Variation in the Coat Protein Gene Among Citrus Tristeza Virus Isolates from Khyber Pakhtunkhwa and Punjab Provinces, and Islamabad Capital Territory of Pakistan

Citrus tristeza virus (CTV) is a plant pathogenic virus belonging to the genus Closterovirus and family Closteroviridae. It is transmitted by vegetative propagation and by several aphid species. It has been reported that CTV has killed millions of citrus trees worldwide. CTV has previously been reported in Pakistan. Symptom based sampling was carried out from the orchards of citrus rich districts of Punjab and Khyber Pakhtunkhwa (KPK) provinces of Pakistan and screened by double antibody sandwich enzyme linked immunosorbent assay (DAS-ELISA) and 48 samples were positive. The major coat protein-coding gene of the positive samples were amplified, sequenced and phylogenetic analysis was carried out. Nucleotide sequence analysis revealed 90-100% similarity within indigenous 48 isolates, 91.1 to 100% similarity with six isolates previously reported from Pakistan and 97.7 to 99.7% similarity with T3 USA, VT USA, VT Israel, RB New Zealand, VT India and an Indian isolate of unknown genotype. A maximum likelihood phylogenetic tree indicated that the CTV population is diverse in Pakistan with different isolates consisting of one major isolate of T3, and three minor isolates of VT, RB and recombinant VT IND genotypes. The most common group (T3 like) is comprised of 36 of samples and is dispersed all over the country irrespective of the region and province. The remaining three groups are related to VT Israel, VT India and RB New Zealand confined to specific regions. These results indicated that a citrus virus free certification program could reduce the risk of spreading these isolates. (C) 2019 Friends Science Publishers