First report of novel assemblages and mixed infections of Giardia duodenalis in human isolates from New Zealand

•First report of a human sample from New Zealand with uncommon Giardia duodenalis assemblage E.•A second human sample was infected with unusual Giardia duodenalis sub-assemblage AIII.•Sample identified with assemblage E also reported a low presence (~5% of the matched total reads) of the zoonotic sub-assemblage BIV.•The first identification of assemblage E and sub-assemblage AIII suggest single and recent zoonotic infection events in humans in New Zealand.