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

doi:10.3969/j.issn.1004-1524.20231172

Acta Agriculturae Zhejiangensis ›› 2024, Vol. 36 ›› Issue (10): 2193-2203.DOI: 10.3969/j.issn.1004-1524.20231172

• Animal Science • Previous Articles Next Articles

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

Abstract

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

CLC Number:

S858.28

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.

Figures/Tables 8

References 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

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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