Citrus tristeza Virus Variants and their Distribution in Mandarin Orchards in Northeastern Himalayan Hill Region of India

Abstract

Northeastern Himalayan hill region of India is known to produce quality mandarin (C. reticulata) commercially. Citrus tristeza virus (CTV), an aphid (Toxoptera citricidus) transmitted closterovirus, is a major problem to cause decline of mandarin in this region. The different orchards of Mirik in the Darjeeling and Rumtek of East Sikkim were surveyed. CTV incidence of 48-53.3% in Mirik and 40-60% in Rumtek were estimated using direct antigen coated-ELISA and polymerase chain reaction. Nine CTV isolates; 6 from Mirik and 3 from Rumtek were characterized based on sequencing of 5’ORF1a gene fragments (404nt) and CP gene (672nt). The present isolates shared 85-100% nt identity and formed 3 genogroups for 5’ ORF1a; and 91-100% nt identity and formed 4 genogroups for CP gene, among them. Majorities of the present isolates are related with decline inducing Indian isolate Kpg3 indicating decline inducing CTV isolates are common in this region. CTV isolates of Sikkim were characterized for the first time and all the Sikkim isolates are genetically related with CTV isolate Kpg3. One new CTV isolate K38 related to the severe Florida isolate T3 was reported from Mirik. The recombination detecting program RDP4 identified two CTV isolates K37 and K38 of Mirik as putative recombinants. The previous and the present studies report occurrence of at least five CTV variants in Northeastern Himalayan hill region of India.