Adane D. Abraham

Analysis of the tomato mild mottle virus genome indicates that it is the most divergent member of the genus Ipomovirus (family Potyviridae)

The complete genome of a tomato mild mottle virus (ToMMV) isolate was analysed, and some biological features were characterized. The ssRNA genome of ToMMV from Ethiopia encompasses 9283 nucleotides (excluding the 3′ poly(A) tail) and encodes a polyprotein of 3011 amino acids. Phylogenetic and pairwise comparisons with other members of the family Potyviridae revealed that ToMMV is the most divergent member of the genus Ipomovirus, with a genome organization similar to that of members of the species Sweet potato mild mottle virus, the type species of the genus. In contrast to earlier reports, ToMMV isolates from Yemen and Ethiopia were not transmitted by the aphid Myzus persicae, but they were transmitted very erratically by the whitefly Bemisia tabaci. A comparison of the 3′-proximal sequences of different isolates provided evidence for geographically associated genetic variation.

Three Distinct Nanoviruses, One of Which Represents a New Species, Infect Faba Bean in Ethiopia

In all, 70 of 296 leaf samples (23.6%) collected from faba bean (Vicia faba) plants showing leaf yellowing and stunting in Ethiopia gave nanovirus-positive reactions when studied by triple-antibody sandwich enzyme-linked immunosorbent assay using broad-spectrum monoclonal antibodies (MAbs) specific to nanoviruses. Further analysis of these samples with seven discriminating MAbs revealed contrasting epitope profiles that were categorized into roughly three serogroups, designated A, B, and C. Serogroup A was found in 89% of the nanovirus-positive samples whereas serogroups B and C were infrequently encountered. Sequence analysis of DNA-S and DNA-U1 of serogroup A, B, and C isolates suggested that each represents a distinct nanovirus species. Serogroup A comprised isolates of Faba bean necrotic stunt virus reported earlier only from Ethiopia and Morocco. The DNA-R, -S, -U1, and -U2 sequences of a serogroup B isolate closely resembled those of Faba bean necrotic yellows virus, providing first molecular evidence for its occurrence in Ethiopia. Sequence analysis of the eight genomic DNAs of a representative serogroup C isolate (Eth-231) showed that it shared overall nucleotide and amino acid sequence identities of only ≤70 and ≤74%, respectively, with other nanoviruses. This suggests that Eth-231 represents a new nanovirus species, for which the name faba bean yellow leaf virus is proposed.

Characterization of an Australian isolate of taro bacilliform virus and development of an infectious clone

The badnavirus taro bacilliform virus (TaBV) has been reported to infect taro (Colocasia esculenta L.) and other edible aroids in several South Pacific island countries, but there are no published reports from Australia. Using PCR and RCA, we identified and characterized an Australian TaBV isolate. A terminally redundant cloned copy of the TaBV genome was generated and shown to be infectious in taro following agro-inoculation. This is the first report of TaBV from Australia and also the first report of an infectious clone for this virus.

