High-throughput sequencing of Potato virus M from tomato in Slovakia reveals a divergent variant of the virus

Potato viral disease has been a major problem in potato production worldwide including Russia. Here, we detected Potato Virus M (PVM), P (PVP), S (PVS), Y (PVY), and X (PVX) and Potato Leaf Roll Virus (PLRV) by RT‐PCR on potato leaves and tubers from the Northwestern (NW), Volga (VF), and Far Eastern (FE) federal districts of Russia. Each sample was co‐infected with up to five viruses. RT‐PCR disclosed all six viruses in NW, three in VF, and five in FE. Phylogenetic analyses of PVM and PVS strains resolved all PVM isolates in Group O (ordinary) and all PVS isolates in Group O. Seven PVY strains were detected, and they included only recombinants. PVY recombinants were thus the dominant potato virus strains in Russia, although they widely varied among the regions. Our research provides insights into the geographical distribution and genetic variability of potato viruses in Russia.

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“…2017; Glasa et al . 2019). Group O includes genotypes O‐1–O‐9, and group D consist of D‐1–D‐7 genotypes (Tabasinejad et al .…”

Section: Resultsmentioning

confidence: 99%

“…2014; Glasa et al . 2019). For PVS phylogenetic tree mapping, the PVS isolates detected here and those previously reported were included (Vallejo et al .…”

Section: Methodsmentioning

confidence: 99%

Occurrence and distribution of viruses infecting potato in Russia

Yanagisawa

Matsushita

Хютти

et al. 2021

Lett Appl Microbiol

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“…The virus detection sensitivity ranged from 35 to 100%, reproducibility was 91.6% and the false-positive detection rate was poor. High-throughput sequencing also significantly unveiled the presence of 03 isolates of Potato virus M in tomato plants in Slovakia ( Glasa et al, 2019 ). One viroid and eight viruses have also been reported by sequencing of sRNA libraries from infected Prunus persica cv.…”

Section: Next-generation Sequencing Technologies As Go-to Tool For Plant Virologymentioning

confidence: 99%

Integrating CRISPR-Cas and Next Generation Sequencing in Plant Virology

et al. 2021

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Plant pathology has been revolutionized by the emergence and intervention of next-generation sequencing technologies (NGS) which provide a fast, cost-effective, and reliable diagnostic for any class of pathogens. NGS has made tremendous advancements in the area of research and diagnostics of plant infecting viromes and has bridged plant virology with other advanced research fields like genome editing technologies. NGS in a broader perspective holds the potential for plant health improvement by diagnosing and mitigating the new or unusual symptoms caused by novel/unidentified viruses. CRISPR-based genome editing technologies can enable rapid engineering of efficient viral/viroid resistance by directly targeting specific nucleotide sites of plant viruses and viroids. Critical genes such as eIf (iso) 4E or eIF4E have been targeted via the CRISPR platform to produce plants resistant to single-stranded RNA (ssRNA) viruses. CRISPR/Cas-based multi-target DNA or RNA tests can be used for rapid and accurate diagnostic assays for plant viruses and viroids. Integrating NGS with CRISPR-based genome editing technologies may lead to a paradigm shift in combating deadly disease-causing plant viruses/viroids at the genomic level. Furthermore, the newly discovered CRISPR/Cas13 system has unprecedented potential in plant viroid diagnostics and interference. In this review, we have highlighted the application and importance of sequencing technologies on covering the viral genomes for precise modulations. This review also provides a snapshot vision of emerging developments in NGS technologies for the characterization of plant viruses and their potential utilities, advantages, and limitations in plant viral diagnostics. Furthermore, some of the notable advances like novel virus-inducible CRISPR/Cas9 system that confers virus resistance with no off-target effects have been discussed.

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“…PVM-O isolates are reported from several EU MSs, i.e. Czech Republic, Germany, Latvia, Poland and Slovakia (Plchova et al, 2015;Glasa et al, 2019;He et al, 2019).…”

Section: Pest Distribution In the Eumentioning

confidence: 99%

“…In addition, two EU isolates (PVM-Hu from Hungary (GQ923785) and PVM-T20 from Slovakia (MH558035)) have been reported to group outside the PVM-O and PVM-D strains based on phylogenetic trees (Fox et al, 2009;Glasa et al, 2019). A BLASTn analysis shows that they are genetically similar one to each other.…”

Section: Intraspecific Diversitymentioning

confidence: 99%

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

Bragard¹,

Dehnen‐Schmutz²,

Gonthier³

et al. 2020

EFS2

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Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of non-EU isolates of potato virus M (PVM). 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 PVM has been evaluated with regard to the criteria to qualify as a potential Union quarantine pest. Because non-EU isolates of PVM are absent from the EU, they do not meet one of the requirements to be regulated as a regulated non-quarantine pest (RNQP) (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. Populations of PVM can be subdivided into two strains: the ordinary strain (PVM-O) is present in the EU, while the divergent strain (PVM-D) is absent from the EU or considered to have at most a limited distribution in the EU. Non-EU isolates of PVM-O are not expected to have an additional impact in the EU compared to EU isolates and therefore do not meet the corresponding criterion to qualify as a potential Union quarantine pest. The Panel is unable to conclude on the potential impact of non-EU PVM-D isolates in the EU territory, but PVM-D isolates meet all the other criteria to qualify as a potential Union quarantine pest.

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High-throughput sequencing of Potato virus M from tomato in Slovakia reveals a divergent variant of the virus

Cited by 8 publications

References 24 publications

Occurrence and distribution of viruses infecting potato in Russia

Occurrence and distribution of viruses infecting potato in Russia

Integrating CRISPR-Cas and Next Generation Sequencing in Plant Virology

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

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