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Nucleic-Acid Based Techniques for the Fine Diagnosis of Plant Viruses in India

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A Century of Plant Virology in India

Abstract

Field and horticultural crops are infected by large number of viruses and virus-like pathogens in India, which can be managed only by preventive measures and for that sensitive diagnosis is a prerequisite. Bioassay was initially utilized in detection of plant viruses. Following this, serological assay enzyme-linked immunosorbent assay (ELISA) was widely employed. In the last two decades, nucleic acid based detection assays were developed for the correct and fine diagnosis of plant viruses in India. Nucleic acid based detection assays in addition to providing sufficient sensitivity, specificity and accuracy are also robust and easily applicable. Correct identity of a large number of viruses which were misdiagnosed earlier was now diagnosed to their correct taxonomic status using nucleic acid based assays. Most commonly used nucleic acid based detection assays employed in India are nucleic acid spot hybridization (NASH), polymerase chain reaction (PCR) and reverse transcription-polymerase chain reaction (RT-PCR). These methods have been utilized for detection of large number of viruses and virus-like pathogens. Multiplex detection assays (multiplex PCR and multiplex–RT-PCR) were also developed for simultaneous detection of more than one virus in same reaction tube. Isothermal detection assay where amplification reaction can be carried out at constant temperature is developed and employed for simple and robust detection as well as characterization of plant viruses in India. The most commonly employed isothermal detection assays includes the rolling circle amplification (RCA) which has been employed to detect DNA viruses of the genera Begomovirus, Babuvirus and Badnavirus. Loop-mediated isothermal amplification (LAMP) are latest in the application of isothermal detection methods, which provides simple and easy detection of plant viruses and such detection assays have been developed for some viruses in India. The next generation sequencing (NGS) or deep sequencing, which involves massive parallel sequencing approach followed by bioinformatics analysis, has revolutionized the field of novel virus discovery in India. This chapter aims to highlight the application of various nucleic acid based detection assays in diagnosis and characterization of viruses infecting different crops in India. In this chapter, a crop-wise review of the application of different nucleic acid based detection methods in India has been presented.

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References

  • Adkar-Purushothama CR, Kanchepalli PR, Yanjarappa SM, Zhang Z, Sano T (2014) Detection, distribution, and genetic diversity of Australian grapevine viroid in grapevines in India. Virus Genes 49:304–311

    Article  CAS  PubMed  Google Scholar 

  • Adsule PG, Upadhyay A, Sawant IS (2011) Vision 2030. National Research Centre for Grapes (Indian Council for Agricultural Research), Pune. http://nrcgrapes.nic.in/zipfiles/NRCG-Vision-2030.pdf

    Google Scholar 

  • Ahlawat YS (1989) Psorosis- a disease of citrus in India. Indian Phytopathol 42:21–25

    Google Scholar 

  • Ahlawat YS (1997) Viruses, greening bacterium and viroids associated with citrus (Citrus species) decline in India. Indian J Agric Sci 67:51–57

    Google Scholar 

  • Ahuja SL, Monga D, Dhayal LS (2007) Genetics of resistance to cotton leaf curl disease in Gossypium hirsutum L. under field conditions. J Hered 98:79–83

    Article  CAS  PubMed  Google Scholar 

  • Alshami AAA, Ahlawat YS, Pant RP (2003) A hitherto unreported yellow vein clearing disease of citrus in India and its viral etiology. Indian Phytopathol 56:422–427

    Google Scholar 

  • Anderson PK, Cunningham AA, Patel NG, Morales FJ, Epstein PR, Daszak P (2004) Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers. Trends Ecol Evol 10:535–544

    Article  Google Scholar 

  • Anindya R, Joseph J, Gowri TDS, Savithri HS (2004) Complete genomicsequence of Pepper vein banding virus (PVBV): a distinct memberof the genus Potyvirus. Arch Virol 149:625–632

    Article  CAS  PubMed  Google Scholar 

  • Anonymous (2013) Central potato research institute news letter, Shilma-171001, Himachal Pradesh, India; 54

    Google Scholar 

  • Anthony Johnson AM, Dasgupta I, Sai Gopal DVR (2014) Development of loop-mediated isothermal amplification and SYBR green real-time PCR methods for the detection of Citrus yellow mosaic badnavirus in citrus species. J Virol Methods 203:9–14

    Article  CAS  PubMed  Google Scholar 

  • Arya M, Baranwal VK, Ahlawat YS, Singh L (2006) RT-PCR detection and molecular characterization of Onion yellow dwarf virus associated with garlic and onion. Curr Sci 91:1230–1234

    CAS  Google Scholar 

  • Awasthi LP, Singh SP, Chaubey AN, Abhishek, Kumar R (2014) Molecular characterization of potato viruses through RT-PCR and electron-microscopy. Caribb J Sci Technol 2:405–410

    Google Scholar 

  • Babu B, Hegde V, Makeshkumar T, Jeeva ML (2011) Detection and identification of Dasheen mosaic virus infecting Colocasia esculenta in India. Indian J Virol 22:59–62

    Article  PubMed  PubMed Central  Google Scholar 

  • Bagyalakshmi K, Parameswari B, Chinnaraja C, Karuppaiah R, Ganesh Kumar V, Viswanathan R (2012) Genetic variability and potential recombination events in the HC-Pro gene of sugarcane streak mosaic virus. Arch Virol 157:1371–1375

    Article  CAS  PubMed  Google Scholar 

  • Bajet NB, Unruh TR, Druffel KL, Eastwell KC (2008) Occurrence of two little cherry viruses in sweet cherry in Washington State. Plant Dis 92:234–238

    Article  CAS  Google Scholar 

  • Balaji V, Vanitharani R, Karthikeyan AS, Anbalagan S (2004) Veluthambi K Infectivity analysis of two variable DNA B components of Mungbean yellow mosaic virus-Vigna in Vigna mungo and Vigna radiata. J Biosci 29:297–308

    Article  CAS  PubMed  Google Scholar 

  • Balasubramanian V, Selvarajan R (2012) Complete genome sequence of a Banana bract mosaic virus isolate infecting the French plantain cv. Nendran in India. Arch Virol 157:397–400

    Article  CAS  PubMed  Google Scholar 

  • Banerjee A, Roy S, Tarafdar J (2011) Phylogenetic analysis of Rice tungro bacilliform virus ORFs revealed strong correlation between evolution and geographical distribution. Virus Genes 43:398–408

    Article  CAS  PubMed  Google Scholar 

  • Banerjee A, Dutta R, Roy S, Ngachan SV (2014a) First report of Chilli veinal mottle virus in Naga chilli (Capsicum chinense) in Meghalaya, India. Virusdisease 25:142–143

    Article  PubMed  Google Scholar 

  • Banerjee A, Chandra S, Swer EKP, Sharma SK, Ngachan SV (2014b) First molecular evidence of Soybean mosaic virus (SMV) infection in soybean from India. Australas Plant Dis Notes 9:150

    Article  Google Scholar 

  • Banerjee A, Roy S, Behere GT, Roy SS, Dutta SK, Ngachan SV (2014c) Identification and characterization of a distinct Banana bunchy top virus isolate of Pacific-Indian Oceans group from North-East India. Virus Res 183:41–49

    Article  CAS  PubMed  Google Scholar 

  • Banerjee A, Roy S, Sharma SK, Dutta SK, Chandra S, Ngachan SV (2016) Reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid diagnosis of chilli veinal mottle virus. Arch Virol. doi:10.1007/s00705-016-2850-7

  • Baranwal VK, Sharma SK (2016) Next generation high throughput diagnostics for management of virus and virus-like pathogens in horticultural crops: status and way forward. In: Souvenir of national seminar on integrating agri-horticultural and allied research for food and nutritional security in the era of global climate disruption, pp 168–178, 4–6 March, 2016. Imphal, Manipur

    Google Scholar 

  • Baranwal VK, Majumdar S, Ahlawat YS, Singh RP (2003) Sodium sulphite yields improved DNA of higher stability for PCR detection of citrus yellow mosaic virus from citrus leaves. J Virol Methods 112:153–156

    Article  CAS  PubMed  Google Scholar 

  • Baranwal VK, Majumder S, Ahlawat YS, Singh RP (2005) A novel approach for simultaneous detection of Citrus yellow mosaic virus and Citrus greening bacterium by multiplex polymerase chain reaction. IJBT 4:228–233

    Google Scholar 

  • Baranwal VK, Jain P, Saritha RK, Jain RK, Gautam NK (2015) Detection and partial characterization of Cowpea mild mottle virus in mungbean and urdbean by deep sequencing and RT-PCR. Crop Prot 75:77–79

    Article  CAS  Google Scholar 

  • Bhardwaj P, Ram R, Zaidi AA, Hallan V (2014) Characterization of Apple stem grooving virus infecting Actinidia deliciosa (Kiwi) in India. Sci Hortic 176:105–111

    Article  Google Scholar 

  • Bhat AI, Siju S (2007) Development of a single tube multiplex RT-PCR for the simultaneous detection of Cucumber mosaic virus and Piper yellow mottle virus associated with stunt disease of black pepper. Curr Sci 93:973–976

    CAS  Google Scholar 

  • Bhat AI, Siljo A (2014) Detection of viruses infecting black pepper by SYBR green-based real-time PCR assay. J Plant Pathol 96:105–109

    Google Scholar 

  • Bhat AI, Jain RK, Ramiah M (2002) Detection of Tobacco streak virus from sunflower and other crops by reverse transcription polymerase chain reaction. Indian Phytopathol 55:216–218

    CAS  Google Scholar 

  • Bhat AI, Hareesh PS, Madhubala R (2005) Sequencing of coat protein gene of an isolate of Cucumber mosaic virus infecting black pepper (Piper nigrum L.) in India. J Plant Biochem Biotechnol 14:37–40

    Article  CAS  Google Scholar 

  • Bhat AI, Siljo A, Jiby MV, Thankamani CK, Mathew PA (2009) Polymerase chain reaction (PCR) based indexing of black pepper (Piper nigrum L.) plants against Piper yellow mottle virus. J Spices Aromat Crops 18:28–32

    Google Scholar 

  • Bhat AI, Siljo A, Deeshma KP (2013) Rapid detection of Piper yellow mottle virus and Cucumber mosaic virus infecting black pepper (Piper nigrum) by loop-mediated isothermal amplification (LAMP). J Virol Methods 193:190–196

    Article  CAS  PubMed  Google Scholar 

  • Biju CN, Siljo A, Bhat AI (2010) Survey and RT-PCR based detection of Cardamom mosaic virus affecting small cardamom in India. Indian J Virol 21:148–150

    Article  CAS  PubMed  Google Scholar 

  • Biswas KK (2008) Molecular diagnosis of Citrus tristeza virus in mandarin (Citrus reticulata) orchards of hills of West Bengal. Indian J Virol 19:26–31

    Google Scholar 

  • Biswas KK (2010) Molecular characterization of Citrus tristeza virus isolates from the Northeastern Himalayan region of India. Arch Virol 155:959–963

    Article  CAS  PubMed  Google Scholar 

  • Biswas KK, Tarafdar A, Sharma SK (2012a) Complete genome of mandarin decline Citrus tristeza virus of Northeastern Himalayan hill region of India: comparative analyses determine recombinant. Arch Virol 157:579–583

    Article  CAS  PubMed  Google Scholar 

  • Biswas KK, Tarafdar A, Diwedi S, Lee RF (2012b) Distribution, genetic diversity and recombination analysis of Citrus tristeza virus of India. Virus Genes 45:139–148

    Article  CAS  PubMed  Google Scholar 

  • Biswas K, Hallen V, Zaidi AA, Pandey PK (2013) Molecular evidence of cucumber mosaic virus subgroup II infecting Capsicum annum L. in the Western region of India. Curr Discov 2:97–105

