Isolation, identification and analyses for genetic features of one bovine viral diarrhea virus strain from yak

doi:10.3969/j.issn.1004-1524.2022.11.06

Acta Agriculturae Zhejiangensis ›› 2022, Vol. 34 ›› Issue (11): 2368-2378.DOI: 10.3969/j.issn.1004-1524.2022.11.06

• Animal Science • Previous Articles Next Articles

Isolation, identification and analyses for genetic features of one bovine viral diarrhea virus strain from yak

WANG Huihui¹^,²(), FENG Xili¹^,², WANG Mengzhu¹^,², ZHAO Zeyang¹^,², LI Yicong¹^,², PU Feiyang¹^,², MA Peng¹^,², LI Yong³, GONG Zhenli³, MA Zhongren¹, MA Xiaoxia¹^,^*()

1. Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
2. College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730010, China
3. Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China

Received:2021-10-28 Online:2022-11-25 Published:2022-11-29
Contact: MA Xiaoxia

Abstract

Abstract:

In this study, one bovine viral diarrhea virus (BVDV) strain was successfully isolated and termed as GSTZ. By electron microscopy, several 50-60 nm viral particles were observed. GSTZ strain displayed the TCID₅₀ (50% tissue culture infection dose) value of 5.0×10^6.5 mL^-1 as revealed by Karber method. Via reverse transcription-PCR (RT-PCR), the whole open reading frame (ORF) of GSTZ strain was sequenced (whole length of 11 691 nt) and classified into the genotype 1 group at either nucleotide level or synonymous codon usage level. The appearance frequency of A+U was higher than that of G+C in GSTZ ORF, and the synonymous codon usage pattern of GSTZ strain displayed the obvious usage bias in synonymous codons with U/A. It was worth noting that, this strain had a tendency of avoiding the selection of the synonymous codons containing CpG dinucleotides, which strongly suggested that the GSTZ strain might weaken the immune responses from host in order to successfully generate its viral particles. The isolated BVDV strain and the above findings could provide biological materials for the related mechanism study of BVDV, and lay foundations for the analysis of antigen relationship of different genotypes of BVDV and vaccine development.

Key words: bovine viral diarrhoea virus, yak, genotype 1, synonymous codon, cytopathogenic effect

CLC Number:

S852.653

WANG Huihui, FENG Xili, WANG Mengzhu, ZHAO Zeyang, LI Yicong, PU Feiyang, MA Peng, LI Yong, GONG Zhenli, MA Zhongren, MA Xiaoxia. Isolation, identification and analyses for genetic features of one bovine viral diarrhea virus strain from yak[J]. Acta Agriculturae Zhejiangensis, 2022, 34(11): 2368-2378.

Figures/Tables 8

References 38

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引物 Primers	正向引物序列 Forward primer sequences(5'→3')	反向引物序列 Reverse primer sequences(5'→3')	产物长度 Product length/bp
BVDV1	CCACCCACTACAAAGAGCAG	CACCGTAGGTATGTTTCAGATTAG	541
BVDV2	GATAGCAGGACTAAACCACC	CCATGTAGGCTCCTATTGAC	293
BVDV3	AACAGACCCACGCTACTGA	CCTGCCCAACTTCTTCAAAT	728
BVDV4	CGAAAGCCTTACCACCGTCTG	CGCCCTTTAGGAATCTGTAACCAC	578
BVDV5	AACTTTAACATTGTTGGTGGCT	CCCTGGGTGTAGTTCCTCTT	1 283
BVDV6	CATCATACGGATATTTCTGCC	TTCCTCTATTGGGTGCTTTT	221
BVDV7	TTGTAAAGTCCCAAGCAGAA	AGTCCATACCCAGTAGTTCG	954
BVDV8	GCAGCAGTTGATTTGGTAGT	GTTCGGGTTATTGTCAGCAT	1 638
BVDV9	GCGGAAGGGTAGTTGGTAGA	GCAAGTCCTCGGAGATGAGC	1 233
BVDV10	AAAGCAAGTGATGGGTCTGT	ACTGGAGGTGGGTGGTATCT	158
BVDV11	GGAAAGGGAAGAGTGATGGA	AGCCTGGTCAGGTTGGAGAT	1 069
BVDV12	TGGATTAGATGATGGCAGTT	TTTATTTGATGTTTGGTGGG	586
BVDV13	TATCGGAGAAATCCAGAAGT	TGGATTAGATGAGGCAGTT	449

