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

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.