    Google Scholar 

  • Biswas C, Dey P, Mitra S, Bera A, Satpathy S, Karmakar PG (2014a) First report of Potato leaf roll virus (PLRV) naturally occurring on jute (Corchorus olitorius) in India. Plant Dis 98:1592–1593

    Article  Google Scholar 

  • Biswas KK, Tarafdar A, Sharma SK, Singh JK, Dwivedi S, Biswas K, Jayakumar BK (2014b) Current status of Citrus tristeza virus incidence and its spatial distribution in citrus growing geographical zones of India. Indian J Agric Sci 84:184–189

    Google Scholar 

  • Boonham N, Kreuzeb J, Winterc S, Vlugtd R, Bergervoetd J, Tomlinsona J, Mumforda R (2014) Methods in virus diagnostics: From ELISA to next generation sequencing. Virus Res 186:20–31

    Article  CAS  PubMed  Google Scholar 

  • Borah BK, Johnsonb AMA, Sai Gopal DVR, Dasgupta I (2008) A comparison of four DNA extraction methods for the detection of Citrus yellow mosaic badna virus from two species of citrus using PCR and dot-blot hybridization. J Virol Methods 151:321–324

    Google Scholar 

  • Brakta A, Thakur PD, Handa A (2013) First report of apple top working disease caused by viruses (Apple stem grooving virus, Apple chlorotic leaf spot virus, and Apple stem pitting virus) in apple in India. Plant Dis 97:1001

    Article  Google Scholar 

  • Briddon RW, Bull SE, Mansoor S, Amin I, Markham PG (2002) Universal primers for the PCR-mediated amplification of DNA É‘ a molecule associated with some monopartite begomoviruses. Mol Biotechnol 20:315–318

    Article  CAS  PubMed  Google Scholar 

  • Byadgi AS, Ahlawat YS (1995) A new viral ringspot disease of citrus (Citrus species) in India. Indian J Agric Sci 65:61–68

    Google Scholar 

  • Chakrabarty PK, Sable S, Monga D, Mayee CD (2005) Polymerase chain reaction-based detection of Xanthomonas axonopodis pv. malvacearum and cotton leaf curl virus. Indian J Agric Sci 75:524–528

    CAS  Google Scholar 

  • Chakraborty S, Pandey PK, Banerjee MK, Kalloo G, Fauquet CM (2003) Tomato leaf curl Gujarat virus, a new begomovirus species causing a severe leaf curl disease of tomato in Varanasi. India Phytopathol 93:1485–1495

    Article  CAS  Google Scholar 

  • Chakraborty S, Vanitharani R, Chattopadhyay B, Fauquet CM (2008) Super virulent pseudorecombination and asymmetric synergism between genomic components of two distinct species of begomovirus associated with severe tomato leaf curl disease in India. J Gen Virol:818–828

    Google Scholar 

  • Chang C, Chen CY, Hsu YH, Wu JT, Hu CC, Chang WC, Lin NS (2005) Transgenic resistance to Cymbidium mosaic virus in Dendrobium expressing the viral capsid protein gene. Transgenic Res 14:41–46

    Article  PubMed  CAS  Google Scholar 

  • Cherian S, Joseph J, Muniyappa V, Savithri HS (1999) Characterization of tobacco mosaic virus isolated from tomato in India. http://www.iisc.ernet.in/currsci/may25/articles30.htm

  • Cherian AK, Baranwal VK, Malathi VG, Pant RP, Ahlawat YS (2004) Banana streak virus from India and its detection by polymerase chain reaction. Indian J Biotechnol 3:409–413

    CAS  Google Scholar 

  • Chinnaraja C, Viswanathan R, Karuppaiah R, Bagyalakshmi K, Malathi P, Parameswari B (2013) Complete genome characterization of Sugarcane yellow leaf virus from India: Evidence for RNA recombination. Eur J Plant Pathol 135:335–349

    Article  CAS  Google Scholar 

  • Chowda Reddy RV, Colvin J, Muniyappa V, Seal S (2005) Diversity and distribution of begomoviruses infecting tomato in India. Arch Virol 150:845–867

    Article  CAS  Google Scholar 

  • Clark MF, Adams AN (1977) Characteristics of the microplate method of enzyme-linked immunosorbent assay for the detection of plant viruses. J Gen Virol 34:475–483

    Article  CAS  PubMed  Google Scholar 

  • Colinet D, Nguyen M, Kummert J, Lepoivre P (1998) Differentiation among potyviruses infecting sweet potato based on genus- and virus-specific reverse transcription polymerase chain reaction. Plant Dis 82:223–229

    Article  CAS  Google Scholar 

  • Das AK, Shivankar VJ, Singh S (2002) Presence of citrus (Citrus species) greening diseases (Candidatus Liberobacter asiaticum) and its psyllid vector (Diaphorina citri) in maharashtra. Indian J Agric Sci 72:188–191

    Google Scholar 

  • Dasgupta I, Das BK, Nath PS, Mukhopadhyay S, Niazi FR, Varma A (1996) Detection of rice tungro bacilliform virus in field and glasshouse samples from India using the polymerase chain reaction. J Virol Methods 58:53–58

    Article  CAS  PubMed  Google Scholar 

  • De LC, Devadas R, Barman D, Chakrabarti S (2013) VISION 2050. National Research Centre for Orchids, Pakyong

    Google Scholar 

  • Deng S, Hiruki C (1991) Amplification 16S rRNA genes from culturable and non-culturable mollicutes. J Microbiol Methods 14:53–61

    Article  CAS  Google Scholar 

  • Deng D, McGrath PF, Robinson DJ, Harrison BD (1994) Detection and differentiation of whitefly transmitted geminiviruses in plants and vector insects by the polymerase reaction with degenerate primers. Ann Appl Biol 125:327–336

    Article  CAS  Google Scholar 

  • Dhir S, Tomar M, Thakur PD, Ram R, Hallan V, Zaidi AA (2009) Molecular evidence for Apple stem pitting virus infection in India. New Dis Rep 19:45

    Google Scholar 

  • Dhir S, Ram R, Hallan V, Zaidi AA (2011) Molecular characterization of an Indian variant of Apple stem pitting virus: evidence of recombination. J Plant Pathol 93:471–478

    CAS  Google Scholar 

  • Dubey VK, Aminuddin SVP (2009) First report of Bean yellow mosaic virus in gladiolus in India. J Plant Pathol 91(S4):110

    Google Scholar 

  • Dubey VK, Aminuddin SVP (2010) Molecular characterization of Cucumber mosaic virus infecting Gladiolus, revealing its phylogeny distinct from the Indian isolate and alike the Fny strain of CMV. Virus Genes 41:126–134

    Article  CAS  PubMed  Google Scholar 

  • Duraisamy R, Natesan S, Muthurajan R, Gandhi K, Lakshmanan P, Karuppusamy N, Chokkappan M (2013) Molecular studies on the transmission of Indian cassava mosaic virus (ICMV) and Sri Lankan cassava mosaic virus (SLCMV) in cassava by Bemisia tabaci and cloning of ICMV and SLCMV replicase gene from cassava. Mol Biotechnol 53:150–158

    Article  CAS  Google Scholar 

  • Elbeaino T, Whitfield A, Sharma M, Digiaro M (2013) Emaravirus-specific degenerate PCR primers allowed the identification of partial RNA-dependent RNA polymerase sequences of Maize red stripe virus and Pigeonpea sterility mosaic virus. J Virol Methods 188:37–40

    Article  CAS  PubMed  Google Scholar 

  • Elbeaino T, Digiaro M, Uppala M, Sudini H (2014) Deep sequencing of pigeonpea sterility mosaic virus discloses five RNA segments related to emaraviruses. Virus Res 188:27–31

    Article  CAS  PubMed  Google Scholar 

  • Gaur RK, Singh M, Rao GP (2003) Molecular characterization of Sugarcane mosaic virus isolate from North Eastern region of India. Sugar Technol 5:149–153

    Article  CAS  Google Scholar 

  • Gawande SJ, Khar A, Lawande KE (2010) First report of Iris yellow spot virus on Garlic in India. Plant Dis 94:1066

    Article  Google Scholar 

  • Gawande SJ, Shukla A, Chimote VP, Kaushal N, Kaundal P, Garg ID, Chimote KP (2011) Development of PCR-based techniques for the detection of immobilised Potato virus Y virions. J Plant Pathol 93:127–132

    CAS  Google Scholar 

  • Gawande SJ, Gurav VS, Ingle AA, Gopal J (2014) First report of Iris yellow spot virus infecting Allium tuberosum in India. Plant Dis 98:1161

    Article  Google Scholar 

  • Geering ADW, Olszewski NE, Harper G, Lockhart BEL, Hull R, Thomas JE (2005) Banana contains a diverse array of endogenous badnaviruses. J Gen Virol 86:511–520

    Article  CAS  PubMed  Google Scholar 

  • Geetanjali AS, Kumar R, Srivastava PS, Mandal B (2011) Biological and molecular characterization of two distinct tomato strains of Cucumber mosaic virus based on complete RNA-3 genome and subgroup specific diagnosis. Indian J Virol 22:117–126

    Article  Google Scholar 

  • Ghosh SB, Bapat VA (2006) Development of RT-PCR based method for detection of Potato virus Y in tobacco and potato. Indian J Biotechnol 5:232–235

    CAS  Google Scholar 

  • Ghosh DK, Mathur S, Gupta KN, Ahlawat YS, Ramachandran P (2002a) Viroid infection of citrus in Central India. Indian Phytopathol 55(3):290–293

    Google Scholar 

  • Ghosh SB, Nagi LHS, Ganapathi TR, Paul Khurana SM, Bapat VA (2002b) Cloning and sequencing of Potato virus Y coat protein gene from an Indian isolate and development of transgenic tobacco for PVY resistance. Curr Sci 82:855–859

    CAS  Google Scholar 

  • Ghosh DK, Aglave B, Bhanare K, Baranwal VK (2007) PCR based detection of Citrus yellow mosaic disease from Vidarbha region of Maharastra. Indian Phytopathol 60:520–526

    CAS  Google Scholar 

  • Ghosh DK, Aglave B, Baranwal VK (2008a) Simultaneous detection of one RNA and one DNA virus from naturally infected citrus plants using duplex PCR technique. Curr Sci 94:1314–1318

    CAS  Google Scholar 

  • Ghosh R, Paul S, Palit P, Das S, Das A, Acharyya S, Mir JI, Ghosh SK, Roy A (2008b) Molecular characterization and computational analysis of coat protein gene of an East Indian isolate of Bhendi yellow vein mosaic virus and associated DNA-beta satellite. Indian J Virol. 19:173–182

    Google Scholar 

  • Ghosh DK, Aghave B, Roy A, Ahlawat YS (2009) Molecular cloning, sequencing and phylogenetic analysis of coat protein gene of a biologically distinct CTV isolate occurring in central India. J Plant Biochem Biotechnol 18:105–108

    Article  CAS  Google Scholar 

  • Ghosh R, Palit P, Paul S, Ghosh SK, Roy A (2012) Detection of Corchorus golden mosaic virus associated with yellow mosaic disease of jute (Corchorus capsularis). Indian J Virol 23:70–74

    Article  PubMed  PubMed Central  Google Scholar 

  • Gibbs A, Mackenzie A (1997) A primer pair for amplifying part of the genome of all potyvirids by RT-PCR. J Virol Methods 63:9–16

    Article  CAS  PubMed  Google Scholar 

  • Girish KR, Usha R (2005) Molecular characterization of two soybean-infecting begomoviruses from India and evidence for recombination among legume-infecting begomoviruses from South-East Asia. Virus Res 108:167–176

