Curious Clade A Comments On MERS



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H1N1 Consulting Paradigm Shift Viral Evolution Intervention Monitoring Vaccine Screening Vaccine Development Expression Profiling Drug Discovery Custom Therapies Patents	Audio:Aug15 Sep11 Sep19 MAP twitter Commentary Curious Clade A Comments On MERS Recombinomics Commentary 21:30 September 24, 2013 The EMC/2012 sequence was obtained after extensive cell culture passage to establish a virus isolate;26 there are 76 single nucleotide differences between EMC/2012 and the root of the clade B lineage. EMC/2012 and Jordan-N3 share 44 nucleotide changes not present in any other known MERS-CoV genome. Because of the lack of reported technical details for the Jordan sequence, the tissue culture adaptation of EMC/2012, and the shared polymorphisms despite large difference in geographical origins of clade A, we focused our analysis on sequences obtained directly from patient material, namely those in clade B. Importantly, genome Bisha_1_2012 (figure 2, in light green) was obtained with direct sequencing of nasopharyngeal swab material from the same patient reported as the source of the EMC/2012 virus (figure 2, in light green).26 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. A542G BAT1 T624C BAT1 T1514C BAT1 A2040G T2318C T2456A RY3 T3134C T3277C C3320T RY3 T3442C A4034G T4388G A4995G A4996G A5427C G5516A C6059T C6293T T6332C RY3 T6619C T8207C T8258C T8333C C8546T T8617C G9516A T10505C T10835G C10982T C11984T T12684C A12707G T13022C T17794C C18415A T25926T T26716C C26806T C28772T Media Link Recombinomics Presentations Recombinomics Publications Recombinomics Paper at Nature Precedings

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