Characterization and analysis of the complete genome sequence of two strains of bovine enterovirus in Henan Province of China

doi:10.3969/j.issn.1004-1524.20240356

Acta Agriculturae Zhejiangensis ›› 2025, Vol. 37 ›› Issue (3): 548-558.DOI: 10.3969/j.issn.1004-1524.20240356

• Animal Science • Previous Articles Next Articles

Characterization and analysis of the complete genome sequence of two strains of bovine enterovirus in Henan Province of China

QIAN Mingzhu¹^,²(), WANG Shenfeng¹, CHANG Xiaoran², HU Junying², ZHU Hongbiao³, WANG Xinping²^,^*()

1. Henan Vocational College of Agriculture, Zhengzhou 451450, China
2. College of Veterinary Medicine, Jilin University, Changchun 130012, China
3. Henan Jianheng Animal Pharmaceutical Co., Ltd., Zhengzhou 451476, China

Received:2024-04-25 Online:2025-03-25 Published:2025-04-02

Abstract

Abstract:

This study aimed to investigate the molecular and genetic characteristics of bovine enteroviruses (BEV) and further explore their features and molecular epidemiology. Five pairs of specific primers were designed to amplify and sequence the full-length genomes of the BEVHeN-B78 (EV-E) and HeN-YR91 (EV-F) strains using PCR. After sequencing, the full genomes were assembled, proofread, and analyzed for homology. The results showed that BEVHeN-B78 genome was 7 453 nt long, with a coding region of 6 523 nt, a 5' untranslated region (UTR) of 812 nt, and a 3'UTR of 118 nt. The HeN-YR91 genome was 7 460 nt, with a coding region of 6 502 nt, a 5'UTR of 825 nt, and a 3'UTR of 133 nt. Homology analysis showed that the HeN-B78 strain shared 75.9% to 88.0% similarity with species E, while HeN-YR91 shared 74.6% to 82.4% similarity with species F. Phylogenetic analysis of the whole genome and the VP1-VP4, 2B, 2C, and 3A-3D gene regions, confirmed that the HeN-B78 strain clustered with EV-E and the HeN-YR91 strain with EV-F. In conclusion, this study confirms the presence of bovine enterovirus species E and F in cattle farms in Henan Province, contributing valuable data to GenBank database of BEV in China.

Key words: Henan Province, bovine enterovirus, whole genome sequence, characterization and analysis

CLC Number:

S852.65

QIAN Mingzhu, WANG Shenfeng, CHANG Xiaoran, HU Junying, ZHU Hongbiao, WANG Xinping. Characterization and analysis of the complete genome sequence of two strains of bovine enterovirus in Henan Province of China[J]. Acta Agriculturae Zhejiangensis, 2025, 37(3): 548-558.

Figures/Tables 9

References 24

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片段 Fragment		引物序列 Primer sequences(5'-3')
F1	S	TTTAAAACAGCCTGGGGGTT
	AS	TGGGATTAGCAGCATTCACG
F2	S	ATGGGCGGTCAGTTCAGCAG
	AS	GTACGAGGTGAGGCTAGCCCTGT
F3	S	GGGCCTTTTGGACAACAACAAGG
	AS	TTGAACGAGACCTCGAGATCT
F4	S	GGCCCCGTAACCTACAAAGGTA
	AS	GAATCGAATACATACCATTCGAC
3'	S	TTGTGCGCGATCAGCGCTACC

片段 Fragment		引物序列 Primer sequences(5'-3')
F1	S	TTTAAAACAGCCTGGGGGTT
	AS	TGGGATTAGCAGCATTCACG
F2	S	ATGGGCGGTCAGTTCAGCAG
	AS	GTACGAGGTGAGGCTAGCCCTGT
F3	S	GGGCCTTTTGGACAACAACAAGG
	AS	TTGAACGAGACCTCGAGATCT
F4	S	GGCCCCGTAACCTACAAAGGTA
	AS	GAATCGAATACATACCATTCGAC
3'	S	TTGTGCGCGATCAGCGCTACC

