IDENTIFIKASI VIRUS AVIAN INFLUENZA SUB TIPE H3 BERDASARKAN GEN PENYANDI PROTEIN HA MENGGUNAKAN NEXT GENERATION SEQUENCERPENELITIAN EKSPERIMENTAL LABORATORIS

Influenza virus is an enveloped, single stranded RNA virus and segmented. This virus belongs to Orthomyxoviridae. This virus devided into three types, A, B, C and D, based on antigenicity of two protein, Matrix (M) and Nucleoprotein (NP). Type A influenza virus devided into several subtypes based on two surface proteins, Hemagglutinin (HA) and Neuraminidase (NA). Until now there are 1-18 HA and 1-11 NA. In this study we identify influenza virus H3 subtype using Next Generation Sequencer. Sample used in this study were local isolated viruses from ducks in 2013. Samples were inoculated in embryonated eggs. After harvested and showed agglutination positive by HA test, then carried out to determine type A and H5 subtype using POCube and One Step Real Time RT-PCR. Deep analysis for subtype identification by Next Generation Sequencer. Sequence analysis using CLC Workbench and Genetyx ver. 12 software. POCube detection showed positive results for type A and negative result for H5 subtype. Detection of influenza virus using One Step Real Time RT-PCR showed positive result for Influenza type A virus and negative for H5. Subtype detection using Next Generation Sequencer showed that this virus belongs to H3 subtype based on mapping analysis to HA references. Amino acids sequence analysis of HA cleavage site showed that this virus belongs to Low Pathogenic virus.