Sequence analysis of ORF3 and ORF5 of PRRSV HNHK3-2021 strain isolated in Hainan

doi:10.6048/j.issn.1001-4330.2024.05.028

Xinjiang Agricultural Sciences ›› 2024, Vol. 61 ›› Issue (5): 1292-1300.DOI: 10.6048/j.issn.1001-4330.2024.05.028

• Prataculture·Animal Husbandry Veterinarian • Previous Articles

Sequence analysis of ORF3 and ORF5 of PRRSV HNHK3-2021 strain isolated in Hainan

FAN Yuexuan¹^,²(), MA Jiamei¹^,², HUANG Chunyuan², ZHENG Jiaxin², CHEN Suzhen¹^,², ZHANG Yan², LIU Guangliang¹^,³(), CAO Zongxi¹^,²()

1. College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China
2. Hainan Provincial Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Husbandry and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China
3. Hainan Provincial Academician Innovation Center, Institute of Animal Husbandry and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China

Received:2023-10-12 Online:2024-05-20 Published:2024-07-09
Correspondence author: LIU Guangliang, CAO Zongxi
Supported by:
Technological Innovation Project of Hainan Provincial Scientific Research Institutes(jscx202001);The National Natural Science Foundation of China(32060796);Open Fund of the State Key Laboratory of Pathogenic Biology of Livestock Diseases(SKLVEB2020KFKT021);Hainan Provincial Academy of Agricultural Sciences Research Project at the same level(HAAS2022PT0205);National Key R&D Program of China(2023YFC3404302)

PRRSV HNHK3-2021毒株的ORF5和ORF7序列分析

范悦轩¹^,²(), 马佳镁¹^,², 黄春媛², 郑佳馨², 陈素贞¹^,², 张艳², 刘光亮¹^,³(), 曹宗喜¹^,²()

1.新疆农业大学动物医学学院,乌鲁木齐 830000
2.海南省农业科学院畜牧兽医研究所/海南省热带动物繁育与疫病研究重点实验室,海口 571100
3.海南省农业科学院畜牧兽医研究所海南省院士团队创新中心,海口 571100

通讯作者: 刘光亮,曹宗喜
作者简介:范悦轩(1997-),男,新疆奇台人,硕士研究生,研究方向为家畜传染病学,(E-mial)1245219231@qq.com
基金资助:
海南省省属科研院所技术创新专项(jscx202001);国家自然科学基金项目(32060796);家畜疫病病原生物学国家重点实验室开放基金(SKLVEB2020KFKT021);海南省农业科学院院本级科研项目(HAAS2022PT0205);国家重点研发计划(2023YFC3404302)

Abstract

Abstract:

【Objective】To explore the epidemiological characteristics and genetic variation of PRRSV in Hainan【Methods】Samples were collected from Haikou and surrounding areas.The PRRSV strain HNHK3-2021 was isolated, and the NSP2 genes, as well as the ORF5 and ORF7 gene sequences, were determined.Sequence alignment analysis was conducted using Lasergene 7.1, and genetic evolution analysis was performed using MEGA-X.【Results】The PRRSV HNHK3-2021 strain isolated was found to be of American origin with high nucleotide similarity to EF112447 HEB1, EU109503 GD, and EU624117 XH-GD ORF5 and ORF7 (99.2%~99.3% and 99.5%~100%, respectively).The derived amino acid similarity was 99%~99.5% and 100%.The nucleotide similarities of ORF5 and ORF7 of PRRSV HNHK3-2021 strain and EU864232 SHB, AY262352_HB-2(sh)2002, AY656990 Abst-1, AY032626 CH-1a, EU807840 CH-1R were found to be 87.1% -96.4% and 91.4%-97.3%, respectively.Similarly, the similarity of amino acids was 86.6%-93% and 91.9%-97.6%.The nucleotide similarities of ORF5 and ORF7 of PRRSV HNHK3-2021 strain and JN654459 NADC30, KP860909 FJZ03, MH068878 SD17-38, AY881994 FJ-1 were found to be 85.4%-87.1% and 89%-91.4%.The similarity of amino acids was 86.1%-87.1% and 89.5%-91.9%.【Conclusion】The PRRSV HNHK3-2021 strain and EU624117 XH-GD have the closest genetic distance.

