MERS-CoV spillover at the camel-human interface

eLife

Volumn 7, Issue , 2018, Pages

  Dudas, Gytis ^a   Carvalho, Luiz Max ^b   Rambaut, Andrew ^b,c   Bedford, Trevor ^a  

^a Fred Hutchinson Cancer Research Center   (United States)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CAMEL; HUMAN; MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS; NONHUMAN; TROPISM; ANIMAL; CLASSIFICATION; CLUSTER ANALYSIS; CORONAVIRUS INFECTION; DISEASE TRANSMISSION; DNA SEQUENCE; EPIDEMIC; GENETIC VARIATION; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR EPIDEMIOLOGY; PHYLOGENY; TRANSMISSION; VETERINARY; ZOONOSIS;

ANIMALS; CAMELUS; CLUSTER ANALYSIS; CORONAVIRUS INFECTIONS; DISEASE OUTBREAKS; DISEASE TRANSMISSION, INFECTIOUS; GENETIC VARIATION; HUMANS; MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS; MOLECULAR EPIDEMIOLOGY; PHYLOGENY; SEQUENCE ANALYSIS, DNA; ZOONOSES;

EID: 85042074507     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.31257     Document Type: Article

References (77)

1. Abdallah H, Faye B. 2013. Typology of camel farming system in Saudi Arabia. Emirates Journal of Food and Agriculture 25:250. DOI: https://doi.org/10.9755/ejfa.v25i4.15491
2. Adney DR, van Doremalen N, Brown VR, Bushmaker T, Scott D, de Wit E, Bowen RA, Munster VJ. 2014. Replication and shedding of MERS-CoV in upper respiratory tract of inoculated dromedary camels. Emerging Infectious Diseases 20:1999-2005. DOI: https://doi.org/10.3201/eid2012.141280, PMID: 25418529
3. Ali MA, Shehata MM, Gomaa MR, Kandeil A, El-Shesheny R, Kayed AS, El-Taweel AN, Atea M, Hassan N, Bagato O, Moatasim Y, Mahmoud SH, Kutkat O, Maatouq AM, Osman A, McKenzie PP, Webby RJ, Kayali G, Systematic KG. 2017. Systematic, active surveillance for Middle East respiratory syndrome coronavirus in camels in Egypt. Emerging Microbes & Infections 6:e1. DOI: https://doi.org/10.1038/emi.2016.130, PMID: 2 8050021
4. Almutairi SE, Boujenane I, Musaad A, Awad-Acharari F. 2010. Non-genetic factors influencing reproductive traits and calving weight in Saudi camels. Tropical Animal Health and Production 42:1087-1092. DOI: https://doi.org/10.1007/s11250-010-9529-y, PMID: 20195755
5. Antia R, Regoes RR, Koella JC, Bergstrom CT. 2003. The role of evolution in the emergence of infectious diseases. Nature 426:658-661. DOI: https://doi.org/10.1038/nature02104, PMID: 14668863
6. Assiri A, Al-Tawfiq JA, Al-Rabeeah AA, Al-Rabiah FA, Al-Hajjar S, Al-Barrak A, Flemban H, Al-Nassir WN, Balkhy HH, Al-Hakeem RF, Makhdoom HQ, Zumla AI, Memish ZA, Epidemiological MZA. 2013a. 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 13:752-761. DOI: https://doi.org/10.1016/S1473-3099(13)70204-4, PMID: 23891402
7. Assiri A, McGeer A, Perl TM, Price CS, Al Rabeeah AA, Cummings DA, Alabdullatif ZN, Assad M, Almulhim A, Makhdoom H, Madani H, Alhakeem R, Al-Tawfiq JA, Cotten M, Watson SJ, Kellam P, Zumla AI, Memish ZA, KSA MERS-CoV Investigation Team. 2013b. Hospital outbreak of Middle East respiratory syndrome coronavirus. New England Journal of Medicine 369:407-416. DOI: https://doi.org/10.1056/NEJMoa1306742, PMID: 23782161
8. Bedford T, Cobey S, Pascual M. 2011. Strength and tempo of selection revealed in viral gene genealogies. BMC Evolutionary Biology 11:220. DOI: https://doi.org/10.1186/1471-2148-11-220, PMID: 21787390
9. Blumberg S, Lloyd-Smith JO. 2013. Inference of R(0) and transmission heterogeneity from the size distribution of stuttering chains. PLoS Computational Biology 9:e1002993. DOI: https://doi.org/10.1371/journal.pcbi.1002993, PMID: 23658504
10. Boni MF, Posada D, Feldman MW. 2007. An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176:1035-1047. DOI: https://doi.org/10.1534/genetics.106.068874, PMID: 1740907 8
11. Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ. 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10:e1003537. DOI: https://doi.org/10.1371/journal.pcbi.1003537, PMID: 24722319
12. Bruen TC, Philippe H, Bryant D. 2006. A simple and robust statistical test for detecting the presence of recombination. Genetics 172:2665-2681. DOI: https://doi.org/10.1534/genetics.105.048975, PMID: 16489234
13. Carpenter B, Gelman A, Hoffman M, Lee D, Goodrich B, Betancourt M, Brubaker MA, Guo J, Li P, Riddell A. 2016. Stan: A probabilistic programming language. Journal of Statistical Software 20:1-37. DOI: https://doi.org/10.18637/jss.v076.i01
14. Cauchemez S, Nouvellet P, Cori A, Jombart T, Garske T, Clapham H, Moore S, Mills HL, Salje H, Collins C, Rodriquez-Barraquer I, Riley S, Truelove S, Algarni H, Alhakeem R, AlHarbi K, Turkistani A, Aguas RJ, Cummings DA, Van Kerkhove MD, et al. 2016. Unraveling the drivers of MERS-CoV transmission. PNAS 113: 9081-9086. DOI: https://doi.org/10.1073/pnas.1519235113, PMID: 27457935
15. Chen X, Chughtai AA, Dyda A, MacIntyre CR. 2017. Comparative epidemiology of Middle East respiratory syndrome coronavirus (MERS-CoV) in Saudi Arabia and South Korea. Emerging Microbes & Infections 6:e51. DOI: https://doi.org/10.1038/emi.2017.40, PMID: 28588290
16. Chu DK, Poon LL, Gomaa MM, Shehata MM, Perera RA, Abu Zeid D, El Rifay AS, Siu LY, Guan Y, Webby RJ, Ali MA, Peiris M, Kayali G. 2014. MERS coronaviruses in dromedary camels, Egypt. Emerging Infectious Diseases 20:1049-1053. DOI: https://doi.org/10.3201/eid2006.140299, PMID: 24856660
17. Corman VM, Jores J, Meyer B, Younan M, Liljander A, Said MY, Gluecks I, Lattwein E, Bosch BJ, Drexler JF, Bornstein S, Drosten C, Müller MA. 2014. Antibodies against MERS coronavirus in dromedary camels, Kenya, 1992-2013. Emerging Infectious Diseases 20:1319-1322. DOI: https://doi.org/10.3201/eid2008.140596, PMID: 25075637
18. Cotten M, Watson SJ, Kellam P, Al-Rabeeah AA, Makhdoom HQ, Assiri A, Al-Tawfiq JA, Alhakeem RF, Madani H, AlRabiah FA, Al Hajjar S, Al-nassir WN, Albarrak A, Flemban H, Balkhy HH, Alsubaie S, Palser AL, Gall A, Bashford-Rogers R, Rambaut A, 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. DOI: https://doi.org/10.1016/S0140-6736(13)61887-5, PMID: 24055451
19. De Maio N, Wu CH, O’Reilly KM, Wilson D. 2015. New routes to phylogeography: A Bayesian structured coalescent approximation. PLOS Genetics 11:e1005421. DOI: https://doi.org/10.1371/journal.pgen.1005421, PMID: 26267488
20. Drummond AJ, Ho SY, Phillips MJ, Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biology 4:e88. DOI: https://doi.org/10.1371/journal.pbio.0040088, PMID: 16683862
21. Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29:1969-1973. DOI: https://doi.org/10.1093/molbev/mss075, PMID: 2236774 8
22. Dudas G, Bedford T, Lycett S, Rambaut A. 2015. Reassortment between influenza B lineages and the emergence of a coadapted PB1-PB2-HA gene complex. Molecular Biology and Evolution 32:162-172. DOI: https://doi.org/10.1093/molbev/msu287, PMID: 25323575
23. Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D’Ambrozio J, Dellicour S, Di Caro A, Diclaro JW, Duraffour S, Elmore MJ, Fakoli LS, et al. 2017. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature 544:309-315. DOI: https://doi.org/10.1038/nature22040, PMID: 28405027
24. Dudas G, Rambaut A. 2016. MERS-CoV recombination: implications about the reservoir and potential for adaptation. Virus Evolution 2:vev023. DOI: https://doi.org/10.1093/ve/vev023, PMID: 27774293
25. Dudas G. 2017. mers-structure: Looking into MERS-CoV dynamics through the structured coalescent lens. Bedford Lab. https://github.com/blab/mers-structure
