猪细小病毒1~7型全基因组遗传变异

doi:10.3969/j.issn.1004-1524.20231172

浙江农业学报 ›› 2024, Vol. 36 ›› Issue (10): 2193-2203.DOI: 10.3969/j.issn.1004-1524.20231172

猪细小病毒1~7型全基因组遗传变异

华涛¹^,²^,³^,⁴(), 常晨¹^,²^,³^,⁴, 李倩文¹^,²^,³^,⁴, 张道华¹^,²^,³^,⁴, 唐波¹^,²^,³^,⁴^,^*()

1.江苏省农业科学院动物免疫工程研究所,国家兽用生物制品工程技术研究中心,江苏南京 210014
2.兽用生物制品(泰州)国泰技术创新中心,江苏泰州 225300
3.省部共建国家重点实验室培育基地—江苏省食品质量安全重点实验室,江苏南京 210014
4.江苏省动物重要疫病与人兽共患病防控协同创新中心,江苏扬州 225009

收稿日期:2023-10-07 出版日期:2024-10-25 发布日期:2024-10-30
作者简介:华涛(1981—),男,江苏连云港人,博士,副研究员,从事兽医病毒分子生物学与免疫学研究。E-mail:huatao541121@163.com
通讯作者: ^*唐波,E-mail:tangbojaas@sina.com

Genetic variation of complete genomes of porcine parvovirus types 1 through 7

HUA Tao¹^,²^,³^,⁴(), CHANG Chen¹^,²^,³^,⁴, LI Qianwen¹^,²^,³^,⁴, ZHANG Daohua¹^,²^,³^,⁴, TANG Bo¹^,²^,³^,⁴^,^*()

1. National Research Center of Veterinary Bio-Product Engineering and Technology, Institute of Veterinary Immunology & Engineering, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
2. Guotai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou 225300, Jiangsu, China
3. Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing 210014, China
4. Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, Jiangsu, China

Received:2023-10-07 Online:2024-10-25 Published:2024-10-30

摘要/Abstract

摘要：

猪细小病毒1型(porcine parvovirus type 1,PPV1)是母猪繁殖失败的主要病原体,即通常所称的猪细小病毒。2001—2016年,在猪体相继鉴定出了6种新型猪细小病毒,分别被命名为猪细小病毒2~7型(PPV2~PPV7型)。为确定中国江苏地区PPV1~PPV7型感染情况和遗传变异特征,采用PPV1~PPV7型常规PCR检测方法,从江苏地区猪场收集到2株PPV1、2株PPV2,以及PPV3、PPV4、PPV5、PPV6、PPV7各1株阳性组织病料,对这9株阳性组织病料进行全基因组测序,采用生物信息分析软件与GenBank中PPV1~PPV7型参考毒株进行比较,系统分析全基因组和衣壳蛋白2(VP2)的遗传进化分子特征。结果表明,PPV1~PPV7型测序毒株与GenBank中同型毒株全基因组同源性均高于97%,而不同型基因组间同源性均小于60.40%。PPV1~PPV7型测序毒株的VP2氨基酸序列与同型毒株同源性均高于97%,但不同型毒株之间差异巨大,PPV4与PPV5有55%同源性,其他毒株之间同源性更低,仅为9%~17%。毒力分析结果表明,2株PPV1流行株与PPV1强毒株Kresse存在相似的毒力位点,且存在5处特有的突变,可能为高毒力毒株。研究结果有助于更好地了解中国猪群中PPV1~PPV7型分子流行病学并制定科学的防治措施。

关键词: 猪细小病毒, PCR检测, 基因组, 衣壳蛋白2, 遗传变异, 毒力分析

Abstract:

