Bioinformatics for plant biosecurity and surveillance systems By; Kiguongo Allan. P. K. (KEPHIS).

Introduction Bioinformatics a science where biology, computer science, and IT merge into a single discipline. Bioinformatics is a tool than a discipline, the tools for analysis of Biological Data.

Introduction Algorithms and statistics with to assess relationships among members of large data sets. Analysis and interpretation of data; nucleotide and amino acid sequences, protein domains, and protein structures.

Introduction Development and implementation of tools that enable efficient access and management of different types of information. Sets of data that are maintained in a consistent state over essentially indefinite periods of time.

Biosecurity and Surveillance Detection, identification and prevention of entry of exotic and spread of harmful pests is fundamental for the protection of a country's biodiversity, sustainable trade and food security. Pests and diseases cause yield and quality losses in crops making detection and identification a crucial facet of successful crop production and trade.

Biosecurity and Surveillance Existing post-entry quarantine screening methods rely on biological indicators and/or molecular assays which require knowledge of infecting viral pathogens. Molecular techniques such as RT-PCR has enhanced efficient, quick and accurate test of viruses and in plant samples.

Biosecurity and Surveillance These molecular techniques only allow for the test of known viruses or a small number of known viruses, therefore, missing on other unknown but harmful viruses and viroids. Next-generation sequencing (NGS) has revolutionized sequencing of nucleic acids due to its efficiency and deeper resolution.

Biosecurity and Surveillance Detection and identification of multiple known and emergent pests and in crops, nuclear stocks, germplasm in gene banks and imported plants. Detection using RNA- sequencing (RNA- seq) requires quick and robust bioinformatics methods to enable for host sequence removal and virus classification.

Biosecurity and Surveillance Co-infection of individual plants with more than one virus. Identification of viruses in asymptomatic plants. Different viruses or levels of viruses associated with different parts of the plant. Different analysis tools giving rise to different viruses being detected.

Biosecurity and Surveillance The identification of novel viruses and/or novel virus isolates. Identification of viruses in specific geographical regions or in host species where they have not been observed previously.

Biosecurity and Surveillance

Biosecurity and Surveillance Pest Risk Analysis (PRA) Germplasm clean-ups Pest and disease management systems Impacts quarantine regulation Plant biosecurity and surveillance; early warning and rapid alert response to pests

Biosecurity and Surveillance Major challenges which include biological characterization of newly discovered and their analysis of their impact on biosecurity, commercial, regulatory and scientific fields. Adoption of framework for efficient biological characterization and risk assessment for previously known or new virus detected using NGS methodologies.

Biosecurity and Surveillance Overall, NGS technologies complemented by classical virus study methods is expected to globally promote plant health and plant protection, but may also cause mayhem in trade and agriculture if challenges and questions are not addressed properly. Risks posed by growing trade and climate change, the aim is to reduce the uncertainties linked with risk management and to help NPPOs decide on the importance of a new virus in a quarantined material or a certified seed stock.

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