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Analysis of angiotensin-converting enzyme 2 (ACE2) from different species sheds some light on cross-species receptor usage of a novel coronavirus 2019-nCoV
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Dear Editor,
A novel coronavirus from Wuhan in central China, named 2019-nCoV, has recently caused an epidemic of pneumonia in humans and posed a huge threat to global public health.1 , 2 To the date 06/02/2020, 2019-nCoV has led to more than 31,000 confirmed cases and 637 deaths in China according to National Health Commission of the People's Republic of China (http://en.nhc.gov.cn/index.html). Cases have also been documented in a growing number of other international locations, including the United States (https://www.cdc.gov/coronavirus/2019-ncov/index.html). As a consequence, it is urgent to develop effective measures to control this novel coronavirus on the basis of its pathogenesis.
Host receptor recognition is a determinant for virus infection. During the time of this letter preparation, three works have just been published to explore the receptor usage of 2019-nCoV. A work by Zheng-Li Shi et al. has shown that angiotensin-converting enzyme 2 (ACE2), the receptor for severe acute respiratory syndrome coronavirus (SARS-CoV),3 from human, Rhinolophus sinicus bat, civet, swine but not mouse mediate 2019-nCoV infection in vitro, while the detailed mechanisms are not yet determined.4 The other two works have reported or predicted human ACE2 usage of 2019-nCoV in a similar way to SARS-CoV mainly based on the coronavirus spike (S) glycoproteins.5 , 6 Considering the fact that the S proteins mutate and gain capability to recognize host receptors among species,7 , 8 there is still a lack of analyses on receptor usage of 2019-nCoV from the receptor perspective, which does not evolve as quickly as viruses.
Here, we firstly performed amino acid sequence alignment of ACE2 from different species, including human, five non-human primates (gibbon, green monkey, macaque, orangutan and chimpanzee), two companion animals (cat and dog), six domestic animals (bovine, sheep, goat, swine, horse and chicken), three wild animals (ferret, civet and Chinese horseshoe bat) and two rodents (mouse and rat). The alignment by Clustal W 2.1 shows that they share a high sequence similarity except chicken (data not shown). The result suggests that 2019-nCoV of probable bat origin may not interact with chicken ACE2 and subsequently infect them, which were not considered in the following analyses. In ACE2, the regions at position 30–41, 82–84 and 353–357 are demonstrated to be involved in the interaction with SARS-CoV S protein, where the residues at positions 31, 35, 38, 82 and 353 are critical.9 Therefore, we took a close comparison in these regions and residues. As shown in Fig. 1 , human and non-human primates share the identity sequences in the regions and residues, implying that ACE2 from non-human primates may recognize 2019-nCoV and mediate its infection. As a result, non-human primates may be susceptible to 2019-nCoV and serve as animal models for antiviral research or intermediate hosts for cross-species transmission. In Fig. 1, the residues of most companion, domestic and wild animals are conserved, especially for the critical ones stated above, while certain ones are variable. For example, Lys31, Glu35, Asp/Glu38 and Lys353 are conserved, which probably form salt bridges. Interestingly, the changes at positions 31, 38 and 82 are observed. These changes suggest steric hindrance and electrostatic interference for host-virus interaction. Taking civet ACE2 as an example, the change of Lys31 to Thr31 is likely to form a hydrogen bond instead of a salt bridge. In addition, the polar side chain of Thr82 may influence the hydrophobic interaction of the original Met82. All these changes may result in a lower binding affinity. However, an additional region covering residues 90–93 has been shown to be involved in civet ACE2 binding to SARS-CoV and enhance their interaction.10 Consequently, we can't preclude the existence of other regions to compensate for the residue changes. With most residues in human ACE2, the ones from these compaion, domestic and wild animals may be favorable for 2019-nCoV recognition, which is in consistent with the recent work by Zheng-Li Shi et al. In case cross-species transmission, close contact with sick or asymptomatic companion, domestic and wild animals should be cautious, such as for workers in livestock farming and travellers in the wild.