Porcine parvovirus type 1 (PPV1), commonly known as porcine parvovirus is the main pathogen of reproductive disorder of sows. From 2001 to 2016, six new types of porcine parvoviruses have been identified in pigs and designated consecutively as porcine parvovirus type 2 through 7 (PPV2-PPV7). In order to determine the infection status and genetic variation of PPV1-PPV7 in Jiangsu, China, two strains of PPV1, two strains of PPV2, and one strain of PPV3, PPV4, PPV5, PPV6 and PPV7 positive tissue samples were identified and collected by routine PCR assay of PPV1-PPV7 strains. These 9 complete genomes of PPV1-PPV7 were sequenced and compared with the reference strains of PPV1-PPV7 in GenBank. The genetic and evolutionary molecular characteristics of PPV1-PPV7 genomes and viral capsid protein 2 (VP2) were systematically analyzed by using bioinformatics analysis software. The result showed that the homology of complete genomes between PPV1-PPV7 sequencing strains and homotypic strains from GenBank was higher than 97%, while the homology between the genomes of different PPV types was less than 60.40%. The amino acid sequence of VP2 of PPV1-PPV7 sequencing strains was more than 97% homologous to the homotypic strains from GenBank, but the homology of VP2 of different porcine parvovirus types were significantly different. The homology of VP2 amino acid sequences between PPV4 and PPV5 was only 55%, and the homologies between other PPV1-PPV7 types were even lower, ranging from 9% to 17%. In addition, VP2 of two new PPV1 strains were analyzed for virulence. The analysis showed that two PPV1 epidemic strains had similar virulence sites with PPV1 high-virulence strain Kresse, and 5 unique mutations were found in the endemic strains, which might be high-virulence strains. This study contributes to a better understanding of the molecular epidemiology of PPV1-PPV7 in Chinese pigs and the formulation of scientific control measures.

Key words: porcine parvovirus, PCR detection, genome, viral capsid protein 2, genetic variation, virulence analysis

中图分类号:

S858.28

华涛, 常晨, 李倩文, 张道华, 唐波. 猪细小病毒1~7型全基因组遗传变异[J]. 浙江农业学报, 2024, 36(10): 2193-2203.

HUA Tao, CHANG Chen, LI Qianwen, ZHANG Daohua, TANG Bo. Genetic variation of complete genomes of porcine parvovirus types 1 through 7[J]. Acta Agriculturae Zhejiangensis, 2024, 36(10): 2193-2203.

图/表 8

参考文献 29

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病毒 Virus	上游引物序列 Forward primer sequence(5’→3’)	下游引物序列 Reverse primer sequence(5’→3’)	产物长度 Product length/bp
PPV1	GTTAGAATAGGATGCGAGGAA	TGCTTGGTAACCTTTCTTTACC	162
PPV2	GCGTGCTCAAGCTGTACC	CTCACTGCGAGATGAAGG	286
PPV3	GCTGATAGGTTGATGAATAAGGAG	CCGCATACCCATAACAGG	498
PPV4	CTGAGACTGAATTCATCCCTG	CAGAATCATGTATGGTCTGC	590
PPV5	CCGAGTTAAGAACTTTACCG	CCCAAGTCAGGAGTTCG	942
PPV6	GTGATAATGATGTGACTACGGAG	CAGCAGTATGTGCAATAGCA	396
PPV7	GGAAATGGAACATCCAGG	TTATCTTTCGTGGCGTCC	428

病毒 Virus	上游引物序列 Forward primer sequence(5’→3’)	下游引物序列 Reverse primer sequence(5’→3’)	产物长度 Product length/bp
PPV1	GTTAGAATAGGATGCGAGGAA	TGCTTGGTAACCTTTCTTTACC	162
PPV2	GCGTGCTCAAGCTGTACC	CTCACTGCGAGATGAAGG	286
PPV3	GCTGATAGGTTGATGAATAAGGAG	CCGCATACCCATAACAGG	498
PPV4	CTGAGACTGAATTCATCCCTG	CAGAATCATGTATGGTCTGC	590
PPV5	CCGAGTTAAGAACTTTACCG	CCCAAGTCAGGAGTTCG	942
PPV6	GTGATAATGATGTGACTACGGAG	CAGCAGTATGTGCAATAGCA	396
PPV7	GGAAATGGAACATCCAGG	TTATCTTTCGTGGCGTCC	428

