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FIELD DIAGNOSIS AND GENOTYPING OF CHIKUNGUNYA VIRUS USING A DRIED REVERSE TRANSCRIPTION LOOP-MEDIATED ISOTHERMAL AMPLIFICATION (LAMP) ASSAY AND MINION SEQUENCING
Genome
MinION sequencing
Transcription loop-mediated isothermal amplification (RT-LAMP)
Autor
Afiliación
Research Center for Zoonosis Control. Hokkaido University. Sapporo, Japan.
Research Center for Zoonosis Control. Hokkaido University. Sapporo, Japan.
Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Flavivirus Laboratory. Rio de Janeiro, RJ, Brazil.
Research Center for Zoonosis Control. Hokkaido University. Sapporo, Japan / Global Station for Zoonosis Control. Global Institution for Collaborative Research and Education (GI-CoRE). Hokkaido University. Sapporo, Japan.
Global Station for Zoonosis Control. Global Institution for Collaborative Research and Education (GI-CoRE). Hokkaido University. Sapporo, Japan / Centre for Research in Infectious Diseases. School of Medicine and Medical Science. University College Dublin. Dublin, Ireland / Global Virus Network. Baltimore, Maryland, USA.
Research Center for Zoonosis Control. Hokkaido University. Sapporo, Japan.
Global Virus Network. Baltimore, Maryland, USA.
Global Virus Network. Baltimore, Maryland, USA.
Oswaldo Cruz Foundation. Evandro Chagas National Institute of Infectious Diseases. Acute Febrile Illnesses Laboratory. Rio de Janeiro, RJ, Brazil / Global Virus Network. Baltimore, Maryland, USA.
Oswaldo Cruz Foundation. Evandro Chagas National Institute of Infectious Diseases. Acute Febrile Illnesses Laboratory. Rio de Janeiro, RJ, Brazil / Global Virus Network. Baltimore, Maryland, USA.
Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Flavivirus Laboratory. Rio de Janeiro, RJ, Brazil.
Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Flavivirus Laboratory. Rio de Janeiro, RJ, Brazil.
Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Flavivirus Laboratory. Rio de Janeiro, RJ, Brazil.
Research Center for Zoonosis Control. Hokkaido University. Sapporo, Japan / Global Station for Zoonosis Control. Global Institution for Collaborative Research and Education (GI-CoRE). Hokkaido University. Sapporo, Japan.
Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Flavivirus Laboratory. Rio de Janeiro, RJ, Brazil.
Research Center for Zoonosis Control. Hokkaido University. Sapporo, Japan / Global Station for Zoonosis Control. Global Institution for Collaborative Research and Education (GI-CoRE). Hokkaido University. Sapporo, Japan / Global Virus Network. Baltimore, Maryland, USA.
Research Center for Zoonosis Control. Hokkaido University. Sapporo, Japan.
Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Flavivirus Laboratory. Rio de Janeiro, RJ, Brazil.
Research Center for Zoonosis Control. Hokkaido University. Sapporo, Japan / Global Station for Zoonosis Control. Global Institution for Collaborative Research and Education (GI-CoRE). Hokkaido University. Sapporo, Japan.
Global Station for Zoonosis Control. Global Institution for Collaborative Research and Education (GI-CoRE). Hokkaido University. Sapporo, Japan / Centre for Research in Infectious Diseases. School of Medicine and Medical Science. University College Dublin. Dublin, Ireland / Global Virus Network. Baltimore, Maryland, USA.
Research Center for Zoonosis Control. Hokkaido University. Sapporo, Japan.
Global Virus Network. Baltimore, Maryland, USA.
Global Virus Network. Baltimore, Maryland, USA.
Oswaldo Cruz Foundation. Evandro Chagas National Institute of Infectious Diseases. Acute Febrile Illnesses Laboratory. Rio de Janeiro, RJ, Brazil / Global Virus Network. Baltimore, Maryland, USA.
Oswaldo Cruz Foundation. Evandro Chagas National Institute of Infectious Diseases. Acute Febrile Illnesses Laboratory. Rio de Janeiro, RJ, Brazil / Global Virus Network. Baltimore, Maryland, USA.
Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Flavivirus Laboratory. Rio de Janeiro, RJ, Brazil.
Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Flavivirus Laboratory. Rio de Janeiro, RJ, Brazil.
Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Flavivirus Laboratory. Rio de Janeiro, RJ, Brazil.
Research Center for Zoonosis Control. Hokkaido University. Sapporo, Japan / Global Station for Zoonosis Control. Global Institution for Collaborative Research and Education (GI-CoRE). Hokkaido University. Sapporo, Japan.
Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Flavivirus Laboratory. Rio de Janeiro, RJ, Brazil.
Research Center for Zoonosis Control. Hokkaido University. Sapporo, Japan / Global Station for Zoonosis Control. Global Institution for Collaborative Research and Education (GI-CoRE). Hokkaido University. Sapporo, Japan / Global Virus Network. Baltimore, Maryland, USA.
Resumen en ingles
Detection and sequencing of chikungunya virus (CHIKV) genome was performed using a combination of a modified reverse transcription loop-mediated isothermal amplification (RT-LAMP) method and a MinION sequencer. We developed the protocol for drying all the reagents for the RT-LAMP in a single reaction tube. Using this system, the CHIKV genome was effectively amplified under isothermal conditions, and used as a template for MinION sequencing with a laptop computer. Our in-house RT-LAMP method and MinION sequencing system were also validated with RNAs and serum samples from recent outbreaks of CHIKV patients in Brazil. The obtained sequence data confirmed the CHIKV outbreaks and identified the genotype. In summary, our established inexpensive on-site genome detection and sequencing system is applicable for both diagnosis of CHIKV infected patients and genotyping of the CHIKV virus in future outbreak in remote areas.
Palabras clave en ingles
Chikungunya virus (CHIKV)Genome
MinION sequencing
Transcription loop-mediated isothermal amplification (RT-LAMP)
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