Ion torrent-based nasopharyngeal swab metatranscriptomics in COVID-19

Gubio S Campos; Silvia I Sardi; Melissa B Falcao; Emilia M M A Belitardo; Danilo J P G Rocha; Carolina A Rolo; Aline D Menezes; Carina S Pinheiro; Rejane H Carvalho; João P P Almeida; Eric R G R Aguiar; Luis G C Pacheco

doi:10.1016/j.jviromet.2020.113888

Ion torrent-based nasopharyngeal swab metatranscriptomics in COVID-19

J Virol Methods. 2020 May 21:282:113888. doi: 10.1016/j.jviromet.2020.113888. Online ahead of print.

Affiliations

¹ Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil.
² Núcleo de Pesquisa e Extensão em Vigilância da Saúde, Universidade Estadual de Feira de Santana, Feira de Santana, BA, Brazil.
³ Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
⁴ Department of Biological Sciences, Center of Biotechnology and Genetics, State University of Santa Cruz (UESC), Ilhéus, BA, Brazil. Electronic address: ericgdp@gmail.com.
⁵ Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil. Electronic address: luis.pacheco@ufba.br.

Abstract

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.

Keywords: Covid-19; SARS-CoV-2; metatranscriptomics; next-generation sequencing.