Population structure of blueberry mosaic associated virus: Evidence of reassortment in geographically distinct isolates

Thekke-Veetil, Thanuja; Polashock, James J.; Marn, M. Viršček; Pleško, Irena Mavrič; Schilder, A. M. C.; Keller, Karen E.; Martín, Robert R.; Tzanetakis, Ioannis E.

doi:10.1016/j.virusres.2015.02.022

Cited by 17 publications

(10 citation statements)

References 38 publications

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“…The nucleotide diversity of BLMaV within the population was rather low, similar to previous findings for fig mosaic virus (FMV) and European mountain ash ringspot‐associated virus (EMARaV; Kallinen et al ., ; Walia et al ., ) and for other negative‐sense segmented viruses such as citrus psorosis virus, blueberry mosaic associated virus and rice stripe virus (Martín et al ., ; Wei et al ., ; Thekke‐Veetil et al ., ). Phylogenetic analysis of BLMaV isolates showed geographical segregation, probably attributable to a founder effect, with a population established recently in an area with limited time for diversification (Pappu et al ., ; Kallinen et al ., ; Thekke‐Veetil et al ., ). However, some isolates grouped with others from different growing areas, a deviation possibly caused by movement of infected planting material to new growing areas.…”

Section: Discussionmentioning

confidence: 97%

“…This evolutionary constraint may be to maintain functional integrity for these proteins (Martín et al ., ; Roßbach et al ., ; Thekke‐Veetil et al ., ). The effect of natural selection on the population dynamics, using three different neutrality tests, indicates that a strong negative selection could play a key role in shaping the population under study, probably due to infection of new host plants (e.g.…”

Section: Discussionmentioning

confidence: 97%

“…As a segmented RNA virus, BLMaV is subjected to both micro‐ and macroevolutionary processes because of the high mutation rates of the error‐prone RdRp as well as reassortment and recombination events (Tentchev et al ., ; Savory & Ramakrishnan, ; Walia et al ., ; Thekke‐Veetil et al ., ). Identifying and understanding the factors that affect genetic variability could be instrumental in designing effective disease control measures (Martín et al ., ; Acosta‐Leal et al ., ).…”

Section: Introductionmentioning

confidence: 97%

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Population structure, evolution and detection of blackberry leaf mottle‐associated virus, an emerging emaravirus

Hassan

Tzanetakis

2019

Plant Pathology

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Blackberry leaf mottle-associated virus (BLMaV) is a recently described emaravirus associated with yellow vein disease, the main constraint of blackberry production in the southern USA. The population structure and genetic variation of BLMaV, based on the nucleocapsid and movement protein genes was resolved. BLMaV diversity is low when compared to other emaraviruses, with the genes studied being under strong negative selection. Phylogenetic analyses suggest long distance migration of the virus whereas incongruent phylogenetic relatedness and predicted reassortment events suggest that genetic exchange could play an important role in BLMaV evolution. A quantitative PCR (qPCR) protocol was developed based on the knowledge obtained through the population structure of the virus; this is a sensitive test able to detect all the isolates studied. The assay was optimized and applied successfully on multiple samples collected from several regions in the United States. Comparison between a previously developed test and the new protocol illustrated that the latter is at least 1000 times more sensitive.

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Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 97%

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Population structure, evolution and detection of blackberry leaf mottle‐associated virus, an emerging emaravirus

Hassan

Tzanetakis

2019

Plant Pathology

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“…One option would be to use next-generation sequencing NGS, which allows the generation of considerably larger amount of sequence data in a given time. In recent years, many new plant viruses have been detected from diseased plants using NGS technology [ 9 , 10 , 11 , 12 , 13 , 14 , 15 ]. dsRNAs have been used as the template for NGS to successfully detect plant viruses and viroids [ 11 , 15 ].…”

Section: Introductionmentioning

confidence: 99%

Combined DECS Analysis and Next-Generation Sequencing Enable Efficient Detection of Novel Plant RNA Viruses

Yanagisawa

Tomita

Koji

et al. 2016

Viruses

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The presence of high molecular weight double-stranded RNA (dsRNA) within plant cells is an indicator of infection with RNA viruses as these possess genomic or replicative dsRNA. DECS (dsRNA isolation, exhaustive amplification, cloning, and sequencing) analysis has been shown to be capable of detecting unknown viruses. We postulated that a combination of DECS analysis and next-generation sequencing (NGS) would improve detection efficiency and usability of the technique. Here, we describe a model case in which we efficiently detected the presumed genome sequence of Blueberry shoestring virus (BSSV), a member of the genus Sobemovirus, which has not so far been reported. dsRNAs were isolated from BSSV-infected blueberry plants using the dsRNA-binding protein, reverse-transcribed, amplified, and sequenced using NGS. A contig of 4,020 nucleotides (nt) that shared similarities with sequences from other Sobemovirus species was obtained as a candidate of the BSSV genomic sequence. Reverse transcription (RT)-PCR primer sets based on sequences from this contig enabled the detection of BSSV in all BSSV-infected plants tested but not in healthy controls. A recombinant protein encoded by the putative coat protein gene was bound by the BSSV-antibody, indicating that the candidate sequence was that of BSSV itself. Our results suggest that a combination of DECS analysis and NGS, designated here as “DECS-C,” is a powerful method for detecting novel plant viruses.

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“…Genetic exchanges through reassortment and recombination are major evolutionary factors for RNA plant viruses ( Aranda et al, 1997 ; Domingo and Holland, 1994 ; Nagy, 2008 ; Simon and Bujarski, 1994 ), that can result in differences in symptom severity, host range, or transmission efficiency of plant viruses ( Thekke-Veetil et al, 2015 ). Virus reassortment is a process of genetic recombination for multipartite (segmented) RNA viruses that occurs in host cells co-infected with multiple viruses and generates hybrid progeny viruses with novel genome combinations ( Marshall et al, 2013 ; Vijaykrishna et al, 2015 ).…”

mentioning

confidence: 99%

Phylogenetic Characterization of Tomato chlorosis virus Population in Korea: Evidence of Reassortment between Isolates from Different Origins

et al. 2018

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Population structure of blueberry mosaic associated virus: Evidence of reassortment in geographically distinct isolates

Cited by 17 publications

References 38 publications

Population structure, evolution and detection of blackberry leaf mottle‐associated virus, an emerging emaravirus

Population structure, evolution and detection of blackberry leaf mottle‐associated virus, an emerging emaravirus

Combined DECS Analysis and Next-Generation Sequencing Enable Efficient Detection of Novel Plant RNA Viruses

Phylogenetic Characterization of Tomato chlorosis virus Population in Korea: Evidence of Reassortment between Isolates from Different Origins

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