Abstract
BackgroundInfluenza is an acute respiratory illness and has become a serious public health problem worldwide. The need to study the HA and NA genes in influenza A virus is essential since these genes frequently undergo mutations. This study describes the development of primer sets for RT-PCR to obtain complete coding sequence of Hemagglutinin (HA) and Neuraminidase (NA) genes of influenza A/H3N2 virus from Indonesia. The primers were developed based on influenza A/H3N2 sequence worldwide from Global Initiative on Sharing All Influenza Data (GISAID) and further tested using Indonesian influenza A/H3N2 archived samples of influenza-like illness (ILI) surveillance from 2008 to 2009.ResultsAn optimum RT-PCR condition was acquired for all HA and NA fragments designed to cover complete coding sequence of HA and NA genes. A total of 71 samples were successfully sequenced for complete coding sequence both of HA and NA genes out of 145 samples of influenza A/H3N2 tested.ConclusionsThe developed primer sets were suitable for obtaining complete coding sequences of HA and NA genes of Indonesian samples from 2008 to 2009.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-016-2235-8) contains supplementary material, which is available to authorized users.
Highlights
Influenza is an acute respiratory illness and has become a serious public health problem worldwide
Sample selection The study samples were 145 archival clinical specimens confirmed for H3N2 that were obtained from the influenza-like illness (ILI) surveillance conducted by the National Institute of Health Research and Development (NIHRD), Indonesia, from 2008 to 2009
The annealing temperature 50 °C was selected for further polymerase chain reaction (PCR) testing of HA and NA genes for Indonesian samples
Summary
Influenza is an acute respiratory illness and has become a serious public health problem worldwide. This study describes the development of primer sets for RT-PCR to obtain complete coding sequence of Hemagglutinin (HA) and Neuraminidase (NA) genes of influenza A/H3N2 virus from Indonesia. The primers were developed based on influenza A/H3N2 sequence worldwide from Global Initiative on Sharing All Influenza Data (GISAID) and further tested using Indonesian influenza A/H3N2 archived samples of influenza-like illness (ILI) surveillance from 2008 to 2009. Influenza virus is usually detected by isolation of the virus from respiratory specimen in cell culture, commonly Madin–Darby canine kidney (MDCK) cell line, and the presence of virus is confirmed by hemagglutination test [3]. Other molecular methods for the diagnosis of influenza virus have been developed, of which methods based on polymerase chain reaction (PCR) have the highest specificity and sensitivity for viral genome detection [4]
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