Staff Profile
Professor Neil Boonham
Chair of Applied Crop Science
- Email: neil.boonham@ncl.ac.uk
- Telephone: 07780825544
- Address: Agriculture Building
School of Natural and Environmental Sciences
University of Newcastle
Newcastle Upon Tyne
NE1 7RU
Background
Area of Expertise
Neil has a background in plant virology and molecular biology and in recent years has focused on the application of post-genomic technologies to provide applied solutions to detection problems in agricultural and environmental analysis.
In the agricultural and biosecurity work the research is focused on development of targeted techniques for in-field and automated detection of pathogens. This encompasses development of diagnostic techniques to enable rapid decision making in the agri-food supply chain to the automated measurement of airborne inoculum; the goal is to provide end users with data enabling them to make more timely and effective management decisions. In addition the use of next generation sequencing for detection and characterisation of the causal agents of disease and virus discovery through to investigating the impact microbial communities have in modulating disease symptoms and severity.
Neil maintains a keen interest in Virology in particular the interaction between viruses and plant hosts, the evolution of virus species and the characterisation of persistent viruses in plants. Neil has authored more than 100 peer reviewed publications and is an editor for the Journal of Virological Methods and a special associate Professor at the University of Nottingham. Neil regularly provides keynote and plenary lectures at international conferences and lectures at undergraduate and masters degree courses at the Universities of Nottingham, Leeds and Harper Adams.
Area of Expertise
Plant pathology and diagnostics.
For a full list of my publications please see my Google Scholar Profile and Orcid profile
Publications
- Martín-Hernández R, Higes M, Sagastume S, Juarranz Á, Dias-Almeida J, Budge GE, Meana A, Boonham N. Microsporidia infection impacts the host cells cycle and reduces cell apoptosis. PLoS ONE 2017, 12(2), e0170183.
- Sabbadin F, Glover R, Stafford R, Rozado-Aguirre Z, Boonham N, Adams I, Mumford R, Edwards R. Transcriptome sequencing identifies novel persistent viruses inherbicide resistant wild-grasses. Scientific Reports 2017, 7, 41987.
- Hodgetts J, Ostojá-Starzewski JC, Prior T, Lawson R, Hall J, Boonham N. DNA barcoding for biosecurity: case studies from the UK plant protection programme. Genome 2016, 59(11), 1033-1048.
- Duff-Farrier CR, Candresse T, Bailey AM, Boonham N, Foster GD. Evidence for different host-dependent functioning of RX against both wild-type and recombinant pepino mosaic virus. Molecular Plant Pathology 2016, 17(1), 120-126.
- Budge GE, Adams I, Thwaites R, Pietravalle S, Drew GC, Hurst GDD, Tomkies V, Boonham N, Brown M. Identifying bacterial predictors of honey bee health. Journal of Invertebrate Pathology 2016, 141, 41-44.
- Adams IP, Harju VA, Hodges T, Hany U, Skelton A, Rai S, Deka MK, Smith JJ, Fox A, Uzayisenga B, Ngaboyisonga C, Uwumukiza B, Rutikanga A, Rutherford M, Ricthis B, Phiri N, Boonham N. First report of maize lethal necrosis disease in Rwanda. New Disease Reports 2014, 29, 22-22.
- Blaser S, Diem H, von Felten A, Gueuning M, Andreou M, Boonham N, Tomlinson J, Muller P, Utzinger J, Frey JE, Buhlmann A. From laboratory to point of entry: Development and implementation of a loop-mediated isothermal amplification (LAMP)-based genetic identification system to prevent introduction of quarantine insect species. Pest Management Science 2018, 74(6), 1504-1512.
- Franco Ortega S, Tomlinson J, Gilardi G, Spadaro D, Gullino ML, Garibaldi A, Boonham N. Rapid detection of Fusarium oxysporum f. sp. lactucae on soil, lettuce seeds and plants using loop-mediated isothermal amplification. Plant Pathology 2018, 67(7), 1462-1473.
- Stainton K, Hall J, Budge GE, Boonham N, Hodgetts J. Rapid molecular methods for in-field and laboratory identification of the yellow-legged Asian hornet (Vespa velutina nigrithorax). Journal of Applied Entomology 2018, 142(6), 610-616.