26. Fagbo SF, Skakni L, Chu DK, Garbati MA, Joseph M, Peiris M, Hakawi AM. 2015. Molecular epidemiology of hospital outbreak of Middle East respiratory syndrome, Riyadh, Saudi Arabia, 2014. Emerging Infectious Diseases 21:1981-1988. DOI: https://doi.org/10.3201/eid2111.150944, PMID: 26484549
27. Faria NR, Suchard MA, Rambaut A, Streicker DG, Lemey P. 2013. Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints. Philosophical Transactions of the Royal Society B: Biological Sciences 368:20120196. DOI: https://doi.org/10.1098/rstb.2012.0196, PMID: 23382420
28. Frost SD, Volz EM. 2010. Viral phylodynamics and the search for an ’effective number of infections’. Philosophical Transactions of the Royal Society B: Biological Sciences 365:1879-1890. DOI: https://doi.org/10.1098/rstb.2010.0060, PMID: 20478883
29. Gill MS, Lemey P, Faria NR, Rambaut A, Shapiro B, Suchard MA. 2013. Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Molecular Biology and Evolution 30:713-724. DOI: https://doi.org/10.1093/molbev/mss265, PMID: 23180580
30. Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, et al. 2014. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345:1369-1372. DOI: https://doi.org/10.1126/science.1259657, PMID: 25214632
31. Grubaugh ND, Ladner JT, Kraemer MUG, Dudas G, Tan AL, Gangavarapu K, Wiley MR, White S, Thézé J, Magnani DM, Prieto K, Reyes D, Bingham AM, Paul LM, Robles-Sikisaka R, Oliveira G, Pronty D, Barcellona CM, Metsky HC, Baniecki ML, et al. 2017. Genomic epidemiology reveals multiple introductions of Zika virus into the United States. Nature 546:401-405. DOI: https://doi.org/10.1038/nature22400, PMID: 28538723
32. Guindon S, Gascuel O, A Simple RB. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52:696-704. DOI: https://doi.org/10.1080/10635150390235520, PMID: 14530136
33. Hasegawa M, Kishino H, Yano T, Ta Y. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22:160-174. DOI: https://doi.org/10.1007/BF02101694, PMID: 3934395
34. Heled J, Bouckaert RR. 2013. Looking for trees in the forest: summary tree from posterior samples. BMC Evolutionary Biology 13:221. DOI: https://doi.org/10.1186/1471-2148-13-221, PMID: 24093883
35. Herrewegh AA, Smeenk I, Horzinek MC, Rottier PJ, de Groot RJ. 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 72:4508-4514. PMID: 9557750
36. Hon CC, Lam TY, Shi ZL, Drummond AJ, Yip CW, Zeng F, Lam PY, Leung FC. 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 82:1819-1826. DOI: https://doi.org/10.1128/JVI.01926-07, PMID: 18057240
37. Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30:772-780. DOI: https://doi.org/10.1093/molbev/mst010, PMID: 23329690
38. Keck JG, Matsushima GK, Makino S, Fleming JO, Vannier DM, Stohlman SA, Lai MM. 1988. In vivo RNA-RNA recombination of coronavirus in mouse brain. Journal of Virology 62:1810-1813. PMID: 2833625
39. Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD. 2006. GARD: a genetic algorithm for recombination detection. Bioinformatics 22:3096-3098. DOI: https://doi.org/10.1093/bioinformatics/btl474, PMID: 17110367
40. Kottier SA, Cavanagh D, Britton P. 1995. Experimental evidence of recombination in coronavirus infectious bronchitis virus. Virology 213:569-580. DOI: https://doi.org/10.1006/viro.1995.0029, PMID: 7491781
41. Kühnert D, Stadler T, Vaughan TG, Drummond AJ. 2016. Phylodynamics with migration: A computational framework to quantify population structure from genomic data. Molecular Biology and Evolution 33:2102-2116. DOI: https://doi.org/10.1093/molbev/msw064, PMID: 27189573
42. Lai MM, Baric RS, Makino S, Keck JG, Egbert J, Leibowitz JL, Stohlman SA. 1985. Recombination between nonsegmented RNA genomes of murine coronaviruses. Journal of Virology 56:449-456.
