Variability in P1 gene redefines phylogenetic relationships among cassava brown streak viruses

Willard Mbewe,Peter Sseruwagi,Fred Tairo,Joseph Ndunguru,Ssetumba Mukasa,Marianne Koerbler,Samar Sheat,Ibrahim Benesi,Stephan Winter,Siobain Duffy

doi:10.1186/s12985-017-0790-9

Abstract

BackgroundCassava brown streak disease is emerging as the most important viral disease of cassava in Africa, and is consequently a threat to food security. Two distinct species of the genus Ipomovirus (family Potyviridae) cause the disease: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). To understand the evolutionary relationships among the viruses, 64 nucleotide sequences from the variable P1 gene from major cassava producing areas of east and central-southern Africa were determined.MethodsWe sequenced an amplicon of the P1 region of 31 isolates from Malawi and Tanzania. In addition to these, 33 previously reported sequences of virus isolates from Uganda, Kenya, Tanzania, Malawi and Mozambique were added to the analysis.ResultsPhylogenetic analyses revealed three major P1 clades of Cassava brown streak viruses (CBSVs): in addition to a clade of most CBSV and a clade containing all UCBSV, a novel, intermediate clade of CBSV isolates which has been tentatively called CBSV-Tanzania (CBSV-TZ). Virus isolates of the distinctive CBSV-TZ had nucleotide identities as low as 63.2 and 63.7% with other members of CBSV and UCBSV respectively.ConclusionsGrouping of P1 gene sequences indicated for distinct sub-populations of CBSV, but not UCBSV. Representatives of all three clades were found in both Tanzania and Malawi.

Highlights

Cassava brown streak disease is emerging as the most important viral disease of cassava in Africa, and is a threat to food security
The plants were classified by having symptoms that were consistent with cassava brown streak disease (CBSD), or potentially were coinfected with agents causing both CBSD and Cassava mosaic disease (CMD) and were taken to The Leibniz Institute – Deutsche Sammlung von Mikroorganismen and Zellkulturen GmbH (DSMZ) Plant Virus Department, where they were maintained under greenhouse conditions
Seven isolates; five from Tanzania (TZ-Nal:07, TZ_Mari_1_13, TZ clade (TZ):Kor6:08, TZ-19-1, Tan_70) and two from Malawi (MW16, MW40) formed a clade which is significantly divergent from other Cassava brown streak virus (CBSV) isolates and the Ugandan cassava brown streak virus (UCBSV) isolates respectively (Fig. 1)

Summary

Introduction

Cassava brown streak disease is emerging as the most important viral disease of cassava in Africa, and is a threat to food security. Recent developments in cassava research have shown that CBSD is emerging as the most important viral disease of cassava in Africa, and is a threat to food security [1]. Two distinct species of the genus Ipomovirus (family Potyviridae), Cassava brown streak virus [3] and Ugandan cassava brown streak virus (UCBSV [4, 5]) cause the disease. CBSD was reported only from the coastal lowlands of East Africa, but recently it has spread throughout the Great Lakes region of East and CentralSouthern Africa [8,9,10,11,12,13,14]

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