Thanks for the feedback Andrew and Richard. I’ve updated https://nextstrain.org/groups/blab/sars-like-cov to split ORF1a and ORF1b. This makes it clearer how nucleotide mutations map to amino acid substitutions.
Ignoring the divergent BetaCoV/Wuhan/IVDC-HB-05/2019 sequence and masking the initial 11 bases of the alignment, we have the following 5 strains and their mutations relative to the base of the outbreak clade:
- WIV04/2019 - no mutations
- IVDC-HB-01/2019 - no mutations
- IPBCAMS-WH-01/2019 - 3 nucleotide mutations / 2 AA changes
- IVDC-HB-04/2020 - 3 nucleotide mutations / 3 AA changes (includes C1023T and C1025T which are suspect being so close together)
- WH-Human_1 - 2 nucleotide mutations / 1 AA change
This alignment was stripped to map to reference https://github.com/blab/sars-like-cov/blob/master/config/sars-like-cov_reference.gb and so lacks indels.