- Woodhall JW, Brown MJ, Perkins K, Valdeolmillos ES, Boonham N, Ray RV. A TaqMan real-time PCR assay for Rhizoctonia cerealis and its use in wheat and soil. European Journal of Plant Pathology 2017, 148(2), 237-245.
- Rozado-Aguirre Z, Adams I, Fox A, Dickinson M, Boonham N. Complete sequence and genomic annotation of carrot torradovirus 1. Archives of Virology 2017, 162(9), 2815-2819.
- Harrison C, Tomlinson J, Ostoja-Starzewska S, Boonham N. Evaluation and validation of a loop-mediated isothermal amplification test kit for detection of Hymenoscyphus fraxineus. European Journal of Plant Pathology 2017, 149(2), 253-259.
- Adams IP, Boonham N, Jones RAC. First complete genome sequence of Arracacha virus A isolated from a 38-year-old sample from Peru. Genome Announcements 2017, 5(18), e00141-17.
- Rozado-Aguirre Z, Marais A, Svanella-Dumas L, Faure C, Latour F, Villeneuve F, Dickinson M, Fox A, Boonham N, Candresse T. First report of Carrot torradovirus 1 (CaTV1), a member of the Torradovirus genus, infecting carrots in France. Plant Disease 2017, 101(7), 1333-1333.
- Fox A, Rozado Z, Adams IP, Skelton A, Dickinson M, Boonham N. Investigating the viral causes of internal necrosis in carrot. Acta Horticulturae 2017, 1153, 245-250.
- Pecman A, Kutnjak D, Gutierrez-Aguirre I, Adams I, Fox A, Boonham N, Ravnikar M. Next generation sequencing for detection and discovery of plant viruses and viroids: Comparison of two approaches. Frontiers in Microbiology 2017, 8, 1998.
- Maxwell DJ, Partridge JC, Roberts NW, Boonham N, Foster GD. The effects of surface structure mutations in Arabidopsis thaliana on the polarization of reflections from virus-infected leaves. PLoS ONE 2017, 12(3), e0174014.
- Rozado-Aguirre Z, Adams I, Collins L, Fox A, Dickinson M, Boonham N. Detection and transmission of Carrot torrado virus, a novel putative member of the Torradovirus genus. Journal of Virological Methods 2016, 235, 119-124.
- Gandolfo DS, Mortimer H, Woodhall JW, Boonham N. Fourier transform infra-red spectroscopy using an attenuated total reflection probe to distinguish between Japanese larch, pine and citrus plants in healthy and diseased states. Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy 2016, 163, 181-188.
- Gil JF, Adams I, Boonham N, Nielsen SL, Nicolaisen M. Molecular and biological characterisation of two novel pomo-like viruses associated with potato (Solanum tuberosum) fields in Colombia. Archives of Virology 2016, 161(6), 1601-1610.
- Gil JF, Adams I, Boonham N, Nielsen SL, Nicolaisen M. Molecular and biological characterization of Potato mop-top virus (PMTV, Pomovirus) isolates from the potato-growing regions of Colombia. Plant Pathology 2016, 65(7), 1210-1220.
- Peters JC, Harper G, Brierley JL, Lees AK, Wale SJ, Hilton AJ, Gladders P, Boonham N, Cunnington AC. The effect of post-harvest storage conditions on the development of black dot (Colletotrichum coccodes) on potato in crops grown for different durations. Plant Pathology 2016, 65(9), 1484-1491.
- Maxwell DJ, Partridge JC, Roberts NW, Boonham N, Foster GD. The effects of plant virus infection on polarization reflection from leaves. PLoS ONE 2016, 11(4), e0152836.
- Mumford RA, Macarthur R, Boonham N. The role and challenges of new diagnostic technology in plant biosecurity. Food Security 2016, 8(1), 103-109.
- Duff-Farrier CRA, Bailey AM, Boonham N, Foster GD. A pathogenicity determinant maps to the N-terminal coat protein region of the Pepino mosaic virus genome. Molecular Plant Pathology 2015, 16(3), 308-315.
