Genomic features of 3 bovine viral diarrhea viruses isolated from newborn claves

doi:10.3969/j.issn.1004-1524.20221234

Acta Agriculturae Zhejiangensis ›› 2023, Vol. 35 ›› Issue (8): 1814-1822.DOI: 10.3969/j.issn.1004-1524.20221234

• Animal Science • Previous Articles Next Articles

Genomic features of 3 bovine viral diarrhea viruses isolated from newborn claves

WANG Mengzhu¹^,²^,³(), YANG Guangmei³, WU Yuhu¹^,²^,³, YANG Xuanye¹^,²^,³, WANG Huihui¹^,²^,³, CAO Xiaoan⁴, LI Yong⁴, MA Zhongren¹^,², MA Xiaoxia¹^,²^,^*()

1. Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
2. Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
3. College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730010, China
4. Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China

Received:2022-08-22 Online:2023-08-25 Published:2023-08-29

Abstract

Abstract:

To study the genetic evolution of Bovine viral diarrhea virus(BVDV)-infected newborn calves in different regions of China, the newborn Holstein calf serum from Shandong, Inner Mongolia and Ningxia provinces preserved in the laboratory was used as the material, and the calf serum was detected by RT-PCR for BVDV RNA, and the positive serum was inoculated into Madin-Darby bovine kidney cells (MDBK). Three isolates were identified as BVDV and named as 21NM-44, 21NX-53 and 21SD-16, respectively. According to the cytopathic ability of the 3 isolates to MDBK cells, 21NM-44 was determined to be a non-cytopathic strain, while 21NX-53 and 21SD-16 could cause cytopathic and were determined to be cytopathic strains. Using specific PCR primers, the whole genome sequences of the 3 viruses were cloned and identified. Based on the whole genome sequences, a phylogenetic tree was established and their genetic evolution relationship was analyzed. The results showed that the 3 wild BVDV isolates from different regions had a high degree of genetic evolution relationship with the BVDV GXNN1 strain (BVDV-1c). This study made a foundation for further research on the evolution of BVDV in China.

Key words: Bovine viral diarrhea virus, newborn calf, whole genome, Madin-Darby bovine kidney cell, cytopathic ability

CLC Number:

S852.653

WANG Mengzhu, YANG Guangmei, WU Yuhu, YANG Xuanye, WANG Huihui, CAO Xiaoan, LI Yong, MA Zhongren, MA Xiaoxia. Genomic features of 3 bovine viral diarrhea viruses isolated from newborn claves[J]. Acta Agriculturae Zhejiangensis, 2023, 35(8): 1814-1822.

