MERS-CoV recombination: Implications about the reservoir and potential for adaptation

Virus Evolution

Volumn 2, Issue 1, 2016, Pages

  Dudas, Gytis ^a   Rambaut, Andrew ^a,b  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

co infection; coronavirus; homoplasy; MERS CoV; MERS.; recombination

Indexed keywords

EID: 84988911740     PISSN: None     EISSN: 20571577     Source Type: Journal    
DOI: 10.1093/ve/vev023     Document Type: Article

References (77)

1. Aburizaiza, A. S. et al. (2014) 'Investigation of Anti-MERSCoronavirus Antibodies in Blood Donors and Abbatoir Workers in Jeddah and Makkah, Kingdom of Saudi Arabia, Fall 2012', Journal of Infectious Diseases, 209(2): 243-6. doi: 10.1093/infdis/ jit589.
2. Adney, D. R. et al. (2014) 'Replication and Shedding of MERS-CoV in Upper Respiratory Tract of Inoculated Dromedary Camels', Emerging Infectious Diseases, 20: 1999-2005.
3. Anisimova, M., Nielsen, R., and Yang, Z. (2003) 'Effect of Recombination on the Accuracy of the Likelihood Method for Detecting Positive Selection at Amino Acid Sites', Genetics, 164: 1229-36.
4. Assiri, A. et al. (2013) 'Epidemiological, Demographic, and Clinical Characteristics of 47 Cases of Middle East Respiratory Syndrome Coronavirus Disease from Saudi Arabia: A Descriptive Study', The Lancet Infectious Diseases, 13: 752-61.
5. Baele, G. et al. (2012) 'Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty', Molecular Biology and Evolution, 29: 2157-67.
6. Baric, R. S. et al. (1987) 'Analysis of Intracellular Small RNAs of Mouse Hepatitis Virus: Evidence for Discontinuous Transcription', Virology, 156: 342-54.
7. Bielejec, F. et al. (2014) 'pBUSS: A Parallel BEAST/BEAGLE Utility for Sequence Simulation under Complex Evolutionary Scenarios', BMC Bioinformatics, 15: 133.
8. Boni, M. F., Posada, D., and Feldman, M. W. (2007) 'An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence Triplets', Genetics, 176: 1035-47.
9. (2010) 'Guidelines for Identifying Homologous Recombination Events in Influenza A Virus', PLoS One, 5: E10434.
10. Boucher, C. A. et al. (1993) 'High-Level Resistance to (-) Enantiomeric 2'-Deoxy-3'-Thiacytidine in vitro is due to One Amino Acid Substitution in the Catalytic Site of Human Immunodeficiency Virus Type 1 reverse Transcriptase', Antimicrobial Agents and Chemotherapy, 37: 2231-4.
11. Bruen, T. C., Philippe, H., and Bryant D. (2006) 'A Simple and Robust Statistical Test for Detecting the Presence of Recombination', Genetics, 172: 2665-81.
12. Cauchemez, S. et al. (2014) 'Middle East Respiratory Syndrome Coronavirus: Quantification of the Extent of the Epidemic, Surveillance Biases, and Transmissibility', The Lancet Infectious Diseases, 14: 50-6.
13. Chang, S. F., Sgro, J. Y., and Parrish, C. R. (1992) 'Multiple Amino Acids in the Capsid Structure of Canine Parvovirus Coordinately Determine the Canine Host Range and Specific Antigenic and Hemagglutination Properties', Journal of Virology, 66: 6858-67.
14. Chare, E. R., Gould, E. A., and Holmes, E. C. (2003) 'Phylogenetic Analysis Reveals a Low Rate of Homologous Recombination in Negative-Sense RNA Viruses', Journal of General Virology, 84: 2691-703.
15. Chu, D. K. et al. (2014) 'MERS Coronaviruses in Dromedary Camels, Egypt', Emerging Infectious Diseases, 20: 1049-53.