43. PMID: 2997467
44. Lemey P, Rambaut A, Drummond AJ, Suchard MA. 2009. Bayesian phylogeography finds its roots. PLoS Computational Biology 5:e1000520. DOI: https://doi.org/10.1371/journal.pcbi.1000520, PMID: 19779555
45. Lipsitch M, Barclay W, Raman R, Russell CJ, Belser JA, Cobey S, Kasson PM, Lloyd-Smith JO, Maurer-Stroh S, Riley S, Beauchemin CA, Bedford T, Friedrich TC, Handel A, Herfst S, Murcia PR, Roche B, Wilke CO, Russell CA. 2016. Viral factors in influenza pandemic risk assessment. eLife 5:e18491. DOI: https://doi.org/10.7554/eLife.18491, PMID: 27834632
46. Liu D, Shi W, Shi Y, Wang D, Xiao H, Li W, Bi Y, Wu Y, Li X, Yan J, Liu W, Zhao G, Yang W, Wang Y, Ma J, Shu Y, Lei F, Gao GF. 2013. Origin and diversity of novel avian influenza A H7N9 viruses causing human infection: phylogenetic, structural, and coalescent analyses. The Lancet 381:1926-1932. DOI: https://doi.org/10.1016/S0140-6736(13)60938-1, PMID: 23643111
47. Lloyd-Smith JO, Schreiber SJ, Kopp PE, Getz WM. 2005. Superspreading and the effect of individual variation on disease emergence. Nature 438:355-359. DOI: https://doi.org/10.1038/nature04153, PMID: 16292310
48. Lycett S, Bodewes R, Pohlmann A, Banks J, Banyai K, Boni M, Bouwstra R, Breed A, Brown I, Chen H, Global Consortium for H5N8 and Related Influenza Viruses. 2016. Role for migratory wild birds in the global spread of avian influenza H5N8. Science 354:213-217. DOI: https://doi.org/10.1126/science.aaf8852, PMID: 27738169
49. Makino S, Keck JG, Stohlman SA, Lai MM. 1986. High-frequency RNA recombination of murine coronaviruses. Journal of Virology 57:729-737. PMID: 3005623
50. Martinez VP, Bellomo C, San Juan J, Pinna D, Forlenza R, Elder M, Padula PJ. 2005. Person-to-person transmission of Andes virus. Emerging Infectious Diseases 11:1848-1853. DOI: https://doi.org/10.3201/eid1112.050501, PMID: 16485469
51. Martinez-Bakker M, Bakker KM, King AA, Rohani P. 2014. Human birth seasonality: latitudinal gradient and interplay with childhood disease dynamics. Proceedings of the Royal Society B: Biological Sciences 281: 20132438. DOI: https://doi.org/10.1098/rspb.2013.2438, PMID: 24695423
52. Memish ZA, Cotten M, Meyer B, Watson SJ, Alsahafi AJ, Al Rabeeah AA, Corman VM, Sieberg A, Makhdoom HQ, Assiri A, Al Masri M, Aldabbagh S, Bosch BJ, Beer M, Müller MA, Kellam P, Drosten C. 2014. Human infection with MERS coronavirus after exposure to infected camels, Saudi Arabia, 2013. Emerging Infectious Diseases 20:1012-1015. DOI: https://doi.org/10.3201/eid2006.140402, PMID: 24857749
53. Mueller NF, Rasmussen DA, Stadler T. 2017. MASCOT: Parameter and state inference under the marginal structured coalescent approximation. bioRxiv. DOI: https://doi.org/10.1101/188516
54. Müller MA, Corman VM, Jores J, Meyer B, Younan M, Liljander A, Bosch BJ, Lattwein E, Hilali M, Musa BE, Bornstein S, Drosten C. 2014. MERS coronavirus neutralizing antibodies in camels, Eastern Africa, 1983-1997. Emerging Infectious Diseases 20:2093-5. DOI: https://doi.org/10.3201/eid2012.141026, PMID: 25425139
