Abstract: 【Objective】 In order to clarify the genetic variation of p20 of the severe and mild strains of Citrus tristeza virus (CTV) in sweet orange and pummelo, seven CTV strains were studied. 【Method】The CTV p20 populations were established by RT-PCR, cloning and sequencing, and the phylogenetic tree was constructed with MEGA6. The genetic structure and mutation level of the CTV populations were analyzed by DNAStar. Haplotype diversity, nucleotide diversity and neutral test of the CTV populations were analyzed by DnaSP. 【Result】 Seven CTV p20 populations consisted of 162 sequences with 11 haplotypes were established. One or more haplotypes were found in each population. Sequence analysis showed that the original nucleotide sequence identity of the haplotypes from different populations was 88.2%-100.0%, the corresponding amino acid sequence identity was 92.3%-100.0% and the lowest amino acid sequence identity was found between CT23-1 and CT9-2. There were 50 sequences of haplotypes PeraIAC-4, CT22 and CT9-1, the corresponding nucleotide sequence identity was 100.0%, of which were dominant haplotypes and close to the standard strain T36. PeraIAC possessed the most abundant haplotype diversity (0.800±0.051) and CT22 had the lowest haplotype diversity (0.170±0.102). Compared with haplotype diversity (0.170-0.552) and nucleotide diversity (0.00032-0.05919) of the populations from pummelo, the populations from sweet orange had richer haplotype diversity (0.513-0.800) and nucleotide diversity (0.04208-0.05677). Phylogenetic analysis showed that the population structure of the isolates from sweet orange was complex, and the haplotypes detected in the populations from sweet orange were related to the standard strains T30, T36, VT and T3. CT31-2, which is close to the strain T3, was the most distant to the dominant haplotype in the phylogenetic tree, and the identity of the corresponding nucleotide sequences was 88.3%. The results of neutrality test showed that the populations from sweet orange tended to be balanced or contracted, while the populations from pummelo tended to be expanded except for CT23. The Tajima’s D values, Fu and Li’s D* values and Fu and Li's F* values of the TR-514Y, CT31 and CT23 populations were positive and significantly different, while those of the CT9 population were negative and significantly different. Recombination analysis of each population showed that no recombination occurred in any group. The population variation analysis showed that the percentage of mutant clones was 0-30.8% and the base mutation frequency was 0-7.706×10^-4. The highest percentage of mutant clones (30.8%), the highest mutation frequency (7.706×10^-4), the most base mutations (11) and the most mutation sites (7) happened in p20 populations of CTV severe strains from sweet orange. The percentage of mutated clones and mutation frequency of CTV mild populations from sweet orange were significantly lower than those of CTV severe populations from sweet orange. The percentage of mutated clones and mutation frequency of CTV mild populations from pummelo were slightly lower than those of severe populations from pummelo. The analysis of base mutation types showed that the base mutation types were mainly base substitution, and substitution from A to G was dominant. The sole insertion of A was detected between the 156 and 157 sites of CT3 and no deletion was found in p20 populations. 【Conclusion】 The variations of severe and mild populations of CTV p20 from sweet orange and pummelo were different. CTV p20 populations from sweet orange had more complex population structure and higher variation level than those from pummelo, and the severe populations of CTV p20 had higher variation level than those of mild populations.

Key words: Citrus tristeza virus (CTV), p20, population, genetic variation