A Multiplex Nanopore Sequencing Approach for the Detection of Multiple Arboviral Species

• DOI: 10.3390/v16010023
• Publication Date: 2023-12-22T09:44:40Z
• Authors: Joilson Xavier; Vagner Fonseca; Talita Adelino; Felipe C. M. Iani; Glauco C. Pereira; Myrian M. Duarte; Mauricio Lima; Emerson Castro; Carla Oliveira; Hegger Fritsch; Natalia Guimarães; Ludmila O. Lamounier; Fernanda Khouri B...; Camilo M. M. Brag...; Crhistinne C. May...; Danielle Malta Lima; Elaine C. de Oliv...; Gislene G. de Cas...; Iago Gomes; Janaina Mazaro; Janete T. N. Rodr...; Jayra Abrantes; Jeová K. B. Colares; Kleber G. Luz; Luana Barbosa da ...; Luiz Demarchi; Magaly C. B. Câmara; Marina C. S. Umak...; Rafaela Sabatini ...; Rutilene Barbosa ...; Simone K. Haddad; Stephanni Figueir...; Svetoslav N. Slavov; Themis Rocha; Noelia Morel; Hector Chiparelli; Analía Burgueño; Victoria Bórmida; María N. Cortinas; Rosario S. Martín; Allan C. Pereira; Marcelo F. dos Sa...; Walter André Júnior; Jairo Mendez Rico; Leticia Franco; Alexander Rosewell; Rodrigo F. do Car...; Carlos F. C. de A...; Ethel L. Noia Maciel; Marília Santini d...; Rivaldo Venâncio ...; Livia C. Vinhal F...; Ana M. B. de Fili...; Marta Giovanetti; Luiz Carlos Junio...
• Keywords: 0301 basic medicine; orthoflaviviruses; Zika Virus Infection; Brief Report; Zika Virus; Microbiology; QR1-502; Dengue; Nanopore Sequencing; 03 medical and health sciences; arbovirus; genotyping; nanopore sequencing; Humans; Chikungunya virus; Multiplex Polymerase Chain Reaction; Arboviruses

The emergence and continued geographic expansion of arboviruses and the growing number of infected people have highlighted the need to develop and improve multiplex methods for rapid and specific detection of pathogens. Sequencing technologies are promising tools that can help in the laboratory diagnosis of conditions that share common symptoms, such as pathologies caused by emerging arboviruses. In this study, we integrated nanopore sequencing and the advantages of reverse transcription polymerase chain reaction (RT-PCR) to develop a multiplex RT-PCR protocol for the detection of Chikungunya virus (CHIKV) and several orthoflaviviruses (such as dengue (Orthoflavivirus dengue), Zika (Orthoflavivirus zikaense), yellow fever (Orthoflavivirus flavi), and West Nile (Orthoflavivirus nilense) viruses) in a single reaction, which provides data for sequence-based differentiation of arbovirus lineages.