Further investigation of a genetically divergent group of plum pox virus-M strain in Turkey

Gürcan, Kahraman; Teber, S.; Çağlayan, Kadriye

doi:10.1007/s42161-018-0187-7

Cited by 16 publications

(12 citation statements)

References 35 publications

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“…There are several global studies of the population structures of RNA viruses of human and other animals, but few of those of plants [36,37]. Several papers have been published reporting sequence analyses of regional populations of PPV [38][39][40][41], allowing the local spread and evolution of particular strains to be identified [42][43][44]. Despite these efforts, the global structure of the PPV population has not yet been determined, although it is now possible, as currently (January 2019) there are more than 200 complete genomic sequences of various isolates of PPV available in the GenBank database (https://www.…”

Section: Introductionmentioning

confidence: 99%

The global phylogeny of Plum pox virus is emerging

Hajizadeh

Gibbs

Amirnia

et al. 2019

Journal of General Virology

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The 206 complete genomic sequences of Plum pox virus in GenBank (January 2019) were downloaded. Their main open reading frames (ORF)s were compared by phylogenetic and population genetic methods. All fell into the nine previously recognized strain clusters; the PPV-Rec and PPV-T strain ORFs were all recombinants, whereas most of those in the PPV-C, PPV-CR, PPV-CV, PPV-D, PPV-EA, PPV-M and PPV-W strain clusters were not. The strain clusters ranged in size from 2 (PPV-CV and PPV-EA) to 74 (PPV-D). The isolates of eight of the nine strains came solely from Europe and the Levant (with an exception resulting from a quarantine breach), but many PPV-D strain isolates also came from east and south Asia and the Americas. The estimated time to the most recent common ancestor (TMRCA) of all 134 non-recombinant ORFs was 820 (865-775) BCE. Most strain populations were only a few decades old, and had small intra-strain, but large inter-strain, differences; strain PPV-W was the oldest. Eurasia is clearly the 'centre of emergence' of PPV and the several PPV-D strain populations found elsewhere only show evidence of gene flow with Europe, so have come from separate introductions from Europe. All ORFs and their individual genes show evidence of strong negative selection, except the positively selected pipo gene of the recently migrant populations. The possible ancient origins of PPV are discussed.

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Section: Introductionmentioning

confidence: 99%

The global phylogeny of Plum pox virus is emerging

Hajizadeh

Gibbs

Amirnia

et al. 2019

Journal of General Virology

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“…The recombination analysis was performed using eight Turkish PPV-Rec genomic sequences, the GenBank PPV-Rec sequences and all currently available isolates of the other PPV strains including isolates of minor strains (n = 450). As a result of the analysis, the previously identified recombination events involving PPV-An, -D, −M, -Rec, −T, and -W (n = 450) (Garcia et al, 2014;Glasa et al, 2004;Gürcan et al, 2019;James et al, 2016;Teber et al, 2019) were identified (results not shown). The major recombination event with a breakpoint at the position 8443 (8374-8458 with 99% confidence interval) (Garcia et al, 2014;Glasa et al, 2004) of PPV-Rec strain was observed for all Rec isolates including the Turkish PPV-Rec isolates.…”

Section: Recombination Analysismentioning

confidence: 91%

“…The six overlapping first-strand cDNA libraries were amplified with 20 pairs of sequencing primers which included 6 primer pairs used for the first-strand cDNA production. When amplification failed particularly for PPV-M-like NIb-CP-3'NCR region, primer pairs modified for PPV-M (Gürcan et al, 2019) were used. PCR amplification was performed on a T100 Thermal Cycler (Bio-Rad Laboratories, Hercules CA, USA) using a PCR program as follows: initial denaturation of 2 min at 94 °C followed by 35 cycles [30 s at 94 °C, annealing for 30 s at 58 °C (for all primer pairs), and extension for 30 s at 72 °C] and by a final extension for 7 min at 72 °C.…”

Section: Sample Information and Isolate Sequencingmentioning

confidence: 99%

“…Their analysis revealed high genetic diversity, the existence of several monophyletic and, in some cases, geographically limited groups within the PPV-D, and -T strain, thereby strongly suggested a long PPV-D, and -T evolutionary history in Turkey (Gürcan et al, 2020;Teber et al, 2019). European part of Turkey was associated with highest genetic diversity of PPV-D and -T. Recently, a monophyletic subcluster within PPV-M has been also identified in Istanbul in European part Turkey and named PPV-MIs (Gürcan et al, 2019).…”

