广东及周边省份猪繁殖与呼吸综合征病毒2型谱系8毒株变异规律和传播研究

doi:10.16431/j.cnki.1671-7236.2023.05.027

摘要/Abstract

摘要： 【目的】使用贝叶斯系统动力学方法重建猪繁殖与呼吸综合征病毒2型(Porcine reproductive and respiratory syndrome virus 2,PRRSV-2)谱系8毒株在广东、广西、湖南、江西和福建5个省份间的传播及遗传演化规律,为猪繁殖与呼吸综合征(Porcine reproductive and respiratory syndrome,PRRS)的针对性防控提供参考。【方法】本研究对来自上述5省所有可用的PRRSV-2的ORF5序列进行系统发育分析,选取其中的谱系8毒株,剔除重组序列及可疑序列。将空间数据结合病原体的进化与流行病学特征进行分析,利用BEAST及相关软件计算病毒的共同祖先、核苷酸替代速率及不同地理位置间可能的传播方向和迁移速率等。【结果】系统发育分析显示,南方5省猪群中流行的PRRSV-2被分为4个谱系,其中154株被鉴定为谱系8毒株。在剔除1株重组毒株和3株可疑毒株后,来自上述5省的谱系8毒株ORF5序列具有强烈的时间信号,且最佳拟合模型为GTR＋I＋G。贝叶斯系统动力学分析表明,5省间谱系8毒株具有2.748×10^-3核苷酸替换/位点/年(95% HPD:2.053×10^-3~3.428×10^-3)的核苷酸替代速率,它们的最近共同祖先可能出现在2002年(95% HPD:1998-2005年)。据SPREAD3计算,广西的毒株向广东(Rate=0.876)、湖南(Rate=0.892)、江西(Rate=0.883)、福建(Rate=0.889)传播,以及部分福建毒株向广西(Rate=0.897)传播。【结论】自2005年以来,广东、广西、湖南、江西和福建5省猪群中流行的PRRSV-2具有丰富的遗传多样性,其中谱系8毒株具有较高的核苷酸替代速率,且有效种群大小在2006－2007年和2009－2013年明显上升。同时,广东、广西、湖南、江西和福建5省谱系8毒株的最近共同祖先可追溯至2002年,且以广西作为潜在发源地在该地区持续传播。

关键词: 猪繁殖与呼吸综合征病毒(PRRSV); 分子流行病学; 贝叶斯系统动力学; 系统地理学

Abstract: 【Objective】 Bayesian phylodynamics was used to reconstruct the transmission and genetic evolution of Porcine reproductive and respiratory syndrome virus 2 (PRRSV-2) lineage 8 strains among five provinces:Guangdong,Guangxi,Hunan,Jiangxi and Fujian,providing a reference for targeted prevention and control of PRRS.【Method】 In this study,phylogenetic analysis of ORF5 sequences from all available PRRSV-2 strains from the above five provinces was performed,and lineage 8 strains were selected to eliminate recombinant sequences as well as suspicious sequences.The spatial data were combined with the evolution and epidemiological characteristics of pathogens for analysis,using BEAST and related software to calculate the common ancestor of the virus,nucleotide substitution rate,as well as possible transmission direction and migration rate between different geographical locations.【Result】 Phylogenetic analysis showed that PRRSV-2 circulating in pig herds in five southern provinces was divided into four lineages,of which 154 strains were identified as lineage 8 strains.After removing a recombinant strain and three suspected strains,the ORF5 sequences from the above five provinces had a strong temporal signal,and the best-fit model was GTR＋I＋G.Bayesian phylodynamic analysis showed that lineage 8 strains from five provinces had nucleotide evolutionary rates of 2.748×10^-3/site/year (95% HPD:2.053×10^-3-3.428×10^-3),and their most recent common ancestor might have emerged in 2002 (95% HPD:1998-2005).According to SPREAD3 calculations,Guangxi strains spreaded to Guangdong (Rate＝0.876),Hunan (Rate＝0.892),Jiangxi (Rate＝0.883),and Fujian (Rate＝0.889),as well as some Fujian strains spreaded to Guangxi (Rate＝0.897).【Conclusion】 Since 2005,PRRSV-2 circulating in pig herds in Guangdong,Guangxi,Hunan,Jiangxi and Fujian provinces had rich genetic diversity,of which lineage 8 strains had a high nucleotide substitution rate,and the effective population size had increased significantly from 2006 to 2007 and 2009 to 2013.The common ancestor of lineage 8 strains of Guangdong,Guangxi,Hunan,Jiangxi and Fujian provinces might have emerged in 2002,and continued to spread in the region with Guangxi as a potential origin.

