Intra-farm diversity and evidence of genetic recombination of Citrus tristeza virus in Delhi region of India

Infection of Citrus tristeza virus (CTV) in different citrus orchards of New Delhi was detected by direct antigen coated-ELISA and RT-PCR. Sweet orange ( Citrus sinensis ) orchards were found to be susceptible to CTV with estimated disease incidence up to 39%. Kagzi kalan ( C. lemon ), Pumello ( C. paradisi ) and Kinnow mandarin ( C. reticulata ) orchards did not show CTV infection. Three CTV isolates, D1, D7 and D15 randomly selected from infected sweet orange orchards were considered for biological and molecular characterization. In the host range study, all the Delhi isolates infected Darjeeling mandarin ( C. reticulata ), Kagzi lime ( C. aurantifolia ), sour orange ( C. aurantium ) and sweet orange but not Kinnow mandarin. A fragment of 5′ORF1a and complete coat protein (CP) gene of these three isolates were cloned, sequenced and compared with other Indian and international CTV isolates. Delhi isolates shared 85–92% sequence identity for 5′ORF1a fragment and 89–91% for CP gene among them. Phylogenetic analysis segregated three Delhi isolates into three genogroups for each of 5′ORF1a fragment and CP gene, however phylogenetic relationships for both the genomic regions was incongruent. Recombination detecting program RDP3 detected CTV isolate D7 as recombinant, indicating genetic variability in CTV isolates might be the outcome of recombination events between divergent CTV sequences. An attempt was made in present study to characterize CTV isolates biologically and at genetic level, and to determine genetic diversity at farm level and study the recombination of CTV isolates in Delhi region.