Volume 10, Issue 1 (3-2022)                   JoMMID 2022, 10(1): 1-9 | Back to browse issues page

XML Print

Download citation:
BibTeX | RIS | EndNote | Medlars | ProCite | Reference Manager | RefWorks
Send citation to:
Lopes L R, Carvalho de Lucca Pina N, Da Silva Junior A C, Bandiera-Paiva P. Evolutionary Analysis of Mammalian ACE2 and the Key Residues Involved in Binding to the Spike Protein Revealed Potential SARS-CoV-2 Hosts. JoMMID 2022; 10 (1) :1-9
URL: http://jommid.pasteur.ac.ir/article-1-436-en.html
Evolutionary Analysis of Mammalian ACE2 and the Key Residues Involved in Binding to the Spike Protein Revealed Potential SARS-CoV-2 Hosts
Luciano Rodrigo Lopes * , Natália Carvalho de Lucca Pina , Antonio Carlos Da Silva Junior , Paulo Bandiera-Paiva
Bioinformatics and Bio-Data Science Division, Health Informatics Department, Universidade Federal de São Paulo, UNIFESP, São Paulo, SP, Brazil
Abstract:   (1745 Views)
Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spilled over to humans via wild mammals, entering the host cell using angiotensin-converting enzyme 2 (ACE2) as receptor through Spike (S) protein binding. While SARS-CoV-2 became fully adapted to humans and globally spread, some mammal species were infected back. The present study evaluated the potential risk of mammals becoming hosts for SARS-CoV-2 through bioinformatics prediction based on ACE2 receptors. Methods: We used evolutionary bioinformatic approaches and comparative analysis of ACE2 critical residues that bind SARS-CoV-2 S-protein and predicted potential SARS-CoV-2 hosts among mammals and assessed their risk. Results: ACE2 phylogenetic tree placed primates close to rodents and rabbits. Felines, rodents, and rabbits had higher ACE2 similarities than human ACE2 (hACE2). Farmed animals, such as bovids, swine, and equids, had similar ACE2 compared to hACE2; however, these animals showed low SARS-CoV-2 susceptibility. Some cetaceans also presented high similarities in ACE2 key residues with hACE2. Conclusion: Here, we showed wild and domestic mammals with a low divergence of ACE2 compared to humans, discussing their possible chance of being infected, especially those animals kept as livestock or pets. Regarding the feasible transmission through contaminated water, cetaceans can be at risk of SARS-CoV-2 infection. Extensive surveillance of SARS-CoV-2 should be applied to prevent new coronavirus outbreaks and preserve mammals from infectious threats.
Keywords: SARS-CoV-2, Coronavirus, ACE2, Mammals, Wildlife
Full-Text [PDF 1557 kb]   (393 Downloads)    
Type of Study: Original article | Subject: Host-pathogen interactions and susceptibility factors
Received: 2021/12/19 | Accepted: 2022/03/11 | Published: 2022/04/4
attachement [JPG 6866 KB]  (79 Download)
References
1. 1. Jelinek HF, Mousa M, Alefishat E, Osman W, Spence I, Bu D, et al. Evolution, Ecology, and Zoonotic Transmission of Betacoronaviruses: A Review. Front Vet Sci. 2021; 8: 380. [DOI:10.3389/fvets.2021.644414]
2. Islam A, Ferdous J, Islam S, Sayeed MdA, Dutta Choudhury S, Saha O, et al. Evolutionary Dynamics and Epidemiology of Endemic and Emerging Coronaviruses in Humans, Domestic Animals, and Wildlife. Viruses. 2021; 13 (10): 1908. [DOI:10.3390/v13101908]
