Molecular detection and coat protein gene based characterization of Citrus tristeza virus prevalent in Sikkim state of India

Citrus tristeza virus (CTV), an important graft transmissible pathogen infecting citrus (Citrus spp.) is prevalent in different citrus growing areas of the country. Sikkim is one of important citrus producing states in the Northeast region of India where Khasi mandarin (C. reticulata) is commercially cultivated. Apart from this, there is limited plantation of Assam lemon (C. limon), Rangpur lime (C. limonia) and Pomelo (C. grandis) in this region. We performed molecular characterization based on coat protein sequence analysis of CTV isolates from Sikkim state of India. Thirty six field samples suspected with Tristeza disease were tested by reverse transcription-polymerase chain reaction (RT-PCR) using CP specific primers (CN150/CN151). Out of 36, 11 samples were found CTV positive. Eight of the 36 samples showing prominent field symptoms were bio-indexed on Mexican lime (C. aurantifolia) indicator plant for CTV. Five of them showed CTV specific vein clearing and vein flecking symptoms. CTV incidence of 30.55% was recorded in the Sikkim based on combined results of ELISA and PCR. In phylogenetic analysis, all CTV isolates were grouped into eight clades, which represented as a genogroup, Gr-I to Gr-VIII. The Sikkim isolates used in the present study were segregated into two genogroup, namely Gr-I and Gr-VI. Sikkim CTV isolates SK13, SK20, SK18, SK6, SK11, SK14, SK12 and SK19 showed 98–100 per cent nucleotide identity among them and clustered with previously reported Indian isolate K10 and Florida severe isolate T3. Other isolates viz. SK5, SK7 and SK22 shared 97–99% nucleotide identity within themselves and clustered with Indian isolate K5. These results suggest the presence of genetic diversity among CTV isolates and at least two strains of CTV in Sikkim. © 2019, Indian Phytopathological Society.