病毒 Virus	引物 Primer	位置 Location	序列 Sequence (5’→3’)	产物长度 Product length/bp
PPV1	PPV1-1F	47-73	AGGTGGAGCCTAACACTATAAATACA	1 342
	PPV1-1R	1 374-1 395	ATTGGCTGCATTGTAGCAACCA
	PPV1-2F	1 245-1 273	AGTCTGCCATGCTATAACTTGTGTACTAA	1 462
	PPV1-2R	2 683-2 706	TCATTTCCTGTTGCAGACAATTCA
	PPV1-3F	2 494-2 521	TACATCTCAACAACCAGAGGTAAGAAGA	1 449
	PPV1-3R	3 918-3 942	TTCCCTCCTATTGGATCTGAAGGTA
	PPV1-4F	3 738-3 766	ATGAACCAAATGGTGCTATAAGATTTACA	986
	PPV1-4R	4 694-4 723	CTAAAGACATAAGGTCATATAAGTGTGGTT
PPV2	PPV2-1F	1-22	GCTTTCTAGTCGGACCGGAAGT	1 586
	PPV2-1R	1 567-1 586	AGTGACCTTGAGCATGCGGC
	PPV2-2F	1 375-1 402	AAGGGAAGATGTCTGAGAAGTTTGTAGA	1 729
	PPV2-2R	3 081-3 104	CTATATCCAGGCAGGGTGAGTCCT
	PPV2-3F	2 918-2 936	CAGCCGGCACCTGAAGAGA	1 424
	PPV2-3R	4 324-4 341	CGGAGGTTCAACGTGCCC
	PPV2-4F	4 097-4 122	CTGAGTATTCAGTGGTACAACCCTCC	1 405
	PPV2-4R	5 481-5 501	AGGTGAGTCAGCACTTCCGGA
PPV3	PPV3-1F	1-19	CGGTTCCGGTTGTGACGTC	1 574
	PPV3-1R	1 557-1 574	TGGCAACGGAGCTAGGCC
	PPV3-2F	1 410-1 437	TCAGAGGATTTTATACCTACCTGTGTCA	1 593
	PPV3-2R	2 983-3 002	TCGTGGTGTTTCGCTGCTTC
	PPV3-3F	2 823-2 842	AGCCGATAGCTACGGTGGCA	1 291
	PPV3-3R	4 088-4 113	TCCAGAATTATCTACCCCTGTCATGA
	PPV3-4F	3 902-3 923	TGGGAATTGCTGACCATAGGTC	1 283
	PPV3-4R	5 165-5 184	ACACAATTCCGGTTCCGGTT
PPV4	PPV4-1F	1-29	TGTAAATTTATYTATGCAAAGTAGGAGGA	1 395
	PPV4-1R	1 372-1 395	CGTTTGTTTCATGCTCCAAAAGTA
	PPV4-2F	1 189-1 213	AGAATCGCTCAGCAAAAGTTATTGA	1 587
	PPV4-2R	2 748-2 775	TAAACACATATTCTGGTTCTTGCTGAAT
	PPV4-3F	2 552-2 577	ATGGAGAACAGAAAGCAAACTGAGAT	1 618
	PPV4-3R	4 147-4 169	TTGGATGTCCTGGTCCTTGATCT
	PPV4-4F	4 021-4 042	TGGTGGTCAAGTATCTGTGCCA	1 392
	PPV4-4R	5 383-5 412	CAATAAAGAGGAAGTCTTTTTTTTAACTTC
PPV5	PPV5-1F	62-82	TCAAAGGTCACTTCCGGGTCA	1 289
	PPV5-1R	1 324-1 350	AGAACAAATATTATTGTCCACCAACCA
	PPV5-2F	1 177-1 201	ATTGGAGGTACAATAGGTGAAGCCT	1 612
	PPV5-2R	2 763-2 788	ACTTTCATATATGGAAACGCAGCTTC
	PPV5-3F	2 606-2 629	TTTGCTTGCCAGAATAGCTGATTT	1 545
	PPV5-3R	4 127-4 150	ACTGTGTCACAGCATTGTTTCCCT
	PPV5-4F	3 951-3 979	CATATACCTAGCCTTGTTGTCTGTACTCC	1 557
	PPV5-4R	5 482-5 507	TTATCTTCTCGCTCTAACACGTTGCT
PPV6	PPV6-1F	1-28	GTGCACAAAATAAAAGTGTGATGTTTTC	1 629
	PPV6-1R	1 604-1 629	ACATTCAACCACATCCTCTGTCATCT
	PPV6-2F	1 428-1 453	CCAAACGGGTAAGAGAAACAGTATTT	1 657
	PPV6-2R	3 057-3 084	ATATAGGCTAGCATATAGGGGATCTGCT
	PPV6-3F	2 853-2 876	AGATCGGTGAGAGTGTTTCATGGA	1 587
	PPV6-3R	4 415-4 439	AACAGTATTTATCAGGCCAGGGTGA
	PPV6-4F	4 180-4 201	TCCAGTAGACCCATCTGCCACC	1 645
	PPV6-4R	5 798-5 824	ATATTGATTGATGAAGGTCTGACCAGA
	PPV6-5F	5 624-5 646	CCTGCCTGTTTAGAGTCCCAGAT	765
	PPV6-5R	6 373-6 388	GCTTCGCGGCCCATGC
PPV7	PPV7-1F	1-22	GGAACGACAAGGACGACACTTC	1 619
	PPV7-1R	1 602-1 619	CGCGCACTCCGGACTGAT
	PPV7-2F	1 393-1 414	ACAACTTCGACGCGACCATGTA	1 557
	PPV7-2R	2 925-2 949	AGACCTTCTTTGTAGGCCACGTACC
	PPV7-3F	2 764-2 785	CACCACCGTCTTCAATCCCATA	1 236
	PPV7-3R	3976-3999	TGGCGTTGAGAAGACACTGGTTTA