Key words: porcine reproductive and respiratory syndrome; genetic evolution analysis; ORF5; ORF7

摘要：

【目的】研究海南猪繁殖与呼吸综合征病毒PRRSV的流行病学特征和遗传变异规律。【方法】采集海南省海口市及周边地区样品,分离出PRRSV HNHK3-2021 毒株,并测定NSP2基因以及 ORF5 和ORF7基因序列,采用Lasergene 7.1进行序列比对分析,用MEGA-X进行遗传演化分析。【结果】分离出的PRRSV HNHK3-2021株为美洲型毒株,PRRSV HNHK3-2021株和EF112447 HEB1、EU109503 GD、EU624117 XH-GD的ORF5和ORF7的核苷酸相似性较高,分别为99.2%~99.3%和99.5%~100%,推导氨基酸相似性为99%~99.5%和100%;PRRSV HNHK3-2021株和EU864232 SHB、AY262352_HB-2(sh)2002、AY656990 Abst-1、AY032626 CH-1a、EU807840 CH-1R的ORF5和ORF7的核苷酸相似性为87.1%~96.4%和91.4%~97.3%,推导氨基酸的相似性为86.6%~93%和91.9%~97.6%;PRRSV HNHK3-2021株和JN654459 NADC30、KP860909 FJZ03、MH068878 SD17-38、AY881994 FJ-1的ORF5和ORF7的核苷酸相似性为85.4%~87.1%和89%~91.4%。氨基酸的相似性为86.1%~87.1%和89.5%~91.9%。【结论】RRSV HNHK3-2021 毒株和EU624117 XH-GD具有最近的遗传距离。

关键词: 猪繁殖与呼吸综合征, 遗传进化, ORF5, ORF7

CLC Number:

FAN Yuexuan, MA Jiamei, HUANG Chunyuan, ZHENG Jiaxin, CHEN Suzhen, ZHANG Yan, LIU Guangliang, CAO Zongxi. Sequence analysis of ORF3 and ORF5 of PRRSV HNHK3-2021 strain isolated in Hainan[J]. Xinjiang Agricultural Sciences, 2024, 61(5): 1292-1300.

范悦轩, 马佳镁, 黄春媛, 郑佳馨, 陈素贞, 张艳, 刘光亮, 曹宗喜. PRRSV HNHK3-2021毒株的ORF5和ORF7序列分析[J]. 新疆农业科学, 2024, 61(5): 1292-1300.

Figures/Tables 7

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项目 Items	引物名称 Name of primer	引物序列 Primer sequences	扩增长度 Amplification length
NSP2	NSP2-F	5'-TCGGTGCACGTGTACCC-3'	1 968
NSP2	NSP3-R	5'-GGCGGGGAAACTCTCTC-3'	1 968
ORF5	ORF5-F	5'-ATGTTGGGGAAGTGCTTGACCGC-3'	602
ORF5	ORF5-R	5'-CTAGAGACGACCCCATTGTTC-3'	602
ORF7	ORF7-F	5'-GAATTCATGCCAAATAACAACGGC-3'	372
ORF7	ORF7-R	5'-TCTAGATCATGTTGGGGGTGATGC-3'	372

项目 Items	引物名称 Name of primer	引物序列 Primer sequences	扩增长度 Amplification length
NSP2	NSP2-F	5'-TCGGTGCACGTGTACCC-3'	1 968
NSP2	NSP3-R	5'-GGCGGGGAAACTCTCTC-3'	1 968
ORF5	ORF5-F	5'-ATGTTGGGGAAGTGCTTGACCGC-3'	602
ORF5	ORF5-R	5'-CTAGAGACGACCCCATTGTTC-3'	602
ORF7	ORF7-F	5'-GAATTCATGCCAAATAACAACGGC-3'	372
ORF7	ORF7-R	5'-TCTAGATCATGTTGGGGGTGATGC-3'	372

