Evolution of Plant Viruses

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Viral Pathogens".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 14812

Special Issue Editor

Department of Biological Science, The University of Tulsa, Tulsa, OK, USA
Interests: emerging and re-emerging of virus diseases; genetic diversity; mutations; recombination; reassortment; bottlenecks
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant viruses infect a variety of agricultural crops and cause significant losses in product yield. To effectively control plant viruses, an understanding of the mechanisms of virus evolution and emergence of new strains are crucial in unfolding the evolutionary trajectories of both RNA and DNA viruses.

Once a plant virus infects the host, RNA viruses in particular, generate a tremendous number of genetic variants called quasispecies, which may result in the evolution of new strains of the same virus. The three driving forces (mutation, recombination, and reassortment) play a major role in plant virus evolution. Further understanding of each mechanism for both RNA and DNA viruses will allow us to use the information for effective management strategies and long-term control of plant virus diseases.

In this special issue, we are inviting researchers to submit a manuscript (original research articles, reviews, opinions, short communication) which focuses on the evolution of RNA and DNA viruses which are infecting any plants, including important agricultural crops and weeds.


References

  1. Wijayasekara, D. and Ali. 2020. Complete genome characterization and coat protein genealogy of isolates of Maize dwarf mosaic virus from Johnsongrass and maize in Oklahoma and Missouri. Plant Disease 104:1214-1223.
  2. A. Ali and Ulrich Melcher. 2019. Modelling of Mutational Events in the Evolution of Viruses. Viruses, 11:(5), 418; https://0-doi-org.brum.beds.ac.uk/10.3390/v11050418.
  3. Ali, A. and M. J. Roossinck. 2017. Analysis of quasispecies variation in single and mixed viral Virus Evolution, 3(2): vex037.
  4. Ali*, and I. Ali. 2015. The Complete genome phylogeny of geographically distinct Dengue virus serotype 2 isolates (1944-2013) supports further groupings in cosmopolitan genotype. Plos One, September 28, 2015.
  5. Abdalla, O. A. and Ali*. 2012. Genetic diversity in the 3’-terminal regions of Papaya ringspot virus (PRSV-W) isolated from watermelon in Oklahoma. Archives of Virology, 157:405-412.
  6. Ali*, A., M. Shafiekhani and J. Olsen 2011. Molecular characterization of the complete genomes of two new field isolates of Cowpea chlorotic mottle virus, and their phylogenetic analysis. Virus Genes, 43: 120-129.
  7. Ali, and M. J. Roossinck. 2010. Genetic bottlenecks during systemic movement of Cucumber mosaic virus vary in different host plants. Virology, 404:279-283.
  8. Ali, A. and M. J. Roossinck. 2008. Genetic Bottlenecks. In “Plant Virus Evolution” (eds M.J. Roossinck). Springer, pp123-131.
  9. Roossinck, M. J. and Ali. 2007. Mechanisms of plant virus evolution and identification of genetic bottlenecks: impact on disease management. In “Biotechnology and Plant Disease Management”, (eds Z.K. Punja, S. DeBoer and H. Sanfacon). CAB International, pp109-124.

Prof. Dr. Akhtar Ali
Guest Editor

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Published Papers (5 papers)

