Artic-rabv

Repository of material for rabies virus genomic surveillance using MinION sequencing (forked and modified from artic-base and the latest conda environment from artic-ncov2019 Includes resources and datasets used in publication: Brunker K, Jaswant G, Thumbi SM et al. Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes [version 1; peer review: awaiting peer review]. Wellcome Open Res 2020, 5:3 (https://doi.org/10.12688/wellcomeopenres.15518.1)

To install:

• Install the GitHub repository:

git clone --recursive https://github.com/kirstyn/artic-rabv.git 

• Install mamba, which massively speeds up conda environment install:

conda install mamba -n base -c conda-forge

• Create conda environment to install tools (using mamba). Modify the filepath after -f to reflect where you have installed artic-rabv on your computer.
• This will take a few minutes

mamba env create -f artic-rabv/environment.yml

• Use this command to activate your environment

source activate artic-rabv  

• To update your environment after changes to environment file

conda env update --file artic-rabv/environment.yml

Primer schemes

Multiplex primer schemes for rabies virus whole genome sequencing, designed using Primal Scheme (http://primal.zibraproject.org/)
rabvTanzDg= primers designed to target Tanzanian rabies virus (2016) rabv_ea=updated primers for East Africa rabies virus lineages (2018) rabvSEasia= primers designed to target SE Asia lineages of rabies virus
rabvPeru2= primers designed to target lineages of rabies virus in Puno/Arequipa, Peru

Protocols

Full "sample-to-sequence" laboratory protocol for sequencing rabies virus samples on the MinION platform

Sequence data

Rabies virus consensus sequence datasets used for the publication "Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes" (Brunker et al, 2020, Wellcome Open Research).
Gel results from PCR validation tests on archived RABV samples.