16. Corman, V. M. et al. (2014a) 'Rooting the Phylogenetic Tree of Middle East Respiratory Syndrome Coronavirus by Characterization of a Conspecific Virus from an African Bat', Journal of Virology, 88: 11297-303.
17. (2014b) 'Antibodies against MERS Coronavirus in Dromedary Camels, Kenya, 1992-2013', Emerging Infectious Diseases, 20.
18. Cotten, M. et al. (2013) 'Transmission and Evolution of the Middle East Respiratory Syndrome Coronavirus in Saudi Arabia: A Descriptive Genomic Study', The Lancet, 382: 1993- 2002.
19. (2014) 'Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus', MBio, 5: E01062-13.
20. Didelot, X., and Falush, D. (2007) 'Inference of Bacterial Microevolution Using Multilocus Sequence Data', Genetics, 175: 1251-66.
21. Dong, G. et al. (2011) 'Phylogenetic Diversity and Genotypical Complexity of H9N2 Influenza a Viruses Revealed by Genomic Sequence Analysis', PLoS One, 6: E17212.
22. Drosten, C. et al. (2015) 'An Observational, Laboratory-Based Study of Outbreaks of MERS-Coronavirus in Jeddah and Riyadh, Kingdom of Saudi Arabia, 2014', Clinical Infectious Diseases, 60(3): 369-77. doi: 10.1093/cid/ciu812.
23. (2013) 'Clinical Features and Virological Analysis of a Case of Middle East Respiratory Syndrome Coronavirus Infection', The Lancet Infectious Diseases, 13: 745-51.
24. Drummond, A. J. et al. (2006) 'Relaxed Phylogenetics and Dating with Confidence', PLoS Biology, 4: E88.
25. (2012) 'Bayesian Phylogenetics with BEAUti and the BEAST 1.7', Molecular Biology and Evolution, 29(8): 1969-73.
26. Excoffier, L. et al. (2013) 'Robust Demographic Inference from Genomic and SNP Data', PLoS Genetics, 9: E1003905.
27. Ferreira, M. A. R., and Suchard, M. A. (2008) 'Bayesian Analysis of Elapsed Times in Continuous-Time Markov Chains', Canadian Journal of Statistics, 36: 355-68.
28. Gierer, S. et al. (2013) 'Lack of MERS Coronavirus Neutralizing Antibodies in Humans, Eastern Province, Saudi Arabia', Emerging Infectious Diseases, 19: 2034-6.
29. Gill, M. S. et al. (2013) 'Improving Bayesian Population Dynamics Inference: A Coalescent-Based Model for Multiple Loci', Molecular Biology and Evolution, 30: 713-24.
30. Gire, S. K. et al. (2014) 'Genomic Surveillance Elucidates Ebola Virus Origin and Transmission during the 2014 Outbreak', Science, 345: 1369-72.
31. Goldman, N., and Yang Z. (1994) 'A Codon-Based Model of Nucleotide Substitution for Protein-Coding DNA Sequences', Molecular Biology and Evolution, 11: 725-36.
32. Gubareva, L. V. et al. (2001) 'Selection of Influenza Virus Mutants in Experimentally Infected Volunteers Treated with Oseltamivir', Journal of Infectious Diseases, 183: 523-31.
33. Guindon, S., and Gascuel, O. (2003) 'A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood', Systematic Biology, 52: 696-704.
34. Hasegawa, M., Kishino, H., and Yano, T. A. (1985) 'Dating of the Human-Ape Splitting by a Molecular Clock of Mitochondrial DNA', Journal of Molecular Evolution, 22: 160-74.
35. Hedrick, P. W., and Thomson, G. (1986) 'A Two-Locus Neutrality Test: Applications to Humans, E. coli and Lodgepole Pine', Genetics, 112: 135-56.
36. Herrewegh, A. A. et al. (1998) '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, 72: 4508-14.
