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.

Cassava brown streak disease (CBSD) has emerged as a major threat to cassava (Manihot esculenta) in eastern and southern Africa. CBSD was first reported in Malawi in the 1950s, but little data on the distribution and epidemiology of the disease are available. A diagnostic survey was therefore conducted in Malawi to determine the distribution, incidence and diversity of viruses causing the disease, and to characterize its effects on local cassava cultivars. Diagnostic tests confirmed the presence of cassava brown streak viruses (CBSVs) in 90% of leaf samples from symptomatic plants. Average CBSD foliar severity was 2.5, although this varied significantly between districts. Both Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) (genus Ipomovirus, family Potyviridae) were detected from sampled plants. UCBSV was widespread, whereas CBSV was detected only in the two most northerly districts. The average abundance of the whitefly vector (Bemisia tabaci) was 0.4 per plant, a low value that was partly attributable to the fact that the survey was conducted during the cool part of the year known to be unfavourable for B. tabaci whiteflies. Spearman's correlation analyses showed a positive correlation between CBSD foliar incidence and CBSD severity and between CBSD severity and CBSD stem incidence. Of the 31 cassava varieties encountered, 20-20 was most severely affected, whilst Mtutumusi was completely unaffected. Although data from this study do not indicate a significant CBSD deterioration in Malawi, strengthened management efforts are required to reduce the current impact of the disease.

A survey was carried out in 19 districts to investigate the prevalence and distribution of sweetpotato virus disease (SPVD) and its implication on the sustainability of clean seed system in Malawi. A total of 166 leaf samples were collected and tested for the presence of 8 viruses using nitrocellulose membrane enzyme-linked immunosorbent assay (NCM-ELISA). SPVD foliar symptoms were observed in 68.42% of the surveyed districts. There were significant variations in disease incidence and severity (p < 0.001) among districts, with the highest incidence in Mulanje (28.34%). Average SPVD severity score was 3.05. NCM-ELISA detected sweet potato feathery mottle virus (SPFMV, 30.54%), sweet potato mild mottle virus (SPMMV, 31.14%), sweet potato mild speckling virus (SPMSV, 16.17%), sweet potato C-6 virus (SPC6V, 13.77%), sweet potato chlorotic stunt virus (SPCSV, 22.16%), sweet potato collusive virus (SPCV, 30.54%), sweet potato virus G (SPVG, 11.38%), cucumber mosaic virus (CMV, 7.78%) either in single or mixed infections. Data from this study indicate a significant SPVD occurrence in the country, and the consequence implications towards national sweetpotato seed system.

Illumina sequencing of RNA from a cassava cutting from northern Malawi produced a genome of Ugandan cassava brown streak virus (UCBSV-MW-NB7_2013). Sequence comparisons revealed stronger similarity to an isolate from nearby Tanzania (93.4% pairwise nucleotide identity) than to those previously reported from Malawi (86.9 to 87.0%).

Viral diseases are part of the limiting factors to tomato (Solanum lycopersicum L.) cultivation worldwide, reducing both the quality and quantity of yield. Tomato mosaic virus (ToMV) is one of the damaging viruses of tomato. This paper describes molecular characteristics of the full length genome of ToMV isolated from tomato in Uganda (ToMV-Ug). The genomic, ribonucleic acid (RNA), of this isolate is 6383 nucleotides (nts) in length, encoding four open reading frames (ORFs). Based on the homology with other ToMV strains, the 5' proximal 130 kilo dalton (kDa) ORF and its read-through product (180 kDa) are expected to encode two proteins required for viral genome replication; while the 30 kDa middle ORF and the 17.5 kDa 3' proximal ORF are expected to encode the movement protein (MP) and coat protein (CP), respectively. The 5'-and 3'-untranslated regions (UTRs) are 71 and 201 nts, respectively. Comparison with previously published ToMV sequences showed that ToMV-Ug is 99% identical to ToMV strains from Africa (Egypt and Zimbabwe), as well as diverse locations such as China, Australia, Germany and Japan; suggesting high levels of sequence conservation within this virus. This is the first report detailing molecular analysis of a ToMV isolate from Uganda and the Eastern and Central Africa regions.

No abstract

Manihot carthaginensis subsp. glaziovii (Müll.Arg.) Allem., a wild relative of cassava, native to Brazil, is one of the popular agroforestry trees used for hedges and/or boundary plants surrounding homesteads and farms and also harbours cassava mosaic begomoviruses (CMBs) and cassava brown streak ipomoviruses. Sequences of the DNA-A component of East African cassava mosaic virus (EACMV) isolates from M. carthaginensis subsp. glaziovii (Müll.Arg.) Allem., collected from non-cassava growing areas of Tanzania were characterized. Thirteen full length DNA-A sequences were analysed together with 15 already reported EACMV sequences and six CMB species reference genomes. The results show 96 to 100% nucleotide sequence identity with EACMV isolates from Kenya. Phylogenetic analysis revealed that EACMV isolates from M. carthaginensis subsp. glaziovii (Müll.Arg.) Allem, belong to a single cassava mosaic begomovirus species. The EACMV monophyletic clade is distinct from all other CMB species. The presence of Cassava infecting begomoviruses in wild cassava relative growing from traditionally non cassava growing region serve as inoculum sources for cassava-infecting begomoviruses and therefore their eradication is key in the sustainable management of CMBs, especially in the non-cassava growing areas.

The epidemiology of Potato Foliar Late Blight (PFLB) disease (Phytophthora infestans) was quantified in major potato production areas of Malawi. Seed multiplication fields, tests clones and local farmers’ fields were sampled basing on Area Under Disease Progress Curve (AUDPC). The determined severity values were transformed into AUDPC coefficients characterizing rate of disease spreading across the crop. Results indicate minimum and maximum AUDPC values of 0 and 1050 respectively, with an average value of 233.57. The results show significant statistical differences in PLB disease across seed multiplication fields, test clones and local farmers’ fields. AUDPC values differed significantly (p < 0.001) among potato growing districts, as well as sources of seed (aeroponics, sandponics, and vendors). Post-harvest survey targeting potato tubers showed that tubers that were sampled from Mzimba district had the highest likelihood of being infected with Potato Tuber Late Blight (PTLB), followed by potatoes that were sampled from Lilongwe (coefficients, b= 1.89, t = 6.11, p-value<0.001) while the potatoes tubers that were sampled from Ntcheu did not vary in the severity with those that were sampled in Dedza. Susceptibility to potato PTLB among potato varieties were varied, with Rosita likelihood to PTLB disease, while there were no other significant differences to PTLB in the rest varieties (b=1.12, t=4.23, p-value<0.001). An extended study on bacterial wilt (PBW) revealed that disease was influenced by the district where the tubers were sampled (x2= 9.26, p-value < 0.001) while the type of variety sampled did not have any significant difference on PBW (x2= 3.59, p-value = 0.268). The presence of potato tuber moth which varied among the sampled districts, was not influenced by variety sampled. The paper has documented and quantified increasing epidemic spread of late blight disease and the consequent effect on sustainable potato production and clean seed systems in Malawi.