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Phylogenetic and geographic distribution of bat sarbecoviruses and their bat ACE2 tropism. Nazia Thakur (9904162) Joseph Newman (5638340) Dongchun Ni (15188356) Jeffrey Seow (9415776) Abigail L. Hay (25157576) Yeonjae Lee (12256119) Ayush Upadhyay (25157573) Babatunde E. Ekundayo (25157578) John A. Hammond (7431785) Thomas P. Peacock (6536120) Kelvin Lau (1847764) Katie J. Doores (346210) Dalan Bailey (193037) Microbiology Cell Biology Evolutionary Biology Environmental Sciences not elsewhere classified Ecology Immunology Biological Sciences not elsewhere classified Cancer Infectious Diseases Virology multiple bat coronaviruses g ., rc g ., civet clade 1 viruses restricted ace2 usage mammalian ace2 proteins g ., rhgb07 using monoclonal antibodies clade 1 sarbecoviruses div >< p determined host range converting enzyme 2 2 convalescent individuals ace2 ), via using binding assays antigenicity using sera related bat sarbecoviruses using sarbecoviruses host range clade 3 pangolin ), neutralising antibodies entry assays binding domain sarbecoviruses interact sarbecoviruses exhibited rodent ace2 like rhgb07 generalist ace2 related antigenicity zoonotic potential vitally important still evidence specialist </ shifting pattern robust evidence research indicates racoon dog novel structure largely maintained including human immunodominant target human primate generalist phenotypes generalist </ especially omicron entry phenotypes diverse panel continued evolution breakthrough infections (A) Evolutionary history of bat sarbecovirus RBDs (NCBI reference shown for 124 amino acid sequences) was inferred by using the Maximum Likelihood method and Whelan and Goldman model. Initial tree(s) for the heuristic search were obtained automatically by Neighbour-Join and BioNJ algorithms to a matrix of pairwise distances (225 total positions) estimated using the JTT model with discrete Gamma distribution (5 categories (+G, parameter = 0.3524)), and then selecting the topology with superior log-likelihood value. Evolutionary analyses were conducted in MEGA 11. Bat sarbecovirus RBDs cluster into clades: clade Ia (yellow), clade Ib (orange), clade II (blue), clade III (green), clade IV (purple) and clade V (red). Viruses selected for analysis in this study are highlighted in red. (B) World map highlighting the geographic location where sarbecoviruses investigated in this study were first isolated (coloured in blue), along with the distribution of the bat species these were isolated from (<a href="https://www.iucnredlist.org/" target="_blank">https://www.iucnredlist.org/</a>). (C) Structural images showing the binding of Rhinolophus affinis ACE2 with SARS-CoV-2 RBD (PDB 7XA7). Offset images highlight the conserved amino acid residues across the different bat ACE2s relative to Rh. affinis ACE2, and the conservation of bat sarbecovirus RBDs compared to SARS-CoV-2, screened in this study. The ACE2-RBD interacting residues are denoted. (D) Maximum likelihood phylogeny of the bat sarbecoviruses full-length Spike and bat ACE2 amino acid sequences are shown. Bat sarbecovirus Spikes were used to generate lentiviral-based pseudotypes and used to infect BHK-21 cells overexpressing different bat ACE2s or human ACE2. A heatmap illustrating receptor usage is shown, representing the mean log RLU of 3−5 separate experiments. A vector-only control (pDISPLAY) was included to demonstrate specificity and to set the background signal. The cognate bat receptor for each virus, where possible is highlighted with a red box. Absence of a red square is indicative of the lack of cognate receptor from our screen, either due to unavailability of ACE2 sequence, or because the original bat host is yet unknown (RhGB07: Rh. hipposideros; SARS-CoV-2, SARS-CoV-1: unknown; BANAL-20-52: Rh. malayanus; BANAL-20-236: Rh. marshalli; RacCS203 – Rh. acuminatus). (E) Sequence alignment of bat sarbecovirus RBDs at the ACE2-binding interface, with key amino acid residues denoted, using SARS-CoV-2 numbering. Regions of amino acid deletions between sequences are denoted in red. The corresponding human and Rh.affinis ACE2 residues that bind SARS-CoV-2 RBD are highlighted, with black indicating amino acid residues that are the same between human ACE2 and Rh. affinis ACE2, green indicating the same residues but a different amino acid, and the remainder highlighting unique binding residues for human ACE2 (blue) or Rh. affinis ACE2 (pink) only. The data underlying this Figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3003944#pbio.3003944.s017" target="_blank">S1 Data</a>. 2026-10-01T17:40:07Z Image Figure 10.1371/journal.pbio.3003944.g001 https://figshare.com/articles/figure/_p_Phylogenetic_and_geographic_distribution_of_bat_sarbecoviruses_and_their_bat_ACE2_tropism_p_/34047367 CC BY 4.0