, “relative dating” was obtained using a single maximum-likelihood phylogeny of PVA and PVY sequences and PVY’s well-supported 157 CE “time to most common recent ancestor”. The PVA datings obtained were supported by several independent historical coincidences. The PVA and PVY populations apparently arose in the Andes approximately 18 centuries ago, and were taken to Europe during the Columbian Exchange, radiating there after the mid-19th century potato late blight pandemic. PVA’s phylogroup A population diverged more recently in the Andean region, probably after new cultivars were bred locally using newly introduced Solanum tuberosum subsp. tuberosum as a parent. Such cultivars became widely grown, and apparently generated the A × W phylogroup recombinants. Phylogroup A, and its interphylogroup recombinants, might pose a biosecurity risk.

Item Type: Article
Authors/Creators:Fuentes, S and Gibbs, AJ and Adams, IP and Wilson, C and Botermans, M and Fox, A and Kreuze, J and Boonham, N and Kehoe, MA and Jones, RAC
Keywords: American lineage, biosecurity significance, dating, disease resistance, evolution, genomics, high-throughput sequencing, interpretation, pathotyping, phylogenetic analysis, population biology, Potato virus A, prehistory, strain groups, vir, diversity
Journal or Publication Title: Phytopathology
Publisher: Amer Phytopathological Soc
ISSN: 0031-949X
DOI / ID Number: 10.1094/PHYTO-08-20-0354-FI
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Copyright © 2021 The Author(s). This is an open access article distributed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license, (

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