- Hodgetts J, Karamura G, Johnson G, Hall J, Perkins K, Beed F, Nakato V, Grant M, Studholme DJ, Boonham N, Smith J. Development of a lateral flow device for in-field detection and evaluation of PCR-based diagnostic methods for Xanthomonas campestris pv. musacearum, the causal agent of banana xanthomonas wilt. Plant Pathology 2015, 64(3), 559-567.
- Kogovsek P, Hodgetts J, Hall J, Prezelj N, Nikolic P, Mehle N, Lenarcic R, Rotter A, Dickinson M, Boonham N, Dermastia M, Ravnikar M. LAMP assay and rapid sample preparation method for on-site detection of flavescence dorée phytoplasma in grapevine. Plant Pathology 2015, 64(2), 286-296.
- Adams I, Harrison C, Tomlinson J, Boonham N. Microarray platform for the detection of a range of plant viruses and viroids. In: Christophe Lacomme, ed. Plant Pathology: Techniques and Protocols. Humana Press Inc, 2015, pp.273-282.
- Hodgetts J, Hall J, Karamura G, Grant M, Studholme DJ, Boonham N, Karamura E, Smith JJ. Rapid, specific, simple, in-field detection of Xanthomonas campestris pathovar musacearum by loop-mediated isothermal amplification. Journal of Applied Microbiology 2015, 119(6), 1651-1658.
- Tomlinson J, Boonham N. Real-Time LAMP for Chalara fraxinea Diagnosis. In: Christophe Lacomme, ed. Plant Pathology: Techniques and Protocols. Humana Press Inc, 2015, pp.75-83.
- Adams IP, Skelton A, Macarthur R, Hodges T, Hinds H, Flint L, Nath PD, Boonham N, Fox A. Carrot yellow leaf virus is associated with carrot internal necrosis. PLoS ONE 2014, 9(11), e109125.
- Adams IP, Rai S, Deka M, Harju V, Hodges T, Hayward G, Skelton A, Fox A, Boonham N. Genome sequence of vanilla distortion mosaic virus infecting Coriandrum sativum. Archives of Virology 2014, 159(12), 3463-3465.
- Tomlinson J, Harrison C, Boonham N, Goodchild SA, Weller SA. Influence of the length of target DNA overhang proximal to the array surface on discrimination of single-base mismatches on a 25-mer oligonucleotide array. BMC Research Notes 2014, 7(1), 251.
- Boonham N, Kreuze J, Winter S, van der Vlugt R, Bergervoet J, Tomlinson J, Mumford R. Methods in virus diagnostics: From ELISA to next generation sequencing. Virus Research 2014, 186, 20-31.
- Hany U, Adams IP, Glover R, Bhat AI, Boonham N. The complete genome sequence of Piper yellow mottle virus (PYMoV). Archives of Virology 2014, 159(2), 385-388.
- Souza Richards R, Adams IP, Kreuze JF, De Souza J, Cuellar W, Dullemans AM, van der Vlugt RAA, Glover R, Hany U, Dickinson M, Boonham N. The complete genome sequences of two isolates of potato black ringspot virus and their relationship to other isolates and nepoviruses. Archives of Virology 2014, 159(4), 811-815.
- Hodgetts J, Johnson G, Perkins K, Ostoja-Starzewska S, Boonham N, Mumford R, Dickinson M. The development of monoclonal antibodies to the secA protein of Cape St. Paul wilt disease phytoplasma and their evaluation as a diagnostic tool. Molecular Biotechnology 2014, 56(9), 803-813.
- Buhlmann A, Pothier JF, Rezzonico F, Smits THM, Andreou M, Boonham N, Duffy B, Frey JE. Erwinia amylovora loop-mediated isothermal amplification (LAMP) assay for rapid pathogen detection and on-site diagnosis of fire blight. Journal of Microbiological Methods 2013, 92(3), 332-339.
- Tomlinson JA, Ostoja-Starzewska S, Webb K, Cole J, Barnes A, Dickinson M, Boonham N. A loop-mediated isothermal amplification-based method for confirmation of Guignardia citricarpa in citrus black spot lesions. European Journal of Plant Pathology 2013, 136(2), 217-224.
