SARS-Coronavirus ancestor's foot-prints in South-East Asian bat colonies and the refuge theory

Infection, Genetics and Evolution

Volumn 11, Issue 7, 2011, Pages 1690-1702

  Gouilh, Meriadeg Ar ^a,d   Puechmaille, Sébastien J ^b   Gonzalez, Jean Paul ^c   Teeling, Emma ^b   Kittayapong, Pattamaporn ^d   Manuguerra, Jean Claude ^a  

^a INSTITUT PASTEUR   (France)

^b UNIVERSITY COLLEGE DUBLIN   (Ireland)

^c CENTRE INTERNATIONAL DE RECHERCHES MÉDICALES DE FRANCEVILLE   (Gabon)

^d MAHIDOL UNIVERSITY   (Thailand)

Author keywords

Betacoronavirus; Emergence; Hipposideridae; Phylogeny; SARS CoV; Thailand

Indexed keywords

RNA DIRECTED RNA POLYMERASE;

ALPHACORONAVIRUS; ARTICLE; BAT; BETACORONAVIRUS; CONTROLLED STUDY; CORONAVIRUS; GENETIC CONSERVATION; GENETIC VARIABILITY; GENOTYPE ENVIRONMENT INTERACTION; GEOGRAPHIC DISTRIBUTION; HIPPOSIDEROS ARMIGER; HIPPOSIDEROS LARVATUS; HOST PATHOGEN INTERACTION; LAST COMMON ANCESTOR; METAGENOME; MOLECULAR PATHOLOGY; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; ORGANISM COLONY; PHYLOGENETIC TREE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; SARS CORONAVIRUS; SEQUENCE ANALYSIS; SEVERE ACUTE RESPIRATORY SYNDROME; SOUTHEAST ASIA; VIRUS CARRIER; VIRUS DETECTION; VIRUS TRANSMISSION; VIRUS VIRULENCE;

ANIMALS; ASIA, SOUTHEASTERN; BASE SEQUENCE; CHIROPTERA; COMMUNICABLE DISEASES, EMERGING; CORONAVIRUS; CORONAVIRUS INFECTIONS; EVOLUTION, MOLECULAR; HOST-PATHOGEN INTERACTIONS; HUMANS; MODELS, BIOLOGICAL; PHYLOGENY; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; SARS VIRUS; SEVERE ACUTE RESPIRATORY SYNDROME; THAILAND; VIRULENCE;

CORONAVIRUS; HIPPOSIDEROS ARMIGER; HIPPOSIDEROS LARVATUS; RHINOLOPHIDAE; SARS CORONAVIRUS; VIVERRIDAE;

EID: 80053571110     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2011.06.021     Document Type: Article

References (82)