Figures/Tables 7

References 30

[1]	SCHARNBÖCK B, ROCH F F, RICHTER V, et al. A meta-analysis of bovine viral diarrhoea virus (BVDV) prevalences in the global cattle population[J]. Scientific Reports, 2018, 8(1): 14420.
[2]	YITAGESU E, JACKSON W, KEBEDE N, et al. Prevalence of bovine abortion, calf mortality, and bovine viral diarrhea virus (BVDV) persistently infected calves among pastoral, peri-urban, and mixed-crop livestock farms in central and Northwest Ethiopia[J]. BMC Veterinary Research, 2021, 17(1): 87.
[3]	史慧君, 袁圆圆, 郭妍婷, 等. 囊泡相关膜蛋白A调控牛病毒性腹泻病毒复制[J]. 微生物学通报, 2022, 49(2): 635-644.
	SHI H J, YUAN Y Y, GUO Y T, et al. Regulation of bovine viral diarrhea virus replication by vesicle-associated membrane protein A[J]. Microbiology China, 2022, 49(2): 635-644. (in Chinese with English abstract)
[4]	VAN ROON A M, MERCAT M, VAN SCHAIK G, et al. Quantification of risk factors for bovine viral diarrhea virus in cattle herds: a systematic search and meta-analysis of observational studies[J]. Journal of Dairy Science, 2020, 103(10): 9446-9463.
[5]	ALOCILLA O A, MONTI G. Bovine Viral Diarrhea Virus within and herd prevalence on pasture-based dairy systems, in southern Chile dairy farms[J]. Preventive Veterinary Medicine, 2022, 198: 105533.
[6]	王怀禹, 刘强, 李彩虹, 等. 南充地区牛病毒性腹泻病的分子流行病学调查及防控措施[J]. 中国动物保健, 2022, 24(3): 107-108.
	WANG H Y, LIU Q, LI C H, et al. Molecular epidemiological investigation and control measures of bovine viral diarrhea in Nanchong area[J]. China Animal Health, 2022, 24(3): 107-108. (in Chinese)
[7]	LAASSRI M, MEE E T, CONNAUGHTON S M, et al. Detection of bovine viral diarrhoea virus nucleic acid, but not infectious virus, in bovine serum used for human vaccine manufacture[J]. Biologicals, 2018, 55: 63-70.
[8]	KOKKONOS K G, FOSSAT N, NIELSEN L, et al. Evolutionary selection of pestivirus variants with altered or no microRNA dependency[J]. Nucleic Acids Research, 2020, 48(10): 5555-5571.
[9]	AL-KUBATI A A G, HUSSEN J, KANDEEL M, et al. Recent advances on the bovine viral diarrhea virus molecular pathogenesis, immune response, and vaccines development[J]. Frontiers in Veterinary Science, 2021, 8: 665128.
[10]	SCHEEL T K H, LUNA J M, LINIGER M, et al. A broad RNA virus survey reveals both miRNA dependence and functional sequestration[J]. Cell Host & Microbe, 2016, 19(3): 409-423.
[11]	周小凯, 马晓霞, 田立, 等. 牛病毒性腹泻病毒分子生物学特性研究进展[J]. 生命的化学, 2017, 37(5): 797-804.
	ZHOU X K, MA X X, TIAN L, et al. Research progress of molecular and biological characteristics of bovine viral diarrhea virus[J]. Chemistry of Life, 2017, 37(5): 797-804. (in Chinese with English abstract)
[12]	马鹏, 李林杰, 常秋燕, 等. BVDV SYBR Green Ⅰ荧光定量PCR方法与RT-PCR方法的建立与应用[J]. 华北农学报, 2017, 32(S1): 49-53.
	MA P, LI L J, CHANG Q Y, et al. The developments of SYBR green Ⅰ real-time PCR and conventional RT-PCR for detection of BVDV[J]. Acta Agriculturae Boreali-Sinica, 2017, 32(S1): 49-53. (in Chinese with English abstract)
[13]	邓宇, 孙春清, 张宏彪, 等. 1株猪源牛病毒性腹泻病毒的分离与鉴定[J]. 畜牧兽医学报, 2012, 43(3): 416-423.
	DENG Y, SUN C Q, ZHANG H B, et al. Isolation and identification of a pig bovine viral diarrhea virus[J]. Chinese Journal of Animal and Veterinary Sciences, 2012, 43(3): 416-423. (in Chinese with English abstract)
[14]	WRIGHT F. The ‘effective number of codons’ used in a gene[J]. Gene, 1990, 87(1): 23-29.
[15]	FUGLSANG A. The ‘effective number of codons’ revisited[J]. Biochemical and Biophysical Research Communications, 2004, 317(3): 957-964.
[16]	巨星, 黄锡霞, 葛建军, 等. 中国荷斯坦奶牛体况评分及其影响因素分析[J]. 中国畜牧杂志, 2019, 55(4): 49-52.
	JU X, HUANG X X, GE J J, et al. Analysis of physical condition score and its influencing factors of Holstein cows in China[J]. Chinese Journal of Animal Science, 2019, 55(4): 49-52. (in Chinese)
[17]	SANJUÁN R, DOMINGO-CALAP P. Mechanisms of viral mutation[J]. Cellular and Molecular Life Sciences: CMLS, 2016, 73(23): 4433-4448.
[18]	DIAO N C, GONG Q L, LI J M, et al. Prevalence of bovine viral diarrhea virus (BVDV) in yaks between 1987 and 2019 in mainland China: a systematic review and meta-analysis[J]. Microbial Pathogenesis, 2020, 144: 104185.
[19]	RAN X H, CHEN X H, MA L L, et al. A systematic review and meta-analysis of the epidemiology of bovine viral diarrhea virus (BVDV) infection in dairy cattle in China[J]. Acta Tropica, 2019, 190: 296-303.
[20]	CHANG L L, QI Y P, LIU D, et al. Molecular detection and genotyping of bovine viral diarrhea virus in Western China[J]. BMC Veterinary Research, 2021, 17(1): 66.
[21]	WANG L N, WU X M, WANG C B, et al. Origin and transmission of bovine viral diarrhea virus type 1 in China revealed by phylodynamic analysis[J]. Research in Veterinary Science, 2020, 128: 162-169.
[22]	HOU P L, ZHAO G M, WANG H M, et al. Prevalence of bovine viral diarrhea virus in dairy cattle herds in Eastern China[J]. Tropical Animal Health and Production, 2019, 51(4): 791-798.
[23]	DENG Y, WANG S L, LIU R X, et al. Genetic diversity of bovine viral diarrhea virus infection in goats in southwestern China[J]. Journal of Veterinary Medicine, 2018, 2018: 1-5.
[24]	DENG M L, CHEN N, GUIDARINI C, et al. Prevalence and genetic diversity of bovine viral diarrhea virus in dairy herds of China[J]. Veterinary Microbiology, 2020, 242: 108565.
[25]	ZHOU Y, REN Y, DAI G, et al. Genetic characterization and clinical characteristics of bovine viral diarrhea viruses in cattle herds of Heilongjiang Province, China[J]. Iranian Journal of Veterinary Research, 2022, 23(1): 69-73.
[26]	MANRUBIA S C. Modelling viral evolution and adaptation: challenges and rewards[J]. Current Opinion in Virology, 2012, 2(5): 531-537.
[27]	GE Z Y, LI X R, CAO X A, et al. Viral adaption of staphylococcal phage: a genome-based analysis of the selective preference based on codon usage Bias[J]. Genomics, 2020, 112(6): 4657-4665.
[28]	ZHOU J H, ZHANG J, CHEN H T, et al. Analysis of synonymous codon usage in foot-and-mouth disease virus[J]. Veterinary Research Communications, 2010, 34(4): 393-404.
[29]	MA X X, MA P, CHANG Q Y, et al. The analyses of relationships among nucleotide, synonymous codon and amino acid usages for E2 gene of bovine viral diarrhea virus[J]. Gene, 2018, 660: 62-67.
[30]	GRENFELL B T, PYBUS O G, GOG J R, et al. Unifying the epidemiological and evolutionary dynamics of pathogens[J]. Science, 2004, 303(5656): 327-332.