Key words: Porcine reproductive and respiratory syndrome virus (PRRSV); molecular epidemiology; Bayesian phylodynamics; phylogeography

中图分类号:

S852.65^＋1

康溥, 任照文, 蔡汝健, 吕宗吉, 黄育浩, 王晓虎. 广东及周边省份猪繁殖与呼吸综合征病毒2型谱系8毒株变异规律和传播研究[J]. 中国畜牧兽医, 2023, 50(5): 2001-2011.

KANG Pu, REN Zhaowen, CAI Rujian, LYU Zongji, HUANG Yuhao, WANG Xiaohu. Variation Regularity and Transmission of PRRSV-2 Lineage 8 Strains in Guangdong and Surrounding Provinces[J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 2001-2011.

参考文献

[1] 陈溥言.兽医传染病学[M].北京:中国农业出版社,2006. CHEN P Y.Veterinary Infectious Diseases[M].Beijing:China Agriculture Press,2006.(in Chinese)
[2] FANG Y,SNIJDER E J J V R.The PRRSV replicase:Exploring the multifunctionality of an intriguing set of nonstructural proteins[J].Virus Research,2010,154(1-2):61-76.
[3] FORSBERG R J M B,EVOLUTION.Divergence time of Porcine reproductive and respiratory syndrome virus subtypes[J].Molecular Biology and Evolution,2005,22(11):2131-2134.
[4] SHI M,LAM T T,HON C C,et al.Phylogeny-based evolutionary,demographical,and geographical dissection of North American type 2 Porcine reproductive and respiratory syndrome viruses[J].Journal of Virology,2010,84(17):8700-8711.
[5] BAO H,LI X.Emergence and spread of NADC34-like PRRSV in China[J].Transboundary and Emerging Diseases,2021,68(6):3005-3008.
[6] 周峰,常洪涛,赵军,等.2012-2013年猪繁殖与呼吸综合征病毒河南流行株的分离鉴定及分子流行病学调查[J].中国兽医学报,2014,34(9):1398-1404. ZHOU F,CHANG H T,ZHAO J,et al.Isolation,identification and molecular epidemiological investigation of henan epidemic strains of Porcine reproductive and respiratory syndrome virus from 2012 to 2013[J].Chinese Journal of Veterinary Science,2014,34(9):1398-1404.(in Chinese)
[7] 王丙雷,王晶,刘媛.2016-2020年华北地区猪繁殖与呼吸综合征病毒分子流行病学调查[J].中国兽医学报,2022,42(1):12-19. WANG B L,WANG J,LIU Y.Molecular epidemiology investigation of Porcine reproductive and respiratory syndrome virus in North China from 2016 to 2020[J].Chinese Journal of Veterinary Medicine,2022,42(1):12-19.(in Chinese)
[8] 覃思楠,宝志鹏,阮文强,等.2016年-2017年四川省部分地区猪繁殖与呼吸综合征病毒的分子流行病学调查[J].动物医学进展,2017,38(12):29-33. QIN S N,BAO Z P,RUAN W Q,et al.Molecular epidemiological investigation of Porcine reproductive and respiratory syndrome virus in some areas of sichuan province from 2016 to 2017[J].Progress in Veterinary Medicine,2017,38(12):29-33.(in Chinese)
[9] SUCHARD M A,WEISS R E,SINSHEIMER J S,et al.Bayesian selection of continuous-time Markov chain evolutionary models[J].Molecular Biology and Evolution,2001,18(6):1001-1013.
[10] LEMEY P,RAMBAUT A,DRUMMOND A J,et al.Bayesian phylogeography finds its roots[J].PLoS Computational Biology,2009,5(9):e1000520.
[11] DUDAS G,CARVALHO L M,BEDFORD T,et al.Virus genomes reveal factors that spread and sustained the Ebola epidemic[J].Nature,2017,544(7650):309-315.
[12] LEMEY P,SUCHARD M,RAMBAUT A.Reconstructing the initial global spread of a human influenza pandemic:A Bayesian spatial-temporal model for the global spread of H1N1pdm[J].PLoS Currents,2009,1:RRN1031.
[13] 王培培.华南地区猪繁殖与呼吸综合征病毒分子流行病学及HY毒株分离鉴定研究[D].郑州:河南农业大学,2016. WANG P P.Molecular epidemiology and isolation and identification of HY strains of Porcine reproductive and respiratory syndrome virus in South China[D].Zhengzhou:Henan Agricultural University,2016.(in Chinese)
[14] 白小磊.华南部分地区PRRSV流行病学调查及Nsp1α和Nsp1β的原核表达[D].广州:华南农业大学,2016. BAI X L.Epidemiological investigation of PRRSV in parts of South China and prokaryotic expression of Nsp1α and Nsp1β[D]. Guangzhou:South China Agricultural University,2016.(in Chinese)