引物 Primers	正向引物序列 Forward primer sequences(5'→3')	反向引物序列 Reverse primer sequences(5'→3')	产物长度 Product length/bp
BVDV1	CCACCCACTACAAAGAGCAG	CACCGTAGGTATGTTTCAGATTAG	541
BVDV2	GATAGCAGGACTAAACCACC	CCATGTAGGCTCCTATTGAC	293
BVDV3	AACAGACCCACGCTACTGA	CCTGCCCAACTTCTTCAAAT	728
BVDV4	CGAAAGCCTTACCACCGTCTG	CGCCCTTTAGGAATCTGTAACCAC	578
BVDV5	AACTTTAACATTGTTGGTGGCT	CCCTGGGTGTAGTTCCTCTT	1 283
BVDV6	CATCATACGGATATTTCTGCC	TTCCTCTATTGGGTGCTTTT	221
BVDV7	TTGTAAAGTCCCAAGCAGAA	AGTCCATACCCAGTAGTTCG	954
BVDV8	GCAGCAGTTGATTTGGTAGT	GTTCGGGTTATTGTCAGCAT	1 638
BVDV9	GCGGAAGGGTAGTTGGTAGA	GCAAGTCCTCGGAGATGAGC	1 233
BVDV10	AAAGCAAGTGATGGGTCTGT	ACTGGAGGTGGGTGGTATCT	158
BVDV11	GGAAAGGGAAGAGTGATGGA	AGCCTGGTCAGGTTGGAGAT	1 069
BVDV12	TGGATTAGATGATGGCAGTT	TTTATTTGATGTTTGGTGGG	586
BVDV13	TATCGGAGAAATCCAGAAGT	TGGATTAGATGAGGCAGTT	449

同义密码子(氨基酸) Synonymous codon (Amino acid)	RSCU	同义密码子(氨基酸) Synonymous codon (Amino acid)	RSCU
UUU(F)	0.98	GCC(A)	1.24
UUC(F)	1.02	GCA(A)	1.52
UUA(L)	0.90	GCG(A)	0.31
UUG(L)	1.34	UAU(Y)	0.92
CUU(L)	0.50	UAC(Y)	1.08
CUC(L)	0.53	CAU(H)	0.72
CUA(L)	1.34	CAC(H)	1.27
CUG(L)	1.39	CAA(Q)	0.97
AUU(I)	0.62	CAG(Q)	1.03
AUC(I)	0.69	AAU(N)	0.86
AUA(I)	1.69	AAC(N)	1.14
GUU(V)	0.59	AAA(K)	0.99
GUC(V)	1.01	AAG(K)	1.01
GUA(V)	0.95	GAU(D)	1.14
GUG(V)	1.45	GAC(D)	0.86
UCU(S)	0.79	GAA(E)	1.06
UCC(S)	0.71	GAG(E)	0.94
UCA(S)	1.74	UGU(C)	1.13
UCG(S)	0.09	UGC(C)	0.87
AGU(S)	1.29	CGU(R)	0.06
AGC(S)	1.38	CGC(R)	0.19
CCU(P)	1.01	CGA(R)	0.19
CCC(P)	0.92	CGG(R)	0.30
CCA(P)	1.66	AGA(R)	2.70
CCG(P)	0.41	AGG(R)	2.56
ACU(T)	0.91	GGU(G)	0.82
ACC(T)	1.04	GGC(G)	0.72
ACA(T)	1.58	GGA(G)	0.95
ACG(T)	0.46	GGG(G)	1.51
GCU(A)	0.93

同义密码子(氨基酸) Synonymous codon (Amino acid)	RSCU	同义密码子(氨基酸) Synonymous codon (Amino acid)	RSCU
UUU(F)	0.98	GCC(A)	1.24
UUC(F)	1.02	GCA(A)	1.52
UUA(L)	0.90	GCG(A)	0.31
UUG(L)	1.34	UAU(Y)	0.92
CUU(L)	0.50	UAC(Y)	1.08
CUC(L)	0.53	CAU(H)	0.72
CUA(L)	1.34	CAC(H)	1.27
CUG(L)	1.39	CAA(Q)	0.97
AUU(I)	0.62	CAG(Q)	1.03
AUC(I)	0.69	AAU(N)	0.86
AUA(I)	1.69	AAC(N)	1.14
GUU(V)	0.59	AAA(K)	0.99
GUC(V)	1.01	AAG(K)	1.01
GUA(V)	0.95	GAU(D)	1.14
GUG(V)	1.45	GAC(D)	0.86
UCU(S)	0.79	GAA(E)	1.06
UCC(S)	0.71	GAG(E)	0.94
UCA(S)	1.74	UGU(C)	1.13
UCG(S)	0.09	UGC(C)	0.87
AGU(S)	1.29	CGU(R)	0.06
AGC(S)	1.38	CGC(R)	0.19
CCU(P)	1.01	CGA(R)	0.19
CCC(P)	0.92	CGG(R)	0.30
CCA(P)	1.66	AGA(R)	2.70
CCG(P)	0.41	AGG(R)	2.56
ACU(T)	0.91	GGU(G)	0.82
ACC(T)	1.04	GGC(G)	0.72
ACA(T)	1.58	GGA(G)	0.95
ACG(T)	0.46	GGG(G)	1.51
GCU(A)	0.93

Isolation, identification and analyses for genetic features of one bovine viral diarrhea virus strain from yak

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