First Report of Cowpea Polero Virus 1 (CPPV1) Infecting Cowpea in Kenya

Orakha Odhiambo Patrick; Hassan Were; Millicent Ndonga; Mukoye Benard

doi:doi:10.11648/j.ijgg.20190704.16

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First Report of Cowpea Polero Virus 1 (CPPV1) Infecting Cowpea in Kenya

Orakha Odhiambo Patrick, Hassan Were, Millicent Ndonga, Mukoye Benard

Published in International Journal of Genetics and Genomics (Volume 7, Issue 4)

Received: 14 September 2019 Accepted: 4 November 2019 Published: 19 November 2019

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Abstract

Cowpea is an important legume crop for nutritional security, livestock feed and source of income in Kenya. Cowpea yield in Kenya is very low and declining further due to high incidences of pests and diseases among other factors. Like other pathogens, viruses have continued to cause yield losses of up to 100% depending on the prevailing epidemiological factors. This study had sought to determine the distribution, prevalence and genetic diversity of Cowpea Mild Mottle Virus (CPMMV) in western Kenya. Two surveys were conducted in the main legume growing areas of western Kenya. A total of 139 legume leafy samples were collected from 5 Counties; Bungoma, Nandi, Vihiga, Kakamega and Busia in June and October 2016. Collected samples were analyzed by Double Antibody Sandwich Enzyme Linked Immunosorbent Assay (DAS–ELISA) for detection CPMMV. ELISA was not carried out to test for CPPV1. Total RNA was extracted from the symptomatic leaf samples using RNeasy Mini Kit (Qiagen) according to the manufacturers’ protocol. Next Generation Sequencing (NGS) protocol proceeded. Assembled contigs were then subjected to a BLASTn search against the Genbank database. Phylogenetic analyses and comparisons were performed using MEGA X. Symptoms observed on legumes in the fields were mosaic, severe yellowing, chlorotic blotches and downward leaf curling. Some of the groundnut, cowpea and common bean samples collected in June and October tested CPMMV positive by DAS-ELISA. Legume samples of soybean, lablab, green grams, bambara nuts and legume weed collected tested negative for CPMMV. Results from Next Generation Sequencing technique revealed the presence of Cowpea Polero Virus 1 (CPPV1), the first full-length CPPV1 report and sequence to be reported in Eastern Africa. Phylogenetic analysis of VCP1 Kenyan isolate sequence revealed 98.27% similarity with that of Burkina faso isolate BE 167 (KY364846.1) (Palanga et al., 2017) and they clustered together. Kenyan isolate VCP1 and the Burkina faso BE 167 isolate are closely related. It is not clear if the spread of CPPV1 is through international trade from either country. Revelation of CPPV1 show that there could be more viruses affecting legume crops in the region whose identities are still unknown. There is need to conduct more diagnosis using NGS technique to detect more unknown but occurring viruses in the region. CPPV1 has been found infecting cowpea in Burkina faso, to the best of our knowledge this is the first report of CPPV1 in Kenya.

Published in	International Journal of Genetics and Genomics (Volume 7, Issue 4)
DOI	10.11648/j.ijgg.20190704.16
Page(s)	119-123
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2019. Published by Science Publishing Group

Keywords

Cowpea Mild Mottle Virus (CPMMV), Cowpea Polero Virus 1 (CPPV1), Next Generation Sequencing