    Article  CAS  PubMed  Google Scholar 

  • Gopi V, Kuruba G, Sankar TG, Palanivel (2010) A detection of citrus yellow mosaic virus by PCR and nucleic acid spot hybridisation using non-radioactive probes in commercial citrus species. Arch Phytopathol Pfl 43:892–899

    Article  CAS  Google Scholar 

  • Govindappa MR, Shankergoud I, Shankarappa KS, Wickramaarachchi WART, Reddy BA, Rangaswamy KT (2011) Molecular detection and partial characterization of Begomovirus associated with the leaf curl disease of sunflower (Helianthus annuus) in Southern India. Plant Pathol J 10:29–35

    Article  Google Scholar 

  • Gupta N, Prabha K, Islam S, Baranwal VK (2013) First report of Leek yellow stripe virus in garlic from India. J Plant Pathol 95(4):S4.69–S4.77

    Google Scholar 

  • Ha C, Coombs S, Revill PA, Harding RM, Vu M, Dale JL (2008) Design and application of two novel degenerate primer pairs for the detection and complete genomic characterization of potyviruses. Arch Virol 153:25–36

    Article  CAS  PubMed  Google Scholar 

  • Haq QMI, Rouhibakhsh A, Ali A, Malathi VG (2011) Infectivity analysis of a blackgram isolate of Mungbean yellow mosaic virus and genetic assortment with MYMIV in selective hosts. Virus Genes 42:429–439

    Article  CAS  PubMed  Google Scholar 

  • Hareesh PS, Bhat AI (2008) Detection and partial nucleotide sequence analysis of Piper yellow mottle virus infecting black pepper (Piper nigrum L.) in India. Indian J Virol 19:160–167

    Google Scholar 

  • Hareesh PS, Madhubala R, Bhatt AI (2006) Characterization of Cucumber mosaic virus infecting Indian long pepper (Piper longum:L.) and betel vine (Piper betle L.) in India. Indian J Biotechnol 5:89–93

    CAS  Google Scholar 

  • Harper G, Osuji JO, Heslop-Harrison P, Hull R, Harper G, Lockhart BEL (1999) Integration of banana streak badnavirus into the Musa genome: molecular evidence. Virology 255:207–213

    Article  CAS  PubMed  Google Scholar 

  • Hema M, Savithri HS, Sreenivasulu P (2003) Comparison of direct binding polymerase chain reaction with recombinant coat protein antibody based dot-immunobinding assay and immunocapture-reverse transcription-polymerase chain reaction for the detection of sugarcane streak mosaic disease in India. Curr Sci 85:1774–1777

    CAS  Google Scholar 

  • Hoa NV, Ahlawat YS (2004) Characterization of four isolates of Indian citrus ringspot virus. Indian Phytopathol 57:296–302

    Google Scholar 

  • Jacob T, Usha R (2001) 3′ – terminal sequence analysis of the RNA genome of the Indian isolate of Cardamom mosaic virus, a new member of the genus Macluravirus of Potyviridae. Virus Genes 23:81–88

    Article  CAS  PubMed  Google Scholar 

  • Jacob T, Jebasingh T, Venugopal MN, Usha R (2003) High genetic diversity in the coat protein and 3′ untranslated regions among geographical isolates of Cardamom mosaic virus from South India. J Biosci 28:589–595

    Article  CAS  PubMed  Google Scholar 

  • Jaidi M, Srivastava A, Kumar S, Raj SK, Singh R (2015) First report of natural occurence of Papaya leaf crumple virus on soyabean in India. New Dis Rep 32:15

    Article  Google Scholar 

  • Jain RK, Pappu SS, Varma A, Ram RD (1998a) Molecular characterization of papaya ringspot potyvirus isolates from India. Ann Appl Biol 132:413–425

    Article  CAS  Google Scholar 

  • Jain RK, Pappu HR, Pappu SS, Krishanareddy M, Vani A (1998b) Watermelon bud necrosis tospovirus is a distinct virus species belonging to serogroup IV. Arch Virol 143:1637–1644

    Article  CAS  PubMed  Google Scholar 

  • Jain RK, Pappu SS, Pappu HR, Culbreath AK, Todd JW (1998c) Molecular diagnosis of Tomato spotted wilt tospovirus infection of peanut and other field and greenhouse crops. Plant Dis 82:900–904

    Article  CAS  Google Scholar 

  • Jain RK, Sharma J, Sivakumar AS, Sharma PK, Byadgi AS, Verma AK, Varma A (2004) Variability in the coat protein gene of Papaya ringspot virus isolates from multiple locations in India. Arch Virol 149:2435–2442

    Article  CAS  PubMed  Google Scholar 

  • Jain RK, Pandey NA, Krishnareddy M, Mandal B (2005) Immunodiagnosis of groundnut and watermelon bud necrosis viruses using polyclonal antiserum to recombinant nucleocapsid protein of Groundnut bud necrosis virus. J Virol Methods 130:162–164

    Article  CAS  PubMed  Google Scholar 

  • Jeevalatha A, Kaundal P, Shandil RK, Sharma NN, Chakrabarti SK, Singh BP (2013a) Complete genome sequence of Potato leafroll virus isolates infecting potato in the different geographical areas of India shows low level genetic diversity. Indian J Virol 24:199–204

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jeevalatha A, Kaundal P, Venkatasalam EP, Chakrabarti SK, Singh BP (2013b) Uniplex and duplex PCR detection of geminivirus associated with potato apical leaf curl disease in India. J Virol Methods 193:62–67

    Article  CAS  PubMed  Google Scholar 

  • John P, Sivalingam PN, Haq QMI, Kumar N, Mishra A, Briddon RW, Malathi VG (2008) Cowpea golden mosaic disease in Gujarat is caused by a Mungbean yellow mosaic India virus isolate with a DNA B variant. Arch Virol 153:1359–1365

    Article  CAS  PubMed  Google Scholar 

  • Jose J, Usha R (2000) Extraction of geminiviral DNA from a highly mucilaginous plant (Abelmoschus esculentus). Plant Mol Biol Report 18:349–355

    Article  CAS  Google Scholar 

  • Jose J, Usha R (2003) Bhendi yellow vein mosaic disease in India is caused by association of a DNA β satellite with a Begomovirus. Virology 305:310–317

    Article  CAS  PubMed  Google Scholar 

  • Joseph J, Savithri HS (1999) Determination of 30-terminal nucleotidesequence of pepper vein banding virus RNA and expression of itscoat protein in Escherichia coli. Arch Virol 144:1679–1687

    Article  CAS  PubMed  Google Scholar 

  • Joshi R, Dasgupta I (2001) Cloning and molecular analysis of DNA of rice tungro bacilliform viruses from different rice growing regions of India. Indian Phytopathol 54:469–475

    CAS  Google Scholar 

  • Joshi R, Kumar V, Dasgupta I (2003) Detection of molecular variability in rice tungro bacilliform viruses from India using polymerase chain reaction–restriction fragment length polymorphism. J Virol Methods 109:89–93

    Article  CAS  PubMed  Google Scholar 

  • Kamaal N, Mohammad A, Gupta S (2011) Identification of Mungbean yellow mosaic India virus infecting Vigna mungo var. silvestris L. Phytopathol Mediterr 50:94–100

    Google Scholar 

  • Kamala S, Makeshkumar T, Sreekumar J, Chakrabarti SK (2015) Whole transcriptome sequencing of diseased elephant foot yam reveals complete genome sequence of Dasheen mosaic virus. Virol Rep 5:1–9

    Article  Google Scholar 

  • Kanakala S, Sakhare A, Verma HN, Malathi VG (2013a) Infectivity and the phylogenetic relationship of a mastrevirus causing chickpea stunt disease in India. Eur J Plant Pathol 135:429–438

    Article  Google Scholar 

  • Kanakala S, Verma HN, Vijay P, Saxena DR, Malathi VG (2013b) Response of chickpea genotypes to Agrobacterium-mediated delivery of Chickpea chlorotic dwarf virus (CpCDV) genome and identification of resistance source. Appl Microbiol Biotechnol 97:9491–9501

    Article  CAS  PubMed  Google Scholar 

  • Kang SS, Athar M, Cheema SS, Malathi VG, Radhakrishnan G (2004) Quick detection of cotton leaf curl virus. Indian Phytopathol 57:245–246

    Google Scholar 

  • Karan M, Harding RM, Dale JL (1994) Evidence for two groups of Banana bunchy top virus isolates. J Gen Virol 75:3541–3546

    Article  CAS  PubMed  Google Scholar 

  • Karasev AV, Nikolaeva OV, Koonin EV, Gumpf DJ, Garnsey SM (1994) Screening of the closterovirus genome by degenerate primer mediated polymerase chain reaction. J Gen Virol 75:1415–1422

    Article  CAS  PubMed  Google Scholar 

  • Karthikeyan AS, Vanitharani R, Balaji V, Anuradha S, Thillaichidambaram P, Shivaprasad PV, Parameswari C, Balamani V, Saminathan M, Veluthambi K (2004) Analysis of an isolate of Mungbean yellow mosaic virus (MYMV) with a highly variable DNA B component. Arch Virol 149:1643–1652

    Article  CAS  PubMed  Google Scholar 

  • Karuppaiah R, Viswanathan R, Ganesh KV (2013) Genetic diversity of sugarcane bacilliform virus isolates infecting Saccharum spp. in India. Virus Genes 46:505–516

    Article  CAS  PubMed  Google Scholar 

  • Katoch M, Ram R, Zaidi AA, Garg ID (2002) Status of Bean yellow mosaic virus on Gladiolus. Crop Prot 21:861–865

    Article  Google Scholar 

  • Katoch M, Ram R, Zaidi AA (2003) First report of Tobacco ringspot virus occurring in gladiolus in India. Plant Pathol 52:789

    Article  Google Scholar 

  • Katoch M, Abdin MZ, Zaidi AA (2004) First report of Tobacco rattle virus occurring in gladiolus in India. Plant Pathol 53:236

    Article  Google Scholar 

  • Kaur C, Raj SK, Snehi SK, Goel AK, Roy RK (2011) Natural occurrence of Ornithogalum mosaic virus newly reported on gladiolus in India. New Dis Rep 24:2. http://dx.doi.org/10.5197/j.2044-0588.2011.024.002

    Article  Google Scholar 

  • Kaushal N, Gawande SJ, Kaundal P, Garg ID (2007) Reverse transcriptase polymerase chain reaction (RT-PCR) Based detection of PVS and PVS strain by using degenerate primers. Potato J 34:85–86

    Google Scholar 

  • Khan JA, Siddiqui MK, Singh BP (2002) The association of Begomovirus with bitter melon in India. Plant Dis 86:3

    Article  Google Scholar 

  • Khan S, Jan AT, Aquil B, Haq QMR (2011) Coat protein gene based characterization of Cucumber mosaic virus isolates infecting banana in India. J Phytology 3:94–101

    CAS  Google Scholar 

  • Kirthi N, Maiya SP, Murthy MRN, Savithri HS (2002) Evidence for recombination among the Tomato leaf curl virus strains/species from Bangalore. Indian Arch Virol 147:255–272

    Article  CAS  PubMed  Google Scholar 

  • Kirthi N, Priyadarshini CGP, Sharma P, Maiya SP, Hemalatha V, Sivaraman P, Dhawan P, Rishi N, Savithri HS (2004) Genetic variability of begomoviruses associated with cotton leaf curl disease originating from India. Arch Virol 149:2047–2057

    CAS  PubMed  Google Scholar 

  • Kreuze JF, Perez A, Untiveros M, Quispe D, Fuentes S (2009) Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses. Virology 388:1–7

    Article  CAS  PubMed  Google Scholar 

  • Krishna Reddy M, Venkataravanappa V, Madhuvanthi B, Jalali S (2010) Molecular characterization of begomoviruses associated with papaya leaf curl disease in India. Acta Hortic 851:465–472

