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

Hagberg, Emma Elisabeth; Krarup, Anders; Fahnøe, Ulrik; Larsen, Lars Erik; Dam-Tuxen, Rebekka; Pedersen, Anders Gorm

doi:10.1016/j.jviromet.2016.03.010

Cited by 8 publications

(2 citation statements)

References 36 publications

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“…The limitation of the interpretation of the partial NS1 data could be avoided in future studies by using next generation sequencing (NGS) of the full genome. This method would allow for trace of the transmission of the virus between farms and to draw more valid conclusion using the full genome sequencing compared to the partial NS1 [28]. Furthermore, NGS would ease the identification of herds infected with more than one strain as previously reported [29].…”

Section: Discussionmentioning

confidence: 99%

Outbreak tracking of Aleutian mink disease virus (AMDV) using partial NS1 gene sequencing

Ryt-Hansen

Hjulsager

Hagberg

et al. 2017

Virol J

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BackgroundAleutian Mink Disease (AMD) is an infectious disease of mink (Neovison vison) and globally a major cause of economic losses in mink farming. The disease is caused by Aleutian Mink Disease Virus (AMDV) that belongs to the genus Amdoparvovirus within the Parvoviridae family. Several strains have been described with varying virulence and the severity of infection also depends on the host’s genotype and immune status. Clinical signs include respiratory distress in kits and unthriftiness and low quality of the pelts. The infection can also be subclinical.Systematic control of AMDV in Danish mink farms was voluntarily initiated in 1976. Over recent decades the disease was mainly restricted to the very northern part of the country (Northern Jutland), with only sporadic outbreaks outside this region. Most of the viruses from this region have remained very closely related at the nucleotide level for decades. However, in 2015, several outbreaks of AMDV occurred at mink farms throughout Denmark, and the sources of these outbreaks were not known.MethodsPartial NS1 gene sequencing, phylogenetic analyses data were utilized along with epidemiological to determine the origin of the outbreaks.ResultsThe phylogenetic analyses of partial NS1 gene sequences revealed that the outbreaks were caused by two different clusters of viruses that were clearly different from the strains found in Northern Jutland. These clusters had restricted geographical distribution, and the variation within the clusters was remarkably low. The outbreaks on Zealand were epidemiologically linked and a close sequence match was found to two virus sequences from Sweden. The other cluster of outbreaks restricted to Jutland and Funen were linked to three feed producers (FP) but secondary transmissions between farms in the same geographical area could not be excluded.ConclusionThis study confirmed that partial NS1 sequencing can be used in outbreak tracking to determine major viral clusters of AMDV. Using this method, two new distinct AMDV clusters with low intra-cluster sequence diversity were identified, and epidemiological data helped to reveal possible ways of viral introduction into the affected herds.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-017-0786-5) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Outbreak tracking of Aleutian mink disease virus (AMDV) using partial NS1 gene sequencing

Ryt-Hansen

Hjulsager

Hagberg

et al. 2017

Virol J

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“…In addition to the issue of limited resolution of the phylogeny, a drawback with different partial sequences is that they sometimes result in different and conflicting tree topologies [ 17 , 19 ]. It has however been shown that by sequencing the entire AMDV genome the phylogenetic resolution is increased to a level where transmission routes between farms can be elucidated [ 24 , 25 ], however the costs associated with the next generation sequencing (NGS) approach are substantial.…”

Section: Discussionmentioning

confidence: 99%

Global phylogenetic analysis of contemporary aleutian mink disease viruses (AMDVs)

Ryt-Hansen

Hagberg

Chriél

et al. 2017

Virol J

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BackgroundAleutian mink disease has major economic consequences on the mink farming industry worldwide, as it causes a disease that affects both the fur quality and the health and welfare of the mink. The virus causing this disease is a single-stranded DNA virus of the genus Amdoparvovirus belonging to the family of Parvoviridae. In Denmark, infection with AMDV has largely been restricted to a region in the northern part of the country since 2001, affecting only 5% of the total Danish mink farms. However, in 2015 outbreaks of AMDV were diagnosed in all parts of the country. Initial analyses revealed that the out breaks were caused by two different strains of AMDV that were significant different from the circulating Danish strains. To track the source of these outbreaks, a major investigation of global AMDV strains was initiated.MethodsSamples from 13 different countries were collected and partial NS1 gene was sequenced and subjected to phylogenetic analyses.ResultsThe analyses revealed that AMDV exhibited substantial genetic diversity. No clear country wise clustering was evident, but exchange of viruses between countries was revealed. One of the Danish outbreaks was caused by a strain of AMDV that closely resembled a strain originating from Sweden. In contrast, we did not identify any potential source for the other and more widespread outbreak strain.ConclusionTo the authors knowledge this is the first major global phylogenetic study of contemporary AMDV partial NS1 sequences. The study proved that partial NS1 sequencing can be used to distinguish virus strains belonging to major clusters. The partial NS1 sequencing can therefore be a helpful tool in combination with epidemiological data, in relation to outbreak tracking. However detailed information on farm to farm transmission requires full genome sequencing.Electronic supplementary materialThe online version of this article (10.1186/s12985-017-0898-y) contains supplementary material, which is available to authorized users.

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A comparative molecular characterization of AMDV strains isolated from cases of clinical and subclinical infection

et al. 2018

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The Aleutian mink disease virus (AMDV) is one of the most serious threats to modern mink breeding. The disease can have various courses, from progressive to subclinical infections. The objective of the study was to provide a comparative molecular characterization of isolates of AMDV from farms with a clinical and subclinical course of the disease. The qPCR analysis showed a difference of two orders of magnitude between the number of copies of the viral DNA on the farm with the clinical course of the disease (10) and the farm with the subclinical course (10). The sequencing results confirm a high level of homogeneity within each farm and variation between them. The phylogenetic analysis indicates that the variants belonging to different farms are closely related and occupy different branches of the same clade. The in silico analysis of the effect of differences in the sequence encoding the VP2 protein between the farms revealed no effect of the polymorphism on its functionality. The close phylogenetic relationship between the isolates from the two farms, the synonymous nature of most of the polymorphisms and the potentially minor effect on the functionality of the protein indicate that the differences in the clinical picture may be due not only to polymorphisms in the nucleotide and amino acid sequences, but also to the stage of infection on the farm and the degree of stabilization of the pathogen-host relationship.

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

Cited by 8 publications

References 36 publications

Outbreak tracking of Aleutian mink disease virus (AMDV) using partial NS1 gene sequencing

Outbreak tracking of Aleutian mink disease virus (AMDV) using partial NS1 gene sequencing

Global phylogenetic analysis of contemporary aleutian mink disease viruses (AMDVs)

A comparative molecular characterization of AMDV strains isolated from cases of clinical and subclinical infection

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