References

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[4]	Singh, B. B., and Emechebe, A. M. (1997). Advances in research on cowpea, Striga and Alectra. Pages 215–224 in Advances in cowpea research. Copublication of International Institute of Tropical Agriculture (IITA) and Japan International Research Center for Agricultural Sciences (JIRCAS), edited by B. B. Singh, D. R. Mohan Raj, K. E. Dashiell, and L. E. N. Jackai. IITA, Ibadan, Nigeria.
[5]	Domier LL (2012) Family Luteoviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (eds) Virus taxonomy: Ninth report of the International committee on the Taxonomy of Viruses. Elsevier Academic Press, Amsterdam, pp 1045-1053.
[6]	Pagan I, Holmes EC, (2010) Long term evolution of the Luteoviridae: Time scale and mode of Virus speciation. J Virol 84: 6177-6187.
[7]	Smirnova E, Firth AE, Miller WA, Scheidecker D, Brault V, Reinbold C, Rakotondrafara AM, Chung BY-W, Ziegler-Graff V (2015) Discovery of a small non-AUG initiated ORFin Polero-viruses and Luteoviruses that is required for long distance movement. PLos Pathog 11 (5): e1004868.
[8]	Nono-Womdim, R., Swai I. S., Green S. K., Gebre-Selassie K., Latterot H., Marchoux G., and Opena R. T. (1996). Tomato viruses in Tanzania: Identification, distribution and disease incidence. Journal of South African Society of Horticulture 6: 41–44.
[9]	Has et al., (2013). De novo transcript sequence reconstruction from RNA-Seq using the Trinity platform for reference generation and analysis.
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[11]	Librado & Rozas (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data.
[12]	Lotos L, Maliogka VI and Katis NI. New Polero Viruses Associated with Yellowing Symptoms in Different Vegetable Crops in Greece.
[13]	Peipei Zhang, Yan Liu, Wenwen Liu, Mengji Cao, Sebastien Massart and Xifeng Wang; (2017). Identification, Characterisation and Full Length Sequence. Analysis of a novel Polero-Virus Associated with Wheat Leaf Yellowing Disease.
[14]	Imade Y. NSa and Kehinde T. Kareem. (2015). Additive Interactions of Unrelated Viruses in Mixed Infection of Cowpea (Vigna unguiculata L. Walp).
[15]	Akinjogunla, O. J., (2005). Effects of single and mixed inoculation with viruses on symptomatology, growth, yield and nutritive content of cowpea: (Vigna unquiculata) M. Sc. Thesis. University of Lagos, Nigeria.
[16]	Amayo, R., Arinaitwe, A. B., Mukasa, S. B., Tusiime, G., Kyamanywa, S., Rubaihayo, P. R. & Edema, R. (2012). Prevalence of viruses infecting cowpea in Uganda and their molecular detection. African Journal of Biotechnology 11: 14132-14139.
[17]	E. Palanga., D. P. Martin., S. Galzi., J. Zabre., Z. Bouda., J. M. Neya., M. Sawadogo., O. Traore., M. Peterschmitt., P. Roumagnac and D. Filloux (2014): Complete genome sequences of Cowpea Polero Virus 1 and Cowpea Polero Virus 2 infecting cowpea plants in Burkina Faso.

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Orakha Odhiambo Patrick, Hassan Were, Millicent Ndonga, Mukoye Benard. (2019). First Report of Cowpea Polero Virus 1 (CPPV1) Infecting Cowpea in Kenya. International Journal of Genetics and Genomics, 7(4), 119-123. https://doi.org/10.11648/j.ijgg.20190704.16

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ACS Style

Orakha Odhiambo Patrick; Hassan Were; Millicent Ndonga; Mukoye Benard. First Report of Cowpea Polero Virus 1 (CPPV1) Infecting Cowpea in Kenya. Int. J. Genet. Genomics 2019, 7(4), 119-123. doi: 10.11648/j.ijgg.20190704.16

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AMA Style

Orakha Odhiambo Patrick, Hassan Were, Millicent Ndonga, Mukoye Benard. First Report of Cowpea Polero Virus 1 (CPPV1) Infecting Cowpea in Kenya. Int J Genet Genomics. 2019;7(4):119-123. doi: 10.11648/j.ijgg.20190704.16

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@article{10.11648/j.ijgg.20190704.16,
  author = {Orakha Odhiambo Patrick and Hassan Were and Millicent Ndonga and Mukoye Benard},
  title = {First Report of Cowpea Polero Virus 1 (CPPV1) Infecting Cowpea in Kenya},
  journal = {International Journal of Genetics and Genomics},
  volume = {7},
  number = {4},
  pages = {119-123},
  doi = {10.11648/j.ijgg.20190704.16},
  url = {https://doi.org/10.11648/j.ijgg.20190704.16},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijgg.20190704.16},
  abstract = {Cowpea is an important legume crop for nutritional security, livestock feed and source of income in Kenya. Cowpea yield in Kenya is very low and declining further due to high incidences of pests and diseases among other factors. Like other pathogens, viruses have continued to cause yield losses of up to 100% depending on the prevailing epidemiological factors. This study had sought to determine the distribution, prevalence and genetic diversity of Cowpea Mild Mottle Virus (CPMMV) in western Kenya. Two surveys were conducted in the main legume growing areas of western Kenya. A total of 139 legume leafy samples were collected from 5 Counties; Bungoma, Nandi, Vihiga, Kakamega and Busia in June and October 2016. Collected samples were analyzed by Double Antibody Sandwich Enzyme Linked Immunosorbent Assay (DAS–ELISA) for detection CPMMV. ELISA was not carried out to test for CPPV1. Total RNA was extracted from the symptomatic leaf samples using RNeasy Mini Kit (Qiagen) according to the manufacturers’ protocol. Next Generation Sequencing (NGS) protocol proceeded. Assembled contigs were then subjected to a BLASTn search against the Genbank database. Phylogenetic analyses and comparisons were performed using MEGA X. Symptoms observed on legumes in the fields were mosaic, severe yellowing, chlorotic blotches and downward leaf curling. Some of the groundnut, cowpea and common bean samples collected in June and October tested CPMMV positive by DAS-ELISA. Legume samples of soybean, lablab, green grams, bambara nuts and legume weed collected tested negative for CPMMV. Results from Next Generation Sequencing technique revealed the presence of Cowpea Polero Virus 1 (CPPV1), the first full-length CPPV1 report and sequence to be reported in Eastern Africa. Phylogenetic analysis of VCP1 Kenyan isolate sequence revealed 98.27% similarity with that of Burkina faso isolate BE 167 (KY364846.1) (Palanga et al., 2017) and they clustered together. Kenyan isolate VCP1 and the Burkina faso BE 167 isolate are closely related. It is not clear if the spread of CPPV1 is through international trade from either country. Revelation of CPPV1 show that there could be more viruses affecting legume crops in the region whose identities are still unknown. There is need to conduct more diagnosis using NGS technique to detect more unknown but occurring viruses in the region. CPPV1 has been found infecting cowpea in Burkina faso, to the best of our knowledge this is the first report of CPPV1 in Kenya.},
 year = {2019}
}