    Article  Google Scholar 

  • Krishnareddy M, Usha-Rani R, Kumar A, Madhavireddy K, Pappu HR (2008) First report of Capsicum chlorosis virus (Genus Tospovirus) infecting chili pepper (Capsicum annuum) in India. Plant Dis 92:1469

    Article  Google Scholar 

  • Kulshrestha S (2005) Molecular characterization of virus causing rose mosaic dis-ease complex. Ph.D.Thesis, Department of Biosciences, Jamia Millia Islamia, New Delhi

    Google Scholar 

  • Kulshrestha S, Hallan V, Sharma A, Seth CA, Chauhan A, Zaidi AA (2013) Molecular characterization and intermolecular interaction of coat protein of Prunus necrotic ringspot virus: implications for virus assembly. Indian J Virol 24:235–241

    Article  PubMed  PubMed Central  Google Scholar 

  • Kumar S (2013) Studies on virus(es) associated with grapevine leafroll disease in India. Ph.D. Thesis, Indian Agricultural Research Institute, New Delhi

    Google Scholar 

  • Kumar PL, Jones AT, Reddy DVR (2003) A novel mite-transmitted virus with a divided RNA genome closely associated with pigeonpea sterility mosaic disease. Phytopathology 93:71–81

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Srivastava A, Raj SK (2005) Molecular detection of Cucumber mosaic virus in Chrysanthemum cultivars. Acta Phytopathol Entomol Hung 40:205–211

    Article  CAS  Google Scholar 

  • Kumar NA, Narasu ML, Zehr UB, Ravi KS (2008) Molecular characterization of Tobacco streak virus causing soybean necrosis in India. IJBT 7:214–217

    CAS  Google Scholar 

  • Kumar J, Kumar A, Khan JA (2009) Aminuddin first report of Papaya leaf curl virus naturally infecting tobacco in India. J Plant Pathol 91:112

    Google Scholar 

  • Kumar S, Baranwal VK, Joshi S, Arya M, Majumder S (2010a) Simultaneous detection of mixed infection of Onion yellow dwarf virus and an Allexivirus in RT-PCR for ensuring virus free onion bulbs. Indian J Virol 21:64–68

    Article  PubMed  PubMed Central  Google Scholar 

  • Kumar A, Kumar J, Khan JA (2010b) Sequence characterization of cotton leaf curl virus from Rajasthan: phylogenetic relationship with other members of geminiviruses and detection of recombination. Virus Genes 40:282–289

    Article  CAS  PubMed  Google Scholar 

  • Kumar J, Kumar A, Roy JK, Tuli R, Khan JA (2010c) Identification and molecular characterization of begomovirus and associated satellite DNA molecules infecting Cyamopsis tetragonoloba. Virus Genes 41:118–125

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Shankar Udaya AC, Nayaka SC, Lund OS, Prakash HS (2011a) Detection of Tobacco mosaic virus and Tomato mosaic virus in pepper and tomato by multiplex RT–PCR. Appl Microbiol 53:359–363

    Article  CAS  Google Scholar 

  • Kumar A, Snehi SK, Raj SK, Kumar J, Khan JA (2011b) Association of Cotton leaf curl Burewala virus and its satellite molecules with leaf distortion symptoms of cotton in India. New Dis Rep 24:18

    Article  Google Scholar 

  • Kumar J, Kumar A, Singh SP, Roy JK, Lalit A, Parmar D, Sharma NC, Tuli R (2012a) First report of Radish leaf curl virus infecting okra in India. New Dis Rep 25:9

    Article  Google Scholar 

  • Kumar S, Singh RM, Ram R, Badyal J, Hallan V, Zaidi AA, Varma A (2012b) Determination of major viral and sub viral pathogens incidence in apple orchards in Himachal Pradesh. Indian J Virol 23:75–79

    Article  PubMed  Google Scholar 

  • Kumar S, Baranwal VK, Singh P, Jain RK, Sawant SD, Singh SK (2012c) Characterization of a Grapevine leafroll-associated virus 3 from India showing incongruence in its phylogeny. Virus Genes 45:195–200

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Sawant SD, Sawant IS, Prabha K, Jain RK, Baranwal VK (2012d) First report of Grapevine leafroll-associated virus 1 infecting grapevines in India. Plant Dis 96:1828

    Article  Google Scholar 

  • Kumar J, Singh SP, Kumar J, Tuli R (2012e) A novel mastrevirus infecting wheat in India. Arch Virol 157:2031–2034

    Google Scholar 

  • Kumar J, Gunapati S, Singh SP, Kumar A, Lalit A, Sharma NC, Puranik R, Tuli R (2013a) A new betasatellite associated with Cotton leaf curl Burewala virus infecting tomato in India: influence on symptoms and viral accumulation. Arch Virol 158:1349–1353

    Article  CAS  PubMed  Google Scholar 

  • Kumar A, Shilpi S, Yogita M, Lal SK, Mandal B (2013b) Identification of a new strain of Tobacco mosaic virus infecting soybean in India based on host reactions and 3′ end genome sequence. Crop Prot 53:20–22

    Google Scholar 

  • Kumar S, Singh L, Ferretti L, Barba M, Zaidi AA, Hallan V (2013c) Evidence of Grapevine leafroll associated virus-1–3, Grapevine fleck virus and Grapevine virus B occurring in Himachal Pradesh, India

    Google Scholar 

  • Kumar S, Gautam KK, Raj SK (2014a) Molecular identification of Cucumber mosaic virus isolates of subgroup IB associated with mosaic disease of eggplant in India. Virus Dis 25:129–131

    Article  Google Scholar 

  • Kumar R, Jeevalatha A, Sharma NN, Sharma S, Chakrabarti SK, Singh BP (2014b) Development of PCR based methods for detection of Potato aucuba mosaic virus in India. Potato J 41:166–174

    Google Scholar 

  • Kumar S, Sankarlingam A, Rabindran R (2014c) Characterization and confirmation of Papaya ringspot virus-W strain infecting Trichosanthese cucumerina at Tamil Nadu. India J Plant Pathol Microbiol 5:225

    CAS  Google Scholar 

  • Kumar J, Gunapati S, Alok A, Lalit A, Gadre R, Sharma NC, Roy JK, Singh SP (2015a) Cotton leaf curl Burewala virus with intact or mutant transcriptional activator proteins: complexity of cotton leaf curl disease. Arch Virol 160:1219–1228

    Article  CAS  PubMed  Google Scholar 

  • Kumar A, Pandey DM, Abraham T, Mathew J, Jyothsna P, Ramachandran P, Malathi VG (2015b) Molecular characterization of viroid associated with tapping panel dryness syndrome of Hevea brasiliensis from India. Curr Sci 108:1520–1527

    CAS  Google Scholar 

  • Kunkalikar SR, Sudarsana P, Rajagopalan P, Zehr UB, Ravi KS (2010) Biological and molecular characterization of Capsicum chlorosis virus infecting chili and tomato in India. Arch Virol 155:1047–1057

    Article  CAS  PubMed  Google Scholar 

  • Kunkalikar SR, Sudarsana P, Arun BM, Rajagopalan P, Chen TC, Yeh SD, Naidu RA, Zehr UB, Ravi KS (2011) Importance and genetic diversity of vegetable-infecting tospoviruses in India. Phytopathology 101:367–376

    Article  PubMed  Google Scholar 

  • Kushwaha N, Achuit K, Singh AK, Chattopadhyay B, Chakraborty S (2010) Recent advances in Geminivirus detection and future perspectives. J Plant Protect Sci 1:1–18

    Google Scholar 

  • Lakshmi V, Hallan V, Ram R, Ahmed N, Zaidi AA, Varma A (2011) Diversity of Apple mosaic virus isolates in India based on coat protein and movement protein genes. Indian J Virol 22:44–49

    Article  PubMed  PubMed Central  Google Scholar 

  • Loconsole G, Onelge N, Potere O, Giampetruzzi A, Bozan O, Satar S, De Stradis A, Savino VN, Yokomi RK, Saponari M (2012) Identification and characterization of citrus yellow vein clearing virus, a putative new member of the genus Mandarivirus. Phytopathology 102:1168–1175

    Article  CAS  PubMed  Google Scholar 

  • Lovisolo O, Lisa V (1978) Virus diseases of carnation. Fitopatol Bras 3:219–233

    Google Scholar 

  • Machida S, Shibuya M, Sano T (2008) Enrichment of viroid small RNAs by hybridization selection using biotinylated RNA transcripts to analyze viroid induced RNA silencing. Gen Plant Pathol 74:203–207

    Article  CAS  Google Scholar 

  • Mackenzie DJ, McLean MA, Mukerji S, Green M (1997) Improved RNA extraction from woody plants for the detection of viral pathogens by reverse transcription-polymerase chain reaction. Plant Dis 81:222–226

    Article  CAS  Google Scholar 

  • Madhubala R, Bhadramurthy V, Bhat AI, Hareesh PS, Retheesh ST, Bhai RS (2005) Occurrence of Cucumber mosaic virus on vanilla (Vanilla planifolia Andrews) in Indian. J Biosci 30:339–350

    Article  CAS  PubMed  Google Scholar 

  • Magie RO, Poe SL (1972) In: Koenig N, Crowley W (eds) Disease and pest associates of bulbs and plant, in the world of gladiolus. North American Gladiolus Council, Edgewood Press, Maryland, pp 155–167

    Google Scholar 

  • Maheshwari R, Panigrahi G, Angappan K (2014) Molecular characterization of distinct YMV (Yellow mosaic virus) isolates affecting pulses in India with the aid of coat protein gene as a marker for identification. Mol Biol Rep 41:2635–2644

    Article  CAS  PubMed  Google Scholar 

  • Majumder S, Baranwal VK (2009) First report of Garlic common latent virus in garlic from India. Plant Dis 93:106

    Article  Google Scholar 

  • Majumder S, Baranwal VK (2014) Simultaneous detection of four garlic viruses by multiplex reversetranscription PCR and their distribution in Indian garlic accessions. J Virol Methods 202:34–38

    Article  CAS  PubMed  Google Scholar 

  • Majumder S, Arya M, Pant RP, Baranwal VK (2007) Shallot virus X in Indian shallot, a new virus report for India. New Dis Rep 15:52

    Google Scholar 

  • Majumder S, Baranwal VK, Joshi S (2008) Simultaneous detection of Onion yellow dwarf virus and Garlic latent virus in infected leaves and cloves of garlic by duplex RT-PCR. J Plant Pathol 90:369–372

    Google Scholar 

  • Mandal B, Varma A, Malathi VG (1997) Systemic infection of Vigna mungo using the cloned DNAs of the blackgram isolate of mungbean yellow mosaic geminivirus through agroinoculation and transmission of the progeny virus by whiteflies. J Phytopathol 145:505–510

    Article  Google Scholar 

  • Mandal B, Jain RK, Chaudhary V, Varma A (2003) First report of natural infection of Luffa acutangula by Watermelon bud necrosis virus in India. Plant Dis 87:598

    Article  Google Scholar 

  • Mandal B, Mandal S, Pun KB, Varma A (2004a) First report of the association of a Nanovirus with foorkey disease of large cardamom in India. Plant Dis 88:428

    Article  Google Scholar 

  • Mandal B, Mandal S, Sohrab SS, Pun KB, Varma A (2004b) A new yellow mosaic disease of chayote in India. Plant Pathol 53:797

    Article  Google Scholar 

  • Mandal B, Kumar A, Rani P, Jain RK (2012a) Complete genome sequence, phylogenetic relationships and molecular diagnosis of an Indian isolate of Potato Virus X. J Phytopathol 160:1–5