片段 Fragment		引物序列 Primer sequences(5'-3')
F1	S	TTTTAAAACCAGCCTGGGGGTT
	AS	TACGCGTTACGACGTAGCAAC
F2	S	ATGGGTGCGCAAGTAAGCAA
	AS	CTGGAGGGCTGCGGTCTGAGTCA
F3	S	GGGGATGTTAAGGACTCAATC
	AS	TTGCAGTCCAGCAAAGAGCTTG
F4	S	GGACCCTACTCAGGGATCCACAC
	AS	GAAGGAGTCGTACCAGGAGCG
3'	S	GCAAAACTGCTCGCGGACGC

片段 Fragment		引物序列 Primer sequences(5'-3')
F1	S	TTTTAAAACCAGCCTGGGGGTT
	AS	TACGCGTTACGACGTAGCAAC
F2	S	ATGGGTGCGCAAGTAAGCAA
	AS	CTGGAGGGCTGCGGTCTGAGTCA
F3	S	GGGGATGTTAAGGACTCAATC
	AS	TTGCAGTCCAGCAAAGAGCTTG
F4	S	GGACCCTACTCAGGGATCCACAC
	AS	GAAGGAGTCGTACCAGGAGCG
3'	S	GCAAAACTGCTCGCGGACGC

序号 Numbers	毒株名称 Strains	GenBank登录号 GenBank accession number	年份 Year	来源国家 Country
1	K2577	AF123432	1999	澳大利亚Australia
2	SL305	AF123433	1999	澳大利亚Australia
3	VG-5-27	NC_001859	2000	美国USA
4	JL-DH13	MN598020	2012	中国China
5	HeN-A2	MN598008	2018	中国China
6	HeN-A3	MN598009	2018	中国China
7	HeN-A12	MN598010	2018	中国China
8	HeN-B81	MN598014	2018	中国China
9	HeN-B83	MN598015	2018	中国China
10	HeN-B84	MN598016	2018	中国China
11	HeN-C4	MN598017	2018	中国China
12	JL-40	MN598019	2018	中国China
13	JL-JY42	MN598032	2018	中国China
14	NX-b-DR47	MN598037	2018	中国China
15	NX-FY40	MN598039	2018	中国China
16	E1_NSWL13	OP020153	2022	澳大利亚Australia
17	SD-S67	MK639928.1	2018	中国China
18	W17_02174-75	MW959114.1	2017	新西兰New Zealand
19	W17_02174-23	MW959113.1	2017	新西兰New Zealand
20	W17_00094-318	MW959112.1	2017	新西兰New Zealand
21	W16_00634-15	MW959109.1	2016	新西兰New Zealand
22	W16_00544-Red6	MW959108.1	2016	新西兰New Zealand
23	W16_00544-CVGW336	MW959107.1	2016	新西兰New Zealand
24	W16_00059-139	MW959105.1	2015	新西兰New Zealand
25	W16_00059-89	MW959104.1	2015	新西兰New Zealand
26	HeN-B62	MN598011.1	2018	中国China
27	NGR_2018	MN650196.1	2018	尼日利亚Nigeria
28	IL-alpaca	KC748420.1	2007	美国USA
29	IS2-Bos_taurus-JPN-1990	LC150010.1	1990	日本Japan
30	Ho12-Bos_taurus-JPN-2014	LC150008.1	2014	日本Japan
31	BEV-261	NC_021220.1	1958	美国USA
32	W1	AY462106.1	2002	新西兰New Zealand
33	BJ001	HQ663846.1	2009	中国China
34	BJ50	HQ917061.1	2008	中国China
35	BHM26	HQ917060.1	2008	中国China
36	3A	AY508697.1	2004	美国USA
37	PS87	AY508696.1	1962	美国USA

Characterization and analysis of the complete genome sequence of two strains of bovine enterovirus in Henan Province of China