1. Armstrong K.N. Phylogeographic structure in Rhinonicteris aurantia (Chiroptera: Hipposideridae): implications for conservation. Acta Chiropterologica 2006, 8(1):63-81.
2. Benda P. et al., 2003. Bats (Mammalia: Chiroptera) of the Eastern Mediterranean. Part 3. Review of bat distribution in Bulgaria, 67, 245-357.
3. Baric R.S., et al. High recombination and mutation rates in mouse hepatitis virus suggest that coronaviruses may be potentially important emerging viruses. Advances in Experimental Medicine and Biology 1995, 380:571-576.
4. Baric R.S., et al. Episodic evolution mediates interspecies transfer of a murine coronavirus. Journal of Virology 1997, 71(3):1946-1955.
5. Baric R.S., et al. Persistent infection promotes cross-species transmissibility of mouse hepatitis virus. Journal of Virology 1999, 73(1):638-649.
6. Van den Brand J.M.A., et al. Pathology of experimental sars coronavirus infection in cats and ferrets. Veterinary Pathology Online 2008, 45(4):551-562.
7. Brandao P., et al. A coronavirus detected in the vampire bat Desmodus rotundus. Brazilian Journal of Infectious Diseases 2008, 12:466-468.
8. Bruyndonckx N., et al. Molecular cophylogenetic relationships between European bats and their ectoparasitic mites (Acari, Spinturnicidae). Molecular Phylogenetics and Evolution 2009, 51(2):227-237.
9. Calisher C.H., et al. Bats: important reservoir hosts of emerging viruses. Clinical Microbiology Review 2006, 19(3):531-545.
10. Carrington C.V.F. Detection and phylogenetic analysis of group 1 coronaviruses in south american bats. Emerging Infectious Diseases 2008, 14(12):1890-1893.
11. Castro C., Arnold J.J., Cameron C.E. Incorporation fidelity of the viral RNA-dependent RNA polymerase: a kinetic, thermodynamic and structural perspective. Virus Research 2005, 107(2):141-149.
12. Chomel B.B. New emerging zoonoses: a challenge and an opportunity for the veterinary profession. Comparative Immunology, Microbiology and Infectious Diseases 1998, 21(1):1-14.
13. Chu D.K.W., et al. Coronaviruses in bent-winged bats (Miniopterus spp.). Journal of General Virology 2006, 87(Pt 9):2461-2466.
14. Cleaveland S., Laurenson M.K., Taylor L.H. Diseases of humans and their domestic mammals: pathogen characteristics, host range and the risk of emergence. Philosophical Transactions of the Royal Society of London. Series B 2001, 356(1411):991-999.
15. Cui J., et al. Evolutionary relationships between bat coronaviruses and their hosts. Emerging Infectious Diseases 2007, 13(10):1526-1532.
16. Daszak P. Bats, in black and white. Science 2010, 329(5992):634-635.
17. Daszak P., Cunningham A.A., Hyatt A.D. Emerging Infectious diseases of wildlife - threats to biodiversity and human health. Science 2000, 287(5452):443-449.
18. Dobson A.P. What links bats to emerging infectious diseases?. Science 2005, 310(5748):628-629.
19. Domingo E., Holland J.J. RNA Virus mutations and fitness for survival. Annual Review of Microbiology 1997, 51(1):151-178.
20. Dominguez S.R., et al. Detection of group 1 coronaviruses in bats in North America. Emerging Infectious Diseases 2007, 13(9):1295-1300.
21. Drexler J.F., et al. Genomic characterization of severe acute respiratory syndrome-related coronavirus in european bats and classification of coronaviruses based on partial rna-dependent rna polymerase gene sequences. Journal of Virology 2010, 84(21):11336-11349.
22. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 2007, 7:214.
23. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 2004, 32(5):1792-1797.
24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39(4):783-791.
25. Gallagher, S.R. and Desjardins, P.R., 2006. Quantitation of DNA and RNA with Absorption and Fluorescence Spectroscopy. Available at: http://onlinelibrary.wiley.com/doi/10.1002/0471140864.psa04ks52/abstract.
26. Gannon W.L., Sikes R.S. Guidelines of the American society of mammalogists for the use of wild mammals in research. Journal of Mammalogy 2007, 88(3):809-823.
27. González J.M., et al. A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae. Archives of Virology 2003, 148(11):2207-2235.