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Research

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19 pages, 29894 KiB  
Article
Role of Diversity and Recombination in the Emergence of Chilli Leaf Curl Virus
by Megha Mishra, Rakesh Kumar Verma, Vineeta Pandey, Aarshi Srivastava, Pradeep Sharma, Rajarshi Gaur and Akhtar Ali
Pathogens 2022, 11(5), 529; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens11050529 - 30 Apr 2022
Cited by 3 | Viewed by 2310
Abstract
Chilli leaf curl virus (ChiLCV), (Genus Begomovirus, family Geminiviridae) and associated satellites pose a serious threat to chilli production, worldwide. This study highlights the factors accountable for genetic diversity, recombination, and evolution of ChiLCV, and associated chilli leaf curl alphasatellite (ChiLCA) [...] Read more.
Chilli leaf curl virus (ChiLCV), (Genus Begomovirus, family Geminiviridae) and associated satellites pose a serious threat to chilli production, worldwide. This study highlights the factors accountable for genetic diversity, recombination, and evolution of ChiLCV, and associated chilli leaf curl alphasatellite (ChiLCA) and chilli leaf curl betasatellite (ChiLCB). Phylogenetic analysis of complete genome (DNA-A) sequences of 132 ChiLCV isolates from five countries downloaded from NCBI database clustered into three major clades and showed high population diversity. The dN/dS ratio and Tajima D value of all viral DNA-A and associated betasatellite showed selective control on evolutionary relationships. Negative values of neutrality tests indicated purified selection and an excess of low-frequency polymorphism. Nucleotide diversity (π) for C4 and Rep genes was higher than other genes of ChiLCV with an average value of π = 18.37 × 10−2 and π = 17.52 × 10−2 respectively. A high number of mutations were detected in TrAP and Rep genes, while ChiLCB has a greater number of mutations than ChiLCA. In addition, significant recombination breakpoints were detected in all regions of ChiLCV genome, ChiLCB and, ChiLCA. Our findings indicate that ChiLCV has the potential for rapid evolution and adaptation to a range of geographic conditions and could be adopted to infect a wide range of crops, including diverse chilli cultivars. Full article
(This article belongs to the Special Issue Evolution of Plant Viruses)
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14 pages, 2783 KiB  
Article
Synonymous Codon Pattern of Cowpea Mild Mottle Virus Sheds Light on Its Host Adaptation and Genome Evolution
by Siqi Yang, Ye Liu, Xiaoyun Wu, Xiaofei Cheng and Xiaoxia Wu
Pathogens 2022, 11(4), 419; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens11040419 - 30 Mar 2022
Cited by 6 | Viewed by 1827
Abstract
Cowpea mild mottle virus (CpMMV) is an economically significant virus that causes severe disease on several legume crops. Aside from recombination, other factors driving its rapid evolution are elusive. In this study, the synonymous codon pattern of CpMMV and factors shaping it were [...] Read more.
Cowpea mild mottle virus (CpMMV) is an economically significant virus that causes severe disease on several legume crops. Aside from recombination, other factors driving its rapid evolution are elusive. In this study, the synonymous codon pattern of CpMMV and factors shaping it were analyzed. Phylogeny and nucleotide composition analyses showed that isolates of different geography or hosts had very similar nucleotide compositions. Relative synonymous codon usage (RSCU) and neutrality analyses suggest that CpMMV prefers A/U-ending codons and natural selection is the dominative factor that affects its codon bias. Dinucleotide composition and codon adaptation analyses indicate that the codon pattern of CpMMV is mainly shaped by the requirement of escaping of host dinucleotide-associated antiviral responses and translational efficiency. Full article
(This article belongs to the Special Issue Evolution of Plant Viruses)
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23 pages, 2354 KiB  
Article
High Mutation Frequency and Significant Population Differentiation in Papaya Ringspot Virus-W Isolates
by Vivek Khanal and Akhtar Ali
Pathogens 2021, 10(10), 1278; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10101278 - 04 Oct 2021
Cited by 2 | Viewed by 2092
Abstract
A total of 101 papaya ringspot virus-W (PRSV-W) isolates were collected from five different cucurbit hosts in six counties of Oklahoma during the 2016–2018 growing seasons. The coat protein (CP) coding region of these isolates was amplified by reverse transcription-polymerase chain reaction, and [...] Read more.
A total of 101 papaya ringspot virus-W (PRSV-W) isolates were collected from five different cucurbit hosts in six counties of Oklahoma during the 2016–2018 growing seasons. The coat protein (CP) coding region of these isolates was amplified by reverse transcription-polymerase chain reaction, and 370 clones (3–5 clones/isolate) were sequenced. Phylogenetic analysis revealed three phylogroups while host, location, and collection time of isolates had minimal impact on grouping pattern. When CP gene sequences of these isolates were compared with sequences of published PRSV isolates (both P and W strains), they clustered into four phylogroups based on geographical location. Oklahoman PRSV-W isolates formed one of the four distinct major phylogroups. The permutation-based tests, including Ks, Ks *, Z *, Snn, and neutrality tests, indicated significant genetic differentiation and polymorphisms among PRSV-W populations in Oklahoma. The selection analysis confirmed that the CP gene is undergoing purifying selection. The mutation frequencies among all PRSV-W isolates were within the range of 1 × 10−3. The substitution mutations in 370 clones of PRSV-W isolates showed a high proportion of transition mutations, which gave rise to higher GC content. The N-terminal region of the CP gene mostly contained the variable sites with numerous mutational hotspots, while the core region was highly conserved. Full article
(This article belongs to the Special Issue Evolution of Plant Viruses)
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19 pages, 3357 KiB  
Article
Genetic Variability and Evidence of a New Subgroup in Watermelon Mosaic Virus Isolates
by Osama A. Abdalla and Akhtar Ali
Pathogens 2021, 10(10), 1245; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10101245 - 26 Sep 2021
Cited by 2 | Viewed by 1656
Abstract
Watermelon mosaic virus (WMV) is one of the important Potyviruses that infect cucurbits worldwide. To better understand the population structure of WMV in the United States (U.S.), 57 isolates were collected from cucurbit fields located in nine southern states. The complete coat protein [...] Read more.
Watermelon mosaic virus (WMV) is one of the important Potyviruses that infect cucurbits worldwide. To better understand the population structure of WMV in the United States (U.S.), 57 isolates were collected from cucurbit fields located in nine southern states. The complete coat protein gene of all WMV isolates was cloned, sequenced and compared with 89 reported WMV isolates. The nucleotide and amino acid sequence identities among the U.S. WMV isolates ranged from 88.9 to 99.7% and from 91.5 to 100%, respectively. Phylogenetic analysis revealed that all the U.S. WMV isolates irrespective of their geographic origin or hosts belonged to Group 3. However, the fifty-seven isolates made three clusters in G3, where two clusters were similar to previously reported subgroups EM1 and EM2, and the third cluster, containing nine WMV isolates, formed a distinct subgroup named EM5 in this study. The ratio of non-synonymous to synonymous nucleotide substitution was low indicating the occurrence of negative purifying selection in the CP gene of WMV. Phylogenetic analysis of selected 37 complete genome sequences of WMV isolates also supported the above major grouping. Recombination analysis in the CP genes confirmed various recombinant events, indicating that purifying selection and recombination are the two dominant forces for the evolution of WMV isolates in the U.S. Full article
(This article belongs to the Special Issue Evolution of Plant Viruses)
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Review

