Phylogenetic and recombination analysis of coronavirus HKU1, a novel coronavirus from patients with pneumonia

doi:10.1007/s00705-005-0573-2

. 2005 Nov;150(11):2299-311.

doi: 10.1007/s00705-005-0573-2. Epub 2005 Jun 28.

Phylogenetic and recombination analysis of coronavirus HKU1, a novel coronavirus from patients with pneumonia

P C Y Woo¹, S K P Lau, Y Huang, H-W Tsoi, K-H Chan, K-Y Yuen

Affiliations

PMID: 15986174
PMCID: PMC7086700
DOI: 10.1007/s00705-005-0573-2

Phylogenetic and recombination analysis of coronavirus HKU1, a novel coronavirus from patients with pneumonia

P C Y Woo et al. Arch Virol. 2005 Nov.

. 2005 Nov;150(11):2299-311.

doi: 10.1007/s00705-005-0573-2. Epub 2005 Jun 28.

Authors

P C Y Woo¹, S K P Lau, Y Huang, H-W Tsoi, K-H Chan, K-Y Yuen

Affiliation

¹ Department of Microbiology, Faculty of Medicine, The University of Hong Kong, Hong Kong.

PMID: 15986174
PMCID: PMC7086700
DOI: 10.1007/s00705-005-0573-2

Abstract

Phylogenetic trees constructed using predicted amino acid sequences of putative proteins of coronavirus HKU1 (CoV-HKU1) revealed that CoV-HKU1 formed a distinct branch among group 2 coronaviruses. Of the 14 trees from p65 to nsp10, nine showed that CoV-HKU1 was clustered with murine hepatitis virus. From nsp11, the topologies of the trees changed dramatically. For the eight trees from nsp11 to N, seven showed that the CoV-HKU1 branch was the first branch. The codon usage patterns of CoV-HKU1 differed significantly from those in other group 2 coronaviruses. Split decomposition analysis revealed that recombination events had occurred between CoV-HKU1 and other coronaviruses.

PubMed Disclaimer

Cited by

The coronavirus recombination pathway.
Wells HL, Bonavita CM, Navarrete-Macias I, Vilchez B, Rasmussen AL, Anthony SJ. Wells HL, et al. Cell Host Microbe. 2023 Jun 14;31(6):874-889. doi: 10.1016/j.chom.2023.05.003. Cell Host Microbe. 2023. PMID: 37321171 Free PMC article. Review.
Correlated sequence signatures are present within the genomic 5'UTR RNA and NSP1 protein in coronaviruses.
Sosnowski P, Tidu A, Eriani G, Westhof E, Martin F. Sosnowski P, et al. RNA. 2022 May;28(5):729-741. doi: 10.1261/rna.078972.121. Epub 2022 Mar 2. RNA. 2022. PMID: 35236777 Free PMC article.
Full Genome Nobecovirus Sequences From Malagasy Fruit Bats Define a Unique Evolutionary History for This Coronavirus Clade.
Kettenburg G, Kistler A, Ranaivoson HC, Ahyong V, Andrianiaina A, Andry S, DeRisi JL, Gentles A, Raharinosy V, Randriambolamanantsoa TH, Ravelomanantsoa NAF, Tato CM, Dussart P, Heraud JM, Brook CE. Kettenburg G, et al. Front Public Health. 2022 Feb 11;10:786060. doi: 10.3389/fpubh.2022.786060. eCollection 2022. Front Public Health. 2022. PMID: 35223729 Free PMC article.
Ecology, evolution and spillover of coronaviruses from bats.
Ruiz-Aravena M, McKee C, Gamble A, Lunn T, Morris A, Snedden CE, Yinda CK, Port JR, Buchholz DW, Yeo YY, Faust C, Jax E, Dee L, Jones DN, Kessler MK, Falvo C, Crowley D, Bharti N, Brook CE, Aguilar HC, Peel AJ, Restif O, Schountz T, Parrish CR, Gurley ES, Lloyd-Smith JO, Hudson PJ, Munster VJ, Plowright RK. Ruiz-Aravena M, et al. Nat Rev Microbiol. 2022 May;20(5):299-314. doi: 10.1038/s41579-021-00652-2. Epub 2021 Nov 19. Nat Rev Microbiol. 2022. PMID: 34799704 Free PMC article. Review.
COVID-19: why not learn from the past?
Zocchi E, Terrazzano G. Zocchi E, et al. Front Med. 2021 Oct;15(5):776-781. doi: 10.1007/s11684-021-0883-0. Epub 2021 Aug 31. Front Med. 2021. PMID: 34463906 Free PMC article. No abstract available.

