Genome evolution at the nucleotide and amino-acid level according to the time and site of sampling.

Positions of nucleotide and amino acid substitutions are listed in reference to both the full-length EV71 polyprotein (number on left of column) and within the affected protein (in parenthesis). BAL: bronchoalveolar lavage sample; CSF: cerebrospinal fluid sample; nt: nucleotide position; aa: amino acid position.*Positions are indicated relative to EV71 BrCr strain (GenBank accession number: U22521).Of note, real-time RT-PCR performed on plasma samples collected at days 1, 5 and 7 presented 27, 32 and 45 ct values, respectively, and immunoglobulins were injected at day 5.