Challenges related to vaccines/diagnosis

Generic detection and pathotyping of influenza viruses by RT-PCR is an established routine diagnostic method, and can be applied to all sub-types and various lineages of AIV. The use of pathotype-specific probes targeting the hemagglutinin cleavage site has been evaluated for the detection and differentiation between H5N1 HPAI and low pathogenicity avian influenza (LPAI) viruses with good results on field samples (H5 cleavage sites of viruses of the goose/Guandong lineage are fairly conserved). On the other hand, the H7 HP cleavage sites are not at all conserved, and degenerate primers to detect the different H7 viruses have been tested. The use of antigenic cartography, NGS sequencing from all isolated viruses, as well as the use of new approaches such as SISPA (Sequencing-independent sub- and pathotyping of avian influenza viruses) and RITA (Riems influenza typing assay) are also recommended.