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

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Abstract
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.
Funding Information
  • Pan American Health Organization (PAHO/WHO) (SCON2021-00180, U01 AI151698, CRP/20/03, 001)
  • Brazilian Ministry of Health (SCON2021-00180, U01 AI151698, CRP/20/03, 001)
  • Programa Inova Fiocruz/Oswaldo Cruz Foundation (SCON2021-00180, U01 AI151698, CRP/20/03, 001)
  • National Institutes of Health USA (SCON2021-00180, U01 AI151698, CRP/20/03, 001)
  • CRP-ICGEB RESEARCH (SCON2021-00180, U01 AI151698, CRP/20/03, 001)
  • Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) (SCON2021-00180, U01 AI151698, CRP/20/03, 001)
  • PON “Ricerca e Innovazione” 2014–2020 (SCON2021-00180, U01 AI151698, CRP/20/03, 001)

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