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Link to original content: https://pubmed.ncbi.nlm.nih.gov/19261195
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. 2009 Mar 5:9:52.
doi: 10.1186/1471-2148-9-52.

Differential stepwise evolution of SARS coronavirus functional proteins in different host species

Xianchun Tang  1 , Gang Li, Nikos Vasilakis, Yuan Zhang, Zhengli Shi, Yang Zhong, Lin-Fa Wang, Shuyi Zhang
Affiliations

Differential stepwise evolution of SARS coronavirus functional proteins in different host species

Xianchun Tang et al. BMC Evol Biol. .

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.

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Figures

Figure 1
Figure 1
Schematic diagram of the SARS-CoV genome organization and viral proteins. The protein coding regions analyzed in this paper were shaded in grey.
Figure 2
Figure 2
Phylogenetic relationships of 59 S gene sequences of SARS-CoVs from human and animals. The tree was generated with MrBayes 3.1.2 program. Posterior probabilities are shown on the nodes of the tree. Branch between BSL group and others was depicted with dotted line, because the branch was too long to be displayed at same scale. Bar, 0.001 nucleotide substitutions per site.
Figure 3
Figure 3
Phylogenetic relationships of 35 replicase domains of SARS-CoVs from human and animals. The tree was generated with MrBayes 3.1.2 program. Posterior probabilities are shown on the nodes of the tree. Bar, 0.001 nucleotide substitutions per site.
Figure 4
Figure 4
Phylogenetic relationships of 56 3'-end ORF sequences of SARS-CoVs from human and animals. The tree was generated with MrBayes 3.1.2 program. Posterior probabilities are shown on the nodes of the tree. Bar, 0.001 nucleotide substitutions per site.
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