First report of maize yellow mosaic virus infecting maize (Zea mays) in Ethiopia

The recent reports of the Polerovirus, Maize yellow mosaic virus (MaYMV) infecting sugarcane (Saccharum spp.) and itch grass (Rottboellia cochinchinensis) in Nigeria (Yahaya et al. 2017) and maize in Burkina Faso (Palanga et al. 2017) provided the motivation for this study. To determine the presence of MaYMV or other poleroviruses, we explored a collection of maize samples of local cultivars taken during virus surveys in August 2015 and July 2016 to assess the distribution of maize lethal necrosis disease (MLND) in three major maize cultivation regions of Ethiopia including Benishangul-Gumuz, Oromia, and South Nations, Nationalities, and People (SNNP). The collection comprised 47 leaf samples from symptomatic maize plants showing yellowing, whitish to yellowish stripes, and mosaic symptoms maintained as dried tissues over anhydrous calcium chloride. Total RNA was extracted using an RNA miniprep kit (Epoch Life Science) following the manufacturer’s instructions. RNA from each sample was screened by one-step RT-PCR with the universal polerovirus primer pair Gen 1 and Gen 2, comprising 322 nucleotides of the coat protein gene (Afouda et al. 2017). By RT-PCR, 78 and 71% of the samples collected in 2015 and 2016, respectively, tested positive for MaYMV. Direct sequencing of the amplified DNA fragments in both directions confirmed near identity (≥99% nt identity) of all Ethiopian sequences and shared 98 to 99% identity to the reference sequence of MaYMV (KU248489). The shared identity to another maize infecting polerovirus species, Maize yellow dwarf virus RMV (MYDV-RMV, NC_021484), ranged from 80 to 81%. To assess the genome variability of the Ethiopian MaYMV isolates, three isolates from three different provinces were selected to perform a deep sequencing analysis. Three independent Illumina libraries were prepared from the respective total RNA and were run on an Illumina MiSeq platform as described by Afouda et al. (2017). De novo and mapped based genome assembly was performed with Geneious v 10.2.3 (Biomatters LTD, NZ). The complete genome sequence of MaYMV isolate MV115 from Basha province was determined with 5,642 nt (MF684369), which was assembled from 36,673 of 2,003,892 reads with an average coverage of 1,141.7. Two near full-length genome sequences were determined, one for isolate MV32 from Wolenchiti Province (5,498 nt, MF684367, 1,820 reads of 2,517,898, mean coverage was 61.3) and for isolate MV90 from Dugda Bora Province (5,504 nt, MF684368, 878 reads of 1,925,886, mean coverage was 33.1). All three determined sequences of MaYMV shared 99.6% identity to each other. The complete MaYMV genome sequence (5,642 nt) of the Ethiopian isolate (MF684369) shared 96.8% nt identity with the Chinese isolate (KU248489), 98.2% with the Nigerian isolate (KY684356), and 95.4% with the isolate from Ecuador (KY052793). This first report of MaYMV in Ethiopia provides evidence for its nationwide distribution and the prevalence of a virus that may have occurred in Ethiopia for some time but was overlooked in targeted surveys focusing on MLND and other prominent maize diseases.

Survey for the identification and geographical distribution of viruses and virus diseases of maize (Zea mays L.) in Ethiopia

A survey to identify the distribution of virus diseases of maize was made in major maize growing regions of Ethiopia. Four surveys were conducted between 2015 and 2017. A total of 284 maize fields have been surveyed, of which 846 leaf samples with virus like disease symptoms were collected from 191 fields. There were no symptoms indicating for virus presence in maize grown in 93 fields which were exempted from sampling, while in contrast up to 100% disease incidence was recorded in maize grown in the Benishangul-Gumuz, Oromia and South Nations, Nationalities and People (SNNP) regions. Symptoms varied in maize ranging from the most common mosaic and streak to severe leaf mottling and necrosis as well as stunting and pre-mature plant death. Double or triple antibody sandwich (DAS or TAS) enzyme-linked immuno-sorbent assay (ELISA) to test for eight common maize viruses such as Maize chlorotic mottle virus (MCMV), Sugarcane mosaic virus (SCMV), Maize streak virus (MSV), Maize dwarf mosaic virus (MDMV), Maize mosaic virus (MMV), Maize stripe virus (MSpV), Wheat streak mosaic virus (WSMV) and Johnsongrass mosaic virus (JGMV) confirmed the presence of MCMV, SCMV and MSV in the leaf samples. Single or mixed infections with MCMV and SCMV frequently occurred and triple infections of MCMV, SCMV and MSV were found in 1% of samples from SNNP region. Sequence analysis of the coat protein genes of randomly selected seropositive samples of the three viruses showed little variability within the studied isolates and those retrieved from the GenBank. Our results indicated maize lethal necrosis disease (MLND) caused by MCMV and SCMV co-infection was the most important disease in SNNP and Oromia while maize streak disease was the predominant virus infecting maize in Benishangul-Gumuz.