Severe acute respiratory syndrome (SARS) coronavirus ORF8 protein is acquired from SARS-related coronavirus from greater horseshoe bats through recombination

Susanna K.P. Lau; Yun Feng; Honglin Chen; Hayes K.H. Luk; Wei Hong Yang; Kenneth S.M. Li; Yu Zhen Zhang; Yi Huang; Zhi Zhong Song; Wang Ngai Chow; Rachel Y.Y. Fan; Syed Shakeel Ahmed; Hazel C. Yeung; Carol S.F. Lam; Jian Piao Cai; Samson S.Y. Wong; Jasper F.W. Chan; Kwok Yung Yuen; Hai Lin Zhang; Patrick C.Y. Woo

doi:10.1128/JVI.01048-15

Severe acute respiratory syndrome (SARS) coronavirus ORF8 protein is acquired from SARS-related coronavirus from greater horseshoe bats through recombination

Susanna K.P. Lau, Yun Feng, Honglin Chen, Hayes K.H. Luk, Wei Hong Yang, Kenneth S.M. Li, Yu Zhen Zhang, Yi Huang, Zhi Zhong Song, Wang Ngai Chow, Rachel Y.Y. Fan, Syed Shakeel Ahmed, Hazel C. Yeung, Carol S.F. Lam, Jian Piao Cai, Samson S.Y. Wong, Jasper F.W. Chan, Kwok Yung Yuen, Hai Lin Zhang, Patrick C.Y. Woo

Research output: Journal article publication › Journal article › Academic research › peer-review

145 Citations (Scopus)

Abstract

Despite the identification of horseshoe bats as the reservoir of severe acute respiratory syndrome (SARS)-related coronaviruses (SARSr-CoVs), the origin of SARS-CoV ORF8, which contains the 29-nucleotide signature deletion among human strains, remains obscure. Although two SARS-related Rhinolophus sinicus bat CoVs (SARSr-Rs-BatCoVs) previously detected in Chinese horseshoe bats (Rhinolophus sinicus) in Yunnan, RsSHC014 and Rs3367, possessed 95% genome identities to human and civet SARSr-CoVs, their ORF8 protein exhibited only 32.2 to 33% amino acid identities to that of human/civet SARSr-CoVs. To elucidate the origin of SARS-CoV ORF8, we sampled 348 bats of various species in Yunnan, among which diverse alphacoronaviruses and betacoronaviruses, including potentially novel CoVs, were identified, with some showing potential interspecies transmission. The genomes of two betacoronaviruses, SARSr-Rf-BatCoV YNLF_31C and YNLF_34C, from greater horseshoe bats (Rhinolophus ferrumequinum), possessed 93% nucleotide identities to human/civet SARSr-CoV genomes. Although these two betacoronaviruses displayed lower similarities than SARSr-Rs-BatCoV RsSHC014 and Rs3367 in S protein to civet SARSr-CoVs, their ORF8 proteins demonstrated exceptionally high (80.4 to 81.3%) amino acid identities to that of human/civet SARSr-CoVs, compared to SARSr-BatCoVs from other horseshoe bats (23.2 to 37.3%). Potential recombination events were identified around ORF8 between SARSr-Rf-BatCoVs and SARSr-Rs-BatCoVs, leading to the generation of civet SARSr-CoVs. The expression of ORF8 subgenomic mRNA suggested that the ORF8 protein may be functional in SARSr-Rf-BatCoVs. The high K_a/K_s ratio among human SARS-CoVs compared to that among SARSr-BatCoVs supported that ORF8 is under strong positive selection during animal- to-human transmission. Molecular clock analysis using ORF1ab showed that SARSr-Rf-BatCoV YNLF_31C and YNLF_34C diverged from civet/human SARSr-CoVs in approximately 1990. SARS-CoV ORF8 originated from SARSr-CoVs of greater horseshoe bats through recombination, which may be important for animal-to-human transmission.