- Woodhall JW, Adams IP, Peters JC, Harper G, Boonham N. A new quantitative real-time PCR assay for Rhizoctonia solani AG3-PT and the detection of AGs of Rhizoctonia solani associated with potato in soil and tuber samples in Great Britain. European Journal of Plant Pathology 2013, 136(2), 273-280.
- Adams IP, Glover R, Souza-Richards R, Bennett S, Hany U, Boonham N. Complete genome sequence of arracacha virus B: A novel cheravirus. Archives of Virology 2013, 158(4), 909-913.
- Buhlmann A, Pothier JF, Tomlinson JA, Frey JE, Boonham N, Smits THM, Duffy B. Genomics-informed design of loop-mediated isothermal amplification for detection of phytopathogenic Xanthomonas arboricola pv. pruni at the intraspecific level. Plant Pathology 2013, 62(2), 475-484.
- Adams IP, Abidrabo P, Miano DW, Alicai T, Kinyua ZM, Clarke J, Macarthur R, Weekes R, Laurenson L, Hany U, Peters D, Potts M, Glover R, Boonham N, Smith J. High throughput real-time RT-PCR assays for specific detection of cassava brown streak disease causal viruses, and their application to testing of planting material. Plant Pathology 2013, 62(1), 233-242.
- Tomlinson JA, Ostoja-Starzewska S, Adams IP, Miano DW, Abidrabo P, Kinyua Z, Alicai T, Dickinson MJ, Peters D, Boonham N, Smith J. Loop-mediated isothermal amplification for rapid detection of the causal agents of cassava brown streak disease. Journal of Virological Methods 2013, 191(2), 148-154.
- Roenhorst JW, Boonham N, Winter S, Menzel W, van der Vlugt RAA. The plant viruses and viroids database and collections of Q-bank. EPPO Bulletin 2013, 43(2), 238-243.
- Villari C, Tomlinson JA, Battisti A, Boonham N, Capretti P, Faccoli M. Use of loop-mediated isothermal ampliflcation for detection of Ophiostoma clavatum, the primary blue stain fungus associated with Ips acuminatus. Applied and Environmental Microbiology 2013, 79(8), 2527-2533.
- Adams IP, Miano DW, Kinyua ZM, Wangai A, Kimani E, Phiri N, Reeder R, Harju V, Glover R, Hany U, Souza-Richards R, Deb Nath P, Nixon T, Fox A, Barnes A, Smith J, Skelton A, Thwaites R, Mumford R, Boonham N. Use of next-generation sequencing for the identification and characterization of Maize chlorotic mottle virus and Sugarcane mosaic virus causing maize lethal necrosis in kenya. Plant Pathology 2013, 62(4), 741-749.
- Woodhall JW, Webb KM, Giltrap PM, Adams IP, Peters JC, Budge GE, Boonham N. A new large scale soil DNA extraction procedure and real-time PCR assay for the detection of Sclerotium cepivorum in soil. European Journal of Plant Pathology 2012, 134(3), 467-473.
- Gil-Salas FM, Peters J, Boonham N, Cuadrado IM, Janssen D. Co-infection with Cucumber vein yellowing virus and Cucurbit yellow stunting disorder virus leading to synergism in cucumber. Plant Pathology 2012, 61(3), 468-478.
- Powell ME, Cuthbertson AGS, Bell HA, Boonham N, Morris J, Northing P. First record of the Q Biotype of the sweetpotato whitefly, Bemisia tabaci, intercepted in the UK. European Journal of Plant Pathology 2012, 133(4), 797-801.
- Hughes KJD, Tomlinson JA, Giltrap PM, Barton V, Hobden E, Boonham N, Lane CR. Development of a real-time PCR assay for detection of Phytophthora kernoviae and comparison of this method with a conventional culturing technique. European Journal of Plant Pathology 2011, 131(4), 695-703.
- Bekele B, Hodgetts J, Tomlinson J, Boonham N, Nikolic P, Swarbrick P, Dickinson M. Use of a real-time LAMP isothermal assay for detecting 16SrII and XII phytoplasmas in fruit and weeds of the Ethiopian Rift Valley. Plant Pathology 2011, 60(2), 345-355.
- Kogovsek P, Pompe-Novak M, Baebler S, Rotter A, Gow L, Gruden K, Foster GD, Boonham N, Ravnikar M. Aggressive and mild Potato virus Y isolates trigger different specific responses in susceptible potato plants. Plant Pathology 2010, 59(6), 1121-1132.
