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Background 2: AMDV-Related Parvoviruses in Wild vs. Farmed Carnivores

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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.

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1. Downloading All Available AMDV Sequences from GenBank

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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/

2. Importing AMDV Sequences and Metadata from GenBank Files

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Now that we've downloaded a set of AMDV sequences, we can incorporate them into the Parvovirus-GLUE project. Load the sequences as follows: