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Determinants of Virus Variation, Evolution, and Host Adaptation. Pathogens 2022; 11:pathogens11091039. [PMID: 36145471 PMCID: PMC9501407 DOI: 10.3390/pathogens11091039] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
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 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.
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Kannan M, Mohamad Saad M, Zainal Z, Kassim H, Ismail I, Talip N, Baharum SN, Bunawan H. Sequence and Phylogenetic Analysis of the First Complete Genome of Ricetungro spherical virus in Malaysia. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 18:e2566. [PMID: 34056024 PMCID: PMC8148635 DOI: 10.30498/ijb.2020.2566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Background: Rice tungro disease (RTD) is a viral disease mainly affecting rice in Asia. RTD caused by Rice tungro bacilliform virus and Rice tungro spherical virus. To date, there are only 5 RTSV isolates have been reported. Objectives: In this study, we aimed to report the complete nucleotide sequence of Malaysian isolate of Rice tungro spherical virus Seberang Perai (RTSV-SP) for the first time. RTSV-SP was characterized and its evolutionary relationship with previously reported Indian and Philippines isolates were elucidated. Materials and Methods: RTSV-SP isolate was isolated from a recent outbreak in a paddy field in Seberang Perai zone of Malaysia. Its complete genome was amplified by RT-PCR, cloned and sequenced. Results: Sequence analysis indicated that the genome of RTSV-SP consisted of 12,173 nucleotides (nt). Comparative analysis of 6 complete genome sequences using Clustal Omega showed that Seberang Perai isolate shared the highest nucleotide identity (96.04%) with Philippine-A isolate, except that the sORF-2 of RTSV-SP is shorter than RTSV Philippine-A by 27 amino acid residues. RTSV-SP found to cluster in Southeast Asia (SEA) group based on the whole genome sequence phylogenetic analysis using MEGA X software. Conclusions: Phylogenetic classification of RTSV isolates based on the complete nucleotide sequences showed more distinctive clustering pattern with the addition of RTSV-SP whole genome to the available isolates. Present study described the isolation and molecular characterization of RTSV-SP.
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Affiliation(s)
- Maathavi Kannan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia
| | - Maisarah Mohamad Saad
- Institute of Rice Research Centre, MARDI Seberang Perai, Jalan Paya Keladi/ Pinang Tunggal, 13200 Kepala Batas, Penang, Malaysia
| | - Zamri Zainal
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia.,School of Biosciences and Biotechnology, Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia
| | - Hakimi Kassim
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia.,School of Biosciences and Biotechnology, Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia
| | - Noraini Talip
- School of Environmental and Natural Resource Sciences, Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia
| | | | - Hamidun Bunawan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia
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Mangrauthia SK, Malathi P, Agarwal S, Ramkumar G, Krishnaveni D, Neeraja CN, Madhav MS, Ladhalakshmi D, Balachandran SM, Viraktamath BC. Genetic variation of coat protein gene among the isolates of Rice tungro spherical virus from tungro-endemic states of the India. Virus Genes 2012; 44:482-7. [PMID: 22234819 DOI: 10.1007/s11262-011-0708-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 12/21/2011] [Indexed: 11/30/2022]
Abstract
Rice tungro disease, one of the major constraints to rice production in South and Southeast Asia, is caused by a combination of two viruses: Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus (RTBV). The present study was undertaken to determine the genetic variation of RTSV population present in tungro endemic states of Indian subcontinent. Phylogenetic analysis based on coat protein sequences showed distinct divergence of Indian RTSV isolates into two groups; one consisted isolates from Hyderabad (Andhra Pradesh), Cuttack (Orissa), and Puducherry and another from West Bengal, Coimbatore (Tamil Nadu), and Kanyakumari (Tamil Nadu). The results obtained from phylogenetic study were further supported with the SNPs (single nucleotide polymorphism), INDELs (insertion and deletion) and evolutionary distance analysis. In addition, sequence difference count matrix revealed 2-68 nucleotides differences among all the Indian RTSV isolates taken in this study. However, at the protein level these differences were not significant as revealed by Ka/Ks ratio calculation. Sequence identity at nucleotide and amino acid level was 92-100% and 97-100%, respectively, among Indian isolates of RTSV. Understanding of the population structure of RTSV from tungro endemic regions of India would potentially provide insights into the molecular diversification of this virus.
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Affiliation(s)
- Satendra K Mangrauthia
- Biotechnology Section, Directorate of Rice Research, Hyderabad, Andhra Pradesh, 500030, India.
