Molecular Analysis of the Global Population of Potato Virus S Redefines Its Phylogeny, and Has Crop Biosecurity Implications

Abstract

In 2020, 264 samples were collected from potato fields in the Turkish provinces of Bolu, Afyon, Kayseri and Niğde. RT-PCR tests, with primers which amplified its coat protein (CP), detected potato virus S (PVS) in 35 samples. Complete CP sequences were obtained from 14 samples. Phylogenetic analysis using non-recombinant sequences of (i) the 14 CP’s, another 8 from Tokat province and 73 others from GenBank; and (ii) 130 complete ORF, RdRp and TGB sequences from GenBank, found that they fitted within phylogroups, PVSI, PVSII or PVSIII. All Turkish CP sequences were in PVSI, clustering within five subclades. Subclades 1 and 4 were in three to four provinces, whereas 2, 3 and 5 were in one province each. All four genome regions were under strong negative selection constraints (ω = 0.0603–0.1825). Considerable genetic variation existed amongst PVSI and PVSII isolates. Three neutrality test methods showed PVSIII remained balanced whilst PVSI and PVSII underwent population expansion. The high fixation index values assigned to all PVSI, PVSII and PVSIII comparisons supported subdivision into three phylogroups. As it spreads more readily by aphid and contact transmission, and may elicit more severe symptoms in potato, PVSII spread constitutes a biosecurity threat for countries still free from it.

Coat protein of alfalfa mosaic alfamovirus (AMV) from Türkiye: genetic inference and in silico docking analysis for potential antiphytoviral purposes

“…Plant virus infections result in significant economic losses in the global agricultural sector (Lecoq and Katis, 2014;Coşkan et al, 2022;Topkaya et al, 2023). The primary focus of defensive strategies in plant virus control is on preventive measures, including the utilization of sanitarily certified propagating material and insect vector management (Fereres and Raccah, 2015;Golino et al, 2017).…”

Genetic Variation between Asian and Mediterranean Populations of Cucurbit Aphid-Borne Yellows Virus

“…Recombination and mutation can affect the evolution of plant virus populations, therefore identifying haplotypes and relationships between CABYV populations based on the CP can shed light on population evolution. The genetic diversity of CABYV populations may be influenced by specific hosts and/or geographic origin [ 19 , 32 ]. In this study, we analyzed the genetic structure of a CABYV population under special circumstances.…”

“…Understanding the genetic diversity and distribution of plant viruses is crucial for developing effective disease management strategies and ensuring global food security [ 18 , 19 ]. The molecular characterization of coat protein genome sequences and comparing genetic variability sampled from different parts of Iran with the isolates from NCBI possibly shed light on the dark part of the information regarding CABYV.…”

Global Population Structure of Apple Mosaic Virus (ApMV, Genus Ilarvirus)

“…Clear understanding on the population structure of a plant virus could be the key for its accurate detection and effective control [ 20 , 21 ]. Therefore, genome sequences of all global ApMV isolates in the National Center for Biotechnology Information (NCBI) GenBank were analyzed in this study to advance our understanding of the virus at the molecular level.…”