猪伪狂犬病病毒gE基因遗传变异及密码子使用偏好性分析

doi:10.16431/j.cnki.1671-7236.2025.07.027

Abstract

Abstract: 【Objective】 The purpose of this experiment was to understand the current epidemic status of Porcine pseudorabies virus (PRV) in China,the genetic status of the epidemic strain,the codon usage bias of PRV gE gene and the influencing factors. 【Method】 In this study,a phylogenetic tree was constructed using Mega 7.0 software for 106 PRV gE gene sequences isolated in China from 2019 to 2023.Launch DnaSP 6.0 software was used for gene selection pressure analysis and gene flow analysis.CodonW 1.4.2 and SPSS 27.0.1 software were used for codon analysis. 【Result】 The results of genetic evolution analysis showed that the PRV strains prevalent in China were genotype Ⅱ,which could be further divided into genotypes 2.1 and 2.2.Gene flow analysis showed that the nucleotide diversity (Pi) of genotypes 2.1 and 2.2 in genotype Ⅱ was 0.006 and 0.002,respectively.The coefficient of genetic differentiation (Fst) was 0.381,the synonymous substitution rate (Ks) and the quantitative index of gene flow (Z) were 1.353 and 6.637,respectively.Gene selection pressure analysis showed that the non-synonymous mutation to synonymous mutation ratio (dN/dS) of genotypes 2.1 and 2.2 was 1.808 and 1.362,respectively.The results of codon base analysis showed that the content of GC3 was more than 50% in the two subtypes of genotype Ⅱ,and the ENC values of different gene coding regions of genotypes 2.1 and 2.2 was 30.04 and 30.06,respectively.Codon usage bias analysis showed that the correlation coefficients of genotypes 2.1 and 2.2 was 0.115 and 0.173,respectively.Relative synonymous codon usage (RSCU) analysis showed that the third codon of high expression in genotypes 2.1 and 2.2 was G/C base,and the third codon of low expression was mainly A/U base.A total of 25 codons with RSCU ＞1 were used as preferred codons,of which 13 had high GC content and 16 ended with base C. 【Conclusion】 Genotype Ⅱ was the dominant PRV strain in China,which had a unique base composition,high GC content and relatively low AU content,showing a low preference.Codon usage was influenced by both mutation pressure and natural selection,in which natural selection played a dominant role.The results of this study provided scientific basis and technical support for the study of the epidemic trend of porcine pseudorabies in China and the formulation of prevention and control strategies.

Key words: Porcine pseudorabies virus (PRV); gE gene; genetic diversity; codon; bias

CLC Number:

S852.65^＋9.1

CHEN Zhian, ZHANG Beiwen, HE Minjia, CHEN Meichun, WENG Chengzhen, HUANG Xinxin, LI Hongxi, ZENG Zhongwen, CHEN Baoliang, QIU Longxin, CHEN Hongbo, LI Xiaobing. Genetic Variation and Codon Usage Bias Analysis of Porcine Pseudorabies Virus gE Gene[J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(7): 3264-3275.

