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Paradigm Shift Intervention Monitoring
Curious Clade A Comments On MERS
The above comments from The Lancet paper on newly released MERS sequences are curious. Clade A (EMC & JOR) are easily distinguished from clade B due to the 39 polymorphisms listed below (cited as 44 polymorphisms above). Prior to the release of the new sequences in the above paper these 39 polymorphisms were limited to clade A. However, two of the newly released sequences share six of these polymorphisms, which are clustered. The Al Batin (BAT1) sequence shares 3 tightly cluster polymorphisms (A542G, T624C, T1514C), while three additional polymorphisms (T2456A, C3320T, T6632C) are shared with Riyadh_3 (RY3).
The sharing of these six polymorphisms, which were identified via direct sequencing, strongly indicates these polymorphisms are not due to tissue culture artifacts. Moreover, these shared polymorphisms cluster within the sequences listed below, and 39 clade A polymorphisms are concentrated in ORF 1a. This clustering strongly supports acquisition by recombination in areas across the Middle East.
Similarly, the Bisha sequence (BIS1) provides more evidence for widespread MERS. In it’s a clade B sequence, but was isolated from the same patient as the clade A sequence, EMC, signaling heavy concentrations of coronavirus. Moreover, BIS1 is virtually identical to Riyadh_1 (RY1) even though the samples were collected more than 4 months apart and in geographically distinct areas (and both sequences have the same 17 BP deletion).
Thus, the hard data supports a genetically distinct clade A. co-infection by clade A and B sequences, and clonal expansion over an extended time period and spread into geographically distinct area, curious comments notwithstanding.