	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21
1		99.2	99.2	99.1	98.7	85.2	99.2	99.6	99.0	95.5	95.8	92.6	93.5	92.6	86.0	86.0	86.3	86.4	85.9	86.5	87.0
2	98.4		100.0	99.9	99.2	85.7	100.0	99.6	99.7	96.2	96.6	93.4	94.3	93.1	86.5	89.4	86.8	86.9	86.2	86.8	87.5
3	98.4	100.0		99.9	99.2	85.7	100.0	99.6	99.7	96.2	96.6	93.4	94.3	93.1	86.5	89.4	86.8	86.9	86.2	86.8	87.5
4	98.4	100.0	100.0		99.1	85.6	99.9	99.5	99.6	96.1	96.5	93.3	94.2	93.0	86.4	89.2	86.6	86.8	86.3	86.6	87.4
5	98.4	100.0	100.0	100.0		85.0	99.2	99.1	99.0	95.8	96.2	92.9	93.8	92.6	85.7	89.4	86.3	86.4	85.7	86.0	86.8
6	84.0	85.2	85.2	85.2	85.2		85.7	85.6	85.7	85.7	86.0	86.8	85.1	86.3	95.6	85.0	95.2	94.6	94.7	94.2	94.2
7	98.4	100.0	100.0	100.0	100.0	85.2		99.6	99.7	96.2	96.6	93.4	94.3	96.1	86.5	89.4	86.8	86.9	86.2	86.8	87.5
8	98.8	99.6	99.6	99.6	99.6	84.8	99.6		99.4	95.8	96.2	93.0	93.9	93.0	86.4	89.5	86.6	86.8	86.3	86.6	87.4
9	97.7	99.2	99.2	99.2	99.2	85.2	99.2	98.8		96.0	96.4	93.1	94.0	92.9	86.5	89.4	86.8	86.9	86.2	87.0	87.5
10	94.6	95.7	95.7	95.7	95.7	85.6	95.7	95.3	94.9		99.1	94.8	95.6	95.1	87.3	90.0	86.9	87.7	86.5	87.5	88.1
11	94.9	96.5	96.5	96.5	96.5	86.0	96.5	96.1	95.7	98.4		95.1	96.2	94.8	87.5	90.3	87.2	87.9	86.7	87.3	88.1
12	91.8	93.4	93.4	93.4	93.4	86.4	93.4	93.0	92.6	93.0	94.2		92.6	95.5	87.7	90.1	87.3	87.0	87.4	87.7	87.4
13	92.2	93.8	93.8	93.8	93.8	82.9	93.8	93.4	93.0	94.6	95.7	90.7		92.6	86.5	88.6	86.5	87.2	85.5	86.0	86.9
14	92.6	93.0	93.0	93.0	93.0	84.0	93.0	93.4	92.2	94.9	94.6	93.0	92.2		87.3	89.9	86.9	86.9	87.1	87.5	87.0
15	85.2	86.4	86.4	86.4	86.4	94.2	86.4	86.0	86.4	88.3	88.7	87.9	86.4	86.4		85.7	96.5	95.6	95.7	95.6	96.0
16	86.8	87.5	87.5	87.5	87.5	83.7	87.5	87.9	87.5	88.3	88.7	89.5	86.8	89.1	86.0		85.3	85.5	85.8	85.6	86.3
17	86.4	87.5	87.5	87.5	87.5	94.2	87.5	87.2	87.5	88.3	88.7	88.7	85.6	87.5	96.1	85.6		94.4	95.2	95.2	95.7
18	86.4	87.5	87.5	87.5	87.5	93.0	87.5	87.2	87.5	89.1	89.5	87.9	86.4	87.2	95.3	86.8	93.4		95.1	94.6	94.6
19	85.9	86.3	86.3	86.3	86.3	93.4	86.3	86.7	86.3	88.3	88.7	88.7	85.5	88.3	96.1	87.9	95.7	94.1		95.1	94.4
20	87.9	88.3	88.3	88.3	88.3	92.6	88.3	87.9	89.1	89.1	88.7	88.3	86.0	87.5	94.6	86.4	95.3	94.2	94.9		94.8
21	85.6	86.8	86.8	86.8	86.8	91.8	86.8	86.4	86.8	88.3	87.9	87.2	84.8	86.4	95.3	87.2	94.6	93.4	94.5	94.6

