Evidence that dicot-infecting mastreviruses are particularly prone to inter-species recombination and have likely been circulating in Australia for longer than in Africa and the Middle East

Kraberger, Simona; Harkins, Gordon William; Kumari, Safaa G.; Thomas, J. E.; Schwinghamer, Mark W.; Sharman, Murray; Collings, David A.; Briddon, R. W.; Martin, Darren P.; Varsani, Arvind

doi:10.1016/j.virol.2013.06.024

Cited by 40 publications

(34 citation statements)

References 52 publications

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“…The recent discoveries of SWSV and other highly divergent mastreviruses [46], [47] suggest that this geminivirus genus likely encompasses a far greater diversity and has a greater global distribution than has been previously appreciated. The SWSV isolate from the Sudanese sugarcane plant that had been propagated in Barbados represents only the third instance of discovery of mastreviruses in the New World [16], [48], and suggests that there may have been other undetected recent introductions of mastreviruses to the Americas.…”

Section: Discussionmentioning

confidence: 99%

Appearances Can Be Deceptive: Revealing a Hidden Viral Infection with Deep Sequencing in a Plant Quarantine Context

et al. 2014

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Comprehensive inventories of plant viral diversity are essential for effective quarantine and sanitation efforts. The safety of regulated plant material exchanges presently relies heavily on techniques such as PCR or nucleic acid hybridisation, which are only suited to the detection and characterisation of specific, well characterised pathogens. Here, we demonstrate the utility of sequence-independent next generation sequencing (NGS) of both virus-derived small interfering RNAs (siRNAs) and virion-associated nucleic acids (VANA) for the detailed identification and characterisation of viruses infecting two quarantined sugarcane plants. Both plants originated from Egypt and were known to be infected with Sugarcane streak Egypt Virus (SSEV; Genus Mastrevirus, Family Geminiviridae), but were revealed by the NGS approaches to also be infected by a second highly divergent mastrevirus, here named Sugarcane white streak Virus (SWSV). This novel virus had escaped detection by all routine quarantine detection assays and was found to also be present in sugarcane plants originating from Sudan. Complete SWSV genomes were cloned and sequenced from six plants and all were found to share >91% genome-wide identity. With the exception of two SWSV variants, which potentially express unusually large RepA proteins, the SWSV isolates display genome characteristics very typical to those of all other previously described mastreviruses. An analysis of virus-derived siRNAs for SWSV and SSEV showed them to be strongly influenced by secondary structures within both genomic single stranded DNA and mRNA transcripts. In addition, the distribution of siRNA size frequencies indicates that these mastreviruses are likely subject to both transcriptional and post-transcriptional gene silencing. Our study stresses the potential advantages of NGS-based virus metagenomic screening in a plant quarantine setting and indicates that such techniques could dramatically reduce the numbers of non-intercepted virus pathogens passing through plant quarantine stations.

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Section: Discussionmentioning

confidence: 99%

Appearances Can Be Deceptive: Revealing a Hidden Viral Infection with Deep Sequencing in a Plant Quarantine Context

et al. 2014

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“…2009, 2014; Grigoras et al. 2010; Kraberger et al. 2013), BBTV is evolving at a sufficient rate that evidence of such movement events should be encoded within the phylogenetic relationships of genomic component sequences sampled from extant BBTV populations.…”

Section: Introductionmentioning

confidence: 99%

The global distribution ofBanana bunchy top virusreveals little evidence for frequent recent, human-mediated long distance dispersal events

et al. 2015

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Banana bunchy top virus (BBTV; family Nanoviridae, genus Babuvirus) is a multi-component single-stranded DNA virus, which infects banana plants in many regions of the world, often resulting in large-scale crop losses. We analyzed 171 banana leaf samples from fourteen countries and recovered, cloned, and sequenced 855 complete BBTV components including ninety-four full genomes. Importantly, full genomes were determined from eight countries, where previously no full genomes were available (Samoa, Burundi, Republic of Congo, Democratic Republic of Congo, Egypt, Indonesia, the Philippines, and the USA [HI]). Accounting for recombination and genome component reassortment, we examined the geographic structuring of global BBTV populations to reveal that BBTV likely originated in Southeast Asia, that the current global hotspots of BBTV diversity are Southeast Asia/Far East and India, and that BBTV populations circulating elsewhere in the world have all potentially originated from infrequent introductions. Most importantly, we find that rather than the current global BBTV distribution being due to increases in human-mediated movements of bananas over the past few decades, it is more consistent with a pattern of infrequent introductions of the virus to different parts of the world over the past 1,000 years.

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“…This could be supported as an evidence of correct recombination events when we know that the first record of CpCDV was reported to infect faba bean in Egypt in 2003 [26]. Through sequencing results put in the study and the through the RDP datasets, it has been noticed that the recombination patterns detected in the dicot-infecting masterviruses compared to the monocot infecting mastervirus are interspecies more than intra-species recombination patterns [23]. CpCDV is the only member of the Geminivirus that is reported to naturally infect faba bean.…”

Section: Discussionmentioning

confidence: 59%

First genome analysis and molecular characterization of Chickpea chlorotic dwarf virus Egyptian isolate infecting squash

2015

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This study aims to identifying and characterizing some molecular properties of geminiviruses co-infection in squash field crop cultivated in Egypt. Squash crops observed to be heavily infected with several insect vectors, also severe chlorosis and stunting was observed. Electron microscopic analysis has revealed geminate capsid particles which indicate the infection of Geminiviruses, especially SqLCV which represent an economic problem to squash filed crop in Egypt. We have investigated possible mixed infections with different plant viruses associated with chlorotic stunt diseases and or other genus groups of geminiviruses. The main objective of this study is to investigate the recombination events, possible recombinants and variants among these genera in the same family differing in vector transmission. This is the first report of the molecular characterization, phylogenetic analysis and putative recombination events of the full length genome of the Chickpea Chlorotic Dwarf Mastrevirus in Egypt. And the first report of co-infection with another begomovirus infecting squash plants. A full length clone of both viruses were isolated and characterized at the molecular level. The complete nucleotide sequence of DNA-A was determined (2,572 bp) and submitted to the genbank under accession no. KF692356. The isolate from Egypt has about 97.8 % homology with the Chickpea chlorotic dwarf virus (CpCDV) isolate from Syria DNA-A isolate FR687959, a 83.2 % homology with the Sudan isolate AM933134 and a 82.7 % homology with Pakistan isolate FR687960. To best of our knowledge this is the first report of complete genome of CpCDV that infect squash plants in Egypt and worldwide.

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Evidence that dicot-infecting mastreviruses are particularly prone to inter-species recombination and have likely been circulating in Australia for longer than in Africa and the Middle East

Cited by 40 publications

References 52 publications

Appearances Can Be Deceptive: Revealing a Hidden Viral Infection with Deep Sequencing in a Plant Quarantine Context

Appearances Can Be Deceptive: Revealing a Hidden Viral Infection with Deep Sequencing in a Plant Quarantine Context

The global distribution ofBanana bunchy top virusreveals little evidence for frequent recent, human-mediated long distance dispersal events

First genome analysis and molecular characterization of Chickpea chlorotic dwarf virus Egyptian isolate infecting squash

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