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Molecular detection of cacao swollen shoot badnavirus species by amplification with four PCR primer pairs, and evidence that Cacao swollen shoot Togo B virus-like isolates are highly prevalent in Côte d’Ivoire

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Abstract

Badnaviruses are plant pararetroviruses that infect economically important crops worldwide, and several badnaviral species have been reported causing significant economic losses in cacao plantations in West Africa. Based on the available full-length genome sequences of cacao swollen shoot disease (CSSD)-associated badnaviruses (n = 66), four primer pairs (CSSD1-CSSD4) were designed to amplify a fragment of the 5′ region of open reading frame (ORF) 3, which comprises the movement protein, by polymerase chain reaction (PCR). Primers were evaluated for their ability to amplify a badnaviral fragment(s) from symptomatic and asymptomatic cacao leaf samples collected in Côte d’Ivoire during 2017–2019. The PCR products obtained by amplification with the CSSD1 primers showed high sequence variability and were phylogenetically related to one of three different badnaviral species, Cacao swollen shoot Togo B virus, Cacao swollen shoot CD virus, and Cacao swollen shoot CE virus, while the CSSD2 and CSSD4 amplicon sequences grouped exclusively with either cacao swollen shoot Togo B virus (CSSTBV) and Cacao swollen shoot Ghana M virus isolates, respectively. The majority of the isolates obtained here were most closely phylogenetically related to CSSTBV, with which they shared 81.0–98.0% nucleotide identity, making the CSSTBV-like isolates the predominant species associated with badnavirus-infected cacao trees tested in Côte d’Ivoire.

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References

  • Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215, 403–410.

    Article  CAS  Google Scholar 

  • Ameyaw, G. A., Dzahini-Obiatey, H. K., & Domfeh, O. (2014). Perspectives on cocoa swollen shoot virus disease (CSSVD) management in Ghana. Crop Protection, 65, 64–70. https://doi.org/10.1016/j.cropro.2014.07.001.

    Article  Google Scholar 

  • Bhat, A. I., Hohn, T., & Selvarajan, R. (2016). Badnaviruses: The current global scenario. Viruses, 177, 1–29.

    Google Scholar 

  • Chingandu, N., Dongo, L., Gutierrez, O. A., & Brown, J. K. (2019). The previously unidentified, divergent badnavirus species cacao red vein-banding virus is associated with cacao swollen shoot disease in Nigeria. Plant Disease, 103, 1302–1308. https://doi.org/10.1094/PDIS-09-18-1561-RE.

    Article  CAS  PubMed  Google Scholar 

  • Chingandu, N., Kouakou, K., Aka, R., Gutierrez, O. A., & Brown, J. K. (2017). Unexpected genome variability at multiple loci suggests cacao swollen shoot virus comprises multiple, divergent molecular variants. Journal of Emerging Diseases and Virology, 3, 1–10.

    Google Scholar 

  • Edgar, R. C. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792–1797.

    Article  CAS  Google Scholar 

  • FAOSTAT. 2017. FAO statistical databases. Available from: http://www.fao.org/faostat/en/#data/QC/visualize. Accessed 10 Jan 2020.

  • Geering, A.D.W.; Hull, R. (2012). Family Caulimoviridae. In virus taxonomy. 9th report of the international committee on taxonomy of viruses; king, a.M.Q., Adams, M.J., Carstens, E.B., Lefkowitz, E.J., Eds.; Elsevier Acad. Press: London, UK, pp. 429-443.

  • Kouakou, K., Kebe, I., Kouassi, N., Aké, S., Cilas, C., & Muller, E. (2012). Geographical distribution of Cacao swollen shoot virus (CSSV) molecular variability in Côte d’Ivoire. Plant Disease, 96, 1445–1450.

    Article  CAS  Google Scholar 

  • Kumar, S., Stecher, G., & Tamura, K. (2015). MEGA7: Molecular evolutionary genetics analysis version 7. Molecular Biology and Evolution, 33, 1870–1874. https://doi.org/10.1093/molbev/msw054.