    Article  CAS  Google Scholar 

  • Mandal B, Vijayanandraj S, Shilpi S, Pun KB, Singh V, Pant RP, Jain RK, Varadarasan S, Varma A (2012b) Disease distribution and characterisation of a new Macluravirus associated with chirke disease of large cardamom. Ann Appl Biol 160:225–236

    Article  CAS  Google Scholar 

  • Mandal B, Jain RK, Krishnareddy M, Kumar NKK, Ravi KS, Pappu HR (2012c) Emerging problems of tospoviruses (Bunyaviridae) and their management in the Indian subcontinent. Plant Dis 96:468–479

    Article  Google Scholar 

  • Mandal B, Shilpi S, Barman AR, Mandal S, Varma A (2013) Nine novel DNA components associated with the foorkey disease of large cardamom: evidence of a distinct Babuvirus species in Nanoviridae. Virus Res 178:297–305

    Article  CAS  PubMed  Google Scholar 

  • Mangal M, Bhardwaj SV, Sharma DR, Kaur R, Mangal AK (2002) Use of meristem tip culture to eliminate carnation latent virus from carnation plants. Indian J Exp Biol:119–122

    Google Scholar 

  • Mangrauthia SK, Parameswari B, Jain RK, Praveen S (2008) Role of genetic recombination in the molecular architecture of papaya ringspot virus. Biochem Genet 46:835–846

    Article  CAS  PubMed  Google Scholar 

  • Mangrauthia SK, Malathi P, Agarwal S, Ramkumar G, KrishnaveniD NCN, Madhav MS, Ladhalakshmi D, Balachandran SM, Viraktamath BC (2012) Genetic variation of coat protein gene among the isolates of Ricetungro spherical virus from tungro-endemic states of the India. Virus Genes 44:482–487

    Article  CAS  PubMed  Google Scholar 

  • Martelli GP (2012) Grapevine virology highlights 2000–2003. In: Extended abstracts of 17th Meeting of the ICVG. Davis, California, USA. pp 13–31

    Google Scholar 

  • Maruthi MN, Rekha AR, Muniyappa V (2007) Pumpkin yellow vein mosaic disease is caused by two distinct begomoviruses: complete viral sequences and comparative transmission by an indigenous Bemisia tabaci and the introduced B-biotype. EPPO Bull 37:412–419

    Article  Google Scholar 

  • Mathur S, Garg AP, Ramachandran P (2002) Detection of viroid infecting chrysanthemum in India. Indian Phytopathol 55:479–482

    Google Scholar 

  • Meena RP, Baranwal VK (2016) Development of multiplex polymerase chain reaction assay for simultaneous detection of clostero-, badna- and mandari-viruses along with huanglongbing bacterium in citrus trees. J Virol Methods 235:58–64

    Google Scholar 

  • Mehra A, Jabeen N, Singh AK, Hallan V, Zaidi AA (2008) A new chrysanthemum potyvirus: a molecular evidence. Arch Phytopathol Plant Protect 42:436–441

    Article  CAS  Google Scholar 

  • Menzel W, Jelkmann W, Maiss E (2002) Detection of four apple viruses by multiplex RT-PCR assays with co-amplification of plant mRNA as internal control. J Virol Methods 99:81–92

    Article  CAS  PubMed  Google Scholar 

  • Minafra A, Hadidi A, Martelli GP (1992) Detection of Grapevine closterovirus A in infected grapevine tissue by reverse transcription-polymerase chain reaction. Vitis 31:221–227

    CAS  Google Scholar 

  • Mishra R, Verma RK, Gaur RK (2015) Analysis of genome comparison of two Indian isolates of Cowpea aphid-borne mosaic virus from India. Virus Genes 51:306–309

    Article  CAS  PubMed  Google Scholar 

  • Monga D, Kumar R, Kumar M (2005) Detection of DNA A and satellite (DNA beta) in cotton leaf curl virus (CLCuV) infected weeds and cotton plants using PCR technique. J Cotton Res Dev 19:105–108

    Google Scholar 

  • Mukherjee K, Verma Y, Chakrabarti SK, Singh MN, Khurana SMP (2003) Cloning and sequencing of coat protein gene of an Indian potato leaf roll virus (PLRV) isolate and its similarity with other members of Luteoviridae. Virus Genes 26:247–253

    Article  CAS  PubMed  Google Scholar 

  • Muniyappa V, Venkatesh HM, Ramappa HK, Kulkarni RS, Zeidan M, Tarba CY, Ghanim M, Czosnek H (2000) Tomato leaf curl virus from Bangalore (ToLCV-Ban4): sequence comparison with Indian ToLCV isolates, detection in plants and insects, and vector relationships. Arch Virol 145:1583–1598

    Article  CAS  PubMed  Google Scholar 

  • Muniyappa V, Maruthi MN, Babitha CR, Colvin J, Briddon RW, Rangaswamy KT (2003) Characterization of Pumpkin yellow vein mosaic virus from India. Ann Appl Biol 142:323–331

    Article  Google Scholar 

  • Naidu RA, Miller JS, Mayo MA, Wesley SV, Reddy AS (2000) The nucleotide sequence of Indian peanut clump virus RNA 2: sequence comparisons among pecluviruses. Arch Virol 145:1857–1866

    Article  CAS  PubMed  Google Scholar 

  • Naimuddin AM, Pratap A (2011) First report of natural infection of Mungbean yellow mosaic India virus in two wild species of Vigna. New Dis Rep 23:21

    Article  Google Scholar 

  • Naimuddin AM, Gupta S, Agnihotri AK (2014) Ageratum conyzoides harbours Mungbean yellow mosaic India virus. Plant Pathol J. doi:10.3923/ppj.2014

  • Nakahara K, Hataya T, Uyeda I (1999) A simple, rapid method of nucleic acid extraction without tissue homogenization for detecting viroids by hybridization and RT-PCR. J Virol Methods 77:47–58

    Article  CAS  PubMed  Google Scholar 

  • Nariani TK (1960) Yellow mosaic of mung (Phaseolus aureus L.) Indian Phytopathol 13:24–29

    Google Scholar 

  • Nath N, Mathur S, Dasgupta I (2002) Molecular analysis of two complete rice tungro bacilliform virus genomic sequences from India. Arch Virol 147:1173–1187

    Article  CAS  PubMed  Google Scholar 

  • Noorani MS, Awasthi P, Singh RM, Ram R, Sharma MP, Singh SR, Ahmed N, Hallan V, Zaidi AA (2010) Complete nucleotide sequence of cherry virus A (CVA) infecting sweet cherry in India. Arch Virol 155:2079–2082

    Article  CAS  PubMed  Google Scholar 

  • Noorania Md S, Awasthia P, Sharma MP, Ram R, Zaidi AA, Hallan V (2013) Simultaneous detection and identification of four cherry viruses by two step multiplex RT-PCR with an internal control of plant nad5 mRNA. J Virol Methods 193:103–107

    Article  CAS  Google Scholar 

  • Padidam M, Beachy RN, Fauquet CM (1995) Tomato leaf curl geminivirus from India has a bipartite genome and coat protein is not essential for infectivity. J Gen Virol 76:249–263

    Article  CAS  PubMed  Google Scholar 

  • Padmavathi M, Srinivas KP, Hema M, Sreenivasulu P (2013) First report of Konjac mosaic virus in elephant foot yam (Amorphophallus paeoniifolius) from India. Australas Plant Dis Notes 8:27–29

    Article  Google Scholar 

  • Pal BF, Tandon RN (1937) Types of tobacco leaf curl in northern India. Indian J Agril Sci 7:363–393

    Google Scholar 

  • Parameswari B, Bagyalakshmi K, Viswanathan R, Chinnaraja C (2013) Molecular characterization of Indian sugarcane streak mosaic virus isolate. Virus Genes 46:186–189

    Article  CAS  PubMed  Google Scholar 

  • Parameswari B, Bagyalakshmi K, Chinnaraja C, Viswanathan R (2014) Molecular characterization of Indian Sugarcane streak mosaic virus isolates reveals recombination and negative selection in the P1 gene. Gene 552:199–203

    Article  CAS  PubMed  Google Scholar 

  • Parveen S, Ahlawat YS, Pant RP, Milne RG (1999) RT-PCR based detection and molecular cloning of coat protein gene of citrus ringspot virus from India. In: International symposium on citriculture. NRCC, Nagpur, p 122

    Google Scholar 

  • Patil BL, Kumar PL (2015) Pigeonpea sterility mosaic virus: a legume-infecting Emaravirus from South Asia. Mol Plant Pathol 16:775–786

    Article  CAS  PubMed  Google Scholar 

  • Patil BL, Rajasubramaniam S, Bagchi C, Dasgupta I (2005) Both Indian cassava mosaic virus and Sri Lankan cassava mosaic virus are found in India and exhibit high variability as assessed by PCR-RFLP. Arch Virol 150:389–397

    Article  CAS  PubMed  Google Scholar 

  • Periasamy M, Niazi FR, Malathi VG (2006) Multiplex RT-PCR, a novel technique for the simultaneous detection of the DNA and RNA viruses causing rice tungro disease. J Virol Methods 134:230–236

    Article  CAS  PubMed  Google Scholar 

  • Prabha K, Baranwal VK (2011) Indian citrus ringspot virus: localization of virus in seed tissues and evidence for lack of seed transmission. Phytoparasitica 39:491–496

    Article  Google Scholar 

  • Prabha K, Baranwal V (2012) The genome sequence of an isolate of Indian citrus ringspot virus infecting the sweet orange in India. J Virol 86:12446–12447

    Article  CAS  Google Scholar 

  • Prabha K, Baranwal VK, Jain RK (2013) Applications of next generation high throughput sequencing technologies in characterization, discovery and molecular interaction of plant viruses. Indian J Virol 24:157–165

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pramesh D, Baranwal VK (2015) Production of virus-free garlic (Allium sativum L.) through meristem tip culture after solar or hot air treatment of cloves. J Hortic Sci Biotechnol 90:180–186

    Article  CAS  Google Scholar 

  • Pramesh D, Islam S, Singh J, Baranwal VK (2012) Serological and PCR detection of Garlic common latent virus associated with garlic accessions of India. Med Plant 4:17–22

    Google Scholar 

  • Prasada Rao RDVJ, Raghunathan V, Joshi NC (1979) Interception of peanut mottle virus. Indian J Pl Prot 7:59–63

    Google Scholar 

  • Prasanth G, Hegde V (2008) Occurrence of Sweet potato feathery mottle virus and Sweet potato leaf curl Georgia viruson Sweet Potato in India. Dis Notes 92:311

    Google Scholar 

  • Pratap D, Kumar S, Raj SK (2008) First molecular identification of a Cucumber mosaic virus isolate causing shoestring symptoms on tomato in India. Australas Plant Dis Notes 3:57–58

    Article  CAS  Google Scholar 

  • Raigond B, Venkateswarlu V, Sridhar J, Jeevalatha A, Sharma S, Singh BP (2014) RT-PCR detection of Potato leaf roll virus (PLRV) in aphids from Northern and North-Eastern India. Indian J Plant Prot 42:430–436

    Google Scholar 

  • Raikhy G, Hallan V, Kulshrestha S, Sharma ML, Ram R, Zaidi AA (2003a) First report of Carnation necrotic fleck virus (CNFV) infecting carnations in India. Plant Pathol 52:801

    Article  Google Scholar 

  • Raikhy G, Hallan V, Kulshrestha S, Sharma ML, Ram R, Zaidi AA (2003b) Molecular characterization of a Carnation etched ring virus isolate from India. Acta Virol 47:105–111

    CAS  PubMed  Google Scholar 

  • Raikhy G, Hallan V, Kulshrestha S, Ram R, Zaidi AA (2006a) Detection of carnation ringspot and Carnation vein mottle virus (es) in carnation cultivars in India. Acta Hortic 722:247–258

