Differential Stepwise Evolution of SARS Coronavirus Functional Proteins in Different Host Species

Overview

Journal BMC Evol Biol

Publisher Biomed Central

Specialty Biology

Date 2009 Mar 6

PMID 19261195

Citations 30

Authors

Xianchun Tang

Gang Li

Nikos Vasilakis

Yuan Zhang

Zhengli Shi

Yang Zhong

Lin-Fa Wang

Shuyi Zhang

Affiliations

Soon will be listed here.

Abstract

Background: SARS coronavirus (SARS-CoV) was identified as the etiological agent of SARS, and extensive investigations indicated that it originated from an animal source (probably bats) and was recently introduced into the human population via wildlife animals from wet markets in southern China. Previous studies revealed that the spike (S) protein of SARS had experienced adaptive evolution, but whether other functional proteins of SARS have undergone adaptive evolution is not known.

Results: We employed several methods to investigate selective pressure among different SARS-CoV groups representing different epidemic periods and hosts. Our results suggest that most functional proteins of SARS-CoV have experienced a stepwise adaptive evolutionary pathway. Similar to previous studies, the spike protein underwent strong positive selection in the early and middle phases, and became stabilized in the late phase. In addition, the replicase experienced positive selection only in human patients, whereas assembly proteins experienced positive selection mainly in the middle and late phases. No positive selection was found in any proteins of bat SARS-like-CoV. Furthermore, specific amino acid sites that may be the targets of positive selection in each group are identified.

Conclusion: This extensive evolutionary analysis revealed the stepwise evolution of different functional proteins of SARS-CoVs at different epidemic stages and different hosts. These results support the hypothesis that SARS-CoV originated from bats and that the spill over into civets and humans were more recent events.

Citing Articles

Adaptive Evolution of the Fox Coronavirus Based on Genome-Wide Sequence Analysis.

Feng C, Liu Y, Lyu G, Shang S, Xia H, Zhang J Biomed Res Int. 2022; 2022:9627961.

PMID: 35463975 PMC: 9020971. DOI: 10.1155/2022/9627961.

The Omic Insights on Unfolding Saga of COVID-19.

Kaur A, Chopra M, Bhushan M, Gupta S, Kumari P H, Sivagurunathan N Front Immunol. 2021; 12:724914.

PMID: 34745097 PMC: 8564481. DOI: 10.3389/fimmu.2021.724914.

Evolution, Ecology, and Zoonotic Transmission of Betacoronaviruses: A Review.

Jelinek H, Mousa M, Alefishat E, Osman W, Spence I, Bu D Front Vet Sci. 2021; 8:644414.

PMID: 34095271 PMC: 8173069. DOI: 10.3389/fvets.2021.644414.

The evolutionary history of ACE2 usage within the coronavirus subgenus .

Wells H, Letko M, Lasso G, Ssebide B, Nziza J, Byarugaba D Virus Evol. 2021; 7(1):veab007.

PMID: 33754082 PMC: 7928622. DOI: 10.1093/ve/veab007.

Variable routes to genomic and host adaptation among coronaviruses.

Montoya V, McLaughlin A, Mordecai G, Miller R, Joy J J Evol Biol. 2021; 34(6):924-936.

PMID: 33751699 PMC: 8242483. DOI: 10.1111/jeb.13771.

References

Bartlam M, Yang H, Rao Z . Structural insights into SARS coronavirus proteins. Curr Opin Struct Biol. 2005; 15(6):664-72. PMC: 7127763. DOI: 10.1016/j.sbi.2005.10.004. View

Yang W, Bielawski J, Yang Z . Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J Mol Evol. 2003; 57(2):212-21. DOI: 10.1007/s00239-003-2467-9. View

Anisimova M, Nielsen R, Yang Z . Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics. 2003; 164(3):1229-36. PMC: 1462615. DOI: 10.1093/genetics/164.3.1229. View

Zhang X, Yap Y, Danchin A . Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus. Arch Virol. 2004; 150(1):1-20. PMC: 7087341. DOI: 10.1007/s00705-004-0413-9. View

Zeng R, Yang R, Shi M, Jiang M, Xie Y, Ruan H . Characterization of the 3a protein of SARS-associated coronavirus in infected vero E6 cells and SARS patients. J Mol Biol. 2004; 341(1):271-9. PMC: 7127270. DOI: 10.1016/j.jmb.2004.06.016. View

Rota P, Oberste M, Monroe S, Nix W, Campagnoli R, Icenogle J . Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science. 2003; 300(5624):1394-9. DOI: 10.1126/science.1085952. View

Yount B, Roberts R, Sims A, Deming D, Frieman M, Sparks J . Severe acute respiratory syndrome coronavirus group-specific open reading frames encode nonessential functions for replication in cell cultures and mice. J Virol. 2005; 79(23):14909-22. PMC: 1287583. DOI: 10.1128/JVI.79.23.14909-14922.2005. View

Zhang C, Wei J, He S . Adaptive evolution of the spike gene of SARS coronavirus: changes in positively selected sites in different epidemic groups. BMC Microbiol. 2006; 6:88. PMC: 1609170. DOI: 10.1186/1471-2180-6-88. View

Kosakovsky Pond S, Frost S . Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics. 2005; 21(10):2531-3. DOI: 10.1093/bioinformatics/bti320. View

10.

Ksiazek T, Erdman D, Goldsmith C, Zaki S, Peret T, Emery S . A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med. 2003; 348(20):1953-66. DOI: 10.1056/NEJMoa030781. View

11.

Yang Z, Swanson W . Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol Biol Evol. 2001; 19(1):49-57. DOI: 10.1093/oxfordjournals.molbev.a003981. View

12.

Tolou H, Couissinier-Paris P, Durand J, Mercier V, De Pina J, De Micco P . Evidence for recombination in natural populations of dengue virus type 1 based on the analysis of complete genome sequences. J Gen Virol. 2001; 82(Pt 6):1283-1290. DOI: 10.1099/0022-1317-82-6-1283. View

13.

Snijder E, Bredenbeek P, Dobbe J, Thiel V, Ziebuhr J, Poon L . Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. J Mol Biol. 2003; 331(5):991-1004. PMC: 7159028. DOI: 10.1016/s0022-2836(03)00865-9. View

14.

Guan Y, Zheng B, He Y, Liu X, Zhuang Z, Cheung C . 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. View

15.

. Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China. Science. 2004; 303(5664):1666-9. DOI: 10.1126/science.1092002. View

16.

Zhao Z, Li H, Wu X, Zhong Y, Zhang K, Zhang Y . Moderate mutation rate in the SARS coronavirus genome and its implications. BMC Evol Biol. 2004; 4:21. PMC: 446188. DOI: 10.1186/1471-2148-4-21. View

17.

Chakraborti S, Prabakaran P, Xiao X, Dimitrov D . The SARS coronavirus S glycoprotein receptor binding domain: fine mapping and functional characterization. Virol J. 2005; 2:73. PMC: 1236967. DOI: 10.1186/1743-422X-2-73. View

18.

Yang Z, Nielsen R . Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol. 2002; 19(6):908-17. DOI: 10.1093/oxfordjournals.molbev.a004148. View

19.

Wang L, Shi Z, Zhang S, Field H, Daszak P, Eaton B . Review of bats and SARS. Emerg Infect Dis. 2007; 12(12):1834-40. PMC: 3291347. DOI: 10.3201/eid1212.060401. View

20.

Drosten C, Gunther S, Preiser W, van der Werf S, Brodt H, Becker S . Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med. 2003; 348(20):1967-76. DOI: 10.1056/NEJMoa030747. View