AMDV Project Build
This tutorial focuses on carnivore amdoparvovirus 1 - also known as Aleutian mink disease virus (AMDV). It comprises the following steps:
- Downloading selected sequences from GenBank.
- Extracting isolate data from GenBank files.
- Constructing an alignment using a codon-aware method.
- Mapping feature coverage of sequence members within an alignment.
- Reconstructing annotated phylogenetic trees.
If you're unclear about the ways in which Parvovirus-GLUE might be used, you may find it useful to skim through this tutorial.
Alternatively, if you're committed to using Parvovirus-GLUE, we recommend you investigate the GLUE example project before attempting this tutorial.
Left to right: stoat/ermine (Mustela ermina); Leonardo da Vinci's 'Lady with an Ermine' (1489--1491); North American mink (Neovison vison); Women posing with mink furs in the 1930s;
Humans have established relatively close relationships with several carnivore species. But whereas some are kept as companion animals, others are hunted or farmed for meat or fur. In Europe, several mustelid species have historically been hunted for fur, including European mink (Mustela lutreola), ermine (Mustela ermina) and European polecat (Mustela putorius). However, the fur of the North American mink (Neovison vison) is considered superior in quality to all of these.
Furthermore, while records of efforts to breed ermine (stoats) in captivity exist, these ventures have apparently been short-lived. By contrast, North American mink are extensively farmed. The first mink farms were founded in the 1860s, in Upstate New York, and farming of American mink was introduced into Europe in the early 1930s. The breeding of various fur colour mutants led to a boom in the mink industry in the two decades that followed.
One unintended consequence of the post-war boom in mink farming was the introduction of American mink into Europe (as escaped animals took up residence in local habitats). American mink (hereafter referred to simply as 'mink') are now a relatively widespread invasive species in Europe.
In the 1930s a severe disease emerged in farmed mink. This disease was originally identified in the Aleutian mink breed and was consequently named Aleutian disease (AD). However, it was soon discovered to afflict American mink in general. AD is caused by an parvovirus in genus (Amdoparvovirus) called Aleutian mink disease virus (AMDV). This virus was originally considered a species in its own right, but has recently been reclassified as a sublineage of carnivore amdoparvovirus 1. AD is presently considered the most important infectious disease affecting farm-raised mink.
Infection with AMDV---or related amdoparvoviruses---is widespread in both wild and farmed mink. Related viruses have also been identified in several other carnivore species, including gray foxes, skunks, raccoon dogs, and red pandas. However, relatively little is known about amdoparvovirus infection biology in the natural environment or the broader distribution of these infections in wild species.
Left to right: Gray fox (Urocyon cinereoargenteus); Striped skunk (Mephitis mephitis); Raccoon dog (Nyctereutes procyonoides); Red panda (Ailurus fulgens).
Most importantly, it is unclear whether the pathology of AD in captive mink is typical of disease in the wild, or if factors associated with fur farming have enabled the disease's emergence.
With the increased availability of molecular sequence data, it may now be feasible to gain insights into the natural history and evolution of amdoparvoviruses, potentially shedding light on the emergence of AD.
In this tutorial, we will use the Parvovirus-GLUE project and published sequence data to investigate the distribution, diversity, and evolution of AMDV.
To download all AMDV entries in NCBI GenBank, we will use a customized version of GLUE's ncbiImporter module. The project-specific configuration of this module can be viewed here. The module is configured to download sequences based on the following query phrase:
"Carnivore amdoparvovirus 1"[Organism] AND 200:5000[SLEN]
This eSearchTerm is a standard NCBI Entrez text query that specifies all GenBank entries labeled "Carnivore amdoparvovirus 1" in the 'Organism' field and with lengths between 200 and 5000 nucleotides (nt).
To use the module, initiate GLUE on the command line as follows:
MyComputer:Parvovirus-GLUE rob$ gluetools.sh
GLUE Version 1.1.103
Copyright (C) 2015-2020 The University of Glasgow
This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you
are welcome to redistribute it under certain conditions. For details see
GNU Affero General Public License v3: http://www.gnu.org/licenses/
Mode path: /
GLUE>
Notice that I’m in the Parvovirus-GLUE directory when I initiate GLUE. This directory will be the default working directory, so when referencing a file from the GLUE console, you’ll need to do so relative to this directory.
Next, navigate to the parvoviridae project as shown:
GLUE> project parvoviridae
OK
Mode path: /project/parvoviridae/
Now create the module using its configuration file, which is contained in the Parvovirus-GLUE project:
Mode path: /project/parvoviridae/
GLUE> create module -f modules/build/genus/amdo/amdoNcbiImporterExample.xml
OK
(1 Module created)
Mode path: /project/parvoviridae/
To run the module, execute the following command in the GLUE shell:
Mode path: /project/parvoviridae/
GLUE> module amdoNcbiImporterExample import
When I ran this command on March 2, 2022, I obtained the following output:
ncbiImporterSummaryResult
totalMatching: 1777
present: 0
surplus: 0
missing: 1777
deleted: 0
downloaded: 1777
Since the GenBank database is continually expanding, you may find that you obtain more sequences when running the same command at a later date. Note that next time the module is run, only the missing sequences will be downloaded.
Now export the sequences to a source directory as follows:
Mode path: /project/parvoviridae
GLUE> export source ncbi-curated-parvo-amdv -p sources/genus/amdo/
Now that we've downloaded a set of AMDV sequences, we can incorporate them into the Parvovirus-GLUE project. Load the sequences as follows:
Parvovirus-GLUE by Robert J Gifford Lab.
For questions, issues, or feedback, please open an issue on the GitHub repository.