Dr Gonçalo Ramalho E Silva
+44 (0)1634 88 3158
Dr Goncalo Silva completed his Biotechnological Engineering degree at the University of Algarve, Faro, Portugal in 2004. Dr Silva has initiated his career in scientific research in 2005 at the University of Algarve, Portugal, working as a Research Assistant on a project about the Evolution and Molecular Epidemiology of Citrus tristeza virus (a plant virus). In January 2008, he was granted a scholarship by Fundação para a Ciência e a Tecnologia (Portugal) to carry out his PhD research on the phylodynamics of citrus tristeza virus at the Plant Molecular Virology Group of BioFig, University of Algarve.
In August 2013, Dr Silva joined the Natural Resources Institute, University of Greenwich, as a Research Fellow. Since then, Dr Silva has been developing diagnostic tools to detect, control and prevent the spread of viral diseases in vegetatively propagated crops. Dr Silva recently started using high throughput sequencing (HTS) technologies for the detection and characterisation of plant viruses and virus discovery.
In addition to playing a direct active role in research, Dr Silva also contributes to strengthening African science capacity through producing training materials, leading training workshops and supervising post-graduate students.
My research focus on the development and application of diagnostic techniques for the rapid and efficient detection of plant viruses and their vectors. These tools enable rapid decision making and support seed systems for the production of virus-free planting material. In addition, the use of high throughput sequencing (HTS) technologies, including MinION (Oxford Nanopore Technologies) for studying plant viral populations and plant virus discovery.
I also have a keen interest in delivering training courses and workshops in diagnostics which allow an effective technology transfer to laboratories in East and West Africa and thereby increasing diagnostics’ capacity in these regions.
Virus survey in UK vineyards
(2021 – 2023, Consultancy service to NIAB EMR Viticulture consortium)
The UK wine industry has grown markedly in recent years and is an important sector to the UK economy. Viral diseases of grapevine can however jeopardize this growth. This work aims at studying the diversity and distribution of viruses infecting UK vineyards and developing on-site diagnostic tools to rapidly identify infected vines in established vineyards. These tools will help in reducing the costs associated with the delayed removal of infected vines and limit the spread of virus diseases in vineyards.
Using High-Throughput Sequencing indexing to strengthen the yam (Dioscorea spp.) seed systems in Sub-Saharan Africa
(2019 – 2022, Royal Society International Collaboration Award)
This collaborative project will transfer state-of-the-art diagnostic techniques to the Biotechnology Laboratory of the Council for scientific and Industrial Research-Crops Research Institute (CSIR-CRI), Ghana thereby improving capacity for yam disease diagnostics and seed certification in the country. The success of this project will ensure the timely availability of disease-free seed yams on a price-competitive basis as the system is producing planting materials to feed the seed yam commercial farmers in Ghana.
Identification of mealybug vectors involved in the transmission of badnavirus infecting yam in Northern Nigeria
(2019-2020, funded by BBSRC Global Challenges Research Fund: “CONNECTED” - Community network for African vector-borne plant diseases award)
Yam productivity is severely compromised by the high impact of yam viruses and their insect vectors. Sap-feeding mealybugs are both direct plant pests and active vectors of badnaviruses, but only little is known about the role they play as vectors of yam badnaviruses. We plan to identify mealybug species infesting yam fields in northern Nigeria and thought to be vectors of Dioscorea bacilliform viruses (DBVs), detect and characterize DBV species in individual mealybugs, and evaluate whether there are potential correlations between certain mealybug- and DBV-species, which could inform vector specificity.
Renewal: Enabling Research Tools for Cassava and Yam Virologists and Breeders
(2016-2021, funded by the Bill and Melinda Gates Foundation)
This project is a continuation of the ‘Development of On-Farm Robust Diagnostic Toolkits for Yam Virus Diseases’ project (ended September 2016). The reinvestment is to optimize the yam virus diagnostic tests developed to date, as well as make further concerted efforts to generate improved antisera for yam potyviruses and badnaviruses to assist both the development of lateral flow devices for field diagnostics, and rapid concentration of virus particles for nucleic acid tests. The reinvestment will focus on the evaluation of the best tests for use in sub-Saharan Africa (SSA), and technology transfer to West African scientists and laboratories. Transfer of the tests will enable W. African National Agricultural Research Systems (NARS) to determine the virus-status of yam breeding lines and certify planting material for distribution to yam smallholders is virus-free.
Building links with the Kent wine industry
(2015–2017, funded by the University of Greenwich)
Grapevine (Vitis vinifera) is a major crop worldwide and produces a valuable agricultural commodity. The UK wine industry is a fast-growing sector and in 2017, an area of c. 2,500 hectares had been planted, a tripling of the area since 2000. Production of wine is projected to increase from the current 6 million bottles of wine per annum to c. 40 million bottles by 2040. This project aims to increase our knowledge about the presence and incidence of viruses in UK vineyards to develop efficient control strategies at this crucial and early stage of vineyard establishment. This project will assist the UK grapevine grower’s network by creating awareness of the presence of economically important viral diseases in UK vineyards and contributing to the sustainability of the UK grapevine industry.