病毒 Virus	引物 Primer	位置 Location	序列 Sequence (5’→3’)	产物长度 Product length/bp
PPV1	PPV1-1F	47-73	AGGTGGAGCCTAACACTATAAATACA	1 342
	PPV1-1R	1 374-1 395	ATTGGCTGCATTGTAGCAACCA
	PPV1-2F	1 245-1 273	AGTCTGCCATGCTATAACTTGTGTACTAA	1 462
	PPV1-2R	2 683-2 706	TCATTTCCTGTTGCAGACAATTCA
	PPV1-3F	2 494-2 521	TACATCTCAACAACCAGAGGTAAGAAGA	1 449
	PPV1-3R	3 918-3 942	TTCCCTCCTATTGGATCTGAAGGTA
	PPV1-4F	3 738-3 766	ATGAACCAAATGGTGCTATAAGATTTACA	986
	PPV1-4R	4 694-4 723	CTAAAGACATAAGGTCATATAAGTGTGGTT
PPV2	PPV2-1F	1-22	GCTTTCTAGTCGGACCGGAAGT	1 586
	PPV2-1R	1 567-1 586	AGTGACCTTGAGCATGCGGC
	PPV2-2F	1 375-1 402	AAGGGAAGATGTCTGAGAAGTTTGTAGA	1 729
	PPV2-2R	3 081-3 104	CTATATCCAGGCAGGGTGAGTCCT
	PPV2-3F	2 918-2 936	CAGCCGGCACCTGAAGAGA	1 424
	PPV2-3R	4 324-4 341	CGGAGGTTCAACGTGCCC
	PPV2-4F	4 097-4 122	CTGAGTATTCAGTGGTACAACCCTCC	1 405
	PPV2-4R	5 481-5 501	AGGTGAGTCAGCACTTCCGGA
PPV3	PPV3-1F	1-19	CGGTTCCGGTTGTGACGTC	1 574
	PPV3-1R	1 557-1 574	TGGCAACGGAGCTAGGCC
	PPV3-2F	1 410-1 437	TCAGAGGATTTTATACCTACCTGTGTCA	1 593
	PPV3-2R	2 983-3 002	TCGTGGTGTTTCGCTGCTTC
	PPV3-3F	2 823-2 842	AGCCGATAGCTACGGTGGCA	1 291
	PPV3-3R	4 088-4 113	TCCAGAATTATCTACCCCTGTCATGA
	PPV3-4F	3 902-3 923	TGGGAATTGCTGACCATAGGTC	1 283
	PPV3-4R	5 165-5 184	ACACAATTCCGGTTCCGGTT
PPV4	PPV4-1F	1-29	TGTAAATTTATYTATGCAAAGTAGGAGGA	1 395
	PPV4-1R	1 372-1 395	CGTTTGTTTCATGCTCCAAAAGTA
	PPV4-2F	1 189-1 213	AGAATCGCTCAGCAAAAGTTATTGA	1 587
	PPV4-2R	2 748-2 775	TAAACACATATTCTGGTTCTTGCTGAAT
	PPV4-3F	2 552-2 577	ATGGAGAACAGAAAGCAAACTGAGAT	1 618
	PPV4-3R	4 147-4 169	TTGGATGTCCTGGTCCTTGATCT
	PPV4-4F	4 021-4 042	TGGTGGTCAAGTATCTGTGCCA	1 392
	PPV4-4R	5 383-5 412	CAATAAAGAGGAAGTCTTTTTTTTAACTTC
PPV5	PPV5-1F	62-82	TCAAAGGTCACTTCCGGGTCA	1 289
	PPV5-1R	1 324-1 350	AGAACAAATATTATTGTCCACCAACCA
	PPV5-2F	1 177-1 201	ATTGGAGGTACAATAGGTGAAGCCT	1 612
	PPV5-2R	2 763-2 788	ACTTTCATATATGGAAACGCAGCTTC
	PPV5-3F	2 606-2 629	TTTGCTTGCCAGAATAGCTGATTT	1 545
	PPV5-3R	4 127-4 150	ACTGTGTCACAGCATTGTTTCCCT
	PPV5-4F	3 951-3 979	CATATACCTAGCCTTGTTGTCTGTACTCC	1 557
	PPV5-4R	5 482-5 507	TTATCTTCTCGCTCTAACACGTTGCT
PPV6	PPV6-1F	1-28	GTGCACAAAATAAAAGTGTGATGTTTTC	1 629
	PPV6-1R	1 604-1 629	ACATTCAACCACATCCTCTGTCATCT
	PPV6-2F	1 428-1 453	CCAAACGGGTAAGAGAAACAGTATTT	1 657
	PPV6-2R	3 057-3 084	ATATAGGCTAGCATATAGGGGATCTGCT
	PPV6-3F	2 853-2 876	AGATCGGTGAGAGTGTTTCATGGA	1 587
	PPV6-3R	4 415-4 439	AACAGTATTTATCAGGCCAGGGTGA
	PPV6-4F	4 180-4 201	TCCAGTAGACCCATCTGCCACC	1 645
	PPV6-4R	5 798-5 824	ATATTGATTGATGAAGGTCTGACCAGA
	PPV6-5F	5 624-5 646	CCTGCCTGTTTAGAGTCCCAGAT	765
	PPV6-5R	6 373-6 388	GCTTCGCGGCCCATGC
PPV7	PPV7-1F	1-22	GGAACGACAAGGACGACACTTC	1 619
	PPV7-1R	1 602-1 619	CGCGCACTCCGGACTGAT
	PPV7-2F	1 393-1 414	ACAACTTCGACGCGACCATGTA	1 557
	PPV7-2R	2 925-2 949	AGACCTTCTTTGTAGGCCACGTACC
	PPV7-3F	2 764-2 785	CACCACCGTCTTCAATCCCATA	1 236
	PPV7-3R	3976-3999	TGGCGTTGAGAAGACACTGGTTTA