3. Shang J, Ye G, Shi K, Wan Y, Luo C, Aihara H, et al. Structural basis of receptor recognition by SARS-CoV-2. Nature. 2020; 581 (7807): 221-4. [DOI:10.1038/s41586-020-2179-y]
4. Zhou P, Yang X-L, Wang X-G, Hu B, Zhang L, Zhang W, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020; 579 (7798): 270-3. [DOI:10.1038/s41586-020-2012-7]
5. Luan J, Lu Y, Jin X, Zhang L. Spike protein recognition of mammalian ACE2 predicts the host range and an optimized ACE2 for SARS-CoV-2 infection. Biochem Biophys Res Commun. 2020; 526 (1): 165-9. [DOI:10.1016/j.bbrc.2020.03.047]
6. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32 (5): 1792-7. [DOI:10.1093/nar/gkh340]
7. Galtier N, Gouy M, Gautier C. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci CABIOS. 1996; 12 (6): 543-8. [DOI:10.1093/bioinformatics/12.6.543]
8. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Bioinformatics. 1992; 8 (3): 275-82. [DOI:10.1093/bioinformatics/8.3.275]
9. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 2018; 35 (6): 1547-9. [DOI:10.1093/molbev/msy096]
10. Brown EEF, Rezaei R, Jamieson TR, Dave J, Martin NT, Singaravelu R, et al. Characterization of Critical Determinants of ACE2-SARS CoV-2 RBD Interaction. Int J Mol Sci. 2021; 22 (5): 2268. [DOI:10.3390/ijms22052268]
11. Wheeler TJ, Clements J, Finn RD. Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models. BMC Bioinformatics. 2014; 15 (1): 7. [DOI:10.1186/1471-2105-15-7]
12. Lu S, Zhao Y, Yu W, Yang Y, Gao J, Wang J, et al. Comparison of SARS-CoV-2 infections among 3 species of non-human primates. 2020; p. 2020.04.08.031807. Available from: https://www.biorxiv.org/content/10.1101/2020.04.08.031807v2. [DOI:10.1101/2020.04.08.031807]
13. Singh DK, Singh B, Ganatra SR, Gazi M, Cole J, Thippeshappa R, et al. Responses to acute infection with SARS-CoV-2 in the lungs of rhesus macaques, baboons and marmosets. Nat Microbiol. 2021; 6 (1): 73-86. [DOI:10.1038/s41564-020-00841-4]
14. Blair RV, Vaccari M, Doyle-Meyers LA, Roy CJ, Russell-Lodrigue K, Fahlberg M, et al. Acute Respiratory Distress in Aged, SARS-CoV-2-Infected African Green Monkeys but Not Rhesus Macaques. Am J Pathol. 2021; 191 (2): 274-82. [DOI:10.1016/j.ajpath.2020.10.016]
15. Sacchetto L, Chaves BA, Costa ER, de Menezes Medeiros AS, Gordo M, Araújo DB, et al. Lack of Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spillover in Free-Living Neotropical Non-Human Primates, Brazil. Viruses. 2021; 13 (10): 1933. [DOI:10.3390/v13101933]
16. Ramilison ML, Andriatsitohaina B, Chell C, Rakotondravony R, Radespiel U, Ramsay MS. Distribution of the critically endangered Coquerel's sifaka (Propithecus coquereli) across a fragmented landscape in NW Madagascar. Afr J Ecol. 2021; 59 (2): 350-8. [DOI:10.1111/aje.12844]
17. Salmona J, Jan F, Rasolondraibe E, Besolo A, Ousseni DS, Beck A, et al. Extensive survey of the Endangered Coquerel's sifaka Propithecus coquereli. Endanger Species Res. 2014; 25 (2): 175-83. [DOI:10.3354/esr00622]
18. Guan Y, Zheng BJ, He YQ, Liu XL, Zhuang ZX, Cheung CL, et al. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science. 2003; 302 (5643): 276-8. [DOI:10.1126/science.1087139]
19. Shi J, Wen Z, Zhong G, Yang H, Wang C, Huang B, et al. Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2. Science. 2020; 368 (6494): 1016-20. [DOI:10.1126/science.abb7015]