See all "Cited by" articles

References

1. Baric RS, Fu K, Schaad MC, Stohlman SA. Establishing a genetic recombination map for murine coronavirus strain A59 complementation groups. Virology. 1990;177:646–656. - PMC - PubMed
1. Eickmann M, Becker S, Klenk HD, Doerr HW, Stadler K, Censini S, Guidotti S, Masignani V, Scarselli M, Mora M, Donati C, Han JH, Song HC, Abrignani S, Covacci A, Rappuoli R. Phylogeny of the SARS coronavirus. Science. 2003;302:1504–1505. - PubMed
1. Fouchier RA, Hartwig NG, Bestebroer TM, Niemever B, de Jong JC, Simon JH, Osterhaus AD. A previously undescribed coronavirus associated with respiratory disease in humans. Proc Natl Acad Sci USA. 2004;101:6212–6216. - PMC - PubMed
1. Fu K, Baric RS. Evidence for variable rates of recombination in the MHV genome. Virology. 1992;189:88–102. - PMC - PubMed
1. Grantham R, Gautier C, Gouy M. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res. 1980;8:1893–1912. - PMC - PubMed

Publication types

Actions

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions

Substances

Actions

LinkOut - more resources

Full Text Sources
Other Literature Sources
- The Lens - Patent Citations

[1] Baric RS, Fu K, Schaad MC, Stohlman SA. Establishing a genetic recombination map for murine coronavirus strain A59 complementation groups. Virology. 1990;177:646–656. - PMC - PubMed

[2] Baric RS, Fu K, Schaad MC, Stohlman SA. Establishing a genetic recombination map for murine coronavirus strain A59 complementation groups. Virology. 1990;177:646–656. - PMC - PubMed

[3] Eickmann M, Becker S, Klenk HD, Doerr HW, Stadler K, Censini S, Guidotti S, Masignani V, Scarselli M, Mora M, Donati C, Han JH, Song HC, Abrignani S, Covacci A, Rappuoli R. Phylogeny of the SARS coronavirus. Science. 2003;302:1504–1505. - PubMed

[4] Eickmann M, Becker S, Klenk HD, Doerr HW, Stadler K, Censini S, Guidotti S, Masignani V, Scarselli M, Mora M, Donati C, Han JH, Song HC, Abrignani S, Covacci A, Rappuoli R. Phylogeny of the SARS coronavirus. Science. 2003;302:1504–1505. - PubMed

[5] Fouchier RA, Hartwig NG, Bestebroer TM, Niemever B, de Jong JC, Simon JH, Osterhaus AD. A previously undescribed coronavirus associated with respiratory disease in humans. Proc Natl Acad Sci USA. 2004;101:6212–6216. - PMC - PubMed

[6] Fouchier RA, Hartwig NG, Bestebroer TM, Niemever B, de Jong JC, Simon JH, Osterhaus AD. A previously undescribed coronavirus associated with respiratory disease in humans. Proc Natl Acad Sci USA. 2004;101:6212–6216. - PMC - PubMed

[7] Fu K, Baric RS. Evidence for variable rates of recombination in the MHV genome. Virology. 1992;189:88–102. - PMC - PubMed

[8] Fu K, Baric RS. Evidence for variable rates of recombination in the MHV genome. Virology. 1992;189:88–102. - PMC - PubMed

[9] Grantham R, Gautier C, Gouy M. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res. 1980;8:1893–1912. - PMC - PubMed

[10] Grantham R, Gautier C, Gouy M. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res. 1980;8:1893–1912. - PMC - PubMed

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Phylogenetic and recombination analysis of coronavirus HKU1, a novel coronavirus from patients with pneumonia

Affiliation

Phylogenetic and recombination analysis of coronavirus HKU1, a novel coronavirus from patients with pneumonia

Authors

Affiliation

Abstract

Similar articles

Cited by

References

Publication types

MeSH terms

Substances

LinkOut - more resources

Full Text Sources

Other Literature Sources

Abstract

Similar articles

Cited by

References

Publication types

MeSH terms

Substances

Related information

LinkOut - more resources

Full Text Sources

Other Literature Sources