Contents lists available at ScienceDirect Journal of Virological Methods journal homepage: www.elsevier.com/locate/jviromet Rapid detection of Tobacco streak virus (TSV) in cotton (Gossypium hirsutum) based on Reverse Transcription Loop Mediated Isothermal Amplification (RT-LAMP) Shailesh Pandurang Gawande a, ⁎ ,1 , Raghavendra K.P. b,1 , Dilip Monga c , Dipak T. Nagrale a , Sandhya Kranthi a a Division of Crop Protection, ICAR-Central Institute for Cotton Research (CICR), Nagpur, 440010, India b Division of Crop Improvement, ICAR-Central Institute for Cotton Research (CICR), Nagpur, 440010, India c ICAR- Central Institute for Cotton Research (CICR), Regional Station, Sirsa, 125055, India ARTICLE INFO Keywords: Tobacco streak virus Cotton RT-LAMP RT-PCR ABSTRACT Tobacco Streak Virus (TSV) belongs to the genus Ilarvirus of the family Bromoviridae an emerging pathogen posing threat to the crop species worldwide. Identification of symptoms due to TSV infection by visual ob- servation of plants often results in misdiagnosis as symptoms produced by this virus can match with those reflecting physiological and nutritional disorders affecting cotton. Development of diagnostic tools with rapidity will have immense role to play in detection and management of the emerging virus. The protocol for rapid diagnosis of TSV infected samples by using Reverse Transcription-Loop Mediated Isothermal Amplification (RT- LAMP) was optimised and this is the first report of its use for diagnosis of TSV on cotton and Soybean. The colorimetric detection for diagnostic simplicity of amplified RT-LAMP product by using different dyes lead to enhanced applicability of this technique. The RT-LAMP diagnostic tool can be utilized not only for laboratory research but also for quarantine and field diagnosis of this important emerging pathogen affecting cotton. The productivity of cotton crops is mainly affected by various biotic and abiotic factors during diverse growth stages of the crop. Among a range of biotic factors, incidence of viral diseases causes serious threat to cotton crop. Tobacco streak virus (TSV) is an emerging and potent pathogen causing severe crop loss in cotton in recent years (Arun Kumar et al., 2008). TSV is a member of genus Ilarvirus (family: Bro- moviridae) and known to be transmitted by thrips in the cotton growing zones of South and Central India (Sdoodee and Teakle, 1987; Prasada Rao et al., 2003). Incidence of TSV in India was first diagnosed in Groundnut and Sunflower affected with Peanut Stem Necrosis Disease (PSND) and Sunflower Necrosis Disease (SND) respectively (Prasada Rao et al., 2000; Ramaiah et al., 2001 and Reddy et al., 2002). TSV has a broad host range comprising of more than 200 plant species belonging to 30 different families (Fulton, 1985; Brunt et al., 1996; EPPO, 2005). In cotton, tobacco streak virus has been reported to cause a maximum of 62.7% yield loss (Rageshwari et al., 2017). Whereas the association of TSV with bud blight of soybean was earlier reported from USA (Fagbenle and Ford, 1970; Rebedeaux et al., 2004) and Brazil (Costa and Cravalho, 1961; Almeida et al., 2005) where it contributed to yield losses of 25 and 100%, respectively. Since, diagnosis of specific virus infection in plant is a challenging task, management of viral disease is becoming difficult in agriculture. Recently, advancement in biochem- istry and biotechnology propelled invention of simpler and cost effec- tive diagnostic tools for detection and management of many pest and diseases affecting crops. The symptoms of TSV on cotton consisting of dark purple necrotic spreading lesions diffuse ring spots with numerous necrotic lesions, necrosis of bracts and square on upper surface (Fig. 1a–c), veinal ne- crosis, and reduction in leaf size of the infected plants which resemble the symptoms developed by physiological and nutritional disorders. Whereas the characteristic symptoms caused by the TSV in soybean are stunting of plant and necrotic patches on the leaves of growing tip of plants (Fig. 1d). Since, the diagnosis of TSV is difficult to distinguish from the physiological and nutritional maladies; there is vital need to develop complementary tool for diagnosis of this menacing TSV. Pre- sently, the TSV prevalence is being diagnosed through serological and nucleic acid based techniques such as ELISA and RT-PCR in Cotton (Bhat et al., 2002; Arun Kumar et al., 2008, Vinod kumar et al., 2017 https://doi.org/10.1016/j.jviromet.2019.04.018 Received 19 December 2018; Received in revised form 6 March 2019; Accepted 20 April 2019 ⁎ Corresponding author. E-mail address: spgawande1@gmail.com (S.P. Gawande). 1 Equally contributed. Journal of Virological Methods 270 (2019) 21–25 Available online 23 April 2019 0166-0934/ © 2019 Elsevier B.V. All rights reserved. T