For those of us with an interest in viral genetics I have started this thread to look at the little data that is now available. What follows is not my analysis but based on the work posted on the Virological.org forum.
1] The consensus is that much of the sequence data is unreliable due to the high number of sequencing errors.
2] Based on the more trusted sequences the MRCA (most recent common ancestor) is probably in early Dec. 2019 giving a recent single common ancestor for all sequences. If accurate this means it probably has not been circulating below the radar for a while.
3] Due to the recent MRCA the cladogram is boringly flat with only a one or two AA variance from WH01 and most being identical. Where there are changes they seem random with no evidence of host adaption.
A note on the Virological site. If you followed the H7N9 discussion thread you may remember Andrew Rambaut from Edinburgh Uni. who posted really useful phylogenetic trees and analysis on the University's Epidemic site (which had sections on MERS, Ebola and flu). When this outbreak occurred I checked the site only to find it had disappeared but Andrew had reappeared as Administrator of Virological which at that time only had a couple of threads. In the main discussion thread I posted a speculation this was a Beta CoV before it was announced, I would not normally have done this based on a single media report but the article was by Lisa at Cidrap and she was quoting Marion Koopmans of Erasmus. I trust MK not to have made the comment without good reason and LS not to use it without reason to think MK had good reason for saying it. Which brings me back to Virological where MK & AR are contributing and which was used to post the first open source sequence. Currently some sequences are being deposited at GISAID and others at Genebank.
1] The consensus is that much of the sequence data is unreliable due to the high number of sequencing errors.
2] Based on the more trusted sequences the MRCA (most recent common ancestor) is probably in early Dec. 2019 giving a recent single common ancestor for all sequences. If accurate this means it probably has not been circulating below the radar for a while.
3] Due to the recent MRCA the cladogram is boringly flat with only a one or two AA variance from WH01 and most being identical. Where there are changes they seem random with no evidence of host adaption.
A note on the Virological site. If you followed the H7N9 discussion thread you may remember Andrew Rambaut from Edinburgh Uni. who posted really useful phylogenetic trees and analysis on the University's Epidemic site (which had sections on MERS, Ebola and flu). When this outbreak occurred I checked the site only to find it had disappeared but Andrew had reappeared as Administrator of Virological which at that time only had a couple of threads. In the main discussion thread I posted a speculation this was a Beta CoV before it was announced, I would not normally have done this based on a single media report but the article was by Lisa at Cidrap and she was quoting Marion Koopmans of Erasmus. I trust MK not to have made the comment without good reason and LS not to use it without reason to think MK had good reason for saying it. Which brings me back to Virological where MK & AR are contributing and which was used to post the first open source sequence. Currently some sequences are being deposited at GISAID and others at Genebank.
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