20. Rudd JM, Tamil Selvan M, Cowan S, Kao Y-F, Midkiff CC, Narayanan S, et al. Clinical and Histopathologic Features of a Feline SARS-CoV-2 Infection Model Are Analogous to Acute COVID-19 in Humans. Viruses. 2021; 13 (8): 1550. [DOI:10.3390/v13081550]
21. McAloose D, Laverack M, Wang L, Killian ML, Caserta LC, Yuan F, et al. From People to Panthera: Natural SARS-CoV-2 Infection in Tigers and Lions at the Bronx Zoo. mBio. 2020; 11 (5): e02220-20 . [DOI:10.1128/mBio.02220-20]
22. Mishra A, Kumar N, Bhatia S, Aasdev A, Kanniappan S, Sekhar AT, et al. SARS-CoV-2 Delta Variant among Asiatic Lions, India. Emerg Infect Dis. 2021; 27 (10): 2723-25. [DOI:10.3201/eid2710.211500]
23. Fernández-Bellon H, Rodon J, Fernández-Bastit L, Almagro V, Padilla-Solé P, Lorca-Oró C, et al. Monitoring Natural SARS-CoV-2 Infection in Lions (Panthera leo) at the Barcelona Zoo: Viral Dynamics and Host Responses. Viruses. 2021; 13 (9): 1683. [DOI:10.3390/v13091683]
24. Chen D, Sun J, Zhu J, Ding X, Lan T, Wang X, et al. Single cell atlas for 11 non-model mammals, reptiles and birds. Nat Commun. 2021; 12 (1): 7083. [DOI:10.1038/s41467-021-27162-2]
25. Giraldo-Ramirez S, Rendon-Marin S, Jaimes JA, Martinez-Gutierrez M, Ruiz-Saenz J. SARS-CoV-2 Clinical Outcome in Domestic and Wild Cats: A Systematic Review. Animals. 2021; 11 (7): 2056. [DOI:10.3390/ani11072056]
26. Hobbs EC, Reid TJ. Animals and SARS-CoV-2: Species susceptibility and viral transmission in experimental and natural conditions, and the potential implications for community transmission. Transbound Emerg Dis. 2021; 68 (4): 1850-67. [DOI:10.1111/tbed.13885]
27. Hammer AS, Quaade ML, Rasmussen TB, Fonager J, Rasmussen M, Mundbjerg K, et al. SARS-CoV-2 Transmission between Mink (Neovison vison) and Humans, Denmark. Emerg Infect Dis. 2021; 27 (2): 547-51. [DOI:10.3201/eid2702.203794]
28. van Aart AE, Velkers FC, Fischer EAJ, Broens EM, Egberink H, Zhao S, et al. SARS-CoV-2 infection in cats and dogs in infected mink farms. Transbound Emerg Dis. 2021; 10.1111/tbed.14173: 1-7. [DOI:10.22541/au.161821264.49927405/v1]
29. Munnink BBO, Sikkema RS, Nieuwenhuijse DF, Molenaar RJ, Munger E, Molenkamp R, et al. Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans. Science. 2021; 371 (6525): 172-7. [DOI:10.1126/science.abe5901]
30. Sun K, Gu L, Ma L, Duan Y. Atlas of ACE2 gene expression reveals novel insights into transmission of SARS-CoV-2. Heliyon. 2021; 7 (1): e05850. [DOI:10.1016/j.heliyon.2020.e05850]
31. Chandler JC, Bevins SN, Ellis JW, Linder TJ, Tell RM, Jenkins-Moore M, et al. SARS-CoV-2 exposure in wild white-tailed deer (Odocoileus virginianus). Proc Natl Acad Sci U S A. 2021; 118 (47): e2114828118. [DOI:10.1073/pnas.2114828118]
32. Palmer MV, Martins M, Falkenberg S, Buckley A, Caserta LC, Mitchell PK, et al. Susceptibility of white-tailed deer (Odocoileus virginianus) to SARS-CoV-2. J Virol. 2021: 95 (11): e00083-21 [DOI:10.1128/JVI.00083-21]
33. McShea WJ. Ecology and management of white-tailed deer in a changing world. Ann N Y Acad Sci. 2012; 1249: 45-56. [DOI:10.1111/j.1749-6632.2011.06376.x]
34. Lopes LR, de Mattos Cardillo G, de Lucca Pina NC, da Silva Junior AC, Kasinski SK, Bandiera-Paiva P. Prediction of SARS-CoV-2 hosts among Brazilian mammals and new coronavirus transmission chain using evolutionary bioinformatics. Anim Dis. 2021; 1 (1): 20. [DOI:10.1186/s44149-021-00020-w]