28. Gonzalez, J.P., Ar Gouilh, M., Reynes, J.M., Leroy, E., 2008. Bat-borne viral diseases. In: Pierce Colfer, C.J., Kleinau, E., (Eds.), Human Health and Forests. A Global Overview of Issues, Practice and Policy (Chapter 8).
29. Gorbalenya Alexander E., Snijder E.J., Spaan W.J.M. Severe acute respiratory syndrome coronavirus phylogeny: toward consensus. Journal of Virology 2004, 78(15):7863-7866.
30. Gouy M., Guindon S., Gascuel O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 2010, 27(2):221-224.
31. Guan Y., et al. Isolation and characterization of viruses related to the sars coronavirus from animals in Southern China. Science 2003, 302(5643):276-278.
32. Hand, S.J. & Kirsch, J.A., 1998. A southern origin for the Hipposideridae (Microchiroptera)? Evidence from the Australian fossil record. Bat biology and conservation. Washington, D.C: T.H. Kunz and P.A. Racey, 72-90.
33. Harvey C.A., et al. Patterns of animal diversity in different forms of tree cover in agricultural landscapes. Ecological Applications: A Publication of the Ecological Society of America 2006, 16(5):1986-1999.
34. Herrewegh A.A., et al. Feline coronavirus type ii strains 79-1683 and 79-1146 originate from a double recombination between feline coronavirus type i and canine coronavirus. Journal of Virology 1998, 72(5):4508-4514.
35. Hutson T., 2003. Bats; ISBN: 089658500X, 9780896585003, 72p, Voyageur Press, 2003.
36. Janies, D.A., Wheeler, W.C. 2002. Theory and practice of parallel direct optimization, Exs (92), 115-123.
37. Jia W., et al. A novel variant of avian infectious bronchitis virus resulting from recombination among three different strains. Archives of Virology 1995, 140(2):259-271.
38. Jones K.E., et al. Global trends in emerging infectious diseases. Nature 2008, 451(7181):990-993.
39. Keck J.G., et al. Multiple recombination sites at the 5'-end of murine coronavirus RNA. Virology 1987, 156(2):331-341.
40. Keesing F., Belden L.K., et al. Impacts of biodiversity on the emergence and transmission of infectious diseases. Nature 2010, 468(7324):647-652.
41. Kuiken T., et al. Emerging viral infections in a rapidly changing world. Current Opinion in Biotechnology 2003, 14(6):641-646.
42. Kunz, T.H. and Fenton, M.B., 2005. Bats, emerging virusinfections, and the rabies paradigm. Dans Bat Ecology. Chicago: Thomas H. Kunz & M. Brock Fenton, 622-679.
43. Lai M.M., et al. Recombination between nonsegmented RNA genomes of murine coronaviruses. Journal of Virology 1985, 56(2):449-456.
44. Lau S.K.P., et al. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proceedings of the National Academy of Science of the United States of America 2005, 102(39):14040-14045.
45. Lau S.K.P., et al. Ecoepidemiology and complete genome comparison of different strains of severe acute respiratory syndrome-related rhinolophus bat coronavirus in china reveal bats as a reservoir for acute, self-limiting infection that allows recombination events. Journal of Virology 2010, 84(6):2808-2819.
46. Lee C.-W., Jackwood M.W. Evidence of genetic diversity generated by recombination among avian coronavirus IBV. Archives of Virology 2000, 145(10):2135-2148.
47. Li W., et al. Bats are natural reservoirs of SARS-like coronaviruses. Science (New York, NY) 2005, 310(5748):676-679.
48. Li W., et al. Animal origins of the severe acute respiratory syndrome coronavirus: insight from ACE2-S-protein interactions. Journal of Virology 2006, 80(9):4211-4219.
49. MacArthur, R.H. & Wilson, E.O., 1967. The theory of island biogeography, Princeton University Press.
50. Makino S., et al. High-frequency RNA recombination of murine coronaviruses. Journal of Virology 1986, 57(3):729-737.
51. Martin D.P., et al. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 2010, 26(19):2462-2463.
52. Martina, Byron E E. et al., 2003. Virology: SARS virus infection of cats and ferrets. Nature, 425(6961), 915.
53. Mueller, O., Lightfoot, S. and Schroeder, A., 2004. RNA Integrity Number (RIN) -Standardization of RNA Quality Control. Available at: http://www.genomics.agilent.com/.
54. Müller M.A., et al. Coronavirus antibodies in African bat species. Emerging Infectious Diseases 2007, 13(9):1367-1370.