	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21
1		99.2	99.2	99.1	98.7	85.2	99.2	99.6	99.0	95.5	95.8	92.6	93.5	92.6	86.0	86.0	86.3	86.4	85.9	86.5	87.0
2	98.4		100.0	99.9	99.2	85.7	100.0	99.6	99.7	96.2	96.6	93.4	94.3	93.1	86.5	89.4	86.8	86.9	86.2	86.8	87.5
3	98.4	100.0		99.9	99.2	85.7	100.0	99.6	99.7	96.2	96.6	93.4	94.3	93.1	86.5	89.4	86.8	86.9	86.2	86.8	87.5
4	98.4	100.0	100.0		99.1	85.6	99.9	99.5	99.6	96.1	96.5	93.3	94.2	93.0	86.4	89.2	86.6	86.8	86.3	86.6	87.4
5	98.4	100.0	100.0	100.0		85.0	99.2	99.1	99.0	95.8	96.2	92.9	93.8	92.6	85.7	89.4	86.3	86.4	85.7	86.0	86.8
6	84.0	85.2	85.2	85.2	85.2		85.7	85.6	85.7	85.7	86.0	86.8	85.1	86.3	95.6	85.0	95.2	94.6	94.7	94.2	94.2
7	98.4	100.0	100.0	100.0	100.0	85.2		99.6	99.7	96.2	96.6	93.4	94.3	96.1	86.5	89.4	86.8	86.9	86.2	86.8	87.5
8	98.8	99.6	99.6	99.6	99.6	84.8	99.6		99.4	95.8	96.2	93.0	93.9	93.0	86.4	89.5	86.6	86.8	86.3	86.6	87.4
9	97.7	99.2	99.2	99.2	99.2	85.2	99.2	98.8		96.0	96.4	93.1	94.0	92.9	86.5	89.4	86.8	86.9	86.2	87.0	87.5
10	94.6	95.7	95.7	95.7	95.7	85.6	95.7	95.3	94.9		99.1	94.8	95.6	95.1	87.3	90.0	86.9	87.7	86.5	87.5	88.1
11	94.9	96.5	96.5	96.5	96.5	86.0	96.5	96.1	95.7	98.4		95.1	96.2	94.8	87.5	90.3	87.2	87.9	86.7	87.3	88.1
12	91.8	93.4	93.4	93.4	93.4	86.4	93.4	93.0	92.6	93.0	94.2		92.6	95.5	87.7	90.1	87.3	87.0	87.4	87.7	87.4
13	92.2	93.8	93.8	93.8	93.8	82.9	93.8	93.4	93.0	94.6	95.7	90.7		92.6	86.5	88.6	86.5	87.2	85.5	86.0	86.9
14	92.6	93.0	93.0	93.0	93.0	84.0	93.0	93.4	92.2	94.9	94.6	93.0	92.2		87.3	89.9	86.9	86.9	87.1	87.5	87.0
15	85.2	86.4	86.4	86.4	86.4	94.2	86.4	86.0	86.4	88.3	88.7	87.9	86.4	86.4		85.7	96.5	95.6	95.7	95.6	96.0
16	86.8	87.5	87.5	87.5	87.5	83.7	87.5	87.9	87.5	88.3	88.7	89.5	86.8	89.1	86.0		85.3	85.5	85.8	85.6	86.3
17	86.4	87.5	87.5	87.5	87.5	94.2	87.5	87.2	87.5	88.3	88.7	88.7	85.6	87.5	96.1	85.6		94.4	95.2	95.2	95.7
18	86.4	87.5	87.5	87.5	87.5	93.0	87.5	87.2	87.5	89.1	89.5	87.9	86.4	87.2	95.3	86.8	93.4		95.1	94.6	94.6
19	85.9	86.3	86.3	86.3	86.3	93.4	86.3	86.7	86.3	88.3	88.7	88.7	85.5	88.3	96.1	87.9	95.7	94.1		95.1	94.4
20	87.9	88.3	88.3	88.3	88.3	92.6	88.3	87.9	89.1	89.1	88.7	88.3	86.0	87.5	94.6	86.4	95.3	94.2	94.9		94.8
21	85.6	86.8	86.8	86.8	86.8	91.8	86.8	86.4	86.8	88.3	87.9	87.2	84.8	86.4	95.3	87.2	94.6	93.4	94.5	94.6