37. Hill, W. G., and Robertson, A. (1968) 'Linkage Disequilibrium in Finite Populations', Theoretical and Applied Genetics. Theoretische und Angewandte Genetik, 38: 226-31.
38. Holmes, E. C., Urwin, R., and Maiden, M. C. (1999) 'The Influence of Recombination on the Population Structure and Evolution of the Human Pathogen Neisseria meningitidis', Molecular Biology and Evolution, 16: 741-9.
39. Hon, C. C. et al. (2008) 'Evidence of the Recombinant Origin of a Bat Severe Acute Respiratory Syndrome (SARS)-Like Coronavirus and Its Implications on the Direct Ancestor of SARS Coronavirus', Journal of Virology, 82: 1819-26.
40. Keck, J. G. et al. (1988) 'in vivo RNA-RNA Recombination of Coronavirus in Mouse Brain', Journal of Virology, 62: 1810-13.
41. Kirkegaard, K., and Baltimore, D. (1986) 'The Mechanism of RNA Recombination in Poliovirus', Cell, 47: 433-43.
42. Kosakovsky Pond, S. L. et al. (2006) 'Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm', Molecular Biology and Evolution, 23: 1891-901.
43. Kottier, S. A., Cavanagh, D., and Britton, P. (1995) 'Experimental Evidence of Recombination in Coronavirus Infectious Bronchitis Virus', Virology, 213: 569-80.
44. Lai, M. M. et al. (1985) 'Recombination between Nonsegmented RNA Genomes of Murine Coronaviruses', Journal of Virology, 56: 449-56.
45. Lau, S. K. P. et al. (2010) '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, 84: 2808-19.
46. Lemey, P., Suchard, M., and Rambaut, A. (2009) 'Reconstructing the Initial Global Spread of a Human Influenza Pandemic', PLoS Currents, 1. doi: 10.1371/currents.RRN1031.
47. Lewontin, R. C. (1964) 'The Interaction of Selection and Linkage. I. General Considerations; Heterotic Models', Genetics, 49: 49-67.
48. Li, K. S. et al. (2004) 'Genesis of a Highly Pathogenic and Potentially Pandemic H5N1 Influenza Virus in Eastern Asia', Nature, 430: 209-13.
49. Lu, L., Lycett, S. J., and Brown, A. J. L. (2014) 'Reassortment Patterns of Avian Influenza Virus Internal Segments among Different Subtypes', BMC Evolutionary Biology, 14: 16.
50. Makino, S. et al. (1986) 'High-Frequency RNA Recombination of Murine Coronaviruses', Journal of Virology, 57: 729-37.
51. Maynard Smith, J., and Smith, N. H. (1998) 'Detecting Recombination from Gene Trees', Molecular Biology and Evolution, 15: 590-9.
52. McVean, G., Awadalla, P., and Fearnhead, P. (2002) 'A Coalescent-Based Method for Detecting and Estimating Recombination from Gene Sequences', Genetics, 160: 1231-41.
53. Memish, Z. A. et al. (2013) 'Family Cluster of Middle East Respiratory Syndrome Coronavirus Infections', New England Journal of Medicine, 368: 2487-94.
54. Meunier, J., and Eyre-Walker, A. (2001) 'The Correlation between Linkage Disequilibrium and Distance: Implications for Recombination in Hominid Mitochondria', Molecular Biology and Evolution, 18: 2132-5.
55. Milkman, R., and Bridges, M. M. (1990) 'Molecular Evolution of the Escherichia coli Chromosome. III. Clonal Frames', Genetics, 126: 505-17.
56. Mitnaul, L. J. et al. (2000) 'Balanced Hemagglutinin and Neuraminidase Activities are Critical for Efficient Replication of Influenza A Virus', Journal of Virology, 74: 6015-20.
57. Muller, H. J. (1932) 'Some Genetic Aspects of Sex', The American Naturalist, 66: 118-38.