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20 pages, 1524 KiB  
Review
Determinants of Virus Variation, Evolution, and Host Adaptation
by Katherine LaTourrette and Hernan Garcia-Ruiz
Pathogens 2022, 11(9), 1039; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens11091039 - 13 Sep 2022
Cited by 12 | Viewed by 5059
Abstract
Virus evolution is the change in the genetic structure of a viral population over time and results in the emergence of new viral variants, strains, and species with novel biological properties, including adaptation to new hosts. There are host, vector, environmental, and viral [...] Read more.
Virus evolution is the change in the genetic structure of a viral population over time and results in the emergence of new viral variants, strains, and species with novel biological properties, including adaptation to new hosts. There are host, vector, environmental, and viral factors that contribute to virus evolution. To achieve or fine tune compatibility and successfully establish infection, viruses adapt to a particular host species or to a group of species. However, some viruses are better able to adapt to diverse hosts, vectors, and environments. Viruses generate genetic diversity through mutation, reassortment, and recombination. Plant viruses are exposed to genetic drift and selection pressures by host and vector factors, and random variants or those with a competitive advantage are fixed in the population and mediate the emergence of new viral strains or species with novel biological properties. This process creates a footprint in the virus genome evident as the preferential accumulation of substitutions, insertions, or deletions in areas of the genome that function as determinants of host adaptation. Here, with respect to plant viruses, we review the current understanding of the sources of variation, the effect of selection, and its role in virus evolution and host adaptation. Full article
(This article belongs to the Special Issue Evolution of Plant Viruses)
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