    Article  CAS  Google Scholar 

  • Miller, M.A.; Holder, M.T.; Vos, R.; Midford, P.E.; Liebowitz, T.; Chan, L.; Hoover, P.; Warnow, T. The CIPRES Portals. (2010). CIPRES. Available online: http://www.phylo.org/sub-sections/portal (accessed on May 1, 2020).

  • Muhire, B. M., Varsani, A., & Martin, D. P. (2014). SDT: A virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One, 9, e108277.

    Article  Google Scholar 

  • Muller, E., Ravel, S., Agret, C., Abrokwah, F., Dzahini-Obiatey, H., Galyuon, I., Kouakou, K., Jeyaseelan, E. C., Allainguillaume, J., & Wetten, A. (2018). Next generation sequencing elucidates cacao badnavirus diversity and reveals the existence of more than ten viral species. Virus Research, 244, 235–251.

    Article  CAS  Google Scholar 

  • Oro, F., Mississo, E., Okassa, M., Guilhaumon, C., Fenouillet, C., & Muller, E. (2012). Geographical differentiation of the molecular diversity of cacao swollen shoot virus in Togo. Archives of Virology, 157, 509–514.

    Article  CAS  Google Scholar 

  • Puig, A.; Ramos-Sobrinho, R.; Keith, C.V.; Kitchen, N.; Gutierrez, O.; Goenaga, R.; Brown, J.K. (2020). First report of cacao mild mosaic virus (CaMMV) associated with symptomatic commercial cacao (Theobroma cacao L.) trees in Puerto Rico. Plant disease, doi: https://doi.org/10.1094/PDIS-04-20-0745-PDN.

  • Ramos-Sobrinho, R., Chingandu, N., Gutierrez, O. A., Marelli, J.-P., & Brown, J. K. (2020). A complex of badnavirus species infecting cacao reveals mixed infections, extensive genomic variability, and interspecific recombination. Viruses, 12, 443. https://doi.org/10.3390/v12040443.

    Article  CAS  PubMed Central  Google Scholar 

  • Rannala, B., & Yang, Z. (1996). Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. Journal of Molecular Evolution, 43, 304–311.

    Article  CAS  Google Scholar 

  • Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Hohna, S., Larget, B., Liu, L., Suchard, M. A., & Huelsenbeck, J. P. (2012). MrBayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61, 539–542.

    Article  Google Scholar 

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Acknowledgments

The authors thank MARS Inc. for supporting this research through Trust Agreement 6038-21000-023-12-T.

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Authors and Affiliations

  1. School of Plant Sciences, The University of Arizona, Tucson, AZ, 85721, USA

    Roberto Ramos-Sobrinho, Cory V. Keith & Judith K. Brown

  2. World Agroforestry Centre (ICRAF), Côte d’Ivoire Country Programme, Abidjan, BP 2823, Côte d’Ivoire

    Koffié Kouakou, Antoine Bolou Bi, Lucien Diby & Christophe Kouame

  3. Université Jean Lorougnon Guédé de Daloa, BP 150, Daloa, Côte d’Ivoire

    Koffié Kouakou

  4. Cocoa program, National Centre for Agronomic Research (CNRA), BP 808, Divo, Côte d’Ivoire

    Romain Aka Aka

  5. Mars Wrigley, 434 G Street Suite 100, Davis, CA, 95616, USA

    Jean-Philippe Marelli

Authors
  1. Roberto Ramos-Sobrinho
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  2. Koffié Kouakou
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  3. Antoine Bolou Bi
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  4. Cory V. Keith
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  5. Lucien Diby
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  6. Christophe Kouame
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  7. Romain Aka Aka
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  8. Jean-Philippe Marelli
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  9. Judith K. Brown
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Correspondence to Judith K. Brown.

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Ramos-Sobrinho, R., Kouakou, K., Bi, A.B. et al. Molecular detection of cacao swollen shoot badnavirus species by amplification with four PCR primer pairs, and evidence that Cacao swollen shoot Togo B virus-like isolates are highly prevalent in Côte d’Ivoire. Eur J Plant Pathol 159, 941–947 (2021). https://doi.org/10.1007/s10658-021-02203-0

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  • DOI: https://doi.org/10.1007/s10658-021-02203-0

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