Fig 1.

Phylogenetic comparison of the GII.4 ORF2 nucleotide sequence isolated longitudinally from subjects with acute and chronic NoV infections. The full-length ORF2 consensus sequences, determined by bulk sequencing, were generated at two time points (ranging 10 days) for the subject with acute infection (green) and at three time points (ranging 288 days) for the subject with chronic infection (blue). In addition, ORF2 sequences from GII.4 epidemic variants detected in NSW, Australia, during 2006 to 2011 and reference sequences derived from GenBank were included in the analysis (n = 248). Each major GII.4 clade was described previously (59), except for the 2009 and 2010 GII.4 variants, which recently emerged. Both subjects were infected with variants that clustered within the GII.4 2006b variant clade (red). For the subject with acute infection, the consensus sequence was identical at both time points. For the subject with chronic infection, the ORF2 sequence at the third time point differed by 4.1% compared to the sequence from the first two time points. The tree shows that subject Ch was persistently infected with the same variant and not reinfected with another circulating 2006b variant. The distance scale represents the number of nucleotide substitutions per position.