References

[1] 何松，汤德元，毛茵茗，等.猪伪狂犬病诊断方法与疫苗研究进展[J].动物医学进展，2024,45(2):95-100.HE S,TANG D Y,MAO Y M,et al.Advances in diagnostic methods and vaccines for porcine pseudorabies[J]. Progress in Veterinary Medicine,2024,45(2):95-100.(in Chinese)
[2] 张映彬.猪伪狂犬病的科学防控[J].特种经济动植物,2024,27(6):63-64.ZHANG Y B.Scientific prevention and control of pseudorabies in pigs[J].Special Economic Animal and Plant,2024,27(6):63-64.(in Chinese)
[3] 程国华，张泽林，刘璐，等.猪伪狂犬病的流行诊断及防控措施[J].浙江畜牧兽医,2024,49(2):31-32.CHENG G H,ZHANG Z L,LIU L,et al.Epidemiological diagnosis and prevention and control measures of porcine pseudorabies[J].Zhejiang Journal Animal Science and Veterinary Medicine,2024,49(2):31-32.(in Chinese)
[4] 杨志刚,汤德元,廖少山,等.猪伪狂犬病病毒新型检测方法研究进展[J].黑龙江畜牧兽医,2021,9:34-38.YANG Z G,TANG D Y,LIAO S S,et al.Research progress of novel detection methods of Porcine pseudorabies virus[J].Heilongjiang Animal Science and Veterinary Medicine,2021,9:34-38.(in Chinese)
[5] 郭镇洋，田志军，彭金美.中国猪伪狂犬病的流行及防控[J].中国科学:生命科学,2023,53(12):1780-1793.GUO Z Y,TIAN Z J,PENG J M.Epidemic prevention and control of porcine pseudorabies in China[J].Scientia Sinica (Vitae),2023,53(12):1780-1793.(in Chinese)
[6] YAO J,LI J,GAO L,et al.Epidemiological investigation and genetic analysis of Pseudorabies virus in Yunnan province of China from 2017 to 2021[J].Viruses,2022,14(5):895.
[7] 郭镇洋，赵静，付军，等.2016—2021年我国猪伪狂犬病病毒的分子流行病学调查与分析[J].中国预防兽医学报,2023,45(2):122-128.GUO Z Y,ZHAO J,FU J,et al.Molecular epidemiological investigation and analysis of Porcine pseudorabies virus in China from 2016 to 2021[J].Chinese Journal of Preventive Veterinary Medicine,2023,45(2):122-128. (in Chinese)
[8] 李雅雯，张莉，丁向彬，等.猪伪狂犬病疫苗研究概况[J].动物医学进展,2024,45(3)：125-128.LI Y W,ZHANG L,DING X B,et al.Progress on porcine pseudorabies vaccine[J].Progress in Veterinary Medicine,2024,45(3):125-128.(in Chinese)
[9] 康笃利.2015—2017年国内部分地区猪伪狂犬病流行病学调查及猪伪狂犬疫苗免疫增强的研究[D].广州：华南农业大学，2018.KANG D L.Epidemiological investigation of Pseudorabies virus in parts of China from 2015 to 2017 and study on PRV immune enhancement[D].Guangzhou：South China Agricultural University,2018.(in Chinese)
[10] 刘运超，杨素珍，尚延丽，等.伪狂犬病病毒研究进展[J].畜牧与兽医,2024,56(2):124-130.LIU Y C,YANG S Z,SHANG Y L,et al.Progress in research on Pseudorabies virus [J].Animal Husbandry & Veterinary Medicine,2024,56(2):124-130.(in Chinese)
[11] 张姗姗，冷雪，时坤，等.猪伪狂犬病流行状况和疫苗应用的研究进展[J].动物医学进展,2018,39(7):81-85.ZHANG S S,LENG X,SHI K,et al.Progress on epidemic situation and vaccine application of porcine pseudorabies[J].Progress in Veterinary Medicine,2018,39(7):81-85.(in Chinese)
[12] LIU Q,KUANG Y,LI Y,et al.The epidemiology and variation in Pseudorabies virus:A continuing challenge to pigs and humans[J].Viruses,2022,14(7):1463.
[13] DENZIN N,CONRATHS FJ,METTENLEITRE T C,et al.Monitoring of pseudorabies in wild boar of Germany—A spatiotemporal analysis[J].Pathogens,2020,9(4):276.
[14] MEIER R K,RUIZ-FONS F,RYSER-DEGIORGIS M P.A picture of trends in Aujeszky’s disease virus exposure in wild boar in the Swiss and European contexts[J].BMC Veterinary Research,2015，11:277.
[15] PEDERSEN K,BEVINS S N,BAROCH J A,et al.Pseudorabies in feral swine in the United States,2009-2012[J].Journal of Wildlife Diseases,2013，49(3):709-713.
