**4. Disease diagnostics and monitoring**

Plant diseases are caused by a wide array of pathogens, including viruses, bacteria, and fungi. A combination of techniques, including microscopy, serological [e.g., enzyme-linked immu‐ nosorbent assay (ELISA)], and molecular (e.g., PCR) techniques, are used in detection and identification of pathogens associated with major diseases of African food staples. Conven‐ tional methods of virus diagnostics, using antibodies and PCR, often lack the sensitivity to detect viruses that exist in low abundance and emerging viruses with unknown genomes. Therefore, next-generation deep sequencing approaches and bioinformatics analysis can be used for de novo assembly of virus and viroid genomes, to perform reliable characterization and diagnostics of known and unknown viruses and viroids [112,154,155]. In the wake of NGS technologies, powerful and high-throughput novel approaches, such as metagenomics, have been developed and widely used to analyze nucleotide sequence of microbial populations in plant samples (see section 2.8) [8,105,156]. In particular, deep sequencing of small RNA families such as short interfering RNAs (siRNAs) can be used to identify and reconstruct any DNA or RNA virus genome and its microvariants with the help of bioinformatics tools [155,157]. Furthermore, the application of NGS can be extended to insect vectors for discovery and characterization of insect viruses [109].

The potential use of NGS technologies for diagnostic programs in quarantine and certification of some fruits have been demonstrated (reviewed in [8]). Existing diagnostics tools that are deployed in several clonally propagated crops (cassava, yam, banana) for quarantine moni‐ toring during exchange of planting material can be enhanced using NGS. In IITA, diagnostic tools have been combined with digital data capture tools for real-time surveillance and rapid diagnosis. This has been put to use for monitoring pathogens of cassava and banana in East Africa.