Fig. 1 Sequence alignment of ACE2 from human (UniProt entry Q9BYF1), Northern white-cheeked gibbon (UniProt entry G1RE79), green monkey (UniProt entry A0A0D9RQZ0), crab-eating macaque (UniProt entry A0A2K5X283), Sumatran orangutan (UniProt entry Q5RFN1), chimpanzee (UniProt entry A0A2J8KU96), cat (UniProt entry Q56H28), dog (UniProt entry J9P7Y2), bovine (UniProt entry Q58DD0), sheep (UniProt entry W5PSB6), goat (UniProt entry A0A452EVJ5), swine (UniProt entry K7GLM4), horse (UniProt entry F6V9L3), ferret (UniProt entry Q2WG88), civet (UniProt entry Q56NL1), Chinese horseshoe bat (UniProt entry E2DHI7), mouse (UniProt entry Q8R0I0) and rat (UniProt entry Q5EGZ1). (A) Region 30–41. (B) Region 82–84. (C) Region 353–357. The conserved residues in the regions are colored in red and the critical residues are marked by asterisks.
In contrast, certain significant changes occur in the mouse and/or rat ACE2 compared to the human one (Fig. 1). The Asn31 and Ser82 in mouse ACE2 may not form favorable interactions with 2019-nCoV due to their electrostatic or hydrophilic characteristics. Importantly, the change into His353 in both mouse and rat ACE2 does not form a strong salt bridge as Lys353 does. Since the structural information for mouse and rat ACE2 is unavailable, we carried out homology modeling using human ACE2 (PDB code 2AJF) as template on online (https://swissmodel.expasy.org) for further analyses. In Fig. 2 A, the change into Ser82 in mouse ACE2 may interfere with the hydrophobic interaction of the original Met82. Additionally, the changes into Asn31 and His353 definitely affect the salt bridge formation and electrostatic potential. The change into His353 in rat ACE2 is similar in the effect on receptor-virus interaction (Fig. 2B). These analyses partially explain why mouse ACE2 does not mediate 2019-nCoV infection reported by Zheng-Li Shi et al. and assume that rodents are not likely to be the susceptible host.
Fig. 2 Structural analyses of the human ACE2 (PDB code 2AJF) with the modeled mouse (A) and rat (B) ones in cartoon diagrams and surface electrostatic potential maps. The regions 30–41, 82–84 and 353–357 are enlarged and the critical residues are labeled. The changed ones affecting the electrostatic potential are labeled and circled in dashed lines. The electrostatic potential is colored from −62 to +62 kiloteslas/charge.
In conclusion, we conducted sequence and structural analyses of angiotensin-converting enzyme 2 (ACE2) from different species, which sheds some light on cross-species receptor usage of 2019-nCoV. All these analyses raise an alert on a potential interspecies transmission of 2019-nCoV and propose further surveillance in other animal populations. Structural studies on human and other species ACE2 in complex with 2019-nCoV spike protein will contribute to understanding cross-species receptor usage of this novel coronavirus.
Declaration of Competing Interest
The authors declare no conflict of interest.
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Dear Editor,
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p
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A novel coronavirus from Wuhan in central China, named 2019-nCoV, has recently caused an epidemic of pneumonia in humans and posed a huge threat to global public health.1 , 2 To the date 06/02/2020, 2019-nCoV has led to more than 31,000 confirmed cases and 637 deaths in China according to National Health Commission of the People's Republic of China (http://en.nhc.gov.cn/index.html). Cases have also been documented in a growing number of other international locations, including the United States (https://www.cdc.gov/coronavirus/2019-ncov/index.html). As a consequence, it is urgent to develop effective measures to control this novel coronavirus on the basis of its pathogenesis.
