Dr Gonçalo Silva is a plant virologist at the Natural Resources Institute (NRI), University of Greenwich, with over 15 years of experience in developing innovative laboratory and field-based diagnostic tools for plant viruses and their vectors. His research focuses on improving plant health and supporting the development of sustainable control strategies.

Since joining NRI in 2013, Gonçalo has led and collaborated on a range of international, multidisciplinary projects with a strong emphasis on molecular diagnostics, virus discovery, and the application of high-throughput sequencing technologies and bioinformatics. His work also includes the development of a novel smart trap for the early detection of regulated plant pests, as part of an Innovate UK-funded initiative. This proof-of-concept technology contributes to strengthening the UK’s biosecurity infrastructure and enhancing the efficiency of pest surveillance and inspection systems

Gonçalo’s work has been supported by major funders including the Bill & Melinda Gates Foundation, the Royal Society, BBSRC, and Innovate UK, and has consistently integrated capacity building and knowledge exchange activities.

• Munguti F.M., Kilalo D.C., Yegon H.K., Macharia I., Seal S.E., Mwango’mbe A.W., Nyaboga E.N., Silva G. (2024) Real-time reverse transcription recombinase polymerase amplification (RT-RPA) assay for detection of cassava brown streak viruses. Scientific Reports 14, 12438 (2024). https://doi.org/10.1038/s41598-024-62249-y
• Festus R.O., Seal S.E., Prempeh R., Quain M.D., Silva G. (2023) Improved Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) for the Rapid and Sensitive Detection of Yam mosaic virus. Viruses 2023, 15, 1592. https://doi.org/10.3390/v15071592
• Diouf M.B., Festus R., Silva G., Guyader S., Umber M., Seal S., Teycheney P.Y. (2022) Viruses of Yams (Dioscorea spp.): Current Gaps in Knowledge and Future Research Directions to Improve Disease Management. Viruses 2022, 14, 1884. https://doi.org/10.3390/v14091884
• Silva G., Bömer M., Turaki A.A., Nkere C.K., Kumar P.L., Seal S.E. (2022) Homing in on Endogenous Badnaviral Elements: Development of Multiplex PCR-DGGE for Detection and Rapid Identification of Badnavirus Sequences in Yam Germplasm. Frontiers in Plant Science. 13:846989. https://doi.org./10.3389/fpls.2022.846989
• 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://doi.org/10.1038/s41598-020-76612-2
• 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

My research focuses on the development and application of innovative diagnostic techniques for the rapid and accurate detection of plant viruses and their insect vectors. These tools are essential for timely decision-making and underpin the production of virus-free planting material, supporting resilient seed systems.

I have a strong interest in leveraging cutting-edge technologies such as loop-mediated isothermal amplification (LAMP), CRISPR-based diagnostics, and portable sequencing platforms like the MinION (Oxford Nanopore Technologies) for virus discovery, molecular characterization, and the study of plant viral populations. My work also includes the development of smart trap technologies for the early detection and identification of insect vectors, contributing to enhanced pest surveillance and biosecurity.

In parallel, I am committed to strengthening diagnostic capacity in low- and middle-income countries. I regularly design and deliver training courses and workshops in virus and vector diagnostics, facilitating effective technology transfer to laboratories across East and West Africa.

Core Relevant Skills

• Development of novel laboratory and field-based diagnostics for plant viruses, including LAMP, CRISPR, and MinION-based platforms
• Molecular characterization and discovery of plant viruses using high-throughput sequencing and bioinformatics
• Design and delivery of capacity-building programmes in diagnostics and vector identification
• Innovation in pest surveillance tools, including smart traps for real-time insect vector monitoring

• MSc Agriculture for Sustainable Development
• BSc Biology
• Module leader of Plant Science

Smart traps for improved surveillance and early detection of plant regulated pests

(2024-2025, funded by Innovate UK)

Bemisia tabaci is a major pest and virus vector affecting economically important crops such as tomato and cucumber. It is a regulated pest in the UK and frequently intercepted on imported plants, particularly poinsettia. Current surveillance relies on visual inspections and sticky traps, which are time-consuming and require expert identification due to similarities with non-quarantine species like Trialeurodes vaporariorum.

This project aims to develop and evaluate a novel smart trap for the automatic, real-time detection of B. tabaci. The prototype combines a suction mechanism with an optical sensor powered by machine learning, enabling passive data collection and remote monitoring. This innovation has the potential to enhance UK biosecurity by improving the efficiency and accuracy of pest surveillance and reducing the burden on inspection services.

Plant virus ecology: the role of parasitic weeds in virus epidemiology and implications for crop production

(2023–2024, funded by the University of Greenwich)

Plant virus ecology seeks to understand the ecological role of viruses and their vectors in managed and natural environments and the reciprocal effects of the ecosystems on virus and vectors distribution and virus evolution.

In this project, we investigated the presence of viruses in parasitic weeds (Cuscuta spp. and Striga spp.) by high-throughput sequencing (HTS) to get an unbiased detection of all DNA and RNA viruses present in these samples. Data from HTS will be used to develop targeted diagnostics to detect vi-ruses in insects to identify potential vectors.

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

(2016-2024, 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 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 has been identified as one 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.

Currently supervising 3 PhD students, with completed supervision of 3.

NRI representative of the Faculty Research Degrees sub-Committee

• Fellow, Higher Education Academy (FHEA)
• Member of the British Society of Plant Pathology