Sequence analysis of Potato leafroll virus isolates reveals genetic stability, major evolutionary events and differential selection pressure between overlapping reading frame products. J Gen Virol

INRA - UMR BiO3P, Domaine de la Motte, BP 35327, 35653 Le Rheu Cedex, France.
Journal of General Virology (Impact Factor: 3.18). 08/2002; 83(Pt 7):1799-807. DOI: 10.1099/0022-1317-83-7-1799
Source: PubMed


In order to investigate the genetic diversity of Potato leafroll virus (PLRV), seven new complete genomic sequences of isolates collected worldwide were compared with the five sequences available in GenBank. Then, a restricted polymorphic region of the genome was chosen to further analyse new sequences. The sequences of PLRV open reading frames (ORFs) 3 and 4 were also compared with those of two other poleroviruses and the non-synonymous to synonymous substitution ratio distribution was analysed in overlapping and non-overlapping regions of the genome using maximum-likelihood models. Results confirmed that PLRV sequences from around the world are very closely related and showed that the region encoding protein P0 allowed the detection of three groups of isolates. When compared to other poleroviruses, PLRV was the most conserved in both ORFs 3 and 4. However, the results suggest that important events, such as deletion, mutation at a stop codon and intraspecific homologous recombination events, have occurred during the evolution of PLRV. Finally, it was shown that the translation products of ORFs 0 and 3 are significantly more conserved than those of the overlapping ORFs 1 and 4, respectively. All together, the results allow the proposal of new hypotheses to explain the apparent genetic stability of PLRV and its evolution.

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    • "It causes serious damage (Guyader and Ducray 2002), which not only causes loss of yield and quality, but also includes the direct costs of virus control measures (Thomas et al. 2000; Nie 2006). PLRV is transmitted in a persistent manner by a few aphid species (Guyader and Ducray 2002), including the green peach aphid (Myzus persicae) and the potato aphid (Macrosiphum euphorbiae ) (Alvarez and Srinivasan 2005). The green peach aphid seems to be the most efficient vector (Rowhani and Stace-Smith 1979). "
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    • "Viruses of the family Luteoviridae including PLRV, belong to the group of ssRNA plant viruses. PLRV infects potatoes worldwide, causing economic yield losses (Guyader and Ducray, 2002). Numerous studies have provided a detailed description of PLRV which is causing characteristic rolling of the leaves, chlorosis, and stunting of infected plants (Alvarez and Srinivasan, 2005). "
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    ABSTRACT: The most common virus affecting potatoes in the field worldwide is Potato leafroll virus (PLRV), belonging to the family Luteoviridae, genius Plerovirus. There are several molecular methods to detect PLRV including polymerase chain reaction (PCR), Multiplex AmpliDet RNA and double antibody sandwich ELISA (DAS-ELISA). But these techniques take a long time for 3hours to two days, requiring sophisticated tools. The aim of this study was to reduce the time required to detect PLRV, using a newly designed Loop-Mediated Isothermal Amplification (LAMP) technique requiring only an ordinary water bath or thermoblock. PLRV RNA was extracted from overall 80 infected naturally potato leaves. A set of six novel primers for the LAMP reaction was designed according to the highly conserved sequence of the viral coat protein (CP) gene. LAMP was carried out under isothermal conditions, applying the Bst DNA polymerase enzyme; The LAMP products were detected visually using the GeneFinder™ florescence dye. A positive result using the GeneFinder™ dye was a color change from the original orange to green. Results confirmed LAMP with GeneFinder™ provides a rapid and safe assay for detection of PLRV. Since with other molecular methods, equipping laboratories with a thermocycler or expensive detector systems is unavoidable, this assay was found to be a simple, cost-effective molecular method that has the potential to replace other diagnostic methods in primary laboratories without the need for expensive equipment or specialized techniques. It can also be considered as a reliable alternative viral detection system in further investigations.
    Journal of virological methods 05/2013; 192(1-2). DOI:10.1016/j.jviromet.2013.04.014 · 1.78 Impact Factor
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    • "Thus, in an overlapping region, if one gene undergoes adaptive evolution (positive selection) with a high ratio of non-synonymous nucleotide mutations (dn/ds >1), the cognate gene often undergoes purifying selection (negative selection; dn/ds <1). This has been observed in many different viruses such as simian immunodeficiency virus [6], potato leaf roll virus [7] and human papilloma virus [8]. "
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    ABSTRACT: Introduction The Hepatitis B Virus (HBV) genome contains four ORFs, S (surface), P (polymerase), C (core) and X. S is completely overlapped by P and as a consequence the overlapping region is subject to distinctive evolutionary constraints compared to the remainder of the genome. Specifically, a non-synonymous substitution in one coding frame may produce a synonymous substitution in the alternative frame, suggesting a possible conflict between requirements for diversifying and purifying forces. To examine how these contrasting requirements are balanced within this region, we investigated the relationship amongst positive selection sites, conserved regions, epitopes and elements of protein structure to consider how HBV balances the contrasting evolutionary pressures. Methodology/Results 323 HBV genotype D genome sequences were collected and analyzed to identify sites under positive selection and highly conserved regions. Epitopes sequences were retrieved from previously published experimental studies stored in the Immune Epitope Database. Predicted secondary structures were used to investigate the association between structure and conservation. Entropy was used as a measure of conservation and bivariate logistic regression was used to investigate the relationship between positive selection/conserved sites and epitope/secondary structure regions. Our results indicate: (i) conservation in S is primarily dictated by α-helix elements in the protein structure, (ii) variable residues are mainly located in PreS, the major hydrophilic region (MHR) and the C-terminus, (iii) epitopes in S, which are directly targeted by the host immune system, are significantly associated with sites under positive selection. Conclusions The highly variable spacer domain in P, which corresponds to PreS in S, appears to act as a harbor for the accumulation of mutations that can provide flexibility for conformational changes and responding to immune pressure.
    PLoS ONE 04/2013; 8(4):e60098. DOI:10.1371/journal.pone.0060098 · 3.23 Impact Factor
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