Section: Introductionmentioning

confidence: 97%

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Genetic diversity and a long evolutionary history of plum pox virus strain rec in Turkey

et al. 2021

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Plum pox virus strain Recombinant (PPV-Rec) is hypothetically considered as homologous recombinant between strains PPV-M and PPV-D. The nucleotide position 8450 up to end of genome is considered to come from PPV-M, and the remaining major genomic part is PPV-D-derived. It is regarded as third major PPV strain due to its wide distribution and prevalence in Europe. However, among over a thousand PPV isolates genetically identified in Turkey, only 10 of them (<1%) were characterized as PPV-Rec. The nearly complete genome of eight of the PPV-Rec isolates from European part of Turkey were obtained and analyzed together with PPV-Rec isolates of other countries. All major genomic features were conserved among Turkish PPV-Rec isolates. The genetic diversity of PPV-Rec isolates in Turkey (n = 8, 0.015 ± 0.001%) was found to be comparable to that observed for the isolates from eight countries (n = 10, 0.014 ± 0.001%). Particularly, genetic diversity of the minor recombinant fragment for Turkish PPV-Rec isolates was apparently higher (0.016 ± 0.001%) than the value for the 10 isolates from eight countries (0.011 ± 0.001%). The high genetic diversity was also demonstrated by high phylogenetic variation in Turkish isolates, indicating a long evolutionary history of PPV-Rec isolates in Turkey. After including Turkish isolates in the recombination analysis, the major putative recombination event of PPV-Rec isolates with a breakpoint around position 8450 was identified again, however the other recently reported putative recombination events were not supported in this study by the algorithms implemented in the RDP software.

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“…Enfekteli ağaçların yakılarak imha edilmesi Figure 7. Destroying infected trees by burning Gürcan et al 2019, Gürcan et al 2020. PPV'nin ülkemizdeki varlığı ve yaygınlığı hakkında yapılan en kapsamlı çalışmada 2007-2010 yılları arasında 56 ilde 5.762 numune alınarak çalışılmış ve Ege, Marmara, Orta Anadolu ve Akdeniz bölgeleri bulaşık bulunmuştur (Akbaş et al 2011).…”

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Assessment of a six-year national survey and eradication program for Plum pox virus in Turkey

Birişik

Morca²,

Erilmez

et al. 2021

Bitki Koruma Bülteni

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Plum pox virus (PPV) is the most dangerous viral agent of stone fruits. PPV can be transmitted by vector aphids and may cause serious damage on fruits, leaves and flowers of Prunus species, especially on plum, apricot, and peach. Eradication of infected plants is one of the most recommended control methods of PPV in the world. The main objective of this study is to evaluate the National PPV survey and eradication program carried by the National Plant Health Authority between 2013 and 2018. During the six years of study, approximately 60.000 trees in 96.26% of Turkey were screened for PPV symptoms and 21.394 samples were collected from suspected plants from seven different fruit species. The samples were tested by ELISA (Enzyme Linked Immunosorbent Assay), and then ELISA questionable samples were verified by RT-PCR (Reverse Transcription Polymerase Chain Reaction). Based on the six years results, 2.718 samples from 161 locations were determined as PPV positive and the infection rate was calculated as 12.70%. During this study, 78.868 trees were eradicated. By the help of intensive monitoring and eradication program, PPV infection rate decreased from 35.72% to 7.47%. On the other hand, PPV infection was firstly recorded and eradicated in seven provinces (Aydın, Bolu, Denizli, Erzincan, Kırıkkale, Sivas, Samsun) which have been knownas PPV-free before. This study showed that eradication is a very effective way to suppress PPV infection and spread. In conclusion, the national survey and eradication program should be operated nationwide and concentrated in nurseries.

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Further investigation of a genetically divergent group of plum pox virus-M strain in Turkey

Cited by 16 publications

References 35 publications

The global phylogeny of Plum pox virus is emerging

The global phylogeny of Plum pox virus is emerging

Genetic diversity and a long evolutionary history of plum pox virus strain rec in Turkey

Assessment of a six-year national survey and eradication program for Plum pox virus in Turkey

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