Ion torrent-based nasopharyngeal swab metatranscriptomics in COVID-19

Gubio Campos; Silvia Sardi; Melissa Falcao; Emilia Belitardo; Danilo Rocha; Carolina Rolo; Aline Menezes; Carina Pinheiro; Rejane Carvalho; João Almeida; Eric Aguiar; Luis Pacheco

doi:10.1590/SciELOPreprints.239

article.authors6a087034006a3

Gubio S. Campos Institute of Health Sciences, Federal University of Bahia, Salvador-BA, Brazil https://orcid.org/0000-0002-1700-2462
Silvia I. Sardi Institute of Health Sciences, Federal University of Bahia, Salvador-BA, Brazil https://orcid.org/0000-0002-2002-8436
Melissa B. Falcao Núcleo de Pesquisa e Extensão em Vigilância da Saúde, Universidade Estadual de Feira de Santana, Feira de Santana-BA, Brazil
Emilia M. M. A. Belitardo Institute of Health Sciences, Federal University of Bahia, Salvador-BA, Brazil https://orcid.org/0000-0003-0818-1582
Danilo J. P. G. Rocha Institute of Health Sciences, Federal University of Bahia, Salvador-BA, Brazil https://orcid.org/0000-0002-2160-2153
Carolina A. Rolo Institute of Health Sciences, Federal University of Bahia, Salvador-BA, Brazil https://orcid.org/0000-0001-8886-6340
Aline D. Menezes Institute of Health Sciences, Federal University of Bahia, Salvador-BA, Brazil https://orcid.org/0000-0002-1416-2874
Carina Pinheiro Institute of Health Sciences, Federal University of Bahia, Salvador-BA, Brazil https://orcid.org/0000-0001-5623-1308
Rejane H. Carvalho Institute of Health Sciences, Federal University of Bahia, Salvador-BA, Brazil
João P. P. Almeida Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte-MG, Brazil https://orcid.org/0000-0001-7532-8420
Eric R. G. R. Aguiar Department of Biological Sciences, Center of Biotechnology and Genetics, State University of Santa Cruz (UESC), Ilhéus-BA, Brazil https://orcid.org/0000-0002-8143-5756
Luis G. C. Pacheco Institute of Health Sciences, Federal University of Bahia, Salvador-BA, Brazil https://orcid.org/0000-0003-2500-0800

DOI:

https://doi.org/10.1590/SciELOPreprints.239

Keywords:

Covid-19, SARS-CoV-2, next-generation sequencing, metatranscriptomics

Resumen

Herein, we describe the detection of a SARS-CoV-2 genome through metatranscriptome next-generation sequencing directly from the nasopharyngeal swab of a suspected case of local transmission of Covid-19, in Brazil. Depletion of human ribosomal RNA and use of an optimized in-house developed bioinformatics strategy contributed to successful detection of the virus.