# Metagenomics Analysis of Viruses Associated with Cassava Brown Streak Disease in Kenya

## TL;DR

This study analyzes viruses causing cassava brown streak disease in Kenya to understand their genetic variation and support better disease control strategies.

## Contribution

The study provides new complete virus sequences and identifies key genomic regions for improved diagnostics and resistance breeding.

## Key findings

- CBSV and UCBSV populations in Kenya show significant genomic variation, particularly in the PI and CP regions.
- The CI protein region is the most stable across CBSV and UCBSV genomes.
- Phylogenetic analysis reveals three major geographical groupings, indicating human-mediated virus spread.

## Abstract

Cassava brown streak disease (CBSD), caused by cassava brown streak virus (CBSV; Ipomovirus brunusmanihotis) and Ugandan cassava brown streak virus (UCBSV; Ipomovirus manihotis) (family Potyviridae, genus Ipomovirus), is increasingly becoming a threat to cassava production in several parts of Africa, especially in Eastern, Central and Southern Africa. In Kenya, the disease continues to wreak havoc on cassava production leading to a significant reduction in crop yields and economic losses of up to USD 1 billion. Variation in virus populations make the control of CBSD challenging as virus genomic variation can affect the accuracy of diagnostic tests, lead to resistance breaking isolates and jeopardize strategies of breeding for resistance. CBSV and UCBSV populations obtained from cassava fields in Kenya were characterized. In total, 44 new complete sequences of CBSV and UCBSV were assembled and 40 sequences successfully submitted to GenBank. Single Nucleotide Polymorphism (SNP) analysis revealed that the cylindrical inclusion protein (CI) is the most stable region across the genome of CBSV and UCBSV. In contrast, protein 1 (PI) and the coat protein (CP) were the most hypervariable regions. Phylogenetic analysis showed three major geographical groupings for both UCBSV and CBSV isolates, suggesting a continued spread of the viruses through human-mediated movement of infected planting materials. The data obtained in this study can support the development of disease management strategies through improved molecular diagnostic tests and targets for breeding for resistance against CBSD.