引物名称 Primer name	正向引物 Forward primer sequence (5'→3')	反向引物 Reverse primer sequence (5'→3')	产物长度 Product length/bp
BVDV1	TGAATCCCCTTCAGCGAAGGC	CATGTGCCATGTACAGCAGAG	319
BVDV2	CTAAAAATCTCTGCTGTACATG	CTGGTGGCTTGTTCTTGTTGTG	759
BVDV3	GAACAAGCCACCAGAGTCACGC	GTTCTTTAAACAGCACATCAC	596
BVDV4	CGATAGTAGTGGATGGGGTCAAG	TGTTACAAGAAGTGTCATCTAC	2 184
BVDV5	CGTCGAGTCATGCAAGTGGTG	GAAGAAACTGTCCCTGGGCTCG	344
BVDV6	CTTCAGATATAAAAGATGGCTG	GCTGCCACGGTCTCATTTCTTAC	736
BVDV7	GATATCCAGGGTTGTGGCAGC	CTCCTCACTTTTAATAAACTTG	696
BVDV8	CAAGTTTATTAAAAGTGAGGAG	GTCATAGTGGTAGTCTTTTGATC	1 469
BVDV9	CGGATCAAAAGACTACCACTATG	GAAGGAAGGCTTATTTATCAC	1 049
BVDV10	CAGACAGGCAGCAGTTGACTTG	CTTCCTATTATTGAGATCCCAAC	1 572
BVDV11	GCAAGGTTAGTGGGGCAAGCAG	TATCCTTTACCCTTGGTTTCTTC	1 427
BVDV12	GTTACAGCAAGAGTAGACTAC	CTATCTCTAGTTGTTCCCATG	1 761
BVDV13	GATACTAAAAAGAATAAAGTTTC	GCTAAAGTGCTATGTGCGTTG	2 036
BVDV14	CAGAGTCAGTCTACCAATATATG	CAGTTCTGGCCATGATGTTC	1 002
BVDV15	CAACTGGCACAAGGTAACTG	TCTGTAGGCAACTTTCATC	1 351
BVDV16	GAGTCATCCAATACCCTGAAGC	TGAGGTCTTTTCCTAGTCCAAC	1 524
BVDV17	CATTACTAAGGTAATGTACAAC	GTTGATTGTAGTGTTATCTTGAG	1 423
BVDV18	CAGAGGGCCGGTCAACTATAAG	CAGTTTTCCAGGATTGAGCATC	1 586
BVDV19	CACATTAACATAATGGACAAGC	CTTTCAAATCCCCTATTCTTAAG	816
BVDV20	GAGAGGATGAAAGTTGCCTAC	GAGGTCTTTTCCTAGTCCAAC	930

