H5N1 Avian Polymorphism in PF11 Traveling Widely through the United States, Italy, Spain, Russia and many of the Ukraine's Neighbors

Bear in mind that these findings are preliminary and this study will be updated as research time permits.  Feel free to inspect closely for precision.

Since the TamiFlu Resistant HK2369 was published in July 2009 from a 2009-06-11 sample of a passenger from San Francisco entering Hong Kong, an increase in count and geographic distribution has been trending with what was once a rare NA polymorphism without a clear progenitor.  The NA sequence carried a G873A, GTg=>GTa, coding for a syn291V.  The sequence also carried an early version of the 206T / 225E RBD revision on HA.

In November, a Swedish sequence from GISAID and then Norway3206-3 (showing a distinctive variant coding for 225G from a post-mortem lung), appeared with the NA syn291V.  In the past month, an accelerating quantity of sequences, primarily carrying 225E, have been published from a widespread geography demonstrating movement of this silent Neuraminidase polymorphism. 

Sequences published on GenBank and GISAID show syn291V spreading thoughout the United States from an early start in New Jersey and Oklahoma (April and May respectively).  Growth occurred by early summer from an extensive base in California to North Dakota, then Texas (September) and onto a recent Kentucky sequence with the predicted HA Triple Combination of 206T / 225E / 300S, a combination that is concurrently found in Moldova, France, Turkey, Japan, Italy, Spain and the United States.  The recent domestic cat sequence from Iowa carries the syn291V suggesting effective Human to Feline transmission.

The worldwide growth is most apparent from recently published sequences.  The syn291