Cattle connection: molecular epidemiology of BVDV outbreaks via rapid nanopore whole-genome sequencing of clinical samples

被引:7
作者
King, Jacqueline [1 ]
Pohlmann, Anne [1 ]
Dziadek, Kamila [1 ]
Beer, Martin [1 ]
Wernike, Kerstin [1 ]
机构
[1] Friedrich Loeffler Inst, Inst Diagnost Virol, Sudufer 10, D-17493 Greifswald, Germany
基金
欧盟地平线“2020”;
关键词
BVDV; Tiling PCR; Amplicon sequencing; Nanopore sequencing; Whole-genome sequencing; MinION; BVDV-1; BVDV-2; Cattle; BOVINE-VIRAL-DIARRHEA; NONHOMOLOGOUS RNA RECOMBINATION; PHYLOGENETIC ANALYSIS; GENETIC DIVERSITY; VIRUS BVDV; HOMOLOGOUS RECOMBINATION; PERSISTENT INFECTION; PESTIVIRUS; IDENTIFICATION; ERADICATION;
D O I
10.1186/s12917-021-02945-3
中图分类号
S85 [动物医学(兽医学)];
学科分类号
0906 ;
摘要
Background As a global ruminant pathogen, bovine viral diarrhea virus (BVDV) is responsible for the disease Bovine Viral Diarrhea with a variety of clinical presentations and severe economic losses worldwide. Classified within the Pestivirus genus, the species Pestivirus A and B (syn. BVDV-1, BVDV-2) are genetically differentiated into 21 BVDV-1 and four BVDV-2 subtypes. Commonly, the 5' untranslated region and the N-pro protein are utilized for subtyping. However, the genetic variability of BVDV leads to limitations in former studies analyzing genome fragments in comparison to a full-genome evaluation. Results To enable rapid and accessible whole-genome sequencing of both BVDV-1 and BVDV-2 strains, nanopore sequencing of twelve representative BVDV samples was performed on amplicons derived through a tiling PCR procedure. Covering a multitude of subtypes (1b, 1d, 1f, 2a, 2c), sample matrices (plasma, EDTA blood and ear notch), viral loads (Cq-values 19-32) and species (cattle and sheep), ten of the twelve samples produced whole genomes, with two low titre samples presenting 96 % genome coverage. Conclusions Further phylogenetic analysis of the novel sequences emphasizes the necessity of whole-genome sequencing to identify novel strains and supplement lacking sequence information in public repositories. The proposed amplicon-based sequencing protocol allows rapid, inexpensive and accessible obtainment of complete BVDV genomes.
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页数:10
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