引物名称 Primer name	正向引物 Forward primer sequence (5'→3')	反向引物 Reverse primer sequence (5'→3')	产物长度 Product length/bp
BVDV1	TGAATCCCCTTCAGCGAAGGC	CATGTGCCATGTACAGCAGAG	319
BVDV2	CTAAAAATCTCTGCTGTACATG	CTGGTGGCTTGTTCTTGTTGTG	759
BVDV3	GAACAAGCCACCAGAGTCACGC	GTTCTTTAAACAGCACATCAC	596
BVDV4	CGATAGTAGTGGATGGGGTCAAG	TGTTACAAGAAGTGTCATCTAC	2 184
BVDV5	CGTCGAGTCATGCAAGTGGTG	GAAGAAACTGTCCCTGGGCTCG	344
BVDV6	CTTCAGATATAAAAGATGGCTG	GCTGCCACGGTCTCATTTCTTAC	736
BVDV7	GATATCCAGGGTTGTGGCAGC	CTCCTCACTTTTAATAAACTTG	696
BVDV8	CAAGTTTATTAAAAGTGAGGAG	GTCATAGTGGTAGTCTTTTGATC	1 469
BVDV9	CGGATCAAAAGACTACCACTATG	GAAGGAAGGCTTATTTATCAC	1 049
BVDV10	CAGACAGGCAGCAGTTGACTTG	CTTCCTATTATTGAGATCCCAAC	1 572
BVDV11	GCAAGGTTAGTGGGGCAAGCAG	TATCCTTTACCCTTGGTTTCTTC	1 427
BVDV12	GTTACAGCAAGAGTAGACTAC	CTATCTCTAGTTGTTCCCATG	1 761
BVDV13	GATACTAAAAAGAATAAAGTTTC	GCTAAAGTGCTATGTGCGTTG	2 036
BVDV14	CAGAGTCAGTCTACCAATATATG	CAGTTCTGGCCATGATGTTC	1 002
BVDV15	CAACTGGCACAAGGTAACTG	TCTGTAGGCAACTTTCATC	1 351
BVDV16	GAGTCATCCAATACCCTGAAGC	TGAGGTCTTTTCCTAGTCCAAC	1 524
BVDV17	CATTACTAAGGTAATGTACAAC	GTTGATTGTAGTGTTATCTTGAG	1 423
BVDV18	CAGAGGGCCGGTCAACTATAAG	CAGTTTTCCAGGATTGAGCATC	1 586
BVDV19	CACATTAACATAATGGACAAGC	CTTTCAAATCCCCTATTCTTAAG	816
BVDV20	GAGAGGATGAAAGTTGCCTAC	GAGGTCTTTTCCTAGTCCAAC	930

长度Length/nt	21NM-44	21NX-53	21SD-16
5'UTR	283	282	153
3'UTR	208	315	217
N^pro	504	504	504
Capsid	312	312	312
E^rns	684	684	684
E1	576	576	585
E2	1 122	1 122	1 122
P7	207	207	207
NS2	1 356	1 362	1 362
NS3	2 049	2 049	2 049
NS4A	192	192	192
NS4B	1 050	1 041	1 041
NS5A	1 488	1 488	1 488
NS5B	2 160	2 160	2 160

长度Length/nt	21NM-44	21NX-53	21SD-16
5'UTR	283	282	153
3'UTR	208	315	217
N^pro	504	504	504
Capsid	312	312	312
E^rns	684	684	684
E1	576	576	585
E2	1 122	1 122	1 122
P7	207	207	207
NS2	1 356	1 362	1 362
NS3	2 049	2 049	2 049
NS4A	192	192	192
NS4B	1 050	1 041	1 041
NS5A	1 488	1 488	1 488
NS5B	2 160	2 160	2 160

Genomic features of 3 bovine viral diarrhea viruses isolated from newborn claves

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