Fig. 2

Sequence similarity across Merbecovirus genomes.  A) HCoV-EMC-2012 was used as the query reference. All MERS-CoV representative isolates from clades A, B and C were converted to a consensus sequence referred to as “MERS-CoVs” in the plot. PDF-2180 and NeoCoV were separated as they were the most closely related virus to MERS-CoVs. PnNL2018B and MOW15-22 were converted to consensus and grouped into “group 2 Bat MCr-CoVs”. SC2013, HKU25, VsCoV-kj15, EjCoV-3 and BtCoV-422 and were converted to consensus into “group 3 Bat MCr-CoVs”. PaGB01 was named into “group 4 Bat MCr-CoVs”. SM3A, GZ131656, BtCoV/133, B04f, B05f, B07f, LMH1f and GX2012 were converted to consensus into “ Tylonycteris HKU4”. MjHKU4-1 and MjHKU4-4 were converted to consensus into “Pangolin MjHKU4”. LMH03f, TT03f, TT06f, TT07f, GD2013 and BY140568 were converted to consensus into “ Pipistrellus HKU5”. Erinaceus-174, Erinaceus-216, and HKU31 were converted to consensus into “Hedgehog-CoV-1”. The groupings were based on the NCBI Taxonomy browser [25]. The x-axis represents the similarity score, while the y-axis represents the genomic coordinates.  B) Maximum likelihood phylogenetic trees inferred based on the fragmented regions of MERS-CoV. This was based on the recombination breakpoints detected at position 21,456 in the NTD and 25,089 in the S2 of the spike region. All trees were rooted by the hedgehog-CoVs clade, consistent with Fig. 1. The red squares represent ACE2 usage, blue circles represent DPP4 usage, and green triangles represent unidentified receptor usage. The numerical node support values are shown above each node. The scale bars represent genetic distance