Analysis of Iranian Potato virus S isolates

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

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, PVS^I, PVS^II or PVS^III. All Turkish CP sequences were in PVS^I, 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 PVS^I and PVS^II isolates. Three neutrality test methods showed PVS^III remained balanced whilst PVS^I and PVS^II underwent population expansion. The high fixation index values assigned to all PVS^I, PVS^II and PVS^III comparisons supported subdivision into three phylogroups. As it spreads more readily by aphid and contact transmission, and may elicit more severe symptoms in potato, PVS^II spread constitutes a biosecurity threat for countries still free from it.

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

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of non‐EU isolates of potato virus S (PVS). The information currently available on geographical distribution, biology, epidemiology, potential entry pathways, potential additional impact compared to the current situation in the EU, and availability of control measures of non‐EU isolates of PVS has been evaluated with regard to the criteria to qualify as potential Union quarantine pest. Because non‐EU isolates of PVS are absent from the EU, they do not meet one of the requirements to be regulated as an RNQP (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. Populations of PVS can be subdivided into two strains: the ordinary strain (PVS‐O) with a worldwide distribution (including the EU), and the Andean strain (PVS‐A) which is absent from the EU or considered to have at most a limited distribution in the EU. Two additional divergent isolates (PVS‐A/PVS‐O recombinants and PVS‐arracacha) have also been categorised. Non‐EU isolates of PVS‐A are expected to have an additional impact as compared to the PVS isolates currently present in the EU, and therefore meet all the criteria to qualify as potential Union quarantine pests; the magnitude of the additional impact is, however, unknown. Non‐EU isolates of PVS‐A/PVS‐O recombinants and of PVS‐arracacha also meet these criteria, with the exception of the criterion regarding the potential additional consequences in the EU territory for which the Panel was unable to conclude. Non‐EU PVS‐O isolates are not expected to have an additional impact in the EU as compared to EU isolates and therefore do not meet the corresponding criterion.

Monoclonal antibody-based serological assays for detection of Potato virus S in potato plants

Potato virus S (PVS) often causes significant losses in potato production in potato-growing countries. In this study, the ordinary strain of PVS (PVS^O) was purified from PVS-infected potato plants and used as the immunogen to produce hybridomas secreting monoclonal antibodies (MAbs). Five highly specific and sensitive murine MAbs (1A3, 16C10, 18A9, 20B12, and 22H4) against PVS were prepared using conventional hybridoma technology. Using these MAbs, tissue print-enzyme-linked immunosorbent assay (ELISA), dot-ELISA, and double-antibody sandwich (DAS)-ELISA were developed for sensitive and specific detection of PVS infection in potato plants. The results of sensitivity assays revealed that PVS could be reliably detected in PVS-infected leaf crude extracts diluted at 1:10 240 and 1:163 840 (w/v, g/ml) in phosphate buffer saline (PBS) by dot-ELISA and DAS-ELISA, respectively. Twenty-two samples collected from potato fields in Yunnan Province, China were tested for PVS infection using the serological assays we had developed, and 14 of them were found to be positive. This indicates that PVS is now prevalent in potato fields in Yunnan Province.

RT-PCR Differentiation, Molecular and Pathological Characterization of Andean and Ordinary Strains of Potato virus S in Potatoes in China

A survey of potatoes in a field in Hubei, China, for common potato viruses revealed that Potato virus S (PVS) was the most abundant virus. To unveil the strain identity of the virus, primers specific to the ordinary and/or Andean strains of PVS (i.e., PVS^O and PVS^A) were designed. RT-PCR using these primers successfully detected PVS^O and PVS^A in the samples. Sequence analysis of the amplicons confirmed the correctness of the RT-PCR assay. Two isolates, PVS HB24 and PVS HB7, representing PVS^O and PVS^A, respectively, were chosen for molecular and biological characterization. Both isolates contained a genome of 8,453 nt in length with six open reading frames. They shared a sequence identity of 79.5% at the complete genome sequence level. Phylogenetic analysis placed PVS HB24 and PVS HB7 to PVS^O and PVS^A clades, respectively. PVS HB24 induced chlorotic local lesions on the inoculated leaves but no visible symptom on the upper uninoculated leaves of Chenopodium quinoa after mechanical inoculation, whereas PVS HB7 induced both local and systemic symptoms on C. quinoa. ELISA and RT-PCR confirmed that PVS HB7 infected C. quinoa systemically whereas PVS HB24 failed to do so. Both isolates infected potato cv. Shepody and Solanum chacoense asymptomatically, but did not infect Nicotiana occidentalis and N. tobaccum cv. Samsun.

Molecular variability in the cysteine rich protein of potato virus M

The potato virus M (PVM), belonging to the genus Carlavirus, is a worldwide endemic pathogen in potato fields. p11 is an 11-16 kDa protein encoded by the last open reading frame of PVM which contains cysteine rich proteins (CRPs) motif. CRPs have been identified as suppressors of gene silencing. In this study the p11 gene from 28 PVM isolates, including 16 new isolates from Iran, were used to determine the global genetic structure of PVM populations. Pairwise nucleotide sequence identity scores showed that global PVM CRP sequence similarity was between 69.3 and 100 %. This genetic diversity divided the 28 isolates into two main divergent phylogenetic clades. The rate of genetic diversity and non-synonymous to synonymous mutations (dN/dS) were significantly different between these two clades. Analysis showed that PVM CP is under significant negative selection pressure with the global ω value of 0.260.

Complete genome sequence of the first Andean strain of potato virus S from Brazil and evidence of recombination between PVS strains

An isolate of the Andean strain of potato virus S (PVS), named BB-AND, was detected for the first time in a Brazilian potato crop, fully sequenced and analyzed. A comparison of BB-AND with other PVS isolates (Andean and Ordinary) showed that BB-AND is quite distinct. The lowest amino acid sequence identity to the only other fully sequenced Andean isolate was found in ORF 1 (82%) and ORF 6 (87%). Recombination analysis showed that the isolate Vltava (AJ863510), from Germany, is a recombinant between PVS(O) and PVS(A) isolates, with the recombination event located between nucleotides 6125 and 8324.