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TY - JOUR
T1 - First Report of Cowpea Polero Virus 1 (CPPV1) Infecting Cowpea in Kenya
AU - Orakha Odhiambo Patrick
AU - Hassan Were
AU - Millicent Ndonga
AU - Mukoye Benard
Y1 - 2019/11/19
PY - 2019
N1 - https://doi.org/10.11648/j.ijgg.20190704.16
DO - 10.11648/j.ijgg.20190704.16
T2 - International Journal of Genetics and Genomics
JF - International Journal of Genetics and Genomics
JO - International Journal of Genetics and Genomics
SP - 119
EP - 123
PB - Science Publishing Group
SN - 2376-7359
UR - https://doi.org/10.11648/j.ijgg.20190704.16
AB - Cowpea is an important legume crop for nutritional security, livestock feed and source of income in Kenya. Cowpea yield in Kenya is very low and declining further due to high incidences of pests and diseases among other factors. Like other pathogens, viruses have continued to cause yield losses of up to 100% depending on the prevailing epidemiological factors. This study had sought to determine the distribution, prevalence and genetic diversity of Cowpea Mild Mottle Virus (CPMMV) in western Kenya. Two surveys were conducted in the main legume growing areas of western Kenya. A total of 139 legume leafy samples were collected from 5 Counties; Bungoma, Nandi, Vihiga, Kakamega and Busia in June and October 2016. Collected samples were analyzed by Double Antibody Sandwich Enzyme Linked Immunosorbent Assay (DAS–ELISA) for detection CPMMV. ELISA was not carried out to test for CPPV1. Total RNA was extracted from the symptomatic leaf samples using RNeasy Mini Kit (Qiagen) according to the manufacturers’ protocol. Next Generation Sequencing (NGS) protocol proceeded. Assembled contigs were then subjected to a BLASTn search against the Genbank database. Phylogenetic analyses and comparisons were performed using MEGA X. Symptoms observed on legumes in the fields were mosaic, severe yellowing, chlorotic blotches and downward leaf curling. Some of the groundnut, cowpea and common bean samples collected in June and October tested CPMMV positive by DAS-ELISA. Legume samples of soybean, lablab, green grams, bambara nuts and legume weed collected tested negative for CPMMV. Results from Next Generation Sequencing technique revealed the presence of Cowpea Polero Virus 1 (CPPV1), the first full-length CPPV1 report and sequence to be reported in Eastern Africa. Phylogenetic analysis of VCP1 Kenyan isolate sequence revealed 98.27% similarity with that of Burkina faso isolate BE 167 (KY364846.1) (Palanga et al., 2017) and they clustered together. Kenyan isolate VCP1 and the Burkina faso BE 167 isolate are closely related. It is not clear if the spread of CPPV1 is through international trade from either country. Revelation of CPPV1 show that there could be more viruses affecting legume crops in the region whose identities are still unknown. There is need to conduct more diagnosis using NGS technique to detect more unknown but occurring viruses in the region. CPPV1 has been found infecting cowpea in Burkina faso, to the best of our knowledge this is the first report of CPPV1 in Kenya.
VL - 7
IS - 4
ER -