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p
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Host receptor recognition is a determinant for virus infection. During the time of this letter preparation, three works have just been published to explore the receptor usage of 2019-nCoV. A work by Zheng-Li Shi et al. has shown that angiotensin-converting enzyme 2 (ACE2), the receptor for severe acute respiratory syndrome coronavirus (SARS-CoV),3 from human, Rhinolophus sinicus bat, civet, swine but not mouse mediate 2019-nCoV infection in vitro, while the detailed mechanisms are not yet determined.4 The other two works have reported or predicted human ACE2 usage of 2019-nCoV in a similar way to SARS-CoV mainly based on the coronavirus spike (S) glycoproteins.5 , 6 Considering the fact that the S proteins mutate and gain capability to recognize host receptors among species,7 , 8 there is still a lack of analyses on receptor usage of 2019-nCoV from the receptor perspective, which does not evolve as quickly as viruses.
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Here, we firstly performed amino acid sequence alignment of ACE2 from different species, including human, five non-human primates (gibbon, green monkey, macaque, orangutan and chimpanzee), two companion animals (cat and dog), six domestic animals (bovine, sheep, goat, swine, horse and chicken), three wild animals (ferret, civet and Chinese horseshoe bat) and two rodents (mouse and rat). The alignment by Clustal W 2.1 shows that they share a high sequence similarity except chicken (data not shown). The result suggests that 2019-nCoV of probable bat origin may not interact with chicken ACE2 and subsequently infect them, which were not considered in the following analyses. In ACE2, the regions at position 30–41, 82–84 and 353–357 are demonstrated to be involved in the interaction with SARS-CoV S protein, where the residues at positions 31, 35, 38, 82 and 353 are critical.9 Therefore, we took a close comparison in these regions and residues. As shown in Fig. 1 , human and non-human primates share the identity sequences in the regions and residues, implying that ACE2 from non-human primates may recognize 2019-nCoV and mediate its infection. As a result, non-human primates may be susceptible to 2019-nCoV and serve as animal models for antiviral research or intermediate hosts for cross-species transmission. In Fig. 1, the residues of most companion, domestic and wild animals are conserved, especially for the critical ones stated above, while certain ones are variable. For example, Lys31, Glu35, Asp/Glu38 and Lys353 are conserved, which probably form salt bridges. Interestingly, the changes at positions 31, 38 and 82 are observed. These changes suggest steric hindrance and electrostatic interference for host-virus interaction. Taking civet ACE2 as an example, the change of Lys31 to Thr31 is likely to form a hydrogen bond instead of a salt bridge. In addition, the polar side chain of Thr82 may influence the hydrophobic interaction of the original Met82. All these changes may result in a lower binding affinity. However, an additional region covering residues 90–93 has been shown to be involved in civet ACE2 binding to SARS-CoV and enhance their interaction.10 Consequently, we can't preclude the existence of other regions to compensate for the residue changes. With most residues in human ACE2, the ones from these compaion, domestic and wild animals may be favorable for 2019-nCoV recognition, which is in consistent with the recent work by Zheng-Li Shi et al. In case cross-species transmission, close contact with sick or asymptomatic companion, domestic and wild animals should be cautious, such as for workers in livestock farming and travellers in the wild.
Fig. 1 Sequence alignment of ACE2 from human (UniProt entry Q9BYF1), Northern white-cheeked gibbon (UniProt entry G1RE79), green monkey (UniProt entry A0A0D9RQZ0), crab-eating macaque (UniProt entry A0A2K5X283), Sumatran orangutan (UniProt entry Q5RFN1), chimpanzee (UniProt entry A0A2J8KU96), cat (UniProt entry Q56H28), dog (UniProt entry J9P7Y2), bovine (UniProt entry Q58DD0), sheep (UniProt entry W5PSB6), goat (UniProt entry A0A452EVJ5), swine (UniProt entry K7GLM4), horse (UniProt entry F6V9L3), ferret (UniProt entry Q2WG88), civet (UniProt entry Q56NL1), Chinese horseshoe bat (UniProt entry E2DHI7), mouse (UniProt entry Q8R0I0) and rat (UniProt entry Q5EGZ1). (A) Region 30–41. (B) Region 82–84. (C) Region 353–357. The conserved residues in the regions are colored in red and the critical residues are marked by asterisks.
