Status and Epidemiology of Maize Lethal Necrotic Disease in Northern Tanzania.

Fatma Hussein Kiruwa,Francesca Stomeo,Joyce Njuguna,Eunice Machuka,Patrick Alois Ndakidemi,Tileye Feyissa,Senait Senay,Samuel Mutiga

doi:10.3390/pathogens9010004

Abstract

Sustainable control of plant diseases requires a good understanding of the epidemiological aspects such as the biology of the causal pathogens. In the current study, we used RT-PCR and Next Generation Sequencing (NGS) to contribute to the characterization of maize lethal necrotic (MLN) viruses and to identify other possible viruses that could represent a future threat in maize production in Tanzania. RT-PCR screening for Maize Chlorotic Mottle Virus (MCMV) detected the virus in the majority (97%) of the samples (n = 223). Analysis of a subset (n = 48) of the samples using NGS-Illumina Miseq detected MCMV and Sugarcane Mosaic Virus (SCMV) at a co-infection of 62%. The analysis further detected Maize streak virus with an 8% incidence in samples where MCMV and SCMV were also detected. In addition, signatures of Maize dwarf mosaic virus, Sorghum mosaic virus, Maize yellow dwarf virus-RMV and Barley yellow dwarf virus were detected with low coverage. Phylogenetic analysis of the viral coat protein showed that isolates of MCMV and SCMV were similar to those previously reported in East Africa and Hebei, China. Besides characterization, we used farmers’ interviews and direct field observations to give insights into MLN status in different agro-ecological zones (AEZs) in Kilimanjaro, Mayara, and Arusha. Through the survey, we showed that the prevalence of MLN differed across regions (P = 0.0012) and villages (P < 0.0001) but not across AEZs (P > 0.05). The study shows changing MLN dynamics in Tanzania and emphasizes the need for regional scientists to utilize farmers’ awareness in managing the disease.

Highlights

Maize is the most important cereal crop and a staple food in sub-Saharan Africa
Maize production is hindered by maize lethal necrosis (MLN), a devastating viral disease that is currently spreading at an alarming rate
In addition to Maize Chlorotic Mottle Virus (MCMV) and Sugarcane Mosaic Virus (SCMV) complete sequences, Next Generation Sequencing (NGS) analysis revealed the occurrence of MSVand signatures of MYDV, Maize dwarf mosaic virus (MDMV), Barley yellow dwarf virus (BYDV), and Sorghum mosaic virus (SrMV) that have been previously reported to cause serious infections in maize [27,28,29]

Summary

Introduction

Maize is the most important cereal crop and a staple food in sub-Saharan Africa. With over million hectares of its land planted with this crop and a per capita consumption of 128 kg, Tanzania is one of the largest producers and consumers of maize in eastern and southern Africa [1]. Pathogens 2020, 9, 4 intensively cultivated in the southern highland, lake, and northern zones of Tanzania [2]. Maize production is hindered by maize lethal necrosis (MLN), a devastating viral disease that is currently spreading at an alarming rate. The disease was first reported in the Southern Rift. Valley region of Kenya in 2011 [3] and Mwanza and Arusha regions in Tanzania in 2012 [4]. MLN has since spread to several other maize-producing African countries, including Rwanda, the Democratic

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