	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21
1		99.5	99.5	99.5	99.5	99.5	100.0	98.9	99.7	93.3	96.0	96.0	93.5	93.3	89.2	90.9	88.4	88.4	99.5	90.6	91.9
2	99.5		99.5	99.5	99.5	99.5	99.5	98.9	99.7	93.3	96.0	96.0	93.5	93.3	89.2	90.9	88.4	87.9	99.5	90.6	91.9
3	99.5	99.5		99.5	99.5	99.5	99.5	98.9	99.7	93.3	96.0	96.0	93.5	93.3	89.2	90.9	88.4	87.9	99.5	90.6	91.9
4	99.5	99.5	99.5		99.5	99.5	99.5	98.9	99.7	93.3	96.0	96.0	93.5	93.3	89.8	91.4	89.0	88.4	99.5	91.1	92.5
5	99.5	99.5	99.5	99.5		99.5	99.5	98.9	99.7	93.3	96.0	96.0	93.5	93.3	89.2	90.9	88.4	88.2	100.0	90.6	92.2
6	99.5	99.5	99.5	99.5	99.5		99.5	98.9	99.7	93.3	96.0	96.0	93.5	93.3	89.8	90.9	88.4	88.4	99.5	91.1	91.9
7	100.0	99.5	99.5	99.5	99.5	99.5		98.9	99.7	93.3	96.0	96.0	93.5	93.3	89.2	90.9	88.4	88.4	99.5	90.6	91.9
8	98.9	98.9	98.9	98.9	98.9	98.9	98.9		99.2	93.0	95.7	95.7	93.5	93.0	89.2	90.6	88.4	87.9	98.9	90.6	91.4
9	99.7	99.7	99.7	99.7	99.7	99.7	99.7	99.2		93.5	96.2.	96.2	93.8	93.5	89.5	91.1	88.7	88.2	99.7	90.9	92.2
10	93.3	93.3	93.3	93.3	93.3	93.3	93.3	93.0	93.5		94.1	94.4	93.3	90.9	91.7	92.7	89.8	90.3	93.3	91.4	92.2
11	96.0	96.0	96.0	96.0	96.0	96.0	96	95.7	96.2	94.1		99.5	95.4	96.0	90.6	92.2	89.2	89.8	96.0	91.4	91.1
12	96.0	96.0	96.0	96.0	96.0	96.0	96	95.7	96.2	94.4	99.5		95.4	96.5	90.9	92.2	89.2	90.1	96.0	91.4	91.1
13	93.5	93.5	93.5	93.5	93.5	93.5	93.5	93.5	93.8	93.3	95.4	95.4		92.7	89.8	90.9	89.0	88.7	93.5	90.1	89.5
14	93.3	93.3	93.3	93.3	93.3	93.3	93.3	93.0	93.5	90.9	96.0	96.5	92.7		89.0	90.3	87.9	88.2	93.3	90.1	90.3
15	89.2	89.2	89.2	89.8	89.2	89.8	89.2	89.2	89.5	91.7	90.6	90.9	89.8	89.0		97.8	94.4	90.0	89.2	97.3	90.9
16	90.9	90.9	90.9	91.4	90.9	90.9	90.9	90.6	91.1	92.7	92.2	92.2	90.9	90.5	97.4		95.4	96.5	90.9	97.8	92.5
17	88.4	88.4	88.4	89.0	88.4	88.4	88.4	88.4	88.7	89.8	89.2	89.2	89.0	87.9	94.4	95.4		94.6	88.4	94.9	88.4
18	88.4	87.9	87.9	88.4	88.2	88.4	88.4	87.9	88.2	90.3	89.8	90.1	88.7	88.2	97.0	96.5	94.6		88.2	96.5	90.1
19	99.5	99.5	99.5	99.5	100.0	99.5	99.5	98.9	99.7	93.3	96.0	86.0	93.5	93.3	89.2	90.9	88.4	88.2		90.6	92.2
20	90.6	90.6	90.6	91.1	90.6	91.1	90.6	90.6	90.9	91.4	91.4	91.4	90.1	90.1	97.3	97.8	94.9	96.5	90.6		91.9
21	91.9	91.9	91.9	92.5	92.2	91.9	91.9	91.4	92.2	92.2	91.1	91.1	89.5	90.3	80.9	92.5	88.4	90.1	92.2	91.9

Sequence analysis of ORF3 and ORF5 of PRRSV HNHK3-2021 strain isolated in Hainan

PRRSV HNHK3-2021毒株的ORF5和ORF7序列分析

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[1]	MA Jiamei, ZHONG Zhiwen, FAN Yuexuan, HUANG Chunyuan, ZHENG Jiaxin, CAO Fangfang, WANG Jinquan, LIU Guangliang, CAO Zongxi. ORF5 gene analysis of two porcine reproductive and respiratory syndrome virus strains from hainan province [J]. Xinjiang Agricultural Sciences, 2023, 60(12): 3049-3056.
[2]	WU Peng;ZHANG Xun;LIANG Tian;CHEN Xin-kai;XIAO Yuan-yuan;SHENG Jin-liang. PRRSV ORF7 Cloning and Genetic Evolution Analysis of Pigs in Northern Xinjiang [J]. , 2016, 53(11): 2149-2156.
[3]	LU Gui-li;WANG Ping;CHENG Jin;XIA Jun;Shayilan·Kayizha;Tuerhong·Nuer;WANG Wen. Clone Andand Sequence Analysis of ORF2-7 Genes of Porcine Reproductive and Respiratory Syndrome Virus of Xinjiang Strains [J]. , 2014, 51(3): 546-551.