35. Pickering BS, Smith G, Pinette MM, Embury-Hyatt C, Moffat E, Marszal P, et al. Susceptibility of Domestic Swine to Experimental Infection with Severe Acute Respiratory Syndrome Coronavirus 2. Emerg Infect Dis. 2021; 27 (1): 104-112 [DOI:10.3201/eid2701.203399]
36. Ulrich L, Wernike K, Hoffmann D, Mettenleiter TC, Beer M. Experimental Infection of Cattle with SARS-CoV-2. Emerg Infect Dis. 2020; 26 (12): 2979-81. [DOI:10.3201/eid2612.203799]
37. Montagutelli X, Prot M, Levillayer L, Salazar EB, Jouvion G, Conquet L, et al. The B1.351 and P.1 variants extend SARS-CoV-2 host range to mice. 2021; p. 2021.03.18.436013. Available from: https://www.biorxiv.org/content/10.1101/2021.03.18.436013v1
38. Lewnard JA, Mora AM, Nkwocha O, Kogut K, Rauch SA, Morga N, et al. Prevalence and Clinical Profile of Severe Acute Respiratory Syndrome Coronavirus 2 Infection among Farmworkers, California, USA, June-November 2020. Emerg Infect Dis. 2021; 27 (5): 1330-42 [DOI:10.3201/eid2705.204949]
39. Sit TH, Brackman CJ, Ip SM, Tam KW, Law PY, To EM, et al. Canine SARS-CoV-2 infection. Nature. 2020; 586 (7831): 776-8. [DOI:10.1038/s41586-020-2334-5]
40. Bosco-Lauth AM, Hartwig AE, Porter SM, Gordy PW, Nehring M, Byas AD, et al. Experimental infection of domestic dogs and cats with SARS-CoV-2: Pathogenesis, transmission, and response to reexposure in cats. Proc Natl Acad Sci. 2020; 117 (42): 26382-8. [DOI:10.1073/pnas.2013102117]
41. Jemeršić L, Lojkić I, Krešić N, Keros T, Zelenika TA, Jurinović L, et al. Investigating the Presence of SARS CoV-2 in Free-Living and Captive Animals. Pathog Basel Switz. 2021; 10 (6): 635. [DOI:10.3390/pathogens10060635]
42. Freuling CM, Breithaupt A, Müller T, Sehl J, Balkema-Buschmann A, Rissmann M, et al. Susceptibility of Raccoon Dogs for Experimental SARS-CoV-2 Infection. Emerg Infect Dis. 2020; 26 (12): 2982-5. [DOI:10.3201/eid2612.203733]
43. Mykytyn AZ, Lamers MM, Okba NMA, Breugem TI, Schipper D, van den Doel PB, et al. Susceptibility of rabbits to SARS-CoV-2. Emerg Microbes Infect. 2021; 10 (1): 1-7. [DOI:10.1080/22221751.2020.1868951]
44. Geller C, Varbanov M, Duval RE. Human Coronaviruses: Insights into Environmental Resistance and Its Influence on the Development of New Antiseptic Strategies. Viruses. 2012; 4 (11): 3044-68. [DOI:10.3390/v4113044]
45. Martin J, Klapsa D, Wilton T, Zambon M, Bentley E, Bujaki E, et al. Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic. Viruses. 2020; 12 (10): E1144. [DOI:10.3390/v12101144]
46. Casanova L, Rutala WA, Weber DJ, Sobsey MD. Survival of surrogate coronaviruses in water. Water Res. 2009; 43 (7): 1893-8. [DOI:10.1016/j.watres.2009.02.002]
47. Loutit MW, Lewis G. Faecal bacteria from sewage effluent in sediments around an ocean outfall. N Z J Mar Freshw Res. 1985; 19 (2): 179-85. [DOI:10.1080/00288330.1985.9516085]
48. Mihindukulasuriya KA, Wu G, St Leger J, Nordhausen RW, Wang D. Identification of a novel coronavirus from a beluga whale by using a panviral microarray. J Virol. 2008; 82 (10): 5084-8. [DOI:10.1128/JVI.02722-07]
Add your comments about this article : Your username or Email:
CAPTCHA
Send email to the article author

Rights and permissions
Creative Commons License This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.