Evolutionary analysis of whole-genome sequences confirms inter-farm transmission of Aleutian mink disease virus

Abstract

Aleutian mink disease virus (AMDV) is a frequently encountered pathogen associated with mink farming. Previous phylogenetic analyses of AMDV have been based on shorter and more conserved parts of the genome, e.g. the partial NS1 gene. Such fragments are suitable for detection but are less useful for elucidating transmission pathways while sequencing entire viral genomes provides additional informative sites and often results in better-resolved phylogenies. We explore how whole-genome sequencing can benefit investigations of AMDV transmission by reconstructing the relationships between AMDV field samples from a Danish outbreak. We show that whole-genome phylogenies are much better resolved than those based on the partial NS1 gene sequences extracted from the same alignment. Well-resolved phylogenies contain more information about the underlying transmission trees and are useful for understanding the spread of a pathogen. In the main case investigated here, the transmission path suggested by the tree structure was supported by epidemiological data. The use of molecular clock models further improved tree resolution and provided time estimates for the viral ancestors consistent with the proposed direction of spread. It was however impossible to infer transmission pathways from the partial NS1 gene tree, since all samples from the case farms branched out from a single internal node. A sliding window analysis showed that there were no shorter genomic regions providing the same phylogenetic resolution as the entire genome. Altogether, these results suggest that phylogenetic analyses based on whole-genome sequencing taking into account sampling dates and epidemiological data is a promising set of tools for clarifying AMDV transmission.

Genetic and evolutionary analysis of a new Asia-4 lineage and naturally recombinant canine distemper virus strains from Thailand

“…However, the complete genomic sequence of the previously described CDV Asia-4 was not available. Even the relatively variable region is essential for exploring more distant relationship among the strains, due to a small number of informative sites, evolutionary analysis of partial genes have resulted in low resolution of phylogenetic trees and is limited for exploring the outbreak 27 . Thus, these partial sequences could not be gathered in this study.…”

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

“…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.…”

Molecular epidemiology of Aleutian mink disease virus causing outbreaks in mink farms from Southwestern Europe: a retrospective study from 2012 to 2019

“…1 ). This has been mentioned previously [ 11 15 22 ], indicating that an analysis of the longer fragments or even the whole genome can build better, higher-resolution phylogenetic relationships.…”

“…Furthermore, the trade of breeding stock/equipment and the circulation of people between farms (workers, visitors, technical staff) can be involved in spreading the virus [ 21 ]. Accordingly, the application of molecular epidemiology has proved useful for tracking possible sources of AMDV infections [ 11 22 ]. This has encouraged many producing countries to characterize their AMDV strains molecularly, and study their relationship with strains from different regions and countries [ 14 15 23 24 ].…”