编号 No.	病毒类型 PPV type	毒株 Strain	地域 Region	收集时间 Collection time	GenBank查询号 GenBank No.	症状 Symptom
1	PPV1	CN-JSYZ201909-1	江苏扬州 Yangzhou, Jiangsu	2019年9月 September 2019	OR046035	腹泻、肠道炎症、皮疹 Diarrhea, intestinal inflammation, rash
2	PPV1	CN-JSZJ202104-1	江苏镇江 Zhenjiang, Jiangsu	2021年4月 April 2021	OR046036	呼吸症状、肺炎 Respiratory symptoms, pneumonia
3	PPV2	CN-JSCZ202011-1	江苏常州 Changzhou, Jiangsu	2020年11月 November 2020	OR046028	健康 Health
4	PPV2	CN-JSYZ201909-2	江苏扬州 Yangzhou, Jiangsu	2019年9月 September 2019	OR046029	腹泻、肠道炎症、皮疹 Diarrhea, intestinal inflammation, rash
5	PPV3	CN-JSZJ202104-2	江苏镇江 Zhenjiang, Jiangsu	2021年4月 April 2021	OR046030	呼吸症状、肺炎 Respiratory symptoms, pneumonia
6	PPV4	CN-JSXZ201804-1	江苏徐州 Xuzhou, Jiangsu	2018年4月 April 2018	OR046031	健康 Health
7	PPV5	CN-JSYZ201610-1	江苏盐城 Yancheng, Jiangsu	2016年10月 October 2016	OR046032	皮炎 Dermatitis
8	PPV6	CN-JSYZ201605-1	江苏盐城 Yancheng, Jiangsu	2016年5月 May 2016	OR046033	发热、肺炎 Fever, pneumonia
9	PPV7	CN-JSCZ201710-1	江苏常州 Changzhou, Jiangsu	2017年10月 October 2017	OR046034	健康 Health

猪细小病毒1~7型全基因组遗传变异

Genetic variation of complete genomes of porcine parvovirus types 1 through 7

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PPV1毒株 PPV1 strain	GenBank查询号 GenBank NO.	氨基酸位点Amino acid site
PPV1毒株 PPV1 strain	GenBank查询号 GenBank NO.	45	215	233	304	320	366	378	383	407	436	565
Kresse	AAC40231	S	T	S	P	I	D	G	Q	K	P	K
CN-JSZJ202104-1	OR0460356	S	T	T	T	T	N	G	Q	N	P	K
CN-JSYZ201909-1	OR046035	S	T	T	P	I	D	G	Q	K	P	K
NADL2	AAA46921	T	I	S	P	I	D	D	H	K	S	R

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