    Article  CAS  Google Scholar 

  • Raikhy G, Hallan V, Kulshrestha S, Ram R, Zaidi AA (2006b) Multiplex PCR and genome analysis of Carnation mottle virus Indian isolate. Curr Sci 90:74–82

    CAS  Google Scholar 

  • Raj SK, Singh BP (1996) Association of geminivirus infection with yellow green mosaic disease of Cucumis sativus: diagnosis by nucleic acid probes. Indian J Exp Biol 34:603–605

    CAS  PubMed  Google Scholar 

  • Raj SK, Saxena S, Hallan V, Singh BP (1998) Biochem Mol Biol Int 44:89–95

    CAS  PubMed  Google Scholar 

  • Raj SK, Srivastava A, Chandra G, Singh BP (2002) Characterization of Cucumber mosaic virus isolate infecting gladiolus cultivars and comparative evaluation of serological and molecular methods for sensitive diagnosis. Curr Sci 83:1132–1137

    Google Scholar 

  • Raj SK, Khan MS, Singh R, Nisha K, Prakash D (2005) Occurrence of yellow mosaic geminiviral disease on bitter gourd (Momordica charantia) and its impact on phytochemical contents. Int J Food Sci Nutr 56:185–192

    Article  CAS  PubMed  Google Scholar 

  • Raj SK, Khan MS, Snehi SK, Srivastava S, Singh HB (2006) A yellow mosaic disease of soybean in Northern India is caused by Cotton leaf curl Kokhran virus. Plant Dis 90:975

    Article  Google Scholar 

  • Raj SK, Kumar S, Choudhari S (2007) Identification of Tomato aspermy virus as the cause of yellow mosaic and flower deformation of chrysanthemums in India. Australas Plant Dis Notes 157:117–125

    Google Scholar 

  • Raj SK, Snehi SK, Khan MS, Singh R, Khan AA (2008) Molecular evidence for association of Tomato leaf curl New Delhi virus with leaf curl disease of papaya (Carica papaya L.) in India. Australas Plant Dis Notes 3:152–155

    Article  CAS  Google Scholar 

  • Raj SK, Kumar S, Choudhary S, Verma DK (2009) Biological and molecular characterization of three isolates of Tomato aspermy virus infecting chrysanthemums in India. J Phytopathol 157:117–125

    Article  CAS  Google Scholar 

  • Raj SK, Snehi SK, Gautam KK, Khan MS (2010) First report of association of Cucumber mosaic virus with blister and leaf distortion of castor bean (Ricinus communis) in India. Phytoparasitica 38:283–289

    Article  Google Scholar 

  • Raj SK, Kumar S, Verma DK, Snehi SK (2011) First report on molecular detection and identification of Tomato aspermy virus naturally occurring on gladiolus in India. Phytoparasitica 39:303–307

    Article  CAS  Google Scholar 

  • Raja P, Jain RK (2006) Molecular diagnosis of Groundnut bud necrosis virus causing bud blight of tomato. Indian Phytopathol 59:359–362

    CAS  Google Scholar 

  • Rajagopalan PA, Naik A, Katturi P, Kurulekar M, Kankanallu RS, Anandalakshmi R (2012) Dominance of resistance-breaking cotton leaf curl Burewala virus (CLCuBuV) in northwestern India. Arch Virol 157:855–868

    Article  CAS  PubMed  Google Scholar 

  • Rajinimala N, Rabindran R (2007) First report of Indian cassava mosaic virus on bittergourd (Momordica charantia) in Tamil Nadu, India. Australas Plant Dis Notes 2:81–82

    Article  Google Scholar 

  • Ramachandran P, Pandey PK, Ahlawat YS, Varma A, Kapur SP (1993) Viroid diseases of citrus in India. In: Proceedings of the 12th Cant. IOCV. IOCV. Riverside, pp 438–440

    Google Scholar 

  • Ramachandran P, Francis L, Mathur S, Varma A, Mathew J, Mathew NM, Sethurajm MR (2000) Evidence for association of a low molecular weight RNA with tapping panel dryness syndrome of rubber. Plant Dis 84:1155

    Article  Google Scholar 

  • Ramachandran P, Roy A, Mathur S, Agarwal J, Ahlawat YS (2003) Diagnostics for Citrus exocortis and Hop stunt viroids associated with yellow corky vein disease in citrus. Indian Phytopathol 56:428–433

    Google Scholar 

  • Rana T (2010) Molecular characterization and diagnostic development for Apple chlorotic leaf spot virus. Ph.D. Thesis, Institute of Himalayan Bioresource Technology, CSIR, Palampur-176061 (H.P.), India

    Google Scholar 

  • Rana T, Chandel V, Hallan V, Zaidi AA (2008) Cydonia oblonga as reservoir of Apple chlorotic leaf spot virus in India. Plant Pathol 57:393

    Article  Google Scholar 

  • Rana T, Chandel V, Kumar Y, Ram R, Hallan V, Zaidi AA (2010) Molecular variability analyses of Apple chlorotic leaf spot virus capsid protein. J Biosci 35:605–615

    Article  CAS  PubMed  Google Scholar 

  • Rana T, Negi A, Dhir S, Thockchom T, Chandel V, Walia Y, Singh RM, Ram R, Hallan V, Zaidi AA (2011) Molecular diagnosis of apple virus and viroid pathogens from India. Arch Phytopathol Plant Protect 44:505–512

    Article  Google Scholar 

  • Rani RV, Karthikeyan AS, Anuradha S, Veluthambi K (1996) Genome homologies among geminiviruses infecting Vigna, cassava, Acalypha Croton and Vernonia. Curr Sci 70:63–69

    Google Scholar 

  • Rao MHP, Reddy DVR (1972) A new strain of tobacco mosaic virus on tomato (Lycopersicon esculentum). Indian Phytopathol 24:672–678

    Google Scholar 

  • Rao RDVJP, Ragunathan V, Joshi NC (1979) Interception of peanut mottle virus. Indian J Plant Prot 7:59–63

    Google Scholar 

  • Rao GP, Chatenet M, Girard JC, Rott P (2006) Distribution of sugarcane mosaic and sugarcane streak mosaic virus in India. Sugar Technol 8:79–81

    Article  Google Scholar 

  • Rao GP, Sharma SK, Singh D, Arya M, Singh P, Baranwal VK (2014) Genetically diverse variants of sugarcane bacilliform virus infecting sugarcane in India and evidence of a novel recombinant Badnavirus variant. J Phytopathol 162:779–787

    Article  CAS  Google Scholar 

  • Ravi K, Joseph J, Nagaraju N, Krishnaprasad S, Reddy H, Savithri HS (1997) Characterization of a pepper vein banding virus from chillipepper in India. Plant Dis 81:673–677

    Article  CAS  Google Scholar 

  • Ravi KS, Kitkaru AS, Winter S (2006) Iris yellow spot virus in onions: a new tospovirus record form India. Plant Pathol 55:288

    Article  Google Scholar 

  • Reddy DVR, Iizuka N, Ghanekar AM, Murthy VK, Kuhn CW, Gibbons RW, Chohan IS (1978) The occurrence of peanut mottle virus in India. Plant Dis Rep 62:978–982

    Google Scholar 

  • Reddy BVB, Obaiah S, Prasanthi L, Sivaprasad Y, Sujitha A, Krishna TG (2015) Mungbean yellow mosaic India virus is associated with yellow mosaic disease of blackgram (Vigna mungo L.) in Andhra Pradesh, India. Arch Phytopathol Plant Protect 48:345–353

    Article  Google Scholar 

  • Renukadevi P, Nagendran K, Nakkeeran S, Karthikeyan G, Jawaharlal M, Alice D, Malathi VG (2015) First report of Tomato spotted wilt virus infection of Chrysanthemum in India. Plant Dis 99:1190

    Article  Google Scholar 

  • Robertson NL, French R, Gray SM (1991) Use of group specific primers and the polymerase chain reaction for the detection and identification of luteoviruses. J Gen Virol 72:1473–1477

    Article  CAS  PubMed  Google Scholar 

  • Rodoni BC, Ahlawat YS, Varma A, Dale JL, Harding RM (1997) The identification and characterisation of Banana bract mosaic virus in India. Plant Dis 81:669–672

    Article  CAS  Google Scholar 

  • Rodoni BC, Dale JL, Harding RM (1999) Characterization and expression of the coat protein-coding region of banana bract mosaic potyvirus, development of diagnostic assays and detection of the virus in banana plants from five countries in Southeast Asia. Arch Virol 144:1725–1737

    Article  CAS  PubMed  Google Scholar 

  • Rojas MR, Gilbertson RL, Russell DR, Maxwell DP (1993) Use of degenerate primers in the polymerase chain reaction to detect whitefly-transmitted geminiviruses. Plant Dis 77:340–347

    Article  CAS  Google Scholar 

  • Roossinck MJ (1999) Cucumoviruses (Bromoviridae)-general features. In: Granoof L, Webster RG (eds) Encyclopedia of virology, 2nd edn. Academic, San Diego, pp 315–320

    Chapter  Google Scholar 

  • Rowhani A, Biardi L, Johnson R, Saldarelli P, Zhang YP, Chin J, Green M (2000) Simplified sample preparation method and one-tube RT-PCR for grapevine viruses. In: Extended abstracts of 13th meeting of ICVG. Adelaide, p 148

    Google Scholar 

  • Roy A, Spoorthi P, Bag MK, Prasad TV, Singh R, Dutta M, Mandal B (2013) A leaf curl disease in germplasm of rapeseed-mustard in India: molecular evidence of a weed-infecting Begomovirus-betasatellite complex emerging in a new crop. J Phytopathol 161:522–535

    Article  CAS  Google Scholar 

  • Roy B, Chakraborty B, Mitra A, Sultana S, Sherpa AR (2015) Natural occurrence of Bhendi yellow vein mosaic virus on Litsea spp. in India. New Dis Rep 31:7

    Article  Google Scholar 

  • Sahana AB, Adkar-Purushothama CR, Chennappa G, Zhang ZX, Sreenivasa MY, Sano T (2013) First report of Grapevine yellow speckle viroid 1 and Hop stunt viroid Infecting Grapevines (Vitis vinifera) in India. Plant Dis 97:1517

    Article  Google Scholar 

  • Sanchez-Navarro JA, Canizares MC, Cano EA, Pallas V (1999) Simultaneous detection of five carnation viruses by nonisotopic molecular hybridization. J Virol Methods 82:167–175

    Article  CAS  PubMed  Google Scholar 

  • Sankaralingam A, Baranwal VK, Ahlawat YS, Devi R, Ramiah M (2006) RT-PCR detection and molecular characterization of Banana bract mosaic virus from the pseudostem and bract of banana. Arch Phytopathol Pfl 39:273–281

    Article  CAS  Google Scholar 

  • Sastry KSM (1964) A new strain of Chrysanthemum aspermy virus from India. Indian J Microbiol. 2007 4:37–40

    Google Scholar 

  • Satyanarayana T, Mitchell SE, Reddy DV, Kresovich S, Jarret R, Naidu RA, Gowda S, Demski JW (1996) The complete nucleotide sequence and genome organization of the M RNA segment of peanut bud necrosis tospovirus and comparison with other tospoviruses. J Gen Virol 77:2347–2352

    Article  CAS  PubMed  Google Scholar 

  • Saxena S, Hallan V, Singh BP, Sane PV (1998) Leaf curl disease of Carica papaya from India may be caused by a bipartite Geminivirus. Plant Dis 82:126

    Article  Google Scholar 

  • Selvarajan R, Balasubramanian V (2013) Natural occurrence of Banana bunchy top virus in Ensete superbum in India. Indian J Virol 24:97–98

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Selvarajan R, Mary Sheeba M, Balasubramanian V, Rajmohan R, Dhevi LN, Sasireka T (2010) Molecular characterization of geographically different Banana bunchy top virus isolates in India. Indian J Virol 21:110–116

