Phylogenetic analysis of MERS-CoV sequence data

Update of this page to include new sequences.

This tree adds the newly published Indiana/USA-1_Saudi_Arabia_2014, Florida/USA-2_Saudi_Arabia_2014 & Greece/Saudi_Arabia_2014 strains (comprising a S gene and an N gene), sequenced by the CDC along with 6 additional sequences from Christian Drosten's group from the Jeddah/Makkah outbreak. These are added to all the other complete or nearly complete sequences currently available

The Greece case is described in Tsiodras et al (2014) Eurosurveillance, Volume 19, Issue 16, 24 April 2014.

Figure 1|Maximum likelihood phylogeny of complete and partial genomes from human and camel cases. Blue shows viruses from the recent Jeddah/Makkah hospital outbreaks. This includes the Florida/USA-2 and Greece-1 exported cases. In green is the recent Indiana/USA-1 strain which was isolated from a hospital doctor who worked in Riyadh. Camel derived sequences have brown labels. The red clade is the previous large nocasomial outbreak in Al-Hasa in 2013.

Indiana/USA-1_Saudi Arabia_2014

This phylogeny suggests that, assuming this doctor was infected through exposure to patients in Riyadh, KSA, this is not directly linked to the large outbreak in Jeddah. Although the USA case is on a lineage that includes many other Riyadh cases from mid to late 2013, the long branch suggests this may be an independent introduction into humans. It seems likely that as some of the recent Riyadh hospital cases are sequenced, they will group with this case.

Florida/USA-2_Saudi Arabia_2014 & Greece-1_Saudia_Arabia_2014

Both these cases group with the recent Jeddah/Makkah nocosomial outbreak. The Greece-1 sequence is only a partial genome (S and N genes comprising about 6kb, 1 fifth of the genome). This probably explains the long branch as this is an artefact of maximum likelihood with short sequences (ML will extrapolate any changes in the region sequenced to be representative of the whole genome).

This is consistent with the reported details of these two cases:

From CDC report:
"On May 1, the patient traveled by plane from Jeddah, Saudi Arabia to London, England, to Boston, Massachusetts, to Atlanta, Georgia, and to Orlando, Florida. The patient reported feeling unwell during the flight from Jeddah to London and continued to feel unwell on subsequent flights with reported symptoms that include fever, chills and a slight cough. On May 9, the patient went to the emergency department of a hospital in Florida and was admitted the same day. The patient is isolated, being well cared for, and is currently doing well."

From WHO report:
"The patient is a 69-year-old male Greek citizen residing in Jeddah, Saudi Arabia, who travelled back to Greece on 17 April. While in Jeddah, the patient consulted a hospital on 8 and 10 April for a febrile illness with diarrhoea. He was diagnosed with probable typhoid fever and treated. He had regularly visited his wife who was hospitalised from 31 March to 5 April in the same hospital for confirmed typhoid fever."

 

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