[16] SHARP P M,STENICO M,PEDEN J F,et al.Codon usage:Mutational bias,translational selection,or both?[J].Biochemical Society Transactions,1993,21(4):835-841.
[17] CHEN H,SUN S,NORENBURG J L,et al.Mutation and selection cause codon usage and bias in mitochondrial genomes of ribbon worms (Nemertea)[J].PLoS One,2014,9(1):e85631.
[18] 魏雪玲,田明明,刘奇.人埃博拉病毒密码子偏爱性与聚类分析[J].病毒学报,2020,36(2):246-254.WEI X L,TIAN M M,LIU Q.Codon usage bias and cluster analysis of the human Ebola virus[J].Chinese Journal of Virology,2020,36(2):246-254.(in Chinese)
[19] PATIL S S,INDRABALAN U B,SURESH K P,et al.Analysis of codon usage bias of Classical swine fever virus[J].Veterinary World,2021,14(6):1450-1458.
[20] 朱小甫,吴旭锦.2013—2017年陕西省猪伪狂犬病病毒分子流行病学调查与gE基因序列变异分析[J].动物医学进展,2019,40(2):22-27.ZHU X F,WU X J.Molecular epidemiological investigation and genetic variation analysis of gE gene of PRV in Shaanxi province from 2013 to 2017[J].Progress in Veterinary Medicine,2019,40(2):22-27.(in Chinese)
[21] 古金元，马梓承，彭涛，等.山东省部分地区猪伪狂犬病病毒分离鉴定及其gE基因遗传变异分析[J].中国兽医学报,2019,39(1):21-24.GU J Y,MA Z C,PENG T,et al.Isolation，identification and phylogenetic analysis of gE gene of Pseudorabies virus in parts of Shandong province[J].Chinese Journal of Veterinary Science,2019,39(1):21-24.(in Chinese)
[22] 柴虹.伪狂犬病病毒gE糖蛋白主要抗原区的原核表达及gE抗体间接ELISA检测方法的初步建立[D].扬州：扬州大学，2006.CHAI H.Expression of major epitope domain of Pseudorabies virus glycoprotein E in Escherichia coli and application of the expression product as antigen of develop an indirect ELISA for detection of viral glycoprotein E antibodies[D].Yanghzou：Yangzhou University,2006.(in Chinese)
[23] 张莉，任卫科，路超，等.2015—2020年天津地区猪伪狂犬病病毒gB、gC、gE基因遗传变异分析[J].中国畜牧兽医,2021,48(10):3741-3751.ZHANG L,REN W K,LU C,et al.Genetic variation analysis of gB,gC and gE genes of Porcine pseudorabies virus isolated in Tianjin during 2015-2020[J].China Animal Husbandry & Veterinary Medicine,2021,48(10):3741-3751.(in Chinese)
[24] 冯华，刘运超，李青梅，等.猪圆环病毒2型主要蛋白编码序列的密码子偏性分析[J].动物医学进展,2022,43(5):36-41.FENG H,LIU Y C,LI Q M,et al.Codon usage bias analysis of the main protein coding sequence of Porcine circovirus 2[J].Progress in Veterinary Medicine,2022,43(5):36-41.(in Chinese)
[25] 杜梦雪，张鑫，高洁，等.紫叶苔(Pleurozia purpurea)线粒体基因组密码子偏好性分析[J].河北科技大学学报,2025,46(1):91-99.DU M X,ZHANG X,GAO J,et al.Analysis of codon usage bias in the mitochondrial genome of Pleurozia purpurea[J].Journal of Hebei University of Science and Technology,2025,46(1):91-99.(in Chinese)
[26] 王媛媛，杨美青.蒙古韭叶绿体基因组密码子使用偏好性分析[J].分子植物育种,2021,19(4):1084-1092.WANG Y Y,YANG M Q.Analysis of the codon usage in the chloroplast genome of Allium mongolicum Regel[J].Molecular Plant Breeding,2021,19(4):1084-1092.(in Chinese)
[27] 李健晴，刘奇，王聪，等.马尔堡病毒密码子偏爱性分析[J].中国人兽共患病学报,2024,40(6):520-528.LI J Q,LIU Q,WANG C,et al.Codon usage bias of Marburg virus[J].Chinese Journal of Zoonoses,2024,40(6):520-528.(in Chinese)
[28] 李荣欣，王波，肖素勤，等.野生稻叶绿体基因组组装与密码子偏好性分析及系统发育研究[J].中国水稻科学,1-16[2024-10-17].http://kns.cnki.net/kcms/detail/33.1146.S.20240905.1405.018.html.LI R X,WANG B,XIAO S Q,et al.Assembly，codon usage bias and phylogenetic analysis of the chloroplast genome of Oryza meyrtiana[J].Chinese Journal of Rice Science,1-16[2024-10-17].http://kns.cnki.net/kcms/detail/33.1146.S.20240905.1405.018.html.(in Chinese)