- Tomlinson JA, Boonham N, Dickinson M. Development and evaluation of a one-hour DNA extraction and loop-mediated isothermal amplification assay for rapid detection of phytoplasmas. Plant Pathology 2010, 59(3), 465-471.
- Budge GE, Shaw MW, Lambourne C, Jennings P, Clayburn R, Boonham N, McPherson M. Characterization and origin of infection of Rhizoctonia solani associated with Brassica oleracea crops in the UK. Plant Pathology 2009, 58(6), 1059-1070.
- Garrido C, Carbu M, Fernandez-Acero FJ, Boonham N, Colyer A, Cantoral JM, Budge G. Development of protocols for detection of Colletotrichum acutatum and monitoring of strawberry anthracnose using real-time PCR. Plant Pathology 2009, 58(1), 43-51.
- Budge GE, Shaw MW, Colyer A, Pietravalle S, Boonham N. Molecular tools to investigate Rhizoctonia solani distribution in soil. Plant Pathology 2009, 58(6), 1071-1080.
- Boonham N, Glover R, Tomlinson J, Mumford R. Exploiting generic platform technologies for the detection and identification of plant pathogens. European Journal of Plant Pathology 2008, 121(3), 355-363.
- Budge GE, Loram J, Donovan G, Boonham N. RNA2 of Soil-borne cereal mosaic virus is detectable in plants of winter wheat grown from infected seeds. European Journal of Plant Pathology 2008, 120(1), 97-102.
- Mumford R, Boonham N, Tomlinson J, Barker I. Advances in molecular phytodiagnostics - New solutions for old problems. European Journal of Plant Pathology 2006, 116(1), 1-19.
- Morris J, Steel E, Smith P, Boonham N, Spence N, Barker I. Host range studies for Tomato chlorosis virus, and Cucumber vein yellowing virus transmitted by Bemisia tabaci (Gennadius). European Journal of Plant Pathology 2006, 114(3), 265-273.
- Boonham N, Hims M, Barker I, Spence N. Potato virus Y from petunia can cause symptoms of potato tuber necrotic ringspot disease (PTNRD). European Journal of Plant Pathology 1999, 105(6), 617-621.
- Ortega SF, Tomlinson J, Hodgetts J, Spadaro D, Gullino ML, Boonham N. Development of loop-mediated isothermal amplification assays for the detection of seedborne fungal pathogens Fusarium fujikuroi and Magnaporthe oryzae in rice seed. Plant Disease 2018, 102(8), 1549-1558.
- Olmos A, Boonham N, Candresse T, Gentit P, Giovani B, Kutnjak D, Liefting L, Maree HJ, Minafra A, Moreira A, Nakhla MK, Petter F, Ravnikar M, Rodoni B, Roenhorst JW, Rott M, Ruiz-Garcia AB, Santala J, Stancanelli G, van der Vlugt R, Varveri C, Westenberg M, Wetzel T, Ziebell H, Massart S. High-throughput sequencing technologies for plant pest diagnosis: challenges and opportunities. EPPO Bulletin 2018, 48(2), 219-224.
- Harper LR, Lawson Handley L, Hahn C, Boonham N, Rees HC, Gough KC, Lewis E, Adams IP, Brotherton P, Phillips S, Hanfling B. Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus). Ecology and Evolution 2018, 8(12), 6330-6341.
- Harper LR, Buxton AS, Rees HC, Bruce K, Brys R, Halfmaerten D, Read DS, Watson HV, Sayer CD, Jones EP, Priestley V, Machler E, Murria C, Garces-Pastor S, Medupin C, Burgess K, Benson G, Boonham N, Griffiths RA, Lawson Handley L, Hanfling B. Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds. Hydrobiologia 2018, 826(1), 25-41.
- Santillan FW, Fribourg CE, Adams IP, Gibbs AJ, Boonham N, Kehoe MA, Maina S, Jones RAC. The biology and phylogenetics of potato virus s isolates from the andean region of south America. Plant Disease 2018, 102(5), 869-885.
