Camel origins of the April Jeddah MERS-CoV outbreak

Some new sequences have been generated by a number of groups that perhaps shed some light on the apparent surge of cases in the area of Jeddah, KSA. The first of these are 3 nearly complete genomes from patients in the Jeddah outbreak sequence by Christian Drosten and his group at the University of Bonn Medical Centre. These are still draft with some (small) gaps that are being completed but are available from Christian's website.

At the same time some new genomes from virus isolated from camels have become available. The first is a genome isolated from a camel in Qatar by Bart Haagmans and colleagues at the Erasmus Medical Center in Rotterdam which will be published shortly in EID. Another recent paper in EID by Ziad Memish, Matt Cotten, Simon Watson, Paul Kellam, Christian Drosten and many others describes the case of an individual apparently infected from his camel herd. Only partial genome is available from the camel so here I have included the human owner genome (Jeddah_1_2013) as the representative. A further camel genome was provided by Maged Hemida of King Faisal University, Al Hofuf, Saudi Arabia and Daniel Chu, Leo Poon, Malik Peiris and colleagues at the University of Hong Kong (this is from Al-Hasa from late November 2013) and published in EID. Finally Thomas Briese, Ian Lipkin and colleagues have published 5 genomes from camels in KSA sampled in November last year (these are full genome sequences for some previously published fragments).

What is interesting is that all these sequences group with a lineage that was first identified in the second MERS case, that of a man from Qatar who was treated in the UK in September 2012 (see England-Qatar_2012, in the tree below). Furthermore, the most recent Qatar camel sequence and 4 of the 5 KSA ones groups closely with the Jeddah outbreak cases suggesting a recent link. It is also relatively unrelated to the other Qatar camel and two linked human cases from October last year and to the camel owner from Jeddah from late 2013.

 

Phylogeny of a sample of complete and mostly-complete MERS-CoV genomes from humans and all complete genomes from camels. Highlighted in yellow is the lineage the recent camel virus from Qatar and KSA which contains a representitave human case involved in the April Jeddah outbreak. Tree is a maximum likelihood phylogeny constructed in PhyML using the GTR+gamma model for the protein coding regions only. Labels coloured red are those from camels (or in the case of Jeddah_1_2013 and Qatar_3_2013, camel owners likely infected from camels). 

Generally, the picture of widely distributed camel sequences across the tree is very indicative of repeated introductions into humans with some limited human to human spread (with a few larger nosocomial outbreaks). The diversity of camel viruses from Qatar and KSA from late 2013, early 2014 provides very strong evidence that at least part of the Jeddah outbreak in April was the result of a recent jump from camels. The important point is that these camels were not selected because of known links to human cases. Further sequencing from camels and human cases is likely to be able to illuminate this relationship further. 

References

Alagaili AN, Briese T, Mishra N, Kapoor V, Sameroff SC, de Wit E, Munster VJ, Hensley LE, Zalmout IS, Kapoor A, Epstein JH, Karesh WB, Daszak P, Mohammed OB, Lipkin WI. (2014) Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia. MBio. 2014 Feb 25;5(2):e00884-14. doi: 10.1128/mBio.00884-14.

Briese T, Mishra N, Jain K, Zalmout IS, Jabado OJ, Karesh WB, Daszak P, Mohammed OB, Alagaili AN, Lipkin WI. (2014) Middle East Respiratory Syndrome Coronavirus Quasispecies That Include Homologues of Human Isolates Revealed through Whole-Genome Analysis and Virus Cultured from Dromedary Camels in Saudi Arabia. MBio. e01146-14. doi: 10.1128/mBio.01146-14.

Chu DKW, Poon LLM, Gomaa MM, Shehata MM, Perera RAPM, Zeid DA, et al. (2014) MERS coronaviruses in dromedary camels, Egypt. Emerg Infect Dis http://dx.doi.org/10.3201/eid2006.140299

Hemida MG, Chu DKW, Poon LLM,. Perera RAPM, Alhammadi MA, Ng H-Y, et al. (2014) MERS coronavirus in dromedary camel herd, Saudi Arabia. Emerg Infect Dis http://dx.doi.org/10.3201/eid2007.140571

Memish ZA, Cotton M, Meyer B, Watson SJ, Alsahafi AJ, Al Rabeeah AA, et al. (2014) Human infection with MERS coronavirus after exposure to infected camels, Saudi Arabia, 2013. Emerg Infect Dis http://dx.doi.org/10.3201/eid2006.140402

Raj VS, Farag EABA, Reusken CBEM,  Lamers MM, et al (2014) Isolation and characterization of MERS coronavirus from a dromedary camel, Qatar, 2014. Emerg Infect Dis In press.

Reusken CBEM, Messadi L, Feyisa A, Ularamu H, Godeke G-J, Danmarwa A, et al. (2014) Geographic distribution of MERS coronavirus among dromedary camels, Africa. Emerg Infect Dis. http://dx.doi.org/10.3201/eid2007.140590

 

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