One-step detection of the 2009 pandemic influenza A(H1N1) virus by the RT-SmartAmp assay and its clinical validation
Authors: Yuki Kawai, Yasumasa Kimura, Alexander Lezhava, Hajime Kanamori, Kengo Usui, Takeshi Hanami, Takahiro Soma, Jean-Étienne Morlighem, Satomi Saga, Yuri Ishizu, Shintaro Aoki, Ryuta Endo, Atsuko Oguchi-Katayama, Yasushi Kogo, Yasumasa Mitani, Takefumi Ishidao, Chiharu Kawakami, Hideshi Kurata, Yumiko Furuya, Takayuki Saito, Norio Okazaki, Masatsugu Chikahira, Eiji Hayashi, Sei-ichi Tsuruoka, Tokumichi Toguchi, Yoshitomo Saito, Toshiaki Ban, Shinyu Izumi, Hideko Uryu, Koichiro Kudo, Yuko Sakai-Tagawa, Yoshihiro Kawaoka, Aizan Hirai, Yoshihide Hayashizaki, Toshihisa Ishikawa
Journal: PLoS One (2012)
MeSH terms: Influenza A Virus, H1N1 Subtype / isolation & purification, Influenza A Virus, H1N1 Subtype / pathogenicity, Influenza, Human / epidemiology, Nucleic Acid Amplification Techniques / methods, Pandemics, RNA-Directed DNA Polymerase / metabolism, Case Reports, Research Support, Non-U.S. Gov't, Validation Study, Aged, Child, DNA Primers / genetics, Drug Resistance, Viral, Female, Hemagglutinin Glycoproteins, Influenza Virus / genetics, Humans, Influenza A Virus, H1N1 Subtype / drug effects, Influenza A Virus, H1N1 Subtype / genetics, Influenza, Human / virology, Oseltamivir / pharmacology, RNA, Viral / genetics, RNA, Viral / isolation & purification, Time Factors, DNA Primers, H1N1 virus hemagglutinin, Hemagglutinin Glycoproteins, Influenza Virus, RNA, Viral, Oseltamivir, RNA-Directed DNA Polymerase

Background:
In 2009, a pandemic (pdm) influenza A(H1N1) virus infection quickly circulated globally resulting in about 18,000 deaths around the world. In Japan, infected patients accounted for 16% of the total population. The possibility of human-to-human transmission of highly pathogenic novel influenza viruses is becoming a fear for human health and society.
Methodology:
To address the clinical need for rapid diagnosis, we have developed a new method, the "RT-SmartAmp assay", to rapidly detect the 2009 pandemic influenza A(H1N1) virus from patient swab samples. The RT-SmartAmp assay comprises both reverse transcriptase (RT) and isothermal DNA amplification reactions in one step, where RNA extraction and PCR reaction are not required. We used an exciton-controlled hybridization-sensitive fluorescent primer to specifically detect the HA segment of the 2009 pdm influenza A(H1N1) virus within 40 minutes without cross-reacting with the seasonal A(H1N1), A(H3N2), or B-type (Victoria) viruses.
Results and conclusions:
We evaluated the RT-SmartAmp method in clinical research carried out in Japan during a pandemic period of October 2009 to January 2010. A total of 255 swab samples were collected from outpatients with influenza-like illness at three hospitals and eleven clinics located in the Tokyo and Chiba areas in Japan. The 2009 pdm influenza A(H1N1) virus was detected by the RT-SmartAmp assay, and the detection results were subsequently compared with data of current influenza diagnostic tests (lateral flow immuno-chromatographic tests) and viral genome sequence analysis. In conclusion, by the RT-SmartAmp assay we could detect the 2009 pdm influenza A(H1N1) virus in patients' swab samples even in early stages after the initial onset of influenza symptoms. Thus, the RT-SmartAmp assay is considered to provide a simple and practical tool to rapidly detect the 2009 pdm influenza A(H1N1) virus.