- Adams IP, Fox A, Boonham N, Massart S, De Jonghe K. The impact of high throughput sequencing on plant health diagnostics. European Journal of Plant Pathology 2018, 152(4), 909-919.
- Glover RH, Adams IP, Budge G, Wilkins S, Boonham N. Detection of honey bee (Apis mellifera) viruses with an oligonucleotide microarray. Journal of Invertebrate Pathology 2011, 107(3), 216-219.
- Gil-Salas FM, Morris J, Cuadrado IM, Budge G, Colyer A, Boonham N, Janssen D. Risk assessment procedure for Cucumber Vein Yellowing Virus (CVYV) and Cucurbit Yellow Stunting Disorder Virus (CYSDV) using a real time RT-PCR assay - study of virus levels in the vector Bemisia tabaci. In: International Symposium on Vegetable Production, Quality and Process Standardization in Chain: a Worldwide Perspective. 2008, Beijing, China: International Society for Horticultural Science.
- Gil-Salas FM, Morris J, Colyer A, Budge G, Boonham N, Cuadrado IM, Janssen D. Development of real-time RT-PCR assays for the detection of Cucumber vein yellowing virus (CVYV) and Cucurbit yellow stunting disorder virus (CYSDV) in the whitefly vector Bemisia tabaci. Journal of Virological Methods 2007, 146(1-2), 45-51.
- Ward L, Koenig R, Budge G, Garrido C, McGrath C, Stubbley H, Boonham N. Occurrence of two different types of RNA-5-containing beet necrotic yellow vein virus in the UK. Archives of Virology 2007, 152(1), 59-73.
- Adams IP, Boonham N, Jones RAC. A 33-year-old plant sample contributes the first complete genomic sequence of Potato Virus U. Microbiology Resource Announcements 2018, 7(23), e01392-18.
- Blaser S, Diem H, von Felten A, Gueuning M, Andreou M, Boonham N, Tomlinson J, Muller P, Utzinger J, Frey B, Frey JE, Buhlmann A. A Loop-mediated Isothermal Amplification (LAMP) Assay for Rapid Identification of Bemisia tabaci. Journal of Visualized Experiments 2018, (140), e58502.
- Maree HJ, Fox A, Al Rwahnih M, Boonham N, Candresse T. Application of HTS for Routine Plant Virus Diagnostics: State of the Art and Challenges. Frontiers in Plant Science 2018, 9, 1082.
- Adams IP, Abad J, Fribourg CE, Boonham N, Jones RAC. Complete genome sequence of Potato virus T from Bolivia, obtained from a 33-year-old sample. Microbiology Resource Announcements 2018, 7(18).
- Adams IP, Fox A, Boonham N, Jones RAC. Complete genomic sequence of the potyvirus mashua virus Y, obtained from a 33-year-old mashua (Tropaeaolum tuberosum) sample. Microbiology Resource Announcements 2018, 7(15).
- Adams IP, Boonham N, Jones RAC. Full-genome sequencing of a virus from a 33-year-old sample demonstrates that Arracacha mottle virus is synonymous with Arracacha virus Y. Microbiology Resource Announcements 2018, 7(21), e01393-18.
- Pecman A, Kutnjak D, Mehle N, Znidaric MT, Gutierrez-Aguirre I, Pirnat P, Adams I, Boonham N, Ravnikar M. High-Throughput Sequencing Facilitates Characterization of a “Forgotten” Plant Virus: The Case of a Henbane Mosaic Virus Infecting Tomato. Frontiers in Microbiology 2018, 9, 2739.
- Fox A, Fowkes AR, Skelton A, Harju V, Buxton-Kirk A, Kelly M, Forde SMD, Pufal H, Conyers C, Ward R, Weekes R, Boonham N, Adams IP. Using high-throughput sequencing in support of a plant health outbreak reveals novel viruses in Ullucus tuberosus (Basellaceae). Plant Pathology 2018, 68(3), 576-587.
- Augustin S, Boonham N, De Kogel WJ, Donner P, Faccoli M, Lees DC, Marini L, Mori N, Petrucco Toffolo E, Quilici S, Roques A, Yart A, Battisti A. A review of pest surveillance techniques for detecting quarantine pests in Europe. EPPO Bulletin 2012, 42(3), 515-551.