Capital of Spain Moving to the Front in the Race for PF11 Antigenic Diversity

The capital area of Spain is generating pandemic strains of particular Antigenic Diversity in Pandemic Influenza H1N1.

Introductions into a pandemic reservoir merit tracking to identify potential vectors of inter-"host species" viral genetic material.  We watch always for something new.  Influenza, as you have read, may be reasonably expected to have a certain level of genetic flux, a certain level . . . but not necessarily the levels we are witnessing within ΣPF11.

Novelty can get very old sometimes, but tempus fugit and so do birds. 

First, Argentina reports genetic novelty corresponding to fatal cases in a sequencing partnership with Columbia University.  Then, Sao Paulo releases 9 sequences splashing across 6 HA backgrounds.  So we studied the data, however sparse.  And we studied closely, under a resigned certainty that the "bad news" was expected, even predicted.  We were confident that ΣPF11's first winter passage in humans would unavoidably derive new sub-clades due to the weather . . . until balmy Spain transparently reported yesterday, somewhat courageously and seemingly with full disclosure. 

Coastal Spain was not in winter during July and August of 2009.  Mallorca's beaches were not covered by tourists bundled against the stark cold.  Yet Spain is demonstrating a very similar rate of genetic acquistion into the pandemic reservoir as nations who were passaging through the cooler weather of their traditional "cold and flu" season.  We would like to say that seeing this rate of change in the summer took us at a complete surprise, but that nagging feeling of knowing gnawing has been persistent every time we discuss tourist areas, the logistics of congregation points, summer camps and the microbiological traits of PF11 (IDRREAV^*).

The first sequence profiled here is certainly not unworthy of mention; however, the pattern shown is also not the most curious of the summer specimens.  The middle of the road may be a good place to plant our feet as this pandemic begins to veer.  So this novel specimen and apparently new sub-clade gets a fresh piece of paper, a clean slate, all to its ungainly self.

A/Catalonia/NS1161, sampled on 2009-07-28, Segment 4 (HA) and Segment 6 (NA).

I only want to discuss the Hemagglutinin in detail today, but you may envelope yourself in the Neuraminidase at your leisure.  I believe you may even find that Segment 7, the Matrix Protein, waits on the rack in your size.

HA Amino Acid Codings to 4 Impractical, but Impressive Polymorphisms

•   48K
• 206A
• 225E
• 264T

None of these changes are prolific within ΣPF11. 

264T occurs on 1 other PF11 background.  225E in the Receptor Binding Domain is rare with a total of 37 occurences worldwide (25 in Catalonia).  206A and 48K are each individually novel to this reservoir.  No permutation of any two of these changes appears to occur together in the sequence record outside of CatS1161.  The probability is calculably low for a series of three independent polymorphisms randomly arising on a single Catalonia background having 225E.  That variability index on the HA would contrast somewhat with the NA.  Did we mention yet that the Neuraminidase gene segment is entirely stable?

48K
Novel to ΣPF11.
Progenitors may include:
1918
WSN33
Seasonal H1N1 1983
Taiwan H1N1 1985
swine Wisconsin H1N1 1997, 1998
swine Hong Kong H1N1 2001

206A
Novel to ΣPF11.
Progenitors may include:
A/South Africa/42/2000(H1N1) - single instance located on GenBank.

225E
37 instances within ΣPF11: Catalonia (25), Europe, Asia, Russia and United States.
Progenitors may include:
Seasonal H1N1 2007

264T
A/New York/3012 from April 2009 within ΣPF11: single instance early in pandemic.
Progenitors are unknown.

Neuraminidase Quadruple Combination
CatS1161 = 106I, 248D, 275H, 286S

The Neuramindase is an exact match for 460 PF11 sequences on file, and is a 100% match (1243/1243) on 11 of those at the nucleotide level.  Though the HA is highly variant, the NA seems to have been spared, matching precisely to 7 other Catalonia sequences in this deposit, to Stockholm37 and to 3 geographically dispersed specimens carrying 225E (NJ01, Sapporo1, Changsha78).

As we have mentioned that the phylogenic tree for these South American sequences have a very low ratio of leaves to branches, you should realise that this sequence is one of several that are defining.  This specimen has gone out on a limb for you, all alone. But don't be remorseful for this single strand of negative-sense RNA because he's not really alone.  That uniqueness creates a commonality if you pull away from the tree a bit and recognise that it's filled with single leaf branches just like this one.  If he could think, I think he would say to you, "Don’t weep for me. I’ve traveled far and vacationed well. I fed at the buffet and chose the best desserts. Don’t worry about me; I’m going shopping now and I'll be back this way soon wearing a stylish new jacket," and then he'd turn and begin training the other branches for the next replication cycle.  He's really not alone.

This sequence is surrounded by others almost as odd as himself, so you could say that he's in good company . . . that is if you consider a gallery of unmasked rogues as good company.  I can hear them musing now, "Somewhere ages and ages hence I shall be telling this with a sigh. Two rogues converged on a sunny beach and I, I selected the one most traveled by and that has made all the difference."

If a virus were non-random, that is.

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