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Wei TY, Yang JG, Liao FL, Gao FL, Lu LM, Zhang XT, Li F, Wu ZJ, Lin QY, Xie LH, Lin HX. Genetic diversity and population structure of rice stripe virus in China. J Gen Virol 2009; 90:1025-1034. [PMID: 19264655 DOI: 10.1099/vir.0.006858-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Rice stripe virus (RSV) is one of the most economically important pathogens of rice and is repeatedly epidemic in China, Japan and Korea. The most recent outbreak of RSV in eastern China in 2000 caused significant losses and raised serious concerns. In this paper, we provide a genotyping profile of RSV field isolates and describe the population structure of RSV in China, based on the nucleotide sequences of isolates collected from different geographical regions during 1997-2004. RSV isolates could be divided into two or three subtypes, depending on which gene was analysed. The genetic distances between subtypes range from 0.050 to 0.067. The population from eastern China is composed only of subtype I/IB isolates. In contrast, the population from Yunnan province (southwest China) is composed mainly of subtype II isolates, but also contains a small proportion of subtype I/IB isolates and subtype IA isolates. However, subpopulations collected from different districts in eastern China or Yunnan province are not genetically differentiated and show frequent gene flow. RSV genes were found to be under strong negative selection. Our data suggest that the most recent outbreak of RSV in eastern China was not due to the invasion of new RSV subtype(s). The evolutionary processes contributing to the observed genetic diversity and population structure are discussed.
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Affiliation(s)
- Tai-Yun Wei
- Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Jin-Guang Yang
- Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Fu-Long Liao
- Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Fang-Luan Gao
- Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Lian-Ming Lu
- Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Xiao-Ting Zhang
- Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Fan Li
- Key Laboratory of Agricultural Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, PR China.,Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Zu-Jian Wu
- Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Qi-Yin Lin
- Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Lian-Hui Xie
- Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Han-Xin Lin
- Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China
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Bousalem M, Durand O, Scarcelli N, Lebas BSM, Kenyon L, Marchand JL, Lefort F, Seal SE. Dilemmas caused by endogenous pararetroviruses regarding the taxonomy and diagnosis of yam (Dioscorea spp.) badnaviruses: analyses to support safe germplasm movement. Arch Virol 2009; 154:297-314. [PMID: 19190853 DOI: 10.1007/s00705-009-0311-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Accepted: 12/12/2008] [Indexed: 11/25/2022]
Abstract
The discovery of endogenous pararetroviral sequences (EPRVs) has had a deep impact on the approaches needed for diagnosis, taxonomy, safe movement of germplasm and management of diseases caused by pararetroviruses. In this article, we illustrate this through the example of yam (Dioscorea spp.) badnaviruses. To enable progress, it is first necessary to clarify the taxonomical status of yam badnavirus sequences. Phylogeny and pairwise sequence comparison of 121 yam partial reverse transcriptase sequences provided strong support for the identification of 12 yam badnavirus species, of which ten have not been previously named. Virus prevalence data were obtained, and they support the presence of EPRVs in D. rotundata, but not in D. praehensilis, D. abyssinica, D. alata or D. trifida. Five yam badnavirus species characterised by a wide host range seem to be of African origin. Seven other yam badnavirus species with a limited host range are probably of Asian-Pacific origin. Recombination under natural circumstances appears to be rare. Average values of nucleotide intra-species genetic distances are comparable to data obtained for other RNA and DNA virus families. The dispersion scenarios proposed here, combined with the fact that host-switching events appear common for some yam badnaviruses, suggest that the risks linked to introduction via international plant material exchanges are high.
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Affiliation(s)
- Mustapha Bousalem
- INRA-URPV, Domaine Duclos, Prise d'Eau, 9170 Petit-Bourg, Guadeloupe, France.
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Harper G, Hart D, Moult S, Hull R, Geering A, Thomas J. The diversity of Banana streak virus isolates in Uganda. Arch Virol 2005; 150:2407-20. [PMID: 16096705 DOI: 10.1007/s00705-005-0610-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2005] [Accepted: 06/24/2005] [Indexed: 11/29/2022]
Abstract
In a study of the variation among isolates of Banana streak virus (BSV) in Uganda, 140 sequences were obtained from 49 samples by PCR across the conserved reverse transcriptase/RNaseH region of the genome. Pairwise comparison of these sequences suggested that they represented 15 different species and phylogenetic analyses showed that all species fell into three major clades based on 28% sequence difference. In addition to the Ugandan sequences, clade I also contained BSV species that are known as both integrated sequences and episomal viruses; clade II also contained integrated BSV sequences but which have not previously been identified as episomal viruses. Clade III comprised of Sugarcane bacilliform virus isolates and Ugandan BSV sequences and for which there is no evidence of integration. The possible reasons for the extraordinary levels of virus sequence variation and the potential origins and epidemiology of these viruses causing banana streak disease are discussed.