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功能区 Function regions	HeN-B78			HeN-YR91
功能区 Function regions	位置 Positions	基因大小 Gene size/nt	氨基酸数量 Amino acid number	位置 Positions	基因大小 Gene size/nt	氨基酸数量 Amino acid number
5'UTR	1~812	812	—	1~825	825	—
VP4	813~1 025	213	71	826~1 032	207	69
VP2	1 026~1 763	738	246	1 033~1 770	738	246
VP3	1 764~2 489	726	242	1 771~2 499	729	243
VP1	2 490~3 329	840	280	2 500~3 324	825	275
2A	3 330~3779	450	150	3 325~3 774	450	150
2B	3 780~4 076	297	99	3 775~4 071	297	99
2C	4 077~5 066	990	330	4 072~5 058	987	329
3A	5 067~5 333	267	89	5 059~5 325	267	89
3B	5 334~5 402	69	23	5 326~5 394	69	23
3C	5 403~5 951	549	183	5 395~5 943	549	183
3D	5 952~7 334	1 383	461	5 944~7 326	1 383	461
P1	813~3 329	2 517	839	826~3 324	2 499	833
P2	3 330~5 066	1 737	579	3 325~5 058	1 734	578
P3	5 067~7 334	2 268	756	5 059~7 326	2 268	756
3'UTR	7 335~7 453	118		7 327~7 460	133

基因名称 Function regions	比对类型 Comparison type	HeN-B78		HeN-YR91
基因名称 Function regions	比对类型 Comparison type	同E种参考毒株 Reference strains of EV-E	同F种参考毒株 Reference strains of EV-F	同E种参考毒株 Reference strains of EV-E	同F种参考毒株 Reference strains of EV-F
Genome	核苷酸Nucleotide	75.9~88.0	67.1~68.1	67.2~68.5	74.6~82.4
	氨基酸Amino acid	—	—	—	—
VP1	核苷酸Nucleotide	71.3~77.7	51.9~56.9	54.1~58.2	61.5~80.7
	氨基酸Amino acid	76.4~97.5	54.6~58.3	54.0~57.0	67.2~90.2
VP2	核苷酸Nucleotide	74.7~79.7	65.0~67.6	65.3~68.8	71.0~81.2
	氨基酸Amino acid	93.0~98.8	74.6~77.5	76.6~78.9	84.6~97.2
VP3	核苷酸Nucleotide	74.5~78.7	59.0~64.6	60.7~63.4	70.2~83.0
	氨基酸Amino acid	89.3~95.5	62.0~66.1	61.2~64.0	78.2~90.5
VP4	核苷酸Nucleotide	69.6~81.2	67.1~72.5	66.7~71.0	78.3~86.0
	氨基酸Amino acid	87.0~92.8	76.8~79.7	71.0~79.7	94.2~100.0
2A	核苷酸Nucleotide	72.0~95.1	66.9~72.0	65.3~70.4	66.9~72.0
	氨基酸Amino acid	84.7~99.3	74.0~79.3	72.7~79.3	78.7~98.0
2B	核苷酸Nucleotide	73.4~96.0	59.6~66.0	63.6~67.0	71.0~83.8
	氨基酸Amino acid	90.9~99.0	67.7~72.7	68.7~72.7	84.8~100.0
2C	核苷酸Nucleotide	77.1~83.8	67.7~71.5	67.0~71.6	78.0~86.2
	氨基酸Amino acid	95.2~99.4	78.4~80.2	78.1~79.3	93.6~99.4
3A	核苷酸Nucleotide	74.9~80.5	61.0~67.0	58.4~64.8	74.5~82.8
	氨基酸Amino acid	85.4~98.9	64.0~69.7	66.3~69.7	89.95~97.8
3B	核苷酸Nucleotide	72.5~85.5	60.9~73.9	59.4~68.1	75.4~85.5
	氨基酸Amino acid	91.3~100.0	69.6~78.3	69.6~78.3	91.3~100.0
3C	核苷酸Nucleotide	73.4~83.8	64.1~68.9	65.4~69.6	72.9~82.9
	氨基酸Amino acid	89.6~97.3	72.1~74.9	72.1~74.3	85.8~97.8
3D	核苷酸Nucleotide	78.6~86.9	70.9~73.3	70.7~73.7	79.2~86.2
	氨基酸Amino acid	92.8~98.5	82.9~84.6	82.9~83.7	93.3~98.3

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