55. Müller MA, Meyer B, Corman VM, Al-Masri M, Turkestani A, Ritz D, Sieberg A, Aldabbagh S, Bosch BJ, Lattwein E, Alhakeem RF, Assiri AM, Albarrak AM, Al-Shangiti AM, Al-Tawfiq JA, Wikramaratna P, Alrabeeah AA, Drosten C, Memish ZA. 2015. Presence of Middle East respiratory syndrome coronavirus antibodies in Saudi Arabia: a nationwide, cross-sectional, serological study. The Lancet Infectious Diseases 15:559-564. DOI: https://doi.org/10.1016/S1473-3099(15)70090-3, PMID: 25863564
56. Notohara M. 1990. The coalescent and the genealogical process in geographically structured population. Journal of Mathematical Biology 29:59-75. DOI: https://doi.org/10.1007/BF00173909, PMID: 2277236
57. Park M, Loverdo C, Schreiber SJ, Lloyd-Smith JO. 2013. Multiple scales of selection influence the evolutionary emergence of novel pathogens. Philosophical Transactions of the Royal Society B: Biological Sciences 368: 20120333. DOI: https://doi.org/10.1098/rstb.2012.0333, PMID: 23382433
58. Quick J, Ashton P, Calus S, Chatt C, Gossain S, Hawker J, Nair S, Neal K, Nye K, Peters T, De Pinna E, Robinson E, Struthers K, Webber M, Catto A, Dallman TJ, Hawkey P, Loman NJ. 2015. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biology 16:114. DOI: https://doi.org/10.1186/s13059-015-0677-2, PMID: 26025440
59. Rasmussen DA, Volz EM, Koelle K. 2014. Phylodynamic inference for structured epidemiological models. PLoS Computational Biology 10:e1003570. DOI: https://doi.org/10.1371/journal.pcbi.1003570, PMID: 24743590
60. Reed KD, Melski JW, Graham MB, Regnery RL, Sotir MJ, Wegner MV, Kazmierczak JJ, Stratman EJ, Li Y, Fairley JA, Swain GR, Olson VA, Sargent EK, Kehl SC, Frace MA, Kline R, Foldy SL, Davis JP, Damon IK. 2004. The detection of monkeypox in humans in the Western Hemisphere. New England Journal of Medicine 350:342-350. DOI: https://doi.org/10.1056/NEJMoa032299, PMID: 14736926
61. Reusken CB, Farag EA, Haagmans BL, Mohran KA, Godeke GJ, Raj S, Alhajri F, Al-Marri SA, Al-Romaihi HE, Al-Thani M, Bosch BJ, van der Eijk AA, El-Sayed AM, Ibrahim AK, Al-Molawi N, Müller MA, Pasha SK, Drosten C, AlHajri MM, Koopmans MP. 2015. Occupational exposure to dromedaries and risk for MERS-CoV infection, Qatar, 2013-2014. Emerging Infectious Diseases 21:1422-1425. DOI: https://doi.org/10.3201/eid2108.150481, PMID: 26196891
62. Reusken CB, Haagmans BL, Müller MA, Gutierrez C, Godeke GJ, Meyer B, Muth D, Raj VS, Smits-De Vries L, Corman VM, Drexler JF, Smits SL, El Tahir YE, De Sousa R, van Beek J, Nowotny N, van Maanen K, Hidalgo-Hermoso E, Bosch BJ, Rottier P, et al. 2013. Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study. The Lancet Infectious Diseases 13:859-866. DOI: https://doi.org/10.1016/S1473-3099(13)70164-6, PMID: 23933067
63. Reusken CB, Messadi L, Feyisa A, Ularamu H, Godeke GJ, Danmarwa A, Dawo F, Jemli M, Melaku S, Shamaki D, Woma Y, Wungak Y, Gebremedhin EZ, Zutt I, Bosch BJ, Haagmans BL, Koopmans MP. 2014. Geographic distribution of MERS coronavirus among dromedary camels, Africa. Emerging Infectious Diseases 20:1370-1374. DOI: https://doi.org/10.3201/eid2008.140590, PMID: 25062254
