Understanding human infection with avian influenza A/H5N1 virus in Indonesia

Since their emergence in Indonesia in 2005, human infections with clade 2.1 avian influenza A/H5N1 virus have been reported, associated with high mortality (84%) compared to regions affected by this virus. This thesis explain the high mortality of A/H5N1 in Indonesia and investigate the genetic evolution during infections relevant to adaptation and virulence in humans, as well as antiviral and vaccine efficacy. We quantified the viral load of respiratory tract specimens as well as fecal and blood samples. Full genome of isolates was analysed for the markers of virulence or human adaptation and antiviral drug resistance. Furthermore, whole genome deep sequencing of clinical respiratory specimens to found within-host viral diversity were also conducted. The study shown that high viral loads are associated with fatal outcomes and the presence of amantadine-resistance mutations in viruses. Across the whole genomes of isolated H5N1 viruses, we found that only a small number of virus associated with human adaptation and virulence. No other known virulence markers were detected, nor antiviral resistance mutations. Antigenic profiling showed two distinct clusters which not associated with time of virus circulation. However, we identified high levels of genetic diversity during human infection and multiple single amino acid variants in all three polymerase (PB2, PB1, and PA) subunits that increased polymerase activity to similar levels as the widely recognized adaptation and virulence marker PB2-E627K. These observations confirm the association of viral load with outcome of human H5N1 infections. Further genome analysis indicates highly dynamic evolutionary processes during human H5N1 virus infection and the potential existence of previously undocumented adaptive pathways.