58. Müller, M. A. et al. (2014) 'MERS Coronavirus Neutralizing Antibodies in Camels, Eastern Africa, 1983-1997', Emerging Infectious Diseases, 20.
59. (2015) 'Presence of Middle East Respiratory Syndrome Coronavirus Antibodies in Saudi Arabia: A Nationwide, Cross-Sectional, Serological Study', The Lancet Infectious Diseases, 15: 559-64.
60. O'Brien, J. D., Minin, V. N., and Suchard, M. A. (2009) 'Learning to Count: Robust Estimates for Labeled Distances between Molecular Sequences', Molecular Biology and Evolution, 26: 801-14.
61. Pond, S. L. K., Frost, S. D. W., and Muse, S. V. (2005) 'HyPhy: Hypothesis Testing Using Phylogenies', Bioinformatics, 21: 676-9.
62. Posada, D., and Crandall, K. A. (2001) 'Evaluation of Methods for Detecting Recombination from DNA Sequences: Computer Simulations', Proceedings of the National Academy of Sciences, 98: 13757-62.
63. (2002) 'The Effect of Recombination on the Accuracy of Phylogeny Estimation', Journal of Molecular Evolution, 54: 396-402.
64. Crandall, K. A., Crandall, K. A., and Holmes, E. C. (2002) 'Recombination in Evolutionary Genomics', Annual Review of Genetics, 36: 75-97.
65. Rambaut, A., and Holmes, E. (2009) 'The Early Molecular Epidemiology of the Swine-Origin A/H1N1 Human Influenza Pandemic', PLoS Currents, 1. doi: 10.1371/currents.RRN1003.
66. Reusken, C. B. et al. (2013) 'Middle East Respiratory Syndrome Coronavirus Neutralising Serum Antibodies in Dromedary Camels: A Comparative Serological Study', The Lancet Infectious Diseases, 13: 859-66.
67. (2014) 'Geographic Distribution of MERS Coronavirus among Dromedary Camels, Africa', Emerging Infectious Diseases, 20: 1370-4.
68. Robertson, D. L., Hahn, B. H., and Sharp, P. M. (1995) 'Recombination in AIDS Viruses', Journal of Molecular Evolution, 40: 249-59.
69. (1995) 'Recombination in HIV-1', Nature, 374: 124-6.
70. Schierup, M. H., and Hein J. (2000) 'Consequences of Recombination on Traditional Phylogenetic Analysis', Genetics, 156: 879-91.
71. Shriner, D. et al. (2003) 'Potential Impact of Recombination on Sitewise Approaches for Detecting Positive Natural Selection', Genetics Research, 81: 115-21.
72. Smith, G. J. D. et al. (2009) 'Origins and Evolutionary Genomics of the 2009 Swine-Origin H1N1 Influenza A Epidemic', Nature, 459: 1122-5.
73. Subbarao, E. K., London, W., and Murphy, B. R. (1993) 'A Single Amino Acid in the PB2 Gene of Influenza A Virus is a Determinant of Host Range', Journal of Virology, 67: 1761-4.
74. Tavaré , S. (1986) Some Mathematical Questions in Biology: DNA Sequence Analysis. Lectures on Mathematics in the Life Sciences, Volume 17, pp. 57-86. American Mathematical Society: Providence, RI, USA.
75. Tisdale, M. et al. (1993) 'Rapid in vitro Selection of Human Immunodeficiency Virus Type 1 Resistant to 3'-Thiacytidine Inhibitors due to a Mutation in the YMDD Region of Reverse Transcriptase', Proceedings of the National Academy of Sciences of the United States of America, 90: 5653-6.
76. Yang, Z. (1994) 'Maximum Likelihood Phylogenetic Estimation from DNA Sequences with Variable Rates Over Sites: Approximate Methods', Journal of Molecular Evolution, 39: 306-14.
77. Zaki, A. M. et al. (2012) 'Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia', New England Journal of Medicine, 367: 1814-20.