    Article  CAS  PubMed  Google Scholar 

  • Selvarajan R, Mary SM, Balasubramanian V (2011) Simultaneous detection of episomal Banana streak Mysore virus and Banana bunchy top virus using multiplex RT-PCR. Curr Sci 100:31–34

    CAS  Google Scholar 

  • Senanayake DMJB, Mandal B, Lodha S, Varma A (2006) Firstreport of chilli leaf curl virus affecting chilli in India. Plant Pathol 56:343

    Article  Google Scholar 

  • Senanayake DMJB, Varma A, Mandal B (2012) Virus–vector relationships, host range, detection and sequence comparisonof Chilli leaf curl virus associated with an epidemic of leaf curl disease of chilli in Jodhpur. India J Phytopathol. doi:10.1111/j.1439-0434.2011.01876.x

  • Seoh ML, Wong SM, Zhang L (1998) Simultaneous TD/RT-PCR detection of Cymbidium mosaic potexvirus and Odontoglossum ringspot tobamovirus with a single pair of primers. J Virol Methods 72:197–204

    Article  CAS  PubMed  Google Scholar 

  • Sharma J, Jain RK, Varma A (2004) Detection of papaya ringspot virus in naturally infected papaya plants by reverse transcription polymerase chain reaction. Indian Phytopathol 57:237–239

    CAS  Google Scholar 

  • Sharma J, Jain RK, Ramiah M, Varma A (2005a) Natural spread of papaya ringspot virus to new areas: occurrence in Coimbatore, Tamil Nadu. Indian Phytopathol 58:245–249

    Google Scholar 

  • Sharma A, Zaidi AA, Sood A, Sharma A, Vij SP, Pathak P, Ahuja PS (2005b) Virus analysis of indigenous orchid germplasm collection. J Orchid Soc India 19:41–46

    Google Scholar 

  • Sharma SK, Tarafdar A, Khatun D, Sumita K, Biswas KK (2012) Intra-farm diversity and evidence of genetic recombination of Citrus tristeza virus isolates in Delhi region of India. J Plant Biochem Biotechnol 21:38–43

    Article  Google Scholar 

  • Sharma P, Verma RK, Mishra RD, Choudhary K, Gaur RK (2013) First report of Turnip yellow virus (TuYV) in Brassica juncea (Indian mustard) in India. New Dis Rep 27:21

    Article  Google Scholar 

  • Sharma SK, Vignesh Kumar P, Baranwal VK (2014a) Immunodiagnosis of episomal Banana streak MY virus using polyclonal antibodies to an expressed putative coat protein. J Virol Methods 207:86–94

    Article  CAS  PubMed  Google Scholar 

  • Sharma SK, Vignesh Kumar P, Poswal R, Rai R, Geetanjali AS, Prabha K, Jain RK, Baranwal VK (2014b) Occurrence and distribution of banana streak disease and standardization of a reliable detection procedure for routine indexing of banana streak viruses in India. Sci Hortic 179:277–283

    Article  CAS  Google Scholar 

  • Sharma SK, Vignesh Kumar P, Geetanjali AS, Pun KB, Baranwal VK (2015) Subpopulation level variation of banana streak viruses in India and common evolution of banana and sugarcane badnaviruses. Virus Genes 50:450–465

    Article  CAS  PubMed  Google Scholar 

  • Sherpa AR, Hallan V, Ram R, Vij SP, Pathak P, Garg ID, Zaidi AA (2003) First report of Cymbidium mosaic virus on Cymbidiums in India. Plant Pathol 52:788

    Article  Google Scholar 

  • Sherpa AR, Bag TK, Hallan V, Zaidi AA (2006) Detection and incidence of Odontoglossum ringspot virus in orchids. Australas Plant Pathol 35:69–71

    Article  Google Scholar 

  • Sherpa AR, Hallan V, Pathak P, Zaidi AA (2007) Complete nucleotide sequence analysis of Cymbidium mosaic virus Indian isolate: further evidence for natural recombination among potex viruses. J Biosci 34:663–669

    Article  Google Scholar 

  • Shetti P, Peter A, Jingade P (2012) Serological and molecular detection of an isolate of Cucumber mosaic virus (CMV) infecting cucumber (Cucumis sativus) and cloning of its coat protein gene. J Biochem Technol 3:198–202

    Google Scholar 

  • Shih SL, Tsai WS, Green SK, Singh D (2006) First report of tomato leaf curl Joydebpur virus infecting chilli in India. New Dis Rep 14:17

    Google Scholar 

  • Siju S, Madhubala R, Bhat AI (2007) Sodium sulphite enhances RNA isolation and sensitivity of Cucumber mosaic virus detection by RT-PCR in black pepper. J Virol Methods 141:107–110

    Article  CAS  PubMed  Google Scholar 

  • Siljo A, Bhat AI, Biju CN, Venugopal MN (2012) Occurrence of Banana bract mosaic virus on cardamom. Phytoparasitica 40:77–85

    Article  Google Scholar 

  • Siljo A, Bhat AI, Biju CN (2013) Analysis of variability in Cardamom mosaic virus isolates occurring in India using symptomatology and coat protein gene sequence. J Spices Aromat Crops 22:70–75

    Google Scholar 

  • Siljo A, Bhat AI, Biju CN (2014) Detection of Cardamom mosaic virus and Banana bract mosaic virus in cardamom using SYBR Green based reverse transcription-quantitative PCR. Virus Dis 25:137–141

    Article  CAS  Google Scholar 

  • Singh R, Raj SK, Chanadra G (2001) Association of monopartite Begomovirus with yellow mosaic disease of pumpkin in India. Plant Dis 85:1029

    Article  Google Scholar 

  • Singh RP, Nie X, Singh M, Coffin R, Duplessis P (2002) Sodium sulphate inhibition of potato and cherry polyphenolics in nucleic acid extraction for virus detection by RT-PCR. J Virol Methods 99:123–131

    Article  CAS  PubMed  Google Scholar 

  • Singh HP, Hallan V, Raikhy G, Kulshrestha S, Sharma ML, Ram R, Garg ID, Zaidi AA (2005) Characterization of an Indian isolate of Carnation mottle virus infecting carnations. Curr Sci 88:594–601

    Google Scholar 

  • Singh L, Hallan V, Jabeen N, Singh AK, Ram R, Martin DP, Zaidi AA (2007a) Coat protein gene diversity among Chrysanthemum virus B isolates from India. Arch Virol 152:405–413

    Article  CAS  PubMed  Google Scholar 

  • Singh MK, Sherpa AR, Hallan V, Zaidi AA (2007b) A potyvirus in Cymbidium spp. In Northern India. Australas Plant Dis 2:11–13

    Article  Google Scholar 

  • Singh R, Raj SK, Prasad V (2008) Molecular characterization of a strain of Squash leaf curl China virus from North India. J Phytopathol 156:222–228

    Article  CAS  Google Scholar 

  • Singh AK, Mishra KK, Chattopadhyay B, Chakraborty S (2009a) Biological and molecular characterization of a Begomovirus associated with yellow mosaic vein mosaic disease of pumpkin from Northern India. Virus Genes 39:359–370

    Article  CAS  PubMed  Google Scholar 

  • Singh D, Tewari AK, Rao GP, Karuppaiah R, Viswanathan R, Arya M, Baranwal VK (2009b) RT-PCR/PCR analysis detected mixed infection of DNA and RNA viruses infecting sugarcane crops in different states of India. Sugar Technol 11:373–380

    Article  CAS  Google Scholar 

  • Singh D, Pathania M, Ram R, Zaidi AA, Verma N (2010) Screening of chrysanthemum cultivars for Chrysanthemum stunt viroid in an Indian scenario. Arch Phytopathol Plant Protect 43:1517–1523

    Article  CAS  Google Scholar 

  • Singh MK, Haq QMR, Mandal B, Varma A (2011a) Evidence of the association of Radish leaf curl virus with tobacco yellow leaf curl disease in Bihar, India. Virus Genes 23:64–69

    Google Scholar 

  • Singh MK, Singh K, Haq QMR, Mandal B, Varma A (2011b) Molecular characterization of Tobacco leaf curl Pusa virus, a new monopartite Begomovirus associated with tobacco leaf curl disease in India. Virus Genes 43:296–306

    Article  CAS  PubMed  Google Scholar 

  • Singh L, Hallan V, Martin DP, Ram R, Zaidi AA (2012) Genomic sequence analysis of four new chrysanthemum virus B isolates: evidence of RNA recombination. Arch Virol 157:531–537

    Article  CAS  PubMed  Google Scholar 

  • Singh JK, Tarafdar A, Sharma SK, Biswas KK (2013) Evidence of recombinant Citrus tristeza virus isolate occurring in acid lime cv. Pant lemon orchard in Uttarakhand terai region of Northern Himalaya in India. Indian J Virol 24:35–41

    Article  PubMed  Google Scholar 

  • Singh R, Banerjee A, Sharma SK, Bhagawati R, Baruah S, Ngachan SV (2015) First report of Turnip mosaic virus occurrence in cole crops (Brassica spp) from Arunachal Pradesh, India. Virus Dis 26:211–213

    Article  Google Scholar 

  • Sivalingam PN (2006) Characterization of begomoviruses affecting tomato in India. Ph.D. Thesis submitted to Indian Agricultural Research Institute, New Delhi-12

    Google Scholar 

  • Sivalingam PN, Varma A (2007) PCR based diagnosis of begomoviruses associated with tomato leaf curl disease in India. J Biochem Biotechnol 16:17–22

    Google Scholar 

  • Smart CD, Schneider B, Blomquist CL, Guerra L, Harrison J, Ahrens NA, Lorenz UKH, SeemĂĽller E, Kirkpatrick BC (1996) Phytoplasma-specific PCR primers based on sequences of the 16S-23S rRNA spacer region. Appl Environ Microbiol 62:2988–2993

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sohrab SS, Mandal B, Pant RP, Varma A (2003) First report of association of Tomato leaf curl New Delhi virus with the yellow mosaic disease of Luffa cylindrica. Plant Dis 87:1148

    Article  Google Scholar 

  • Sohrab SS, Mandal B, Ali A, Varma A (2006) Molecular diagnosis of emerging begomovirus diseases in cucurbits occurring in northern India. Indian J Virol 17:88–95

    Google Scholar 

  • Sohrab SS, Mandal B, Ali A, Varma A (2010) Chlorotic curly stunt: a severe begomovirus disease of bottle gourd in Northern India. Indian J Virol 21:56–63

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Soumya K, Yogita M, Prasanthi Y, Anitha K, Kavi Kishor PB, Jain RK, Mandal B (2014) Molecular characterization of Indian isolate of peanut mottle virus and immuno diagnosis using bacterial expressed core capsid protein. Virus Dis 25:331–337

    Article  CAS  Google Scholar 

  • Srinivasulu M, Sai Gopal DVR (2011) Coat protein sequence comparison of south Indian isolates of Papaya ringspot virus with other Indian subcontinent isolates. Phytopathol Mediterr 50:359–367

    CAS  Google Scholar 

  • Srivastava KM, Raizada RK, Singh BP (1983) Bean yellow mosaic virus on Gladiolus psittacinus in India. Indian J Plant Pathol 1:83–88

    Google Scholar 

  • Srivastava KM, Raj SK, Singh BP (1992) Properties of a Cucumber mosaic virus strain naturally infecting chrysanthemum in India. Plant Dis 76:474–477

    Article  Google Scholar 

  • Subba Reddy CV, Sreenivasulu P, Sekhar G (2011) Duplex-immunocapture-RT-PCR for detection and discrimination of two distinct potyviruses naturally infecting sugarcane (Saccharum spp. hybrids). Indian J Exp Biol 49:68–73