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Affiliation(s)
- G Harper
- Department of Disease and Stress Biology, John Innes Centre, Colney Lane, Norwich, UK.
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Tsompana M, Abad J, Purugganan M, Moyer JW. The molecular population genetics of the Tomato spotted wilt virus (TSWV) genome. Mol Ecol 2004; 14:53-66. [PMID: 15643950 DOI: 10.1111/j.1365-294x.2004.02392.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA viruses are characterized by high genetic variability resulting in rapid adaptation to new or resistant hosts. Research for plant RNA virus genetic structure and its variability has been relatively scarce compared to abundant research done for human and animal RNA viruses. Here, we utilized a molecular population genetic framework to characterize the evolution of a highly pathogenic plant RNA virus [Tomato spotted wilt virus (TSWV), Tospovirus, Bunyaviridae]. Data from genes encoding five viral proteins were used for phylogenetic analysis, and for estimation of population parameters, subpopulation differentiation, recombination, divergence between Tospovirus species, and selective constraints on the TSWV genome. Our analysis has defined the geographical structure of TSWV, attributed possibly to founder effects. Also, we identify positive selection favouring divergence between Tospovirus species. At the species level, purifying selection has acted to preserve protein function, although certain amino acids appear to be under positive selection. This analysis provides demonstration of population structuring and species-wide population expansions in a multisegmented plant RNA virus, using sequence-based molecular population genetic analyses. It also identifies specific amino acid sites subject to selection within Bunyaviridae and estimates the level of genetic heterogeneity of a highly pathogenic plant RNA virus. The study of the variability of TSWV populations lays the foundation in the development of strategies for the control of other viral diseases in floral crops.
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Affiliation(s)
- M Tsompana
- Department of Plant Pathology, North Carolina State University, 2518 Gardner Hall, Raleigh, NC 27695-7616, USA
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Leung H, Zhu Y, Revilla-Molina I, Fan JX, Chen H, Pangga I, Cruz CV, Mew TW. Using Genetic Diversity to Achieve Sustainable Rice Disease Management. PLANT DISEASE 2003; 87:1156-1169. [PMID: 30812716 DOI: 10.1094/pdis.2003.87.10.1156] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Hei Leung
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Youyong Zhu
- Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | | | - Jin Xiang Fan
- Agriculture Department of Yunnan, Kunming, 650032, Yunnan, China
| | - Hairu Chen
- Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Ireneo Pangga
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Casiana Vera Cruz
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Twng Wah Mew
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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Azzam O, Chancellor TCB. The Biology, Epidemiology, and Management of Rice Tungro Disease in Asia. PLANT DISEASE 2002; 86:88-100. [PMID: 30823328 DOI: 10.1094/pdis.2002.86.2.88] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Osmat Azzam
- Monticello Research Australia, Googong, Australia
| | - Tim C B Chancellor
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent, UK
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García-Arenal F, Fraile A, Malpica JM. Variability and genetic structure of plant virus populations. ANNUAL REVIEW OF PHYTOPATHOLOGY 2001; 39:157-86. [PMID: 11701863 DOI: 10.1146/annurev.phyto.39.1.157] [Citation(s) in RCA: 372] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Populations of plant viruses, like all other living beings, are genetically heterogeneous, a property long recognized in plant virology. Only recently have the processes resulting in genetic variation and diversity in virus populations and genetic structure been analyzed quantitatively. The subject of this review is the analysis of genetic variation, its quantification in plant virus populations, and what factors and processes determine the genetic structure of these populations and its temporal change. The high potential for genetic variation in plant viruses, through either mutation or genetic exchange by recombination or reassortment of genomic segments, need not necessarily result in high diversity of virus populations. Selection by factors such as the interaction of the virus with host plants and vectors and random genetic drift may in fact reduce genetic diversity in populations. There is evidence that negative selection results in virus-encoded proteins being not more variable than those of their hosts and vectors. Evidence suggests that small population diversity, and genetic stability, is the rule. Populations of plant viruses often consist of a few genetic variants and many infrequent variants. Their distribution may provide evidence of a population that is undifferentiated, differentiated by factors such as location, host plant, or time, or that fluctuates randomly in composition, depending on the virus.
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Affiliation(s)
- F García-Arenal
- Departamento de Biotecnología, E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain.
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