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Complete sequence and diversity of a maize-associated Polerovirus in East Africa

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Abstract

Since 2011–2012, Maize lethal necrosis (MLN) has emerged in East Africa, causing massive yield loss and propelling research to identify viruses and virus populations present in maize. As expected, next generation sequencing (NGS) has revealed diverse and abundant viruses from the family Potyviridae, primarily sugarcane mosaic virus (SCMV), and maize chlorotic mottle virus (MCMV) (Tombusviridae), which are known to cause MLN by synergistic co-infection. In addition to these expected viruses, we identified a virus in the genus Polerovirus (family Luteoviridae) in 104/172 samples selected for MLN or other potential virus symptoms from Kenya, Uganda, Rwanda, and Tanzania. This polerovirus (MF974579) nucleotide sequence is 97% identical to maize-associated viruses recently reported in China, termed ‘maize yellow mosaic virus’ (MaYMV) and maize yellow dwarf virus (MaYMV; KU291101, KU291107, MYDV-RMV2; KT992824); and 99% identical to MaYMV (KY684356) infecting sugarcane and itch grass in Nigeria; 83% identical to a barley-associated polerovirus recently identified in Korea (BVG; KT962089); and 79% identical to the U.S. maize-infecting polerovirus maize yellow dwarf virus (MYDV-RMV; KT992824). Nucleotide sequences from ORF0 of 20 individual East African isolates collected from Kenya, Uganda, Rwanda, and Tanzania shared 98% or higher identity, and were detected in 104/172 (60.5%) of samples collected for virus-like symptoms, indicating extensive prevalence but limited diversity of this virus in East Africa. We refer to this virus as “MYDV-like polerovirus” until symptoms of the virus in maize are known.

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Acknowledgements

This project was supported in part by funds from Innovative Agriculture Research Initiative (iAGRI-USAID Award Number CA-621-A-00-11-00009-00) supporting D. P. Massawe training by Dr. L. R. Stewart. A PEARL Grant (OPP1112585) to T. Asiimwe from the Bill and Melinda Gates Foundation supported collection and analysis of samples from Rwanda, in part. We thank our collaborators from Uganda (Dr. Andrew Kiggundu) and Kenya (Dr. George Mahuku, IITA) for providing original samples used in this work. The remainder of the work was supported by USDA-ARS intramural funding for project ‘Control of Virus Diseases in Corn and Soybean’ at the Corn, Soybean and Wheat Quality Research Unit in Wooster, OH. We thank Kristen Willie (USDA) for RNA sample preparation, Brian Hodge (OSU) for laboratory troubleshooting, Kelly Barriball (USDA), and Dr. M. Amine Batnini for proofreading this work.

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Authors and Affiliations

  1. Department of Plant Pathology, Ohio State University, Wooster, OH, 44691, USA

    Deogracious P. Massawe, Lucy R. Stewart & Margaret G. Redinbaugh

  2. USDA-ARS Corn, Soybean and Wheat Quality Research Unit, 023 Selby Hall, 1680 Madison Ave, Wooster, OH, 44691, USA

    Lucy R. Stewart & Margaret G. Redinbaugh

  3. Biotechnology Program, Rwanda Agriculture Board, Airport Road 5016, Kigali, Rwanda

    Jovia Kamatenesi & Theodore Asiimwe

Authors
  1. Deogracious P. Massawe
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  2. Lucy R. Stewart
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  3. Jovia Kamatenesi
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  4. Theodore Asiimwe
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  5. Margaret G. Redinbaugh
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Contributions

DPM collected samples in Tanzania, and performed research; Dr. LRS conceived and designed the study, collected samples in Tanzania, analyzed data, supervised project, and directed manuscript preparation; JK assisted in the extraction of the viruses from maize leave samples; Dr. TA lead and designed Rwanda survey supported by a PEARL Grant (OPP1112585); and Dr. MGR, led and supervised on-site collections of samples and metadata in Kenya and Uganda.

Corresponding author

Correspondence to Lucy R. Stewart.

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The authors declare that they have no conflict of interest.

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This research had no human or animal subjects.

Additional information

Edited by Karel Petrzik.

Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.

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Figure S1

P0 partial protein sequence alignment: minimal differences. Nucleotide sequences (249-838 bp) were translated into amino acids (aa) for protein analysis by using CLC workbench program; (Germantown, MD). The first reading frame was selected to allow the translation to start from the first nucleotide. Translated amino acids were aligned together using Gonnet matrix with slow and accurate model of 0.1 extension gap cost on MacVector software (Version 15.5.3; Apex, NC). Supplementary material 1 (PPTX 358 kb)

Table S1

Primers designed from RNA-Seq contigs of MYDV-like polerovirus. Table S2 East African samples testing positive for MYDV-like polerovirus by RT-PCR. Supplementary material 2 (DOCX 32 kb)

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Massawe, D.P., Stewart, L.R., Kamatenesi, J. et al. Complete sequence and diversity of a maize-associated Polerovirus in East Africa. Virus Genes 54, 432–437 (2018). https://doi.org/10.1007/s11262-018-1560-5

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  • DOI: https://doi.org/10.1007/s11262-018-1560-5

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