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Fig. 1 Sequence alignment of ACE2 from human (UniProt entry Q9BYF1), Northern white-cheeked gibbon (UniProt entry G1RE79), green monkey (UniProt entry A0A0D9RQZ0), crab-eating macaque (UniProt entry A0A2K5X283), Sumatran orangutan (UniProt entry Q5RFN1), chimpanzee (UniProt entry A0A2J8KU96), cat (UniProt entry Q56H28), dog (UniProt entry J9P7Y2), bovine (UniProt entry Q58DD0), sheep (UniProt entry W5PSB6), goat (UniProt entry A0A452EVJ5), swine (UniProt entry K7GLM4), horse (UniProt entry F6V9L3), ferret (UniProt entry Q2WG88), civet (UniProt entry Q56NL1), Chinese horseshoe bat (UniProt entry E2DHI7), mouse (UniProt entry Q8R0I0) and rat (UniProt entry Q5EGZ1). (A) Region 30–41. (B) Region 82–84. (C) Region 353–357. The conserved residues in the regions are colored in red and the critical residues are marked by asterisks.
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Fig. 1
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Sequence alignment of ACE2 from human (UniProt entry Q9BYF1), Northern white-cheeked gibbon (UniProt entry G1RE79), green monkey (UniProt entry A0A0D9RQZ0), crab-eating macaque (UniProt entry A0A2K5X283), Sumatran orangutan (UniProt entry Q5RFN1), chimpanzee (UniProt entry A0A2J8KU96), cat (UniProt entry Q56H28), dog (UniProt entry J9P7Y2), bovine (UniProt entry Q58DD0), sheep (UniProt entry W5PSB6), goat (UniProt entry A0A452EVJ5), swine (UniProt entry K7GLM4), horse (UniProt entry F6V9L3), ferret (UniProt entry Q2WG88), civet (UniProt entry Q56NL1), Chinese horseshoe bat (UniProt entry E2DHI7), mouse (UniProt entry Q8R0I0) and rat (UniProt entry Q5EGZ1). (A) Region 30–41. (B) Region 82–84. (C) Region 353–357. The conserved residues in the regions are colored in red and the critical residues are marked by asterisks.
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Sequence alignment of ACE2 from human (UniProt entry Q9BYF1), Northern white-cheeked gibbon (UniProt entry G1RE79), green monkey (UniProt entry A0A0D9RQZ0), crab-eating macaque (UniProt entry A0A2K5X283), Sumatran orangutan (UniProt entry Q5RFN1), chimpanzee (UniProt entry A0A2J8KU96), cat (UniProt entry Q56H28), dog (UniProt entry J9P7Y2), bovine (UniProt entry Q58DD0), sheep (UniProt entry W5PSB6), goat (UniProt entry A0A452EVJ5), swine (UniProt entry K7GLM4), horse (UniProt entry F6V9L3), ferret (UniProt entry Q2WG88), civet (UniProt entry Q56NL1), Chinese horseshoe bat (UniProt entry E2DHI7), mouse (UniProt entry Q8R0I0) and rat (UniProt entry Q5EGZ1). (A) Region 30–41. (B) Region 82–84. (C) Region 353–357. The conserved residues in the regions are colored in red and the critical residues are marked by asterisks.