    Google Scholar 

  • Sudhakar N, Prasad DN, Mohan N, Murugesan K (2006) First report of Cucumber mosaic virus subgroup-II infecting Lycopersicon esculantum in India. Plant Dis 90:1457

    Article  Google Scholar 

  • Swarnalatha P, Reddy MK (2014) Duplex PCR for simultaneous detection of Begomovirus and Phytoplasma from naturally infected tomato. Pest Manag Horticult Ecosyst 20:59–68

    Google Scholar 

  • Tarafdar A, Godara S, Dwivedi S, Jayakumar BK, Biswas KK (2013) Characterization of Citrus tristeza virus and determination of genetic variability in North-east and South India. Indian Phytopathol 66:302–307

    Google Scholar 

  • Thomas KM, Krishnaswamy CS (1939) Leaf crinkle: a transmissible disease of papaya. Curr Sci 8:316

    Google Scholar 

  • Tiwari AK, Mall S, Khan MS, Snehi SK, Sharma PK, Rao GP, Raj SK (2010a) Detection and identification of Tomato leaf curl Palampur virus infecting Cucurbita pepo in India. Guanaxi Agric Sci 41:1291–1295

    Google Scholar 

  • Tiwari N, Padmalatha KV, Singh VB, Haq QMI, Malathi VG (2010b) Tomato leaf curl Bangalore virus (ToLCBV): infectivity and enhanced pathogenicity with diverse betasatellites. Arch Virol 155:1343–1347

    Article  CAS  PubMed  Google Scholar 

  • Tiwari AK, Snehi SK, Singh R, Raj SK, Rao GP, Sharma PK (2011) Molecular identification and genetic diversity among six Begomovirus isolates affecting cultivation of cucurbitaceous crops in Uttar Pradesh, India. Arch Phytopathol Plant Protect 45:1070–1075

    Article  Google Scholar 

  • Tiwari AK, Snehi SK, Khan MS, Sharma PK, Raj SK, Rao GP (2012) Molecular detection and identification of Tomato leaf curl New Delhi virus associated with yellow mosaic and leaf curl disease of Luffa cylindrica in India. Indian Phytopathol 65:80–84

    Google Scholar 

  • Umamaheswaran K, Jain RK, Bhat AI, Ahlawat YS (2003) Biological and molecular characterization of a Tospovirus isolate from tomato and its relationship with other Tospoviruses. Indian Phytopathol 56:168–173

    CAS  Google Scholar 

  • Usharani KS, Surendranath B, Haq QMR, Malathi VG (2004a) Yellow mosaic virus infecting soybean in Northern India is distinct from the species infecting soybean in southern and western India. Curr Sci 86:845–850

    CAS  Google Scholar 

  • Usharani KS, Surendranath B, Paul Khurana SM, Garg ID, Malathi VG (2004b) Potato leaf curl – a new disease of potato in northern India caused by a strain of Tomato leaf curl New Delhi virus. Plant Pathol 53:235

    Article  Google Scholar 

  • Usharani KS, Surendranath B, Haq QMR, Malathi VG (2005) Infectivity analysis of a soybean isolate of Mungbean yellow mosaic India virus by agroinoculation. J Gen Plant Pathol 71:230–237

    Article  CAS  Google Scholar 

  • Usharani TR, Laxmi V, Jalali S, Krishnareddy M (2013) Duplex PCR to detect both Papaya ringspot virus and Papaya leaf curl virus simultaneously from naturally infected papaya (Carica papaya L.) Indian J Biotechnol 12:269–272

    CAS  Google Scholar 

  • Valand GB, Muniyappa V (1992) Epidemiology of Tobacco leaf curl virus in India. Ann Appl Biol 120:257–267

    Article  Google Scholar 

  • Van der Vlugt RAA, Steffens P, Cuperus C, Barg E, Lesemann DE, Bos L, Vetten HJ (1999) Further evidence that shallot yellow stripe virus (SYSV) is a distinct potyvirus and reidentification ofWelsh onion yellow stripe virus as a SYSV strain. Phytopathology 89:148–155

    Article  PubMed  Google Scholar 

  • Varma PM (1955) Ability of the whitefly to carry more than one virus simultaneously. Curr Sci 24:317–318

    Google Scholar 

  • Varma A, Giri BK (1998) Virus disease of cucurbits in India. In: Nayer NM, More TA (eds) Cucurbits. Oxford and IBH Publishing House Pvt Ltd, New Delhi. 1998

    Google Scholar 

  • Varma A, Malathi VG (2003) Emerging geminivirus problems: a serious threat to crop production. Ann Appl Biol 142:145–164

    Article  CAS  Google Scholar 

  • Venkataravanappa V, Reddy CNL, Swaranalatha P, Jalali S, Briddon RW, Krishna Reddy M (2011) Diversity and phylogeography of begomovirus associated beta satellites of okra in India. Virol J 8:555

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Venkataravanappa V, Lakshminarayana Reddy CN, Jalali S, Krishna Reddy M (2012a) Molecular characterization of distinct bipartite Begomovirus infecting bhendi (Abelmoschus esculentus L.) in India. Virus Genes 44:522–535

    Article  CAS  PubMed  Google Scholar 

  • Venkataravanappa V, Reddy CNL, Jalali S, Reddy MK (2012b) Molecular characterization of distinct bipartite begomovirus infecting bhendi (Abelmoschus esculentus L.) in India. Gene 44:522–535

    CAS  Google Scholar 

  • Verma N, Ram R, Sharma A, Hallan V, Zaidi AA, Garg ID (2003) Detection, identification and incidence of Chrysanthemum B carlavirus in chrysanthemum in India. Crop Prot 22:425–429

    Article  Google Scholar 

  • Verma R, Baranwal VK, Prakash S, Tomer SPS, Pant RP, Ahlawat YS (2006) First report of Papaya ringspot virus W in sponge gourd from India. Plant Dis 90:974

    Article  Google Scholar 

  • Verma N, Mehra A, Singh L, Hallan V, Singh AK, Jabeen N, Singh MK, Ram R, Zaidi AA (2007) Screening of viruses infecting chrysanthemum cultivars in India. Sci Hortic 111:260–265

    Article  Google Scholar 

  • Verma N, Kumar K, Kulshrestha S, Raikhy G, Hallan V, Ram R, Zaidi AA, Garg ID (2009) Molecular studies on Tomato aspermy virus isolates infecting chrysanthemums. Arch Phytopathol Plant Protect 42:99–111

    Article  CAS  Google Scholar 

  • Vishnoi R, Raj SK, Prasad V (2009) Molecular characterization of an Indian isolate of Banana bunchy top virus based on six genomic DNA components. Virus Genes 38:334–344

    Article  CAS  PubMed  Google Scholar 

  • Vishnoi R, Kumar S, Raj SK (2013) Molecular characterization of a Cucumber mosaic virus isolate associated with mosaic disease of banana in India. Phytoparasitica 41:545–555

    Article  CAS  Google Scholar 

  • Viswanathan R, Karuppaiah R (2010) Distribution pattern of RNA viruses causing mosaic symptoms and yellow leaf in Indian sugarcane varieties. Sugar Cane Int 28:202–205

    Google Scholar 

  • Viswanathan R, Rao GP (2011) Disease scenario and management of major sugarcane diseases in India. Sugar Technol 13:336–353

    Article  CAS  Google Scholar 

  • Viswanathan R, Balamuralikrishnan M, Karuppaiah R (2008a) Identification of three genotypes of sugarcane yellow leaf virus causing yellow leaf disease from India and their molecular characterization. Virus Genes 37:368–379

    Article  CAS  PubMed  Google Scholar 

  • Viswanathan R, Balamuralikrishnan M, Karuppaiah R (2008b) Characterization and genetic diversity of sugarcane streak mosaic virus causing mosaic in sugarcane. Virus Genes 36:553–564

    Article  CAS  PubMed  Google Scholar 

  • Viswanathan R, Karuppaiah R, Malathi P, Ganesh Kumar V, Chinnaraja C (2009) Diagnosis of Sugarcane yellow leaf virus in asymptomatic sugarcane by RT-PCR. Sugar Technol 11:368–372

    Article  CAS  Google Scholar 

  • Watpade S, Raigond B, Thakur PD, Handa A, Pramanick KK, Sharma YP, Tomar M (2012) Molecular detection of latent Apple chlorotic leaf spot virus in elite mother plants of apple. Indian J Virol 23:359–363

    Article  Google Scholar 

  • Wyatt SD, Brown JK (1996) Detection of subgroup III geminivirus isolates in leaf extracts by degenerate primers and polymerase chain reaction. Phytopathology 86:1288–1293

    Article  Google Scholar 

  • Yadav RK, Shukla RK, Chattopadhyay D (2009) Soybean cultivar resistant to Mungbean Yellow Mosaic India Virus infection induces viral RNA degradation earlier than the susceptible cultivar. Virus Res 144:89–95

    Article  CAS  PubMed  Google Scholar 

  • Yadav MK, Biswas KK, Lal SK, Baranwal VK, Jain RK (2013) A distinct strain of Cowpea mild mottle virus infecting soybean in India. J Phytopathol 161:739–744

    Article  Google Scholar 

  • Yeh SD, Chang TF (1995) Nucleotide sequence of the N gene of Watermelon silver mottle virus, a proposed new member of the genus Tospovirus. Phytopathology 85:58–64

    Article  CAS  Google Scholar 

  • Zaidi AA, Hallan V, Rana T, Raikhy G, Ram R (2009) Viruses in ornamental crops and their management: an Indian scenario. J Ornamental Hortic 12:147–166

    Google Scholar 

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Acknowledgements

Authors are grateful to various researchers in India for sharing the information. We are grateful to anonymous reviewers for critical screening of manuscript.

Author information

Authors and Affiliations

  1. ICAR Research Complex for NEH Region, Manipur Centre, Lamphelpat, Imphal, 795004, India

    Susheel Kumar Sharma & Th. Surjit Singh

  2. ICAR-Directorate of Medicinal and Aromatic Plants Research, Boriavi, Anand, Gujarat, 387310, India

    Ram Prasnna Meena

  3. Department of Plant Pathology, University of Agricultural Sciences, Raichur, Karnataka, 584104, India

    D. Pramesh

  4. AICRP on Medicinal & Aromatic Plants and Betelvine, Orissa University of Agriculture & Technology, Bhubaneswar, 751003, India

    Sandeep Kumar

  5. Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India

    Sandeep Kumar & Virendra Kumar Baranwal

Authors
  1. Susheel Kumar Sharma
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  2. Ram Prasnna Meena
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  3. D. Pramesh
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  4. Sandeep Kumar
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  5. Th. Surjit Singh
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  6. Virendra Kumar Baranwal
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Corresponding author

Correspondence to Susheel Kumar Sharma .

Editor information

Editors and Affiliations

  1. Advanced Center for Plant Virology, Indian Agricultural Research Institute, New Delhi, India

    Bikash Mandal

  2. Advanced Center for Plant Virology, Indian Agricultural Research Institute, New Delhi, India

    Govind Pratap Rao

  3. Advanced Center for Plant Virology, Indian Agricultural Research Institute, New Delhi, India

    Virendra Kumar Baranwal

  4. Advanced Centre for Plant Virology, Indian Agricultural Research Institute, New Delhi, India

    Rakesh Kumar Jain

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© 2017 Springer Nature Singapore Pte Ltd.

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Sharma, S.K., Meena, R.P., Pramesh, D., Kumar, S., Singh, T.S., Baranwal, V.K. (2017). Nucleic-Acid Based Techniques for the Fine Diagnosis of Plant Viruses in India. In: Mandal, B., Rao, G., Baranwal, V., Jain, R. (eds) A Century of Plant Virology in India. Springer, Singapore. https://doi.org/10.1007/978-981-10-5672-7_27

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