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Paradigm Shift Intervention Monitoring
Sequence Matches England1
However, the sequence at Genbank covered multiple regions and provided sufficient information to classify the sequence as a close relative of the England1 sequence. That designation had been suggest from the partial N gene sequence which included A29719T, which was exclusively shared with the England1 sequence which was from the other Qatari resident.
Prior to the release of this longer sequence, full sequences had been generated for nine patients. The first four divided the MERS-CoV sequences into two sub-clades. One was composed of the two earliest sequences, Jordan-N3 (ICU nurse, 40F, in Jordan) and EMC (first confirmed case, 60M, from Jeddah), while the other was composed of England1 (Qatari, 49M, air ambulance to England) and England2 (England resident, 60M, Urah pilgrim to KSA). These two sub-clades were largely defined by clustered polymorphisms in the OFR 1ab gene. All subsequent isolates mapped to the England1/2 branch, which was then divided into England1 and England2.
The recently released Dubai sequence (73M traveled to Germany for treatment) mapped to the England1 branch, while the four sequences from the Al Hasa nosocomial outbreak mapped to England2.
The Essen sequence had two additional polymorphisms (C25597T and C27229T) which were also exclusively shared with England1, as well as two unique polymorphisms (C680T and G12116A). the clustering of the polymorphisms shared with England1 also supports evolution via homologous recombination, which was also seen for the earlier polymorphisms that defined the two major sub-clades.
The shared polymorphisms between England1 and the Essen sequences suggests the Qatari who developed mild symptoms in KSA while performing Umrah, recovered after he returned to Qatar and then was MERS-CoV infected in Qatar, since the patient generating the Essen sequence had not traveled outside of Qatar prior to symptoms.
Thus, England1, Essen, and the Dubai sequences define MERS-CoV in Qatar and UAE, while the Al Hasa and England2 sequences define the other branch of the England1/2 subclade.