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Author Information

Orakha Odhiambo Patrick

Department of Biological Sciences, Masinde Muliro University of Science and Technology (MMUST), Kakamega, Kenya
Hassan Were

Department of Agriculture and Land Use Management, Masinde Muliro University of Science and Technology (MMUST), Kakamega, Kenya
Millicent Ndonga

Department of Biological Sciences, Masinde Muliro University of Science and Technology (MMUST), Kakamega, Kenya
Mukoye Benard

Department of Biological Sciences, Masinde Muliro University of Science and Technology (MMUST), Kakamega, Kenya

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APA Style

Orakha Odhiambo Patrick, Hassan Were, Millicent Ndonga, Mukoye Benard. (2019). First Report of Cowpea Polero Virus 1 (CPPV1) Infecting Cowpea in Kenya. International Journal of Genetics and Genomics, 7(4), 119-123. https://doi.org/10.11648/j.ijgg.20190704.16

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ACS Style

Orakha Odhiambo Patrick; Hassan Were; Millicent Ndonga; Mukoye Benard. First Report of Cowpea Polero Virus 1 (CPPV1) Infecting Cowpea in Kenya. Int. J. Genet. Genomics 2019, 7(4), 119-123. doi: 10.11648/j.ijgg.20190704.16

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AMA Style

Orakha Odhiambo Patrick, Hassan Were, Millicent Ndonga, Mukoye Benard. First Report of Cowpea Polero Virus 1 (CPPV1) Infecting Cowpea in Kenya. Int J Genet Genomics. 2019;7(4):119-123. doi: 10.11648/j.ijgg.20190704.16

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@article{10.11648/j.ijgg.20190704.16,
  author = {Orakha Odhiambo Patrick and Hassan Were and Millicent Ndonga and Mukoye Benard},
  title = {First Report of Cowpea Polero Virus 1 (CPPV1) Infecting Cowpea in Kenya},
  journal = {International Journal of Genetics and Genomics},
  volume = {7},
  number = {4},
  pages = {119-123},
  doi = {10.11648/j.ijgg.20190704.16},
  url = {https://doi.org/10.11648/j.ijgg.20190704.16},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijgg.20190704.16},
  abstract = {Cowpea is an important legume crop for nutritional security, livestock feed and source of income in Kenya. Cowpea yield in Kenya is very low and declining further due to high incidences of pests and diseases among other factors. Like other pathogens, viruses have continued to cause yield losses of up to 100% depending on the prevailing epidemiological factors. This study had sought to determine the distribution, prevalence and genetic diversity of Cowpea Mild Mottle Virus (CPMMV) in western Kenya. Two surveys were conducted in the main legume growing areas of western Kenya. A total of 139 legume leafy samples were collected from 5 Counties; Bungoma, Nandi, Vihiga, Kakamega and Busia in June and October 2016. Collected samples were analyzed by Double Antibody Sandwich Enzyme Linked Immunosorbent Assay (DAS–ELISA) for detection CPMMV. ELISA was not carried out to test for CPPV1. Total RNA was extracted from the symptomatic leaf samples using RNeasy Mini Kit (Qiagen) according to the manufacturers’ protocol. Next Generation Sequencing (NGS) protocol proceeded. Assembled contigs were then subjected to a BLASTn search against the Genbank database. Phylogenetic analyses and comparisons were performed using MEGA X. Symptoms observed on legumes in the fields were mosaic, severe yellowing, chlorotic blotches and downward leaf curling. Some of the groundnut, cowpea and common bean samples collected in June and October tested CPMMV positive by DAS-ELISA. Legume samples of soybean, lablab, green grams, bambara nuts and legume weed collected tested negative for CPMMV. Results from Next Generation Sequencing technique revealed the presence of Cowpea Polero Virus 1 (CPPV1), the first full-length CPPV1 report and sequence to be reported in Eastern Africa. Phylogenetic analysis of VCP1 Kenyan isolate sequence revealed 98.27% similarity with that of Burkina faso isolate BE 167 (KY364846.1) (Palanga et al., 2017) and they clustered together. Kenyan isolate VCP1 and the Burkina faso BE 167 isolate are closely related. It is not clear if the spread of CPPV1 is through international trade from either country. Revelation of CPPV1 show that there could be more viruses affecting legume crops in the region whose identities are still unknown. There is need to conduct more diagnosis using NGS technique to detect more unknown but occurring viruses in the region. CPPV1 has been found infecting cowpea in Burkina faso, to the best of our knowledge this is the first report of CPPV1 in Kenya.},
 year = {2019}
}

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