55. Nixon K.C. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 1999, 15(4):407-414.
56. Nunn C.L., et al. Parasites and the evolutionary diversification of primate clades. The American Naturalist 2004, 164(S5):S90-S103.
57. Pfefferle S., et al. Distant relatives of severe acute respiratory syndrome coronavirus and close relatives of human coronavirus 229e in bats, ghana. Emerging Infectious Diseases 2009, 15(9):1377-1384.
58. Posada D. JModelTest: phylogenetic model averaging. Molecular Biology and Evolution 2008, 25(7):1253-1256.
59. Poon L.L.M., et al. Identification of a novel coronavirus in bats. Journal of Virology 2005, 79(4):2001-2009.
60. Qinfen Z., et al. The life cycle of SARS coronavirus in Vero E6 cells. Journal of Medical Virology 2004, 73(3):332-337.
61. Quan, P.-L. et al., 2010. Identification of a severe acute respiratory syndrome coronavirus-like virus in a leaf-nosed bat in Nigeria. mBio, 1(4).
62. Reperant, L.A., 2010. Applying the theory of island biogeography to emerging pathogens: toward predicting the sources of future emerging zoonotic and vector-borne diseases. Vector Borne and Zoonotic Diseases (Larchmont, N.Y.), 10(2), 105-110.
63. Schrag S.J., Wiener P. Emerging infectious disease: what are the relative roles of ecology and evolution?. Trends in Ecology & Evolution 1995, 10(8):319-324.
64. Simmons, N.B., 2007. Order Chiroptera. Mammalian Species of the world: A Taxonomic and Geographic Reference. D. E. Wilson, D. M. Reeders.
65. Snijder E.J., et al. Comparison of the genome organization of toro- and coronaviruses: evidence for two nonhomologous RNA recombination events during Berne virus evolution. Virology 1991, 180(1):448-452.
66. Snijder E.J., et al. Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. Journal of Molecular Biology 2003, 331(5):991-1004.
67. Song H.-D., et al. Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(7):2430-2435.
68. Stadler K., et al. SARS - beginning to understand a new virus. Nature Reviews Microbiology 2003, 1(3):209-218.
69. Streicker D.G., et al. Host phylogeny constrains cross-species emergence and establishment of rabies virus in bats. Science 2010, 329(5992):676-679.
70. Tang X.C., et al. Prevalence and genetic diversity of coronaviruses in bats from China. Journal of Virology 2006, 80(15):7481-7490.
71. Teeling E.C., et al. A molecular phylogeny for bats illuminates biogeography and the fossil record. Science 2005, 307(5709):580-584.
72. Thackray L.B., Holmes K.V. Amino acid substitutions and an insertion in the spike glycoprotein extend the host range of the murine coronavirus MHV-A59. Virology 2004, 324(2):510-524.
73. Tong S., et al. detection of novel sars-like and other coronaviruses in bats from Kenya. Emerging Infectious Diseases 2009, 15(3):482-485.
74. Trisurat Y., Alkemade R., Verburg P.H. Projecting land-use change and its consequences for biodiversity in northern Thailand. Environmental Management 2010, 45(3):626-639.
75. Troyer J.L., et al. FIV cross-species transmission: an evolutionary prospective. Veterinary Immunology and Immunopathology 2008, 123(1-2):159-166.
76. Turmelle A.S., Olival K.J. Correlates of viral richness in bats (order Chiroptera). EcoHealth 2009, 6(4):522-539.
77. VandeWoude S., Troyer J., Poss M. Restrictions to cross-species transmission of lentiviral infection gleaned from studies of FIV. Veterinary Immunology and Immunopathology 2010, 134(1-2):25-32.
78. Varón A., Vinh L.S., Wheeler W.C. POY version 4: phylogenetic analysis using dynamic homologies. Cladistics 2010, 26(1):72-85.
79. Wheeler W. Optimization alignment: the end of multiple sequence alignment in phylogenetics?. Cladistics 1996, 12(1):1-9.
80. WHO, 2003. WHO Summary of probable SARS cases with onset of illness from 1 November 2002 to 31 July 2003. Available at: http://www.who.int/.
81. Woo P.C.Y., et al. Molecular diversity of coronaviruses in bats. Virology 2006, 351(1):180-187.
82. Woolhouse M.E.J., Gowtage-Sequeria S. Host range and emerging and reemerging pathogens. Emerging Infectious Diseases 2005, 11(12):1842-1847.