Genome organisation of bat alphacoronaviruses (a). Bat coronavirus CDPHE15/USA/2006 (KF430219.1) had previously been annotated to depict the positions of the mature peptides within the ORF1a and ORF1b regions. The annotated bat coronavirus CDPHE15/USA/2006 (KF430219.1) was used as a guide to indicate the position of the mature peptides within Alphacoronavirus sp. isolate WAAlc1 (MK472071.1), Pekapeka alphacoronavirus 2 (B6) and Pekapeka alphacoronavirus 1 (B5). (b) Tanglegram of midpoint rooted phylogenetic trees of the polymerase (ORF1b) and spike protein of alphacoronaviruses on the right.