Original language	English
Pages (from-to)	10532-10547
Number of pages	16
Journal	Journal of Virology
Volume	89
Issue number	20
DOIs	https://doi.org/10.1128/JVI.01048-15
Publication status	Published - Oct 2015
Externally published	Yes

ASJC Scopus subject areas

Microbiology
Immunology
Insect Science
Virology

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10.1128/JVI.01048-15

Cite this

Lau, S. K. P., Feng, Y., Chen, H., Luk, H. K. H., Yang, W. H., Li, K. S. M., Zhang, Y. Z., Huang, Y., Song, Z. Z., Chow, W. N., Fan, R. Y. Y., Ahmed, S. S., Yeung, H. C., Lam, C. S. F., Cai, J. P., Wong, S. S. Y., Chan, J. F. W., Yuen, K. Y., Zhang, H. L., & Woo, P. C. Y. (2015). Severe acute respiratory syndrome (SARS) coronavirus ORF8 protein is acquired from SARS-related coronavirus from greater horseshoe bats through recombination. Journal of Virology, 89(20), 10532-10547. https://doi.org/10.1128/JVI.01048-15

@article{60d4d93f0035490db38a1a6e4a98df97,

title = "Severe acute respiratory syndrome (SARS) coronavirus ORF8 protein is acquired from SARS-related coronavirus from greater horseshoe bats through recombination",

abstract = "Despite the identification of horseshoe bats as the reservoir of severe acute respiratory syndrome (SARS)-related coronaviruses (SARSr-CoVs), the origin of SARS-CoV ORF8, which contains the 29-nucleotide signature deletion among human strains, remains obscure. Although two SARS-related Rhinolophus sinicus bat CoVs (SARSr-Rs-BatCoVs) previously detected in Chinese horseshoe bats (Rhinolophus sinicus) in Yunnan, RsSHC014 and Rs3367, possessed 95% genome identities to human and civet SARSr-CoVs, their ORF8 protein exhibited only 32.2 to 33% amino acid identities to that of human/civet SARSr-CoVs. To elucidate the origin of SARS-CoV ORF8, we sampled 348 bats of various species in Yunnan, among which diverse alphacoronaviruses and betacoronaviruses, including potentially novel CoVs, were identified, with some showing potential interspecies transmission. The genomes of two betacoronaviruses, SARSr-Rf-BatCoV YNLF_31C and YNLF_34C, from greater horseshoe bats (Rhinolophus ferrumequinum), possessed 93% nucleotide identities to human/civet SARSr-CoV genomes. Although these two betacoronaviruses displayed lower similarities than SARSr-Rs-BatCoV RsSHC014 and Rs3367 in S protein to civet SARSr-CoVs, their ORF8 proteins demonstrated exceptionally high (80.4 to 81.3%) amino acid identities to that of human/civet SARSr-CoVs, compared to SARSr-BatCoVs from other horseshoe bats (23.2 to 37.3%). Potential recombination events were identified around ORF8 between SARSr-Rf-BatCoVs and SARSr-Rs-BatCoVs, leading to the generation of civet SARSr-CoVs. The expression of ORF8 subgenomic mRNA suggested that the ORF8 protein may be functional in SARSr-Rf-BatCoVs. The high Ka/Ks ratio among human SARS-CoVs compared to that among SARSr-BatCoVs supported that ORF8 is under strong positive selection during animal- to-human transmission. Molecular clock analysis using ORF1ab showed that SARSr-Rf-BatCoV YNLF_31C and YNLF_34C diverged from civet/human SARSr-CoVs in approximately 1990. SARS-CoV ORF8 originated from SARSr-CoVs of greater horseshoe bats through recombination, which may be important for animal-to-human transmission.",

author = "Lau, {Susanna K.P.} and Yun Feng and Honglin Chen and Luk, {Hayes K.H.} and Yang, {Wei Hong} and Li, {Kenneth S.M.} and Zhang, {Yu Zhen} and Yi Huang and Song, {Zhi Zhong} and Chow, {Wang Ngai} and Fan, {Rachel Y.Y.} and Ahmed, {Syed Shakeel} and Yeung, {Hazel C.} and Lam, {Carol S.F.} and Cai, {Jian Piao} and Wong, {Samson S.Y.} and Chan, {Jasper F.W.} and Yuen, {Kwok Yung} and Zhang, {Hai Lin} and Woo, {Patrick C.Y.}",