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In contrast, certain significant changes occur in the mouse and/or rat ACE2 compared to the human one (Fig. 1). The Asn31 and Ser82 in mouse ACE2 may not form favorable interactions with 2019-nCoV due to their electrostatic or hydrophilic characteristics. Importantly, the change into His353 in both mouse and rat ACE2 does not form a strong salt bridge as Lys353 does. Since the structural information for mouse and rat ACE2 is unavailable, we carried out homology modeling using human ACE2 (PDB code 2AJF) as template on online (https://swissmodel.expasy.org) for further analyses. In Fig. 2 A, the change into Ser82 in mouse ACE2 may interfere with the hydrophobic interaction of the original Met82. Additionally, the changes into Asn31 and His353 definitely affect the salt bridge formation and electrostatic potential. The change into His353 in rat ACE2 is similar in the effect on receptor-virus interaction (Fig. 2B). These analyses partially explain why mouse ACE2 does not mediate 2019-nCoV infection reported by Zheng-Li Shi et al. and assume that rodents are not likely to be the susceptible host.
Fig. 2 Structural analyses of the human ACE2 (PDB code 2AJF) with the modeled mouse (A) and rat (B) ones in cartoon diagrams and surface electrostatic potential maps. The regions 30–41, 82–84 and 353–357 are enlarged and the critical residues are labeled. The changed ones affecting the electrostatic potential are labeled and circled in dashed lines. The electrostatic potential is colored from −62 to +62 kiloteslas/charge.
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Fig. 2 Structural analyses of the human ACE2 (PDB code 2AJF) with the modeled mouse (A) and rat (B) ones in cartoon diagrams and surface electrostatic potential maps. The regions 30–41, 82–84 and 353–357 are enlarged and the critical residues are labeled. The changed ones affecting the electrostatic potential are labeled and circled in dashed lines. The electrostatic potential is colored from −62 to +62 kiloteslas/charge.
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Fig. 2
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Structural analyses of the human ACE2 (PDB code 2AJF) with the modeled mouse (A) and rat (B) ones in cartoon diagrams and surface electrostatic potential maps. The regions 30–41, 82–84 and 353–357 are enlarged and the critical residues are labeled. The changed ones affecting the electrostatic potential are labeled and circled in dashed lines. The electrostatic potential is colored from −62 to +62 kiloteslas/charge.
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Structural analyses of the human ACE2 (PDB code 2AJF) with the modeled mouse (A) and rat (B) ones in cartoon diagrams and surface electrostatic potential maps. The regions 30–41, 82–84 and 353–357 are enlarged and the critical residues are labeled. The changed ones affecting the electrostatic potential are labeled and circled in dashed lines. The electrostatic potential is colored from −62 to +62 kiloteslas/charge.
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In conclusion, we conducted sequence and structural analyses of angiotensin-converting enzyme 2 (ACE2) from different species, which sheds some light on cross-species receptor usage of 2019-nCoV. All these analyses raise an alert on a potential interspecies transmission of 2019-nCoV and propose further surveillance in other animal populations. Structural studies on human and other species ACE2 in complex with 2019-nCoV spike protein will contribute to understanding cross-species receptor usage of this novel coronavirus.
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Declaration of Competing Interest
The authors declare no conflict of interest.
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Declaration of Competing Interest
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The authors declare no conflict of interest.
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Acknowledgments
This work was supported by Henan Emergency Project for Prevention and Control of 2019 Novel Coronavirus, the Earmarked Fund for Modern Agro-industry Technology Research System of China (CARS-35) and the Special Fund for Henan Agriculture Research System (S2012-06). The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
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Acknowledgments
This work was supported by Henan Emergency Project for Prevention and Control of 2019 Novel Coronavirus, the Earmarked Fund for Modern Agro-industry Technology Research System of China (CARS-35) and the Special Fund for Henan Agriculture Research System (S2012-06). The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
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Acknowledgments
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This work was supported by Henan Emergency Project for Prevention and Control of 2019 Novel Coronavirus, the Earmarked Fund for Modern Agro-industry Technology Research System of China (CARS-35) and the Special Fund for Henan Agriculture Research System (S2012-06). The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
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