Fig. 6

Arrival of SARS-CoV-2 lineages and transmission-associated mutations over time. A Number of consensus sequences including each lineage-defining mutation, named by alternative nucleotides and genome position. The first detected occurrence of each derived allele is indicated by an arrow. The nucleotide positions correspond to the following amino positions in genes: A23403G;D614G;S;S, C1059T;T85I;orf1a;NSP2, C11916T;S25L;orf1a;NSP7, C14408T;P323L;orf1b;NSP12, C15324T;N629N;orf1b;NSP12, C3037T;F107F;orf1a;NSP3, G28881A;R203K;N;N, G28882A;R203R;N;N, G28883C;G204R;N;N. Nucleotide positions are coded as follows: ancestral nucleotide allele, genome position, derived nucleotide allele; ancestral amino acid allele, position in protein, derived amino acid allele; ORF; gene. B Introductions that generated transmission lineages of > 2 genomes as a function of the TMRCA (inferred by ML ASR), colored by PANGO lineage name and annotated if the introduction had reported travel history (y) or not (n). Pearson correlation coefficients: r = − 0.30 (− 0.43, − 0.16), p = 6.828e−05, black line. Note that the last inferred introduction event had a TMRCA of April 16th, not shown here because it was a singleton