year = "2015",

month = oct,

doi = "10.1128/JVI.01048-15",

language = "English",

volume = "89",

pages = "10532--10547",

journal = "Journal of Virology",

issn = "0022-538X",

publisher = "American Society for Microbiology",

number = "20",

}

Lau, SKP, Feng, Y, Chen, H, Luk, HKH, Yang, WH, Li, KSM, Zhang, YZ, Huang, Y, Song, ZZ, Chow, WN, Fan, RYY, Ahmed, SS, Yeung, HC, Lam, CSF, Cai, JP, Wong, SSY, Chan, JFW, Yuen, KY, Zhang, HL & Woo, PCY 2015, 'Severe acute respiratory syndrome (SARS) coronavirus ORF8 protein is acquired from SARS-related coronavirus from greater horseshoe bats through recombination', Journal of Virology, vol. 89, no. 20, pp. 10532-10547. https://doi.org/10.1128/JVI.01048-15

Severe acute respiratory syndrome (SARS) coronavirus ORF8 protein is acquired from SARS-related coronavirus from greater horseshoe bats through recombination. / Lau, Susanna K.P.; Feng, Yun; Chen, Honglin et al.
In: Journal of Virology, Vol. 89, No. 20, 10.2015, p. 10532-10547.

Research output: Journal article publication › Journal article › Academic research › peer-review

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AU - Luk, Hayes K.H.

AU - Yang, Wei Hong

AU - Li, Kenneth S.M.

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AU - Lam, Carol S.F.

AU - Cai, Jian Piao

AU - Wong, Samson S.Y.

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AU - Zhang, Hai Lin

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AB - Despite the identification of horseshoe bats as the reservoir of severe acute respiratory syndrome (SARS)-related coronaviruses (SARSr-CoVs), the origin of SARS-CoV ORF8, which contains the 29-nucleotide signature deletion among human strains, remains obscure. Although two SARS-related Rhinolophus sinicus bat CoVs (SARSr-Rs-BatCoVs) previously detected in Chinese horseshoe bats (Rhinolophus sinicus) in Yunnan, RsSHC014 and Rs3367, possessed 95% genome identities to human and civet SARSr-CoVs, their ORF8 protein exhibited only 32.2 to 33% amino acid identities to that of human/civet SARSr-CoVs. To elucidate the origin of SARS-CoV ORF8, we sampled 348 bats of various species in Yunnan, among which diverse alphacoronaviruses and betacoronaviruses, including potentially novel CoVs, were identified, with some showing potential interspecies transmission. The genomes of two betacoronaviruses, SARSr-Rf-BatCoV YNLF_31C and YNLF_34C, from greater horseshoe bats (Rhinolophus ferrumequinum), possessed 93% nucleotide identities to human/civet SARSr-CoV genomes. Although these two betacoronaviruses displayed lower similarities than SARSr-Rs-BatCoV RsSHC014 and Rs3367 in S protein to civet SARSr-CoVs, their ORF8 proteins demonstrated exceptionally high (80.4 to 81.3%) amino acid identities to that of human/civet SARSr-CoVs, compared to SARSr-BatCoVs from other horseshoe bats (23.2 to 37.3%). Potential recombination events were identified around ORF8 between SARSr-Rf-BatCoVs and SARSr-Rs-BatCoVs, leading to the generation of civet SARSr-CoVs. The expression of ORF8 subgenomic mRNA suggested that the ORF8 protein may be functional in SARSr-Rf-BatCoVs. The high Ka/Ks ratio among human SARS-CoVs compared to that among SARSr-BatCoVs supported that ORF8 is under strong positive selection during animal- to-human transmission. Molecular clock analysis using ORF1ab showed that SARSr-Rf-BatCoV YNLF_31C and YNLF_34C diverged from civet/human SARSr-CoVs in approximately 1990. SARS-CoV ORF8 originated from SARSr-CoVs of greater horseshoe bats through recombination, which may be important for animal-to-human transmission.

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Severe acute respiratory syndrome (SARS) coronavirus ORF8 protein is acquired from SARS-related coronavirus from greater horseshoe bats through recombination

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