Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus

Abstract

Recently, a novel coronavirus (2019-nCoV) has emerged from Wuhan, China, causing symptoms in humans similar to those caused by severe acute respiratory syndrome coronavirus (SARS-CoV). Since the SARS-CoV outbreak in 2002, extensive structural analyses have revealed key atomic-level interactions between the SARS-CoV spike protein receptor-binding domain (RBD) and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. Here, we analyzed the potential receptor usage by 2019-nCoV, based on the rich knowledge about SARS-CoV and the newly released sequence of 2019-nCoV. First, the sequence of 2019-nCoV RBD, including its receptor-binding motif (RBM) that directly contacts ACE2, is similar to that of SARS-CoV, strongly suggesting that 2019-nCoV uses ACE2 as its receptor. Second, several critical residues in 2019-nCoV RBM (particularly Gln493) provide favorable interactions with human ACE2, consistent with 2019-nCoV's capacity for human cell infection. Third, several other critical residues in 2019-nCoV RBM (particularly Asn501) are compatible with, but not ideal for, binding human ACE2, suggesting that 2019-nCoV has acquired some capacity for human-to-human transmission. Last, while phylogenetic analysis indicates a bat origin of 2019-nCoV, 2019-nCoV also potentially recognizes ACE2 from a diversity of animal species (except mice and rats), implicating these animal species as possible intermediate hosts or animal models for 2019-nCoV infections. These analyses provide insights into the receptor usage, cell entry, host cell infectivity and animal origin of 2019-nCoV and may help epidemic surveillance and preventive measures against 2019-nCoV.IMPORTANCE The recent emergence of Wuhan coronavirus (2019-nCoV) puts the world on alert. 2019-nCoV is reminiscent of the SARS-CoV outbreak in 2002 to 2003. Our decade-long structural studies on the receptor recognition by SARS-CoV have identified key interactions between SARS-CoV spike protein and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. One of the goals of SARS-CoV research was to build an atomic-level iterative framework of virus-receptor interactions to facilitate epidemic surveillance, predict species-specific receptor usage, and identify potential animal hosts and animal models of viruses. Based on the sequence of 2019-nCoV spike protein, we apply this predictive framework to provide novel insights into the receptor usage and likely host range of 2019-nCoV. This study provides a robust test of this reiterative framework, providing the basic, translational, and public health research communities with predictive insights that may help study and battle this novel 2019-nCoV.

Keywords: 2019-nCoV; SARS coronavirus; angiotensin-converting enzyme 2; animal reservoir; cross-species transmission; human-to-human transmission.

FIG 1

Structural analysis of human ACE2 recognition by 2019-nCoV and SARS-CoV. (A) Overall structure of human SARS-CoV RBD (year 2002) complexed with human ACE2. PDB ID is 2AJF. ACE2 is in green, the core of RBD (receptor-binding domain) is in cyan, and RBM (receptor-binding motif) is in magenta. (B) Critical residue changes in the RBMs of SARS-CoV and 2019-nCoV. All these five residues in SARS-CoV underwent natural selections and were shown to be critical for ACE2 recognition, cell entry, and host range of SARS-CoV. The residue numbers are shown as in SARS-CoV RBD, with the corresponding residue numbers in 2019-nCoV shown in parentheses. For viral adaption to ACE2, > means “is more adapted”, >>> means “is much more adapted,” and = means “is similarly adapted.” Information about the two most critical residues, 479 and 487, is in red. (C) Experimentally determined structure of the interface between a designed SARS-CoV RBD (optimized for human ACE2 recognition) and human ACE2. PDB ID is 3SCI. (D) Modeled structure of the interface between 2019-nCoV RBD and human ACE2. Here, mutations were introduced to the RBD region in panel C based on sequence differences between SARS-CoV and 2019-nCoV. GenBank accession numbers are MN908947.1 for 2019-nCoV spike, NC_004718.3 for human SARS-CoV spike (year 2002; strain Tor2), AGZ48818.1 for bat SARS-CoV spike (year 2013; strain Rs3367), AY304486.1 for civet SARS-CoV spike (year 2002; SZ3), and AY525636 for human/civet SARS-CoV spike (year 2003; strain GD03). References for the other sequences are in parentheses as follows: civet SARS-CoV spike (year 2005) (9); human SARS-CoV spike (year 2008) (8).

FIG 2

Spike phylogeny of representative β-genus lineage b coronaviruses. The spike protein sequences of selected β-genus lineage b coronaviruses were aligned and phylogenetically compared. Sequences were aligned using free end gaps with the Blosum62 cost matrix in Geneious Prime. The tree was constructed using the neighbor-joining method based on the multiple sequence alignment, also in Geneious Prime. Numbers at the end of each sequence correspond to the GenBank accession number. The radial phylogram was exported from Geneious and then rendered for publication using EvolView (evolgenius.info) and Adobe Illustrator CC 2020.

FIG 3

Sequence comparison of 2019-nCoV and SARS-CoV. (A) Sequence alignment of SARS-CoV and 2019-nCoV RBDs. RBM residues are in magenta. The five critical residues in Fig. 1B are in blue. ACE2-contacting residues are shaded. Asterisks indicate positions that have a single, fully conserved residue. Colons indicate positions that have strongly conserved residues. Periods indicate positions that have weakly conserved residues. (B) Sequence similarities of SARS-CoV and 2019-nCoV in the spike protein, RBD, and RBM, respectively. (C) Sequence similarities of MERS-CoV and HKU4 virus in the spike protein, RBD, and RBM, respectively. GenBank accession numbers are JX869059.2 for human MERS-CoV spike and NC_009019.1 for bat HKU4-CoV spike.

FIG 4

Structural analysis of animal ACE2 recognition by 2019-nCoV and SARS-CoV. (A) Critical changes in virus-contacting residues of ACE2 from different host species. GenBank accession numbers for ACE2 are as follows: NM_001371415.1 (human), AAX63775.1 (civet), KC881004.1 (bat), NP_001123985.1 (mouse), AY881244 (rat), NP_001116542.1 (pig), AB208708 (ferret), NM_001039456 (cat), Q5RFN1 (orangutan), and AY996037 (monkey). (B) Experimentally determined structure of the interface between a designed SARS-CoV RBD (optimized for civet ACE2 recognition) and civet ACE2. PDB ID is 3SCK. (C) Modeled structure of the interface between 2019-nCoV RBD and civet ACE2. Here, mutations were introduced to the RBD region in panel B based on sequence differences between SARS-CoV and 2019-nCoV.