Analysis of the genetic characteristics of chitinase gene of Plasmodium vivax along the China-Myanmar border

doi:10.3969/j.issn.1672-2302.2024.02.005

Abstract

Abstract:

Objective To understand the genetic diversity of the Plasmodium vivax chitinase (PvCHT1) gene along the China-Myanmar border, and explore its geographical variations for evidence to invent the malaria vaccines against P. vivax in China. Methods PvCHT1 gene sequences were collected from regions along the China-Myanmar border (Tengchong, Yunnan Province) and inland China (Hefei, Anhui Province; Zhengzhou, Henan Province), as well as from 11 countries, including Myanmar, Cambodia, Thailand, Vietnam, Indonesia, Malaysia, Papua New Guinea, Brazil, Colombia, Peru and Mexico through the National Center for Biotechnology Information (NCBI) of the United States. Mega, DnaSP, KaKs_Calculator, Arlequin, STRUCTURE and NETWORK software were used to analyze the genetic diversity, gene evolution, genetic differentiation, population STRUCTURE and haplotype NETWORK of all the harvested gene sequences. Results A total of 16 PvCHT1 gene sequences were obtained, including 6 from the China-Myanmar border region and 10 from inland China. Besides, another 551 PvCHT1 gene sequences were harvested from 11 other countries via NCBI. Genetic diversity analysis revealed 25 polymorphic sites in the PvCHT1 gene, of which 16 were non-synonymous mutations. The most common mutation sites were E617D (31.57%) and I272M (31.04%). The nucleotide diversity of the PvCHT1 gene in the China-Myanmar border region (π=0.000 79) was slightly higher than that in inland China (π=0.000 71) and Myanmar (π=0.000 75). Gene evolution analysis indicated that the neutral test (Tajima’s D) value of the PvCHT1 gene in the China-Myanmar border region was less than 0, with a ratio of non-synonymous to synonymous mutations (Ka/Ks) greater than 1. Genetic differentiation analysis showed that the fixation (F_ST) of the PvCHT1 gene in the China-Myanmar border region was 0.31 with inland China, -0.05 with Myanmar, and it ranged from 0.04 to 0.15 with Cambodia, Thailand, Vietnam, Indonesia and Malaysia. Additionally, it ranged from 0.24 to 0.56 with Papua New Guinea, Brazil, Colombia, Peru and Mexico. Population structure analysis indicated that the optimal number of clusters for all populations was 7, with the population at the China-Myanmar border comprised primarily of groups K1 to K6, dominated by K5. Haplotype network analysis showed strong geographical differentiation in the PvCHT1 gene, with four haplotype geographical clusters identified. Haplotype H5 was shared in all countries except inland China and Mexico. Conclusion PvCHT1 gene showing high conservation in the China-Myanmar border, which suggests that this gene can be a potential candidate target for transmission-blocking vaccines. Furthermore, significant geographical variation exists in the PvCHT1 gene among different populations. The findings indicate that design of the vaccine should be more targeted.

Key words: Plasmodium vivax, PvCHT1 gene, Genetic diversity, China-Myanmar border

CLC Number:

R382.3+1

ZHANG Man, SHEN Haimo, CHEN Shenbo, CHEN Junhu. Analysis of the genetic characteristics of chitinase gene of Plasmodium vivax along the China-Myanmar border[J]. Journal of Tropical Diseases and Parasitology, 2024, 22(2): 89-96.

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国家/地区	S	H	Hd	π	K	Tajima’s D值	P值
中缅边境	4	3	0.600±0.215	0.000 79	1.533	-0.676 13	>0.05
中国内陆	3	4	0.733±0.120	0.000 71	1.378	1.076 59	>0.05
缅甸	8	9	0.779±0.068	0.000 75	1.460	-1.021 63	>0.05
柬埔寨	13	32	0.840±0.020	0.001 03	2.008	-0.275 26	>0.05
泰国	12	21	0.846±0.020	0.000 95	1.847	-0.434 84	>0.05
越南	8	5	0.653±0.076	0.000 62	1.205	-1.568 91	>0.05
印度尼西亚	4	5	0.905±0.103	0.000 83	1.619	-0.039 84	>0.05
马来西亚	7	9	0.830±0.055	0.000 95	1.847	-0.011 96	>0.05
巴布亚新几内亚	4	7	0.762±0.051	0.000 63	1.230	0.601 27	>0.05
巴西	3	4	0.705±0.074	0.000 57	1.105	0.587 19	>0.05
哥伦比亚	6	6	0.807±0.028	0.000 78	1.522	0.195 00	>0.05
秘鲁	5	6	0.476±0.069	0.000 34	0.664	-0.849 87	>0.05
墨西哥	3	4	0.695±0.063	0.000 53	1.032	0.587 39	>0.05

国家/地区	Ka	Ks	Ka/Ks	P值
中缅边境	0.008 8	0.000 8	1.123 9	>0.05
中国内陆	2.777 3	3.841 8	0.722 9	>0.05
缅甸	0.000 9	0.000 6	1.499 7	>0.05
柬埔寨	2.743 9	3.536 9	0.775 8	<0.05
泰国	2.746 6	3.619 4	0.758 9	<0.05
越南	0.000 6	0.000 9	0.631 6	>0.05
印度尼西亚	2.746 9	3.604 7	0.762 0	>0.05
马来西亚	2.737 5	3.714 8	0.736 9	<0.05
巴布亚新几内亚	0.000 6	0.000 6	0.982 8	>0.05
巴西	2.750 2	3.762 8	0.730 9	>0.05
哥伦比亚	2.759 0	3.745 3	0.736 7	<0.05
秘鲁	2.765 0	3.790 2	0.729 5	<0.05
墨西哥	0.000 4	0.000 9	0.421 4	>0.05

国家/地区	中国内陆	中缅边境	缅甸	柬埔寨	泰国	越南	印度尼西亚	马来西亚	巴布亚新几内亚	巴西	哥伦比亚	秘鲁
中缅边境	0.31*
缅甸	0.33**	-0.05
柬埔寨	0.32**	0.05	0.18**
泰国	0.28**	0.06	0.18**	0.03**
越南	0.45**	0.15	0.25**	0.05*	0.08**
印度尼西亚	0.30*	0.04	0.17**	-0.00	-0.04	0.00
马来西亚	0.28**	0.09	0.21**	0.08**	0.05*	0.23**	0.05**
巴布亚新几内亚	0.52**	0.24*	0.33**	0.07*	0.12**	0.05	0.06	0.29**
巴西	0.29**	0.25**	0.29**	0.18**	0.12**	0.36**	0.13	0.03	0.43**
哥伦比亚	0.33**	0.30*	0.36**	0.25**	0.17**	0.38**	0.18*	0.12**	0.44**	0.05*
秘鲁	0.47**	0.56**	0.53**	0.36**	0.29**	0.59**	0.42**	0.29**	0.63**	0.09*	0.10**
墨西哥	0.49**	0.53**	0.53**	0.37**	0.30**	0.58**	0.42**	0.24**	0.60**	0.20*	0.09**	0.18**