64. Smith GJ, Bahl J, Vijaykrishna D, Zhang J, Poon LL, Chen H, Webster RG, Peiris JS, Guan Y. 2009. Dating the emergence of pandemic influenza viruses. PNAS 106:11709-11712. DOI: https://doi.org/10.1073/pnas.0904991106, PMID: 19597152
65. Turner TL, Hahn MW, Nuzhdin SV. 2005. Genomic islands of speciation in Anopheles gambiae. PLoS Biology 3: e285. DOI: https://doi.org/10.1371/journal.pbio.0030285, PMID: 16076241
66. van Boheemen S, de Graaf M, Lauber C, Bestebroer TM, Raj VS, Zaki AM, Osterhaus AD, Haagmans BL, Gorbalenya AE, Snijder EJ, Fouchier RA. 2012. Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans. mBio 3:e00473-12. DOI: https://doi.org/10.1128/mBio.00473-12, PMID: 23170002
67. Vaughan TG, Kühnert D, Popinga A, Welch D, Drummond AJ. 2014. Efficient Bayesian inference under the structured coalescent. Bioinformatics 30:2272-2279. DOI: https://doi.org/10.1093/bioinformatics/btu201, PMID: 24753484
68. Volz EM, Koelle K, Bedford T. 2013. Viral phylodynamics. PLoS Computational Biology 9:e1002947. DOI: https://doi.org/10.1371/journal.pcbi.1002947, PMID: 23555203
69. Volz EM. 2012. Complex population dynamics and the coalescent under neutrality. Genetics 190:187-201. DOI: https://doi.org/10.1534/genetics.111.134627, PMID: 22042576
70. Wernery U, Corman VM, Wong EY, Tsang AK, Muth D, Lau SK, Khazanehdari K, Zirkel F, Ali M, Nagy P, Juhasz J, Wernery R, Joseph S, Syriac G, Elizabeth SK, Patteril NA, Woo PC, Drosten C. 2015. Acute Middle East respiratory syndrome coronavirus infection in livestock Dromedaries, Dubai, 2014. Emerging Infectious Diseases 21:1019-1022. DOI: https://doi.org/10.3201/eid2106.150038, PMID: 25989145
71. Wernery U. 2001. Camelid immunoglobulins and their importance for the new-born-a review. Journal of Veterinary Medicine Series B 48:561-568. DOI: https://doi.org/10.1046/j.1439-0450.2001.00478.x, PMID: 1170 8675
72. WHO MERS-Cov Research Group. 2013. State of knowledge and data gaps of Middle East respiratory syndromecoronavirus (MERS-CoV) in humans. PLoS Currents 5. DOI: https://doi.org/10.1371/currents.outbreaks.0bf719e352e7478f8ad85fa30127ddb8
73. World Health Organization. 2016. Disease outbreak news. http://www.who.int/csr/don/19-december-2016-2-mers-saudi-arabia/en/ [Accessed August 2017].
74. World Health Organization. 2017. WHO MERS-CoV global summary and assessment of risk. http://www.who.int/emergencies/mers-cov/risk-assessment-july-2017.pdf [Accessed August 2017].
75. Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution 39:306-314. DOI: https://doi.org/10.1007/BF00160154, PMID: 7932792
76. Zaki AM, van Boheemen S, Bestebroer TM, Osterhaus AD, Fouchier RA. 2012. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. New England Journal of Medicine 367:1814-1820. DOI: https://doi.org/10.1056/NEJMoa1211721, PMID: 23075143
77. Zhang Z, Shen L, Gu X. 2016. Evolutionary dynamics of MERS-CoV: potential recombination, positive selection and transmission. Scientific Reports 6:25049. DOI: https://doi.org/10.1038/srep25049, PMID: 27142087