Vol.:(0123456789) 1 3 Indian Phytopathology https://doi.org/10.1007/s42360-019-00169-y RESEARCH ARTICLE Disease incidence and molecular indexing of viruses infecting King chilli (Capsicum chinense Jacq) in North East India Ng. Tombisana Meetei 1,2  · Amit Kumar Singh 1,3  · Brijesh Kumar Singh 3  · Nirmal Mandal 1 Received: 20 September 2018 / Revised: 2 September 2019 / Accepted: 19 September 2019 © Indian Phytopathological Society 2019 Abstract A survey was conducted in King chilli growing areas of four Northeast states of India namely, Assam, Nagaland, Manipur and Meghalaya for virus disease incidence particularly Cucumber mosaic virus (CMV), Chilli veinal mottle virus (ChiVMV) and Chilli leaf curl virus (ChiLCV). The virus disease incidence based on symptomatology ranged from 15 to 65% with highest incidence recorded in Golaghat district of Assam and lowest in the Ukhrul district of Manipur. The polymerase chain reaction based detection using coat protein gene specifc primers for the three viruses revealed the presence of CMV and ChiVMV in all the four states whereas ChiLCV was recorded only in one location from Assam. In two of the samples collected for CMV and ChiVMV, mixed infection of the two viruses was confrmed. Based on molecular method based detection, the incidence of CMV infection in King chilli among all the samples tested for the virus was 32.5% whereas it was 25.97% for ChiVMV. Keywords Cucumber mosaic virus · King chilli · Viruses · Symptomatology · Molecular detection Introduction King chilli, a natural hybrid of Capsicum chinense and C. frutescens is recognised as one of the hottest chilli in the world today with a rating of 1,001,304 Scoville heat units (SHU’s) (Bosland and Baral 2007). It is indigenous to the Northeast region of India and possess a number of variants (Kumar et al. 2011; Murmu et al. 2014) with diferent local names such as Naga chilli in Nagaland, BhutJolokia in Assam, and U-Morok in Manipur (Sanatombi et al. 2010; Verma et al. 2013). The major growing areas for this chilli are in the States of Nagaland, Assam and Manipur and are also sporadically cultivated in Meghalaya, Mizoram and Arunachal Pradesh. The capsaicin content of King chilli is very high (~ 3%), due to which the demand for this crop in the international market is high (Tewksbury and Nabhan 2001). The chilli is vulner- able to several biotic stresses caused by viruses, fungi and bacteria (Talukdar et al. 2012) and as a result the productivity of the crop is substantially reduced. During the crop growth, several diseases attack the plants, the most common diseases being ‘die-back’, ‘anthracnose’ and ‘leaf curl’ (Borgohain and Devi 2007). In a study from Bhutjolokia growing areas in Assam, the incidence of viral, fungal and bacterial infection were reported to be 60%, 10% and 3% respectively (Talukdar et al. 2015), concluding that the occurrence of viral disease in Bhutjolokia is widespread in Assam. Several viruses have been reported to infect Bhutjolokia. These viruses include Cucumber mosaic virus (CMV), Potato virus Y (PVY) (Taluk- dar et al. 2015, 2017; Baruah et al. 2016), Tomato spotted wilt virus (TSWV) (Talukdar et al. 2015), Chilli leaf curl virus (ChiLCV) (Borgohain and Devi 2007; Talukdar et al. 2015; Baruah et al. 2016) Groundnut bud necrosis virus (GBNV) (Baruah et al. 2016) and Chilli veinal mottle virus (ChiVMV) (Banerjee et al. 2014). The infection may be by a single virus or more than one virus together forming a disease complex (Baruah et al. 2016). In this study, a survey was conducted in the major King chilli growing States of Northeast India namely Assam, Nagaland, Manipur and also Meghalaya to detect the occur- rence of three viruses in King chilli based on visible symp- toms and later confrming the presence of particular viruses * Nirmal Mandal nirman_bckv05@yahoo.com 1 Department of Agricultural Biotechnology, Faculty of Agriculture, Bidhan Chandra Krishi Viswavidyalaya, Nadia, Mohanpur 741252, West Bengal, India 2 College of Post Graduate Studies, Central Agricultural University (Imphal), Umiam 793103, Meghalaya, India 3 College of Horticulture and Forestry, Central Agricultural University (Imphal), Pasighat 791102, Arunachal Pradesh, India