[29] 孙涛.猪伪狂犬病毒变异毒株鉴别诊断PCR方法建立与基因缺失灭活疫苗免疫保护效力研究[D].南京：南京农业大学,2016.SUN T.Establishment of PCR assay for discrimination variant strain of Pseudorabies virus and protection efficacy of inactivated Pseudorabies virus deletion gE/gI genes vaccine[D].Nanjing：Nanjing Agricultural University,2016.(in Chinese)
[30] 刘青芸.伪狂犬病病毒猪源和人源分离毒株的遗传变异分析及生物学特性研究[D].武汉：华中农业大学，2022.LIU Q Y.Genetic variation analysis and biological characteristics of clinical stratins of Pseudorabies virus isolated from pigs and humans[D].Wuhan：Huazhong Agricultural University,2022.(in Chinese)
[31] YE C,ZHANG Q Z,TIAN Z J,et al.Genomic characterization of emergent Pseudorabies virus in China reveals marked sequence divergence:Evidence for the existence of two major genotypes[J].Virology,2015,483:32-43.
[32] 王清龙，王瑞宁，王勋，等.猪伪狂犬病病毒gE蛋白的真核表达及其活性鉴定[J].河南农业科学,2023,52(3):127-134.WANG Q L,WANG R N,WANG X,et al.Eukaryotic expression of Porcine pseudorabies virus gE protein and identification of its activity [J].Journal of Henan Agricultural Sciences,2023,52(3):127-134.(in Chinese)
[33] 敖清莹，曾智勇，徐国，等.猪伪狂犬病毒贵州分离株gE基因的克隆及遗传信息分析[J].山地农业生物学报,2018,37(2):80-84.AO Q Y,ZENG Z Y,XU G,et al.Cloning and genetic analysis of gE gene of Porcine pseudorabies virus isolated from Guizhou province[J].Journal of Mountain Agriculture and Biology,2018,37(2):80-84.(in Chinese)
[34] 孙嵬，张柱亭，董辉，等.基于线粒体COI基因序列的黄胫小车蝗不同地理种群的遗传分化及基因流分析[J].昆虫学报,2013,56(8):907-916.SUN W,ZHANG Z T,DONG H,et al.Analysis of genetic differentiation and gene flow among different geographic populations of Oedaleus infernalis (Orthoptera:Acrididae) based on mtDNA COI gene sequences [J].Acta Entomologicala Sinica,2013,56(8):907-916.(in Chinese)
[35] 丁建华,张海军.Excel在模拟遗传漂变中的应用[J].生物学杂志,2016,33(5):109-111.DING J H,ZHANG H J.Application of Excel in simulating genetic drift[J].Journal of Biology,2016,33(5):109-111.(in Chinese)
[36] 康明,黄宏文.湖北海棠的等位酶变异和遗传多样性研究[J].生物多样性,2002,4:376-385.KANG M,HUANG H W.Allozyme variation and genetic diversity of Malus hupehensis[J].Biodiversity,2002,4:376-385.(in Chinese)
[37] WRIGHT F.The 'effective number of codons’ used in a gene[J].Gene,1990,87(1):23-29.
[38] 王玥宁.非洲猪瘟病毒基因组密码子偏性分析及目的蛋白密码子优化表达[D].扬州：扬州大学，2024.WANG Y N.Analysis of codon bias in African swine fever virus genomes and optimization of codon usage for target protein expression[D].Yangzhou：Yangzhou University,2024.(in Chinese)
[39] CHEN Y,LI X,CHI X,et al.Comprehensive analysis of the codon usage patterns in the envelope glycoprotein E2 gene of the Classical swine fever virus[J].PLoS One,2017,12(9):e183646.
[40] 李亚飞，罗春雨，石哲芳，等.新型冠状病毒Omicron变异株密码子偏爱性及其进化分析[J].中国人兽共患病学报,2022,38(7):559-565.LI Y F,LUO C Y,SHI Z F,et al.Analysis of the codon usage bias and evolution of the SARS-CoV-2 Omicron variant[J].Chinese Journal of Zoonoses,2022,38(7):559-565.(in Chinese)
[41] BUTT A M,NASRULLAH I,QAMAR R,et al.Evolution of codon usage in Zika virus genomes is host and vector specific[J].Emerging Microbes & Infections,2016,5(10):e107-e114.
[42] 石秀凡，黄京飞，梁宠荣，等.人类基因中同义密码子的偏好与密码子-反密码子间的结合强度密切相关吗[J].科学通报,2000,23:2520-2525.SHI X F,HUANG J F,LIANG C R,et al.Is the preference of synonymous codons in human genes closely related to the binding strength between codons and anti-codons[J].Chinese Science Bulletin,2000,23:2520-2525.(in Chinese)
[42] PARVATHY S T,UDAYASURIYAN V,BHADANA V.Codon usage bias[J].Molecular Biology Reports,2022,49(1):539-565.

