niman wrote:
N444K
EPI298423 A/Shahriar/5336/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.92613
EPI295741 A/England/139/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.92613
EPI295733 A/England/99/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.92613
EPI295731 A/England/93/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.92613
EPI295729 A/England/91/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.92613
EPI295728 A/England/90/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.92613
EPI295725 A/England/85/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.92613
EPI295724 A/England/79/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.92613
EPI295516 A/Bhutan/72/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.92613
EPI295501 A/Bangladesh/1685/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.92613
EPI295481 A/Pennsylvania/17/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.92613
EPI295474 A/Pennsylvania/16/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.92613
EPI280326 A/Wisconsin/08/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.92613
Here is more info on how to read "pedigrees" or "travel logs". The above travel log is realively short and quite homogeneous. It is for an HA "mutation" that leads to a change in the protein sequence - position 444 changes from N (asparagine) to K (lysine). The only "matches" or "hits" for this change, in the entire GISAID database are the sequences above (all are recent human sequences - if no species is listed in the name it is human).
This group is closely related and if you look at additional HA changes (or travl logs) on this thread, you will see all of the above isolates in one list after another (the lists are order by accession number, which are assigned by GISAID as sequences are received and are loosely chronological). Thus, this is a recent change, and all of the above have that change, even though the were from WI and PA in the US, multiple locations in the UK, as well as Iran, Bangladesh, and Bhutan, which is why I call these "travel logs".
There is additional data in the database, including the actual sequence, which can be used with public software that will put the sequences in phylogenetic trees, which schematically shows which sequences are releated to which.
There is also meta data showing who did the sequencing, when sample was collected, age and gender of patient. Sometimes status is included (like deceased), or more info on location (I included some of the UK locations in today's commentary).
The identity of Pennsylvania/17 was easy because it came from a 45M collected on Nov 16, which matches the index case for the Lehigh death cluster
http://www.recombinomics.com/News/12011 ... irmed.htmlPennsylvania/16 was collected on November 17 from a 22M, which is close to media reports which described a 28M admitted to Lehigh Valley Hospital at about the same time as the 45M (so sample collection a day apart would be expected).
The actual HA sequences are identical, further confirming both patients were probably from the same location and collected at the same time.
Thus, it is clear that these two samples represent the Lehigh death cluster. Samples from the Montogomery County death cluster have not been released, but it is VERY likely that they will be H1N1 and very closely related to PA/16 and PA/17,
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