Re: (almost) no recombination in flu-B
I will check it later. Due to my experiences in the evolution of viruses, I do not think your idea is right. Anyway you should publish your paper in some peer-viewed journals. It is very important for a research. Try it
Here is a quick run-down on G743A, which should make it pretty clear that the acquistions are not due to selection of random errors.
In 2006, G743A on clade 2.2 was concentrated in Europe and on the same clade 2.2.2 background. There were something like 40 isolates from southern Germany, Switzerland, France and the Czech Republic. The only other published clade 2.2 sequence with G743A was in west Africa (one sequence out of many dozen).
I was working with NAMRU-3 on H5N1 in Egypt right after a cluster of 3 fatal infections were found in family members in Gharbiya. The NA sequences had N294S, which confered oseltamivir resistance. Since the resistance was in isolates collected prior to oseltamivir treatment, the frequncy of N294S in birds was of interest.
In February three isolates were received from chickens in Gharbiya. One of the three was closely related to the human sequences, but didn't have N294S. However, it was clear that the isolate was a mixture, so it was plaque pururified to see if a minor species had N294S. Over 40 clones were isolated and the NA's were sequenced. 30 of the clones were closely related to the human sequences, but they did not have N294S. However, they did have G743A, which was not in the human sequences. The other 10 clones matched the other two chicken sequences, which were related to Egyptian H5N1 sequences from 2006. Once again the 2006 sequences did not have G743A, but the 2007 sequences (from the clones or the two independent isolates) did.
Thus, in Gharbiya there were two distinct H5N1 sequences that had acquired the same polymrphism, G743A. The selection for this was not obvious, since the change was silent, and no Egyptian (or Israel, which was similar) sequence had G743A in 2006, but it appeared on two backgrounds at the same time in 2007. Thus, since only two backgrounds were involved, the acquisitions could have been a coincidence, although the number of differences between the 2006 and 2007 sequences was small (2-6 changes), so the chance of a coincidence would have been small.
However, shortly thereafter isolates in southern Egypt picked up the change. Once again earlier versions of the southern sequences had been found in patients and the earlier sequences did not have G743A. These sequences were quite different than those in the Nile Delta, yet they picked up the same change. This happened again, so there were four distinct H5N1 in Egypt that had picked up the same change, which would have been VERY hard to explain by random error / selection mechanism.
However, these "coincidences" did not stop in Egypt. In Feb, 2007 there was also an H5N1 outbreak in Moscow. The sequences were similar to clade 2.2.3 isolates from Azerbaijan in 2006, but the Moscow sequences had also acquired G743A.
NAMRU-3 also had a facility in Ghana, which also reported H5N1 for the first time in the spring of 2007. The sequences were closely related to H5N1 from the Ivory Coast (in 2006), but the Ghana sequences had also acquired G743A.
Thus, there were six different backgrounds in three different countries that had acquired the same change at the same time. However, as additional sequences were released, more examples were revealed.
Kuwait also had an outbreak in Feb, 2007. The sequences were also clade 2.2.3, but were distinct from the sequences in Moscow. The Kuwait sequences were closley related to clade 2.2.3 from Uvs Lake and Russia collected during a wild bird outbreak in the summer of 2006. Similar sequences were in South Korea and Japan at the end of 2006 and none of the 2006 sequences had G743A, but all of the sequences in Kuwait did. These Uvs Lake sequences in Kuwait subsequently spread throuout Europe in the summer and fall, and all Uvs Lake sequences published to date have G743A.
Similarly, there was an H5N1 outbreak in Nigeria in early 2007, which were similar to the first human case there. A small subset of the Nigerian sequences also had G743A.
Thus, the G743A in clade 2.2 which was largely limited to a small geographic region in Europe on a clade 2.2.2 background in 2006, suddenly appeared on multiple genetic backgrounds (including multple versions of clade 2.2.1 and clade 2.2.3) in early 2007, and the 2006 precursors of each of these sub-clades did not have G743A.
Trying to explain the above acquistions of the G743A SNP via selection of a random mutation is a difficult task, especially since the 2006 precusors for each background had already been isolated and the 2006 sequences did not have G743A.
Although the appearance of the same SNP on so many different backgrounds at the same time is unusual, the sharing of the same change by isolates with a smaller number of genetic backgrounds is common, and these acquisition of SNPs via homologous recombination is the MAIN driver of influenza evolution (and accounts for the VAST majority of SNPs).
