The Biology and Phylogenetics of Potato virus S Isolates from the Andean Region of South America

Abstract

Biological characteristics of 11 Potato virus S (PVS) isolates from three cultivated potato species (Solanum spp.) growing in five Andean countries and 1 from Scotland differed in virulence depending on isolate and host species. Nine isolates infected Chenopodium quinoa systemically but two others and the Scottish isolate remained restricted to inoculated leaves; therefore, they belonged to biologically defined strains PVSA and PVSO, respectively. When nine wild potato species were inoculated, most developed symptomless systemic infection but Solanum megistacrolobum developed systemic hypersensitive resistance (SHR) with one PVSO and two PVSA isolates. Andean potato cultivars developed mostly asymptomatic primary infection but predominantly symptomatic secondary infection. In both wild and cultivated potato plants, PVSA and PVSO elicited similar foliage symptoms. Following graft inoculation, all except two PVSO isolates were detected in partially PVS-resistant cultivar Saco, while clone Snec 66/139-19 developed SHR with two isolates each of PVSA and PVSO. Myzus persicae transmitted all nine PVSA isolates but none of the three PVSO isolates. All 12 isolates were transmitted by plant-to-plant contact. In infective sap, all isolates had thermal inactivation points of 55 to 60°C. Longevities in vitro were 25 to 40 days with six PVSA isolates but less than 21 days for the three PVSO isolates. Dilution end points were 10−3 for two PVSO isolates but 10−4 to 10−6 with the other isolates. Complete new genome sequences were obtained from seven Andean PVS isolates; seven isolates from Africa, Australia, or Europe; and single isolates from S. muricatum and Arracacia xanthorhiza. These 17 new genomes and 23 from GenBank provided 40 unique sequences; however, 5 from Eurasia were recombinants. Phylogenetic analysis of the 35 nonrecombinants revealed three major lineages, two predominantly South American (SA) and evenly branched and one non-SA with a single long basal branch and many distal subdivisions. Using least squares dating and nucleotide sequences, the two nodes of the basal PVS trifurcation were dated at 1079 and 1055 Common Era (CE), the three midphylogeny nodes of the SA lineages at 1352, 1487, and 1537 CE, and the basal node to the non-SA lineage at 1837 CE. The Potato rough dwarf virus/Potato virus P (PVS/PRDV/PVP) cluster was sister to PVS and diverged 5,000 to 7,000 years ago. The non-SA PVS lineage contained 18 of 19 isolates from S. tuberosum subsp. tuberosum but the two SA lineages contained 6 from S. tuberosum subsp. andigena, 4 from S. phureja, 3 from S. tuberosum subsp. tuberosum, and 1 each from S. muricatum, S. curtilobum, and A. xanthorrhiza. This suggests that a potato-infecting proto-PVS/PRDV/PVP emerged in South America at least 5,000 years ago, became endemic, and diverged into a range of local Solanum spp. and other species, and one early lineage spread worldwide in potato. Preventing establishment of the SA lineages is advised for all countries still without them.

Pest categorisation of potato virus S (non‐EU isolates)

“…As indicated in the previous section, isolates belonging to the PVS-O strain are reported worldwide, including several EU Member States (Germany, Hungary, the Netherlands and United Kingdom) (Duan et al, 2018;Santillan et al, 2018).…”

“…Pest distribution outside the EU PVS occurs worldwide wherever potato is grown (Jeffries, 1998). Recent phylogenetic analyses show a clear separation between the geographical distribution of PVS isolates at the strain level (Duan et al, 2018;Santillan et al, 2018). PVS-O isolates are reported from all continents (Salari et al, 2011;Duan et al, 2018;Santillan et al, 2018) while PVS-A isolates are only reported from Asia, Oceania and South America (Cox and Jones, 2010;Duan et al, 2018;Khassanov and Vologin, 2018).…”

“…Solanum betaceum is reported as a host of PVS without information of the strain(s) involved (CABI, 2019). (Vallejo et al, 2016), S. tuberosum (Santillan et al, 2018) Natural and experimental hosts in different botanical families (Santillan et al, 2018). Additional natural hosts may exist Solanum sp.…”

Coinfección natural de virus de ARN en cultivos de papa (<i>Solanum tuberosum</i> subsp. Andigena) en Antioquia (Colombia)

“…La situación encontrada para la detección del virus PVS fue contraria a lo antes expuesto, pues el virus se encontró mediante ELISA en el 80,5 % de las muestras y tan sólo en el 25 % de éstas, cuando se utilizó RT-qPCR. Dicha diferencia, indica la necesidad de diseñar nuevos cebadores que cubran toda la variabilidad genética que presenta PVS en los Andes colombianos y que ha sido claramente demostrada en estudios filogenéticos recientes (Gutiérrez et al, 2012;Gutiérrez et al, 2013;Santillan et al, 2018), en donde se han encontrado al menos tres linajes diferentes para este virus: PVS A , PVS O y PVS P ; este último hasta ahora solo encontrado en Antioquia (Colombia) y denominado PVS P haciendo referencia a su detección inicial en papa criolla (S. phureja) (Vallejo et al, 2016). Ya que las secuencias de este linaje sirvieron de base para el diseño de los cebadores PVS_gen_F y qPVS_gen_R utilizados en el presente trabajo, es posible inferir que dichos cebadores presentan desajustes (mismatches) con respecto a sus regiones de unión en algunos genotipos de este virus que se encuentran infectando las muestras evaluadas; mientras que los anticuerpos empleados en las pruebas de ELISA cubren un rango mayor de variación, dada su unión con regiones muy conservadas de la proteína de la cápside de este virus.…”

Full-Genome Sequencing of a Virus from a 33-Year-Old Sample Demonstrates that Arracacha Mottle Virus Is Synonymous with Arracacha Virus Y

“…A fourth virus with 650-nm filamentous particles typical of the genus Carlavirus was also present. It was first named Arracacha latent virus ( 3 ) but was later identified as another Carlavirus , Potato virus S ( 4 ). In 1981, ArVY was recovered from leaves of arracacha plants that were freeze-dried in 1979 in the United Kingdom.…”