Evidence for ACE2-utilizing coronaviruses (CoVs) related to severe acute respiratory syndrome CoV in bats

Abstract

In 2002, severe acute respiratory syndrome (SARS)-coronavirus (CoV) appeared as a novel human virus with high similarity to bat coronaviruses. However, while SARS-CoV uses the human angiotensin-converting enzyme 2 (ACE2) receptor for cellular entry, no coronavirus isolated from bats appears to use ACE2. Here we show that signatures of recurrent positive selection in the bat ACE2 gene map almost perfectly to known SARS-CoV interaction surfaces. Our data indicate that ACE2 utilization preceded the emergence of SARS-CoV-like viruses from bats.

Fig 1

Residues under positive selection in bat ACE2 correspond to human ACE2 residues that interact with the SARS-CoV spike. (a) Six residues under positive selection (red) in bat ACE2 map to the SARS-CoV-binding surface (orange and red) of human ACE2 (green) and are in direct contact with the SARS-CoV spike (gray) in a cocrystal structure (PDB 2AJF) (17). (b) Bat species used in the ACE2 analysis and the amino acids encoded at the six residue positions that directly contact the SARS-CoV spike and are evolving under positive selection. Bat polymorphisms have been reported at some of these positions (11), and a human polymorphism is found at one of them. (c) Detailed view of the side chains of five of these residues under positive selection (red) in ACE2 (green), along with the side chains of cognate contacts in the SARS-CoV spike (light gray). (d) Cocrystal structures have been solved for human ACE2 in complex with the spike proteins of both SARS-CoV (17) and NL63-CoV (39). ACE2 residues that mediate contact with each virus are indicated. Residues under positive selection in bat ACE2 are indicated in red.

Fig 2

Positive selection of residues at the base of a key ACE2 glycan. (a) A linear schematic of the ACE2 protein is shown. Regions of the protein that interact with the SARS-CoV spike are indicated in dark gray (17). Residue positions found to be under positive selection in bats are shown with black tick marks. Six of these fall in the known surface of interaction with the SARS-CoV spike, and 13 more are indicated with numbers. Of these, five (in red type) are positioned at the base of a key glycan on the receptor that is located at position 90. (b) A rotated view of the structure shown in Fig. 1a, with the main SARS-CoV-binding surface now at the left. The glycosylated asparagine at position 90 is shown in orange, with five residues under positive selection sitting in a ridge adjacent to it (red).