A fast and robust method for whole genome sequencing of the Aleutian Mink Disease Virus (AMDV) genome

TY - JOUR

T1 - A fast and robust method for whole genome sequencing of the Aleutian Mink Disease Virus (AMDV) genome

AU - Hagberg, Emma E

AU - Krarup, Anders

AU - Fahnøe, Ulrik

AU - Larsen, Lars E

AU - Dam-Tuxen, Rebekka

AU - Pedersen, Anders G

N1 - Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

PY - 2016/8/1

Y1 - 2016/8/1

N2 - Aleutian Mink Disease Virus (AMDV) is a frequently encountered pathogen associated with commercial mink breeding. AMDV infection leads to increased mortality and compromised animal health and welfare. Currently little is known about the molecular evolution of the virus, and the few existing studies have focused on limited regions of the viral genome. This paper describes a robust, reliable, and fast protocol for amplification of the full AMDV genome using long-range PCR. The method was used to generate next generation sequencing data for the non-virulent cell-culture adapted AMDV-G strain as well as for the virulent AMDV-Utah strain. Comparisons at nucleotide- and amino acid level showed that, in agreement with existing literature, the highest variability between the two virus strains was found in the left open reading frame, which encodes the non-structural (NS1-3) genes. This paper also reports a number of differences that potentially can be linked to virulence and host range. To the authors' knowledge, this is the first study to apply next generation sequencing on the entire AMDV genome. The results from the study will facilitate the development of new diagnostic tools and can form the basis for more detailed molecular epidemiological analyses of the virus.

AB - Aleutian Mink Disease Virus (AMDV) is a frequently encountered pathogen associated with commercial mink breeding. AMDV infection leads to increased mortality and compromised animal health and welfare. Currently little is known about the molecular evolution of the virus, and the few existing studies have focused on limited regions of the viral genome. This paper describes a robust, reliable, and fast protocol for amplification of the full AMDV genome using long-range PCR. The method was used to generate next generation sequencing data for the non-virulent cell-culture adapted AMDV-G strain as well as for the virulent AMDV-Utah strain. Comparisons at nucleotide- and amino acid level showed that, in agreement with existing literature, the highest variability between the two virus strains was found in the left open reading frame, which encodes the non-structural (NS1-3) genes. This paper also reports a number of differences that potentially can be linked to virulence and host range. To the authors' knowledge, this is the first study to apply next generation sequencing on the entire AMDV genome. The results from the study will facilitate the development of new diagnostic tools and can form the basis for more detailed molecular epidemiological analyses of the virus.

KW - Aleutian Mink Disease Virus/genetics

KW - Animals

KW - DNA, Viral/genetics

KW - Genome, Viral

KW - High-Throughput Nucleotide Sequencing/methods

KW - Phylogeny

KW - Polymerase Chain Reaction

U2 - 10.1016/j.jviromet.2016.03.010

DO - 10.1016/j.jviromet.2016.03.010

M3 - Journal article

C2 - 27060623

SN - 0166-0934

VL - 234

SP - 43

EP - 51

JO - Journal of Virological Methods

JF - Journal of Virological Methods

ER -