Development of On-Farm Robust Diagnostic Toolkits for Yam Virus Diseases
(2012-2016, funded by The Bill and Melinda Gates Foundation)
Yams are propagated vegetatively through their tubers, which leads to an accumulation of tuber-borne diseases in farmers' planting material and subsequent serious crop yield losses. The economically important tuber-borne diseases are caused by viruses, and the only effective method of controlling these virus diseases is to use virus-free planting material. The scarcity and associated high expense of such material have been identified as some of the most important critical constraints to increasing yam production and productivity in West Africa. The goal of this project is to develop sensitive and specific cost-effective diagnostic tests for the most important African yam viruses and then adapt these tests to be suitable for on-farm virus-indexing. Due to the presence of integrated pararetrovirus sequences (EPRVs) in some yam breeding line genomes, it is also necessary to identify which lines contain activatable EPRV sequences and identify diagnostic procedures for these EPRVs. The diagnostic toolkits and procedures developed will be suitable for use in West African indexing centres and this will lead to the delivery of high-quality virus-free planting material of preferred yam varieties for multiplication and distribution to yam smallholders in West Africa. This will lead to improved food security and income generation for smallholders in West Africa.
- Kutnjak D., Tamisier L., Adams I., Boonham N., Candresse T., Chiumenti M., De Jonghe K., Kreuze J.F., Lefebvre M., Silva G., Malapi-Wight M., Margaria P., Mavrič Pleško I., McGreig S., Miozzi L., Remenant B., Reynard J-S., Rollin J., Rott M., Schumpp O., Massart S., Haegeman A. (2021) A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses. Microorganisms. 2021; 9:841. https://doi.org/10.3390/microorganisms9040841
- Silva G., Tomlinson J., Onkokesung N., Sommer S., Mrisho L., Legg J., Adams I.P., Gutierrez-Vazquez Y., Howard T.P., Laverick A., Hossain O., Wei Q., Gold K.M., Boonham N. (2021) Plant pest surveillance: from satellites to molecules. Emerging Topics in Life Sciences ETLS20200300. doi: https://doi.org/10.1042/ETLS20200300
- Tembo M., Adediji A.O., Bouvaine S., Chikoti P.C., Seal S.E., Silva G. (2020) A quick and sensitive diagnostic tool for detection of Maize streak virus. Scientific Reports 10, 19633. https://gala.gre.ac.uk/id/eprint/30221/
- Nkere C.K., Otto E., Atiri G.I., Onyeka J., Silva G., Bömer M., Seal S.E and Kumar, P.L. (2020) Assessment of Yam mild mosaic virus coat protein gene sequence diversity reveals the prevalence of cosmopolitan and African group of isolates in Ghana and Nigeria. Current Plant Biology. https://doi.org/10.1016/j.cpb.2020.100156
- Silva G., Bömer M., Rathnayake A.I., Sewe S.O., Visendi P., Oyekanmi J.O., Quain M.D., Akomeah B., Kumar P.L. & Seal S.E. (2019) Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing. Plants 8, 167. https://doi.org/10.3390/plants8060167
- Silva G., Lecourt J., Clover G.R.G. & Seal S.E. (2018) First record of Grapevine Pinot gris virus infecting Vitis vinifera in the United Kingdom. New Disease Reports 38, 7. http://dx.doi.org/10.5197/j.2044-0588.2018.038.007
- Bömer M., Rathnayake A.I., Visendi P., Sewe O.S., Sicat J.P.A., Silva G., Kumar P.L. & Seal S.E. (2018) Tissue culture and next-generation sequencing: A combined approach for detecting yam (Dioscorea spp.) viruses. Physiological and Molecular Plant Pathology 105:54-66. https://doi.org/10.1016/j.pmpp.2018.06.003
- Silva G., Oyekanmi J., Nkere C.K., Bömer M., Kumar P.L. & Seal S.E. (2018) Rapid detection of potyviruses from crude plant extracts. Analytical Biochemistry 546:17–22. https://doi.org/10.1016/j.ab.2018.01.019
- Nkere C.K., Oyekanmi J.O., Silva G., Bömer M., Atiri G.I., Onyeka J., Maroya N.G., Seal S.E. & Kumar P.L. (2018) Chromogenic detection of yam mosaic virus by closed‑tube reverse transcription loop‑mediated isothermal amplification (CT‑RT‑LAMP). Archives of Virology 163:1057–1061. https://doi.org/10.1007/s00705-018-3706-0
- Bömer M., Rathnayake A.I., Visendi P., Silva G. & Seal S.E. (2018) Complete genome sequence of a new member of the genus Badnavirus, Dioscorea bacilliform RT virus 3, reveals the first evidence of recombination in yam badnaviruses. Archives of Virology 163:533–538. https://doi.org/10.1007/s00705-017-3605-9
- Silva G., Lecourt J., Clover G.R.G. & Seal S.E. (2017) First report of Grapevine fanleaf virus infecting grapevine in the United Kingdom. New Disease Reports 36, 9. http://dx.doi.org/10.5197/j.2044-0588.2017.036.009
- Silva G., Bömer M., Nkere C., Kumar P.L. & Seal S.E. (2015) Rapid and specific detection of Yam mosaic virus by reverse-transcription recombinase polymerase amplification. Journal of Virological Methods 222:138-144. https://doi.org/10.1016/j.jviromet.2015.06.011