Genetic Variation and Codon Usage Bias Analysis of Porcine Pseudorabies Virus gE Gene

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	LI Zhishan, ZHOU Zhaoyue, LIU Tianlong, WANG Shuaiyu, JIANG Haiyang. Analysis of the Effects of Platycodon grandiflorum Ultrafine Powder on the Diversity of Intestinal Flora in Mice Based on 16S rRNA Technology [J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(7): 3372-3385.
[2]	WANG Panpan, SHARAMATI·Bodai, BAKHET·Bodai, LI Zhenwei, ORALHAZI·Hazikhan. Analysis of Genetic Structure and Maternal Origin of Seven Kazakh Cattle Populations in Xinjiang Based on D-loop Polymorphism [J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(3): 1166-1179.
[3]	LI Chaojie, MENG Meng, LI Bo, JIN Guang, WANG Kun, CHE Leijie, QIAO Xiaochun, ZHANG Yuanqing, NIU Xiaoyan. Analysis of Genetic Diversity and Genetic Differentiations in 3 Local Cattle Populations of Shanxi Province Using Microsatellite Markers [J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(1): 226-237.
[4]	WANG Xintong, ZHANG Yanli, GONG Ying, LIU Xuexue, JIANG Lin, MA Yuehui, LIU Shuqin, PU Yabin. Construction of Specific Genetic Markers for Tibetan Horses Through Population Structure Analysis of Global Domestic Horses [J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(1): 238-248.
[5]	CAO Ping, LI Ruizhe, CHEN Shengmei, XUE Bin, HAN Shenglan, MEI Sa, DA Sang, CAI Jia, SUN Yonggang, MA Zhijie. Paternal Genetic Molecular Assessment of Four Yak Populations in Golog Tibetan Autonomous Prefecture, Qinghai [J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(9): 3948-3957.
[6]	ZHANG Yan, WEI Zhitong, HU Yehao, ZHANG Huaju, ZHANG Man, FU Tong, LIU Xian, LI Zhigang, QI Xinglei, WANG Eryao, ZHANG Zijing, LIANG Dong, GAO Tengyun. Genetic Diversity and Population Structure Analysis of Jiaxian Red Cattle Based on Whole Genome Sequencing [J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(7): 2933-2942.
[7]	HUANG Xianghui, ZHANG Tianneng, ARZUGUL·Musha, WANG Yutao. Genetic Diversity and Phylogenetic Analysis of Goat Population in Karakoram-Pamir Region [J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(6): 2533-2544.
[8]	LI Xin, LI Wei, LIU Jie, CHENG Jingran, LIU Jinjun, WANG Pengran, HAN Xueliang, REN Erjun, DENG Lufang, ZONG Wenli. Analysis of Codon Usage Bias of MC3R Gene in Nyctereutes procyonoides [J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(4): 1349-1361.
[9]	SHI Haina, WANG Yongjie, LIANG Wanpeng, GENG Zhiguang, LI Shien, XU Zhenfei, LIU Gang, LIU Zhe. Genetic Diversity and Origin Evolution Analysis of Qingyang Donkey Based on mtDNA D-loop Region Sequence [J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(2): 601-613.
[10]	YU Jifeng, XIE Jing, HUANG Yong, XIAO Lu, LIN Yi, CAO Ye, YE Yonggang, WEI Yong, WU Xuejing, LI Jiangling, KANG Runmin. Construction of Codon-optimized RHDV2 Dual VP60 Recombinant Baculovirus and Immunogenicity Analysis of the Expressed Protein [J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(2): 668-677.
[11]	WAN Weican, ZHANG Xu, HUANG Xuan, YAN Haifeng, JIANG Guitao, LI Chuang. Assessment of Conservation Effects of Lingxian White Goose Based on Whole Genome Resequencing [J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(11): 4890-4898.
[12]	DAI Kaiyu, YANG Zhifeng, GUO Yexing. Analysis of Codon Usage Bias of Toll-like Receptor 5 Gene in 15 Species [J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(1): 11-22.
[13]	YUE Yunfeng, HUANG Weiping, LIU Min, JIN Suyu, HUANG Lin, ZHENG Yucai. Genetic Diversity Analysis of Liangshan Black Sheep Population Based on Mitochondrial Cytb Gene [J]. China Animal Husbandry & Veterinary Medicine, 2023, 50(9): 3671-3679.
[14]	LUO Shimin, LI Zhongbo. Genetic Diversity and Genetic Evolution of H and F genes of Canine Distemper Virus in Huaihua District [J]. China Animal Husbandry & Veterinary Medicine, 2023, 50(8): 3248-3257.
[15]	WANG Linqing, ZHAO Li, CHEN Ximeng, WU Shaofeng, HAN Yingying, LIU Fang, JIN Yue, CHEN Hongying. Serological Investigation of Porcine Pseudorabies Virus Infection and Genetic Variation Analysis of gE Gene in Henan Province [J]. China Animal Husbandry & Veterinary Medicine, 2023, 50(8): 3364-3372.