The symptom and genetic diversity of cassava brown streak viruses infecting cassava in East Africa

The genetic and symptom diversity of six virus isolates causing cassava brown streak disease (CBSD) in the endemic (Kenya, Mozambique, and Tanzania) and the recently affected epidemic areas (Uganda) of eastern Africa was studied. Five cassava varieties; Albert, Colombian, Ebwanateraka, TMS60444 (all susceptible) and Kiroba (tolerant) were graft inoculated with each isolate. Based on a number of parameters including the severity of leaf and root symptoms, and the extent of virus transmission by grafting, the viruses were classified as either severe or relatively mild. These results were further confirmed by the mechanical inoculation of 13 herbaceous hosts in which the virulent isolates caused plant death in Nicotiana clevelandii and N. benthamiana whereas the milder isolates did not. Phylogenetic analysis of complete coat protein gene sequences of these isolates together with sequences obtained from 14 other field-collected samples from Kenya and Zanzibar, and reference sequences grouped them into two distinct clusters, representing the two species of cassava brown streak viruses. Put together, these results did not suggest the association of a hypervirulent form of the virus with the current CBSD epidemic in Uganda. Identification of the severe and milder isolates, however, has further implications for disease management and quarantine requirements.

Multiplex RT-PCR assays for the simultaneous detection of both RNA and DNA viruses infecting cassava and the common occurrence of mixed infections by two cassava brown streak viruses in East Africa

Uniplex and multiplex reverse transcription-polymerase chain reaction (RT-PCR) protocols were developed for the detection of cassava brown streak viruses (CBSVs) in single and mixed infections with cassava mosaic begomoviruses (CMBs) in a tropical crop plant, cassava (Manihot esculenta). CMBs contain ssDNA as their genome (genus Begomovirus, family Geminiviridae) while CBSVs are made up of positive sense ssRNA (genus Ipomovirus, family Potyviridae), and they cause the economically important cassava mosaic and cassava brown streak diseases, respectively, in sub-Saharan Africa. Diagnostic methodologies have long been available for CMBs but they are limited for CBSVs especially in mixed infections. In this study, the two CBSVs, Cassava brown streak virus (CBSV) and Cassava brown streak Uganda virus (CBSUV) occurring singly or in mixed infection with CMBs, African cassava mosaic virus and East African cassava mosaic virus were detected in a single RT-PCR using both previously described and newly designed virus-specific primers. These protocols were highly efficient for detecting CBSVs compared to the existing methods and have great potential to minimize sample handling and contamination. As well as improving the diagnosis of cassava viruses, the development of multiplex RT-PCR protocols have revealed the common occurrence of mixed infections by CBSV and CBSUV in cassava fields of Tanzania and Kenya, which was contrary to the common belief until recently that these two viruses have existed separately. These protocols have implications for diagnosis and epidemiological studies on cassava virus diseases in Eastern Africa.

Optimization of diagnostic RT-PCR protocols and sampling procedures for the reliable and cost-effective detection of Cassava brown streak virus

Sampling procedures and diagnostic protocols were optimized for accurate diagnosis of Cassava brown streak virus (CBSV) (genus Ipomovirus, family Potyviridae). A cetyl trimethyl ammonium bromide (CTAB) method was optimized for sample preparation from infected cassava plants and compared with the RNeasy plant mini kit (Qiagen) for sensitivity, reproducibility and costs. CBSV was detectable readily in total RNAs extracted using either method. The major difference between the two methods was in the cost of consumables, with the CTAB 10x cheaper (0.53 pounds sterling=US$0.80 per sample) than the RNeasy method (5.91 pounds sterling=US$8.86 per sample). A two-step RT-PCR (1.34 pounds sterling=US$2.01 per sample), although less sensitive, was at least 3-times cheaper than a one-step RT-PCR (4.48 pounds sterling=US$6.72). The two RT-PCR tests revealed consistently the presence of CBSV both in symptomatic and asymptomatic leaves and indicated that asymptomatic leaves can be used reliably for virus diagnosis. Depending on the accuracy required, sampling 100-400 plants per field is an appropriate recommendation for CBSD diagnosis, giving a 99.9% probability of detecting a disease incidence of 6.7-1.7%, respectively. CBSV was detected at 10(-4)-fold dilutions in composite sampling, indicating that the most efficient way to index many samples for CBSV will be to screen pooled samples. The diagnostic protocols described below are reliable and the most cost-effective methods available currently for detecting CBSV.

Mitochondrial DNA variability and development of a PCR diagnostic test for populations of the whitefly Bemisia afer (Priesner and Hosny)

The whitefly, Bemisia afer (Hemiptera; Aleyrodidae), is emerging as a major agricultural pest. The current identification methods based on adult and pupal morphology are laborious and unreliable. A diagnostic polymerase chain reaction (PCR) protocol was developed for the first time in this study to discriminate B. afer from other whitefly species. Primers specific to mitochondrial cytochrome oxidase I gene (mtCOI) were designed to amplify a band of approx 650 bp. The PCR products were sequenced from B. afer samples collected from Malawi, Tanzania, Uganda, Zanzibar, and the United Kingdom. Phylogenetic analyses of mtCOI sequences and those of reference B. afer sequences clustered the African B. afer separately from the UK and Chinese populations and from other whitefly species. The African cluster was divided into two clades by parsimony and neighbor-joining methods. This indicates the existence of at least two genotypic clusters of B. afer, which are diverged by 0.8 to 3.2% nucleotide (nt) identities. Analysis of molecular variance indicated that these differences were the result of within population variation but were insufficient to identify discrete populations. Among the whitefly species used in the analysis, B. afer was equally dissimilar to Bemisia tabaci and Bemisia tuberculata (21.3-26.2% nt identities). As is the case for B. tabaci, these data show that mtCOI sequences are informative also for identifying B. afer variants, which lack distinguishing morphological features.

Re-emergence of Cassava Brown Streak Disease in Uganda

During November 2004, veinal chlorosis on mature cassava leaves, typical of cassava brown streak disease (CBSD), was observed at Mukono in central Uganda. Five out of 11 cultivars at the site showed CBSD symptoms (incidence range 4 to 64%). In a survey of farmers' fields, CBSD was observed in Wakiso and Mukono districts. Incidence of cassava mosaic disease was also recorded and averaged 60% for landraces (range 16.7 to 100%) and 20% for resistant varieties (range 0 to 65%). Leaf samples of plants with CBSD symptoms produced an amplicon of 222 bp using reverse transcription-polymerase chain reaction with primers that amplify a fragment of the coat protein (CP) gene of Cassava brown streak virus. Sequence comparisons based on the amplified CP gene fragment indicated that the isolates have 77 to 82.9% nucleotide and 43.9 to 56.8% amino acid identity with those from Mozambique and Tanzania. There was 95.9 to 99.5% nucleotide and 85.1 to 90.5% amino acid identity among the Ugandan isolates. These results confirm the re-emergence of CBSD in Uganda after it was first observed in the 1930s in cassava introduced from Tanzania and controlled by eradication. Prior to this report, CBSD was known to be restricted to the coastal lowlands of East Africa.