key: cord-0031878-ua3skags
authors: Kumar, Ankeet; Nath, Sujith S.; Sridhar Sudarshan, Ashwin; Iyer, Vinithra; Jadeja, Niti B.; Panchamia, Neha; Banerji, Indrakshi; Vanak, Abi Tamim; Tatu, Utpal
title: Genome Sequences of Five Indian Canine Rabies Virus Isolates Obtained Using Oxford Nanopore Technologies Sequencing
date: 2022-04-26
journal: nan
DOI: 10.1128/mra.01246-21
sha: 20c9787165e2eaf3df48b731ad6288aea4eb3ae3
doc_id: 31878
cord_uid: ua3skags

We report five canine rabies virus genome sequences from India that were obtained from brain samples using Oxford Nanopore Technologies sequencing. The sequences will facilitate understanding of the evolution and transmission of rabies.

The consensus sequence was obtained by using the commands from the file minion.py from the ARTIC protocol (https://github.com/artic-network/fieldbioinformatics/blob/ master/artic/minion.py) (6) , and the parameters used were as specified in the protocol. Reads 200 to 700 bp long were mapped against the reference genome (strain NNV-RAB-H [GenBank accession number EF437215.1]) (normalized to 150Â coverage) using minimap2 v2.17, and the option -x map-ont was used to map ONT reads to the reference. The output SAM files were indexed and sorted for further steps. Variant calling was performed using medaka v1.0.3 (https://github.com/nanoporetech/medaka) as a part of the ARTIC pipeline, and final consensus sequences were obtained. Medaka was run separately for the reads from the first and second rounds to account for the different models needed due to the different Guppy versions and different versions of the flow cells used (r941_min_high_g351 for the initial batch of reads and r103_min_ high_g360 for the gaps sequenced in the second run). The VCF files were merged by sample and category using bcftools merge. Only variants identified in either set of sequencing reads with coverage of $20Â and nonframeshift mutations were considered for building the consensus sequence.

The GC contents ranged from 45.53 to 45.71% among the five genomes. Information related to the data collected, closest relative genome, and percentage of identity to the closest relative is available in Table 1 . Identity among our genomes ranged from 94.14 to 99.4%.

Permissions for animal sampling were granted by concerned authorities of the Ashoka Trust for Research in Ecology and the Environment (ATREE) and the Indian Institute of Science under approval numbers AAEC/101/2016 and CAF/Ethics/831/2021, respectively.

Data availability. The raw reads and the genome sequences were submitted to NCBI with SRA accession numbers SRX13297356, SRX13297357, SRX13297358, SRX13297359, and SRX13297360 and GenBank accession numbers OL422906.1, OL422907.1, OL422908.1, OL422909.1, and OL422910.1. The primers used and the coverage of genes are reported on figshare (https://figshare.com/articles/media/Genome_sequences_of_Indian_canine_Rabies_ virus_using_Oxford_Nanopore_Technology/17694347?file=32385851 and https://figshare .com/articles/media/Genome_sequences_of_Indian_canine_Rabies_virus_using_Oxford_ Nanopore_Technology/17694347?file=32385860, respectively). NNV-RAB-H (GenBank accession number EF437215.1) was used as the reference genome for mapping and primer design. 

Modelling the challenges of managing free-ranging dog populations

Rabies virus transcription and replication

Utility of real-time Taqman PCR for antemortem and postmortem diagnosis of human rabies

Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes

Performance of neural network basecalling tools for Oxford Nanopore sequencing

nCoV-2019 novel coronavirus bioinformatics protocol

This project was funded through a DBT/Wellcome Trust India Alliance Intermediate Fellowship to A.T.V. (grant IA/CPHI/15/1/502028). U.T. acknowledges a DBT-IISC partnership, and A.K. acknowledges funding from the CSIR.