Prevalence and diversity of tomato viruses in Uganda

Abstract

Globalization and climate change favour pathogen establishment and introduction of disease pathogens to new areas, thus necessitating regular and improved disease surveillance strategies for early detection and management of plant diseases. High-throughput or next-generation sequencing (NGS) provides broad-spectrum and accurate identification of viruses that enables quantification, multiplex detection, and discovery of new viruses. This study aim was to determine the prevalence of tomato virus diseases as well as establish the diversity of viruses infecting tomato in Uganda. A biological survey of 45 tomato farms was carried out across nine districts. Samples of ten leaf discs were collected from symptomatic plants on each farm and shipped to the University of Cambridge, virology laboratory in the UK, for nanopore sequencing and virus discovery. Individual (total RNA) leaf samples were pooled to form four samples representing Eastern, West Nile and Albertine, Central and Western regions of Uganda from which samples were picked. Sequences in FASTQ format obtained from the Nanopore flow-cell were used for initial analysis using ‘Centrifuge’, a microbial classification engine that enables rapid, accurate, and sensitive labelling of reads and relative quantification of species. Survey results showed an average virus disease incidence of 43.02% (60% in Central, 48% in Eastern, 37% in Western, and 30.2% in Albertine and West Nile regions). Analysis of variance showed that tomato virus disease incidence and severity varied significantly with tomato varieties grown (Pα0.05 < 0.05), the agroecology (Pα0.05 < 0.001), but there was no significant difference in tomato virus disease incidence (Pα0.05 = 0.24) and severity (Pα0.05 = 0.06), with cropping systems. In terms of diversity of tomato viruses, sequencing results showed significant difference (Pα0.05), the agroecology (Pα0.05 < 0.001), but there was no significant difference in tomato virus disease incidence (Pα0.05 = 0.24) and severity (Pα0.05 < 0.06), with cropping systems. In terms of diversity of tomato viruses, sequencing results showed significant difference (Pα0.05<0.001) among different virus species of tomato in Uganda, but there was no significant difference (Pα0.05 = 0.94) in the distribution of different tomato viruses across the four regions. Virus family Virgaviridae had the highest percentage reads across the regions (76.6% in Central, 50.6% in Eastern, 37.6 in Western and 27.2% in Albertine and West Nile regions), dominated by the genus Tobamovirus, specifically Tomato mosaic virus, suggesting that Tomato mosaic virus is still the most prevalent virus of tomato in Uganda. Two viruses, Tomato brown rugose fruit virus and the Ethiopian tobacco bushy top virus (and its associated satellite RNA) were identified for the first time in Uganda. These results highlight the effects of farming practices, globalization, and climate change in escalating the spread of existing and emerging tomato virus diseases, thus necessitating more interventions in seed trade regulations, movement of plant materials and agricultural practices.