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Molecular identification and phylogenetic characterization of A-strain isolates of maize streak virus from western Ethiopia

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Abstract

The A-strain of maize streak virus (MSV) causes maize streak disease (MSD), which is a major biotic threat to maize production in sub-Saharan Africa. Previous studies have described different MSV strains of economic importance from southern and eastern African countries and how eastern African regions are hubs for MSV diversification. Despite these efforts, due to a lack of extensive sampling, there is limited knowledge about the MSV-A diversity in Ethiopia. Here, field sampling of maize plants and wild grasses with visible MSD symptoms was carried out in the western Ethiopian regions of Gambela, Oromia, and Benishangul-Gumuz during the maize-growing season of 2019. The complete genomes of MSV isolates (n = 60) were cloned and sequenced by the Sanger method. We used a model-based phylogenetic approach to analyse 725 full MSV genome sequences available in the GenBank database together with newly determined genome sequences from Ethiopia to determine their subtypes and identify recombinant lineages. Of the 127 fields accessed, MSD prevalence was highest, at 96%, in the Gambela region and lowest in Oromia, at 66%. The highest mean symptom severity of 4/5 (where 5 is the highest and 1 the lowest) was observed in Gambela and Benishangul-Gumuz. Our results show that these newly determined MSV isolates belong to recombinant lineage V of the A1 subtype, with the widest dissemination and greatest economic significance in sub-Saharan Africa and the adjacent Indian Ocean islands.

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Acknowledgements

The authors would like to express sincere gratitude to Mr. Tolcha Tufa for producing the map of the surveyed areas. The facilitation and support provided by Associate Professor Darren Martin in getting samples tested at the University of Cape Town in South Africa deserve our special appreciation.

Funding

KAO was supported by the National Research Foundation (NRF) South Africa and The World Academy of Science (TWAS) Grant number 105461. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

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Author notes

  1. Daniel Ketsela and Kehinde A. Oyeniran contributed equally to this work.

Authors and Affiliations

  1. Virology Research Laboratory, Ambo Agricultural Research Centre, Ethiopian Institute of Agricultural Research, P.O. Box 37, Ambo, Ethiopia

    Daniel Ketsela & Berhanu Feyissa

  2. Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa

    Kehinde A. Oyeniran

  3. Department of Biological Sciences, Bamidele Olumilua University of Education, Science and Technology, Ikere-Ekiti, Nigeria

    Kehinde A. Oyeniran

  4. The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA

    Rafaela S. Fontenele, Simona Kraberger & Arvind Varsani

  5. Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa

    Arvind Varsani

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  1. Daniel Ketsela
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Correspondence to Kehinde A. Oyeniran.

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Ketsela, D., Oyeniran, K.A., Feyissa, B. et al. Molecular identification and phylogenetic characterization of A-strain isolates of maize streak virus from western Ethiopia. Arch Virol 167, 2753–2759 (2022). https://doi.org/10.1007/s00705-022-05614-4

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