[15] 方奎.华南部分地区PRRSV的分离、遗传进化分析及综合防控措施研究[D].武汉:华中农业大学,2022. FANG K.Isolation,evolutionary analysis and prevention and control measures of PRRSV in some areas of South China[D].Wuhan:Huazhong Agricultural University,2022.(in Chinese)
[16] 赵静,李超,许浒,等.非洲猪瘟暴发前后我国猪繁殖与呼吸综合征病毒的流行变化[J].中国预防兽医学报,2022,44(4):349-356. ZHAO J,LI C,XU H,et al.Epidemic changes of Porcine reproductive and respiratory syndrome virus in China before and after African swine fever outbreak[J].Chinese Journal of Preventive Veterinary Medicine,2022,44(4):349-356.(in Chinese)
[17] HONG S,WEI Y,LIN S,et al.Genetic analysis of Porcine productive and respiratory syndrome virus between 2013 and 2014 in Southern parts of China:Identification of several novel strains with amino acid deletions or insertions in nsp2[J].BMC Veterinary Research,2019,15(1):171.
[18] SUN Y K,HAN X L,WEI Y F,et al.Phylogeography,phylodynamics and the recent outbreak of lineage 3 Porcine reproductive and respiratory syndrome viruses in China[J].Transboundary and Emerging Diseases,2019,66(5):2152-2162.
[19] SHI M,LAM T T Y,HON C C,et al.Molecular epidemiology of PRRSV:A phylogenetic perspective[J].Virus Research,2010,154(1-2):7-17.
[20] GAO J C,XIONG J Y,YE C,et al.Genotypic and geographical distribution of Porcine reproductive and respiratory syndrome viruses in mainland China in 1996-2016[J].Veterinary Microbiology,2017,208:164-172.
[21] DUFFY S,SHACKELTON L A,HOLMES E C.Rates of evolutionary change in viruses:Patterns and determinants[J].Nature Reviews Genetics,2008,9(4):267-276.
[22] CHAIKHUMWANG P,TANTITUVANONT A,TRIPIPAT T,et al.Dynamics and evolution of highly pathogenic Porcine reproductive and respiratory syndrome virus following its introduction into a herd concurrently infected with both types 1 and 2[J].Infection, Genetics and Evolution,2015,30:164-174.
[23] NGUYEN V,KIM H K,MOON H,et al.A Bayesian phylogeographical analysis of type 1 Porcine reproductive and respiratory syndrome virus (PRRSV)[J].Transboundary and Emerging Diseases,2014,61(6):537-545.
[24] NILUBOL D,TRIPIPAT T,HOONSUWAN T,et al.Dynamics and evolution of Porcine reproductive and respiratory syndrome virus (PRRSV) ORF5 following modified live PRRSV vaccination in a PRRSV-infected herd[J].Archives of Virology,2014,159(1):17-27.
[25] NILUBOL D,TRIPIPAT T,HOONSUWAN T,et al.Genetic diversity of the ORF5 gene of Porcine reproductive and respiratory syndrome virus (PRRSV) genotypes Ⅰ and Ⅱ in Thailand[J].Archives of Virology,2013,158(5):943-953.
[26] KIM H K,PARK S J,RHO S M,et al.One year's study of dynamic and evolution of types Ⅰ and Ⅱ PRRSV in a swine farm[J].Veterinary Microbiology,2011,150(3-4):230-238.
[27] GOSSMANN T I,KEIGHTLEY P D,EYRE-WALKER A.The effect of variation in the effective population size on the rate of adaptive molecular evolution in eukaryotes[J].Genome Biology and Evolution,2012,4(5):658-667.
[28] TIAN K,YU X,ZHAO T,et al.Emergence of fatal PRRSV variants:Unparalleled outbreaks of atypical PRRS in China and molecular dissection of the unique hallmark[J].PLoS One,2007,2(6):e526.
[29] 卢景.广西猪繁殖与呼吸综合征的流行病学调查[D].北京:中国农业大学,2005. LU J.Epidemiological investigation of Porcine reproductive and respiratory syndrome in Guangxi[D].Beijing:China Agricultural University,2005.(in Chinese)
[30] ALKHAMIS M A,MOORE B R,PEREZ A M.Phylodynamics of H5N1 highly pathogenic avian influenza in Europe,2005-2010:Potential for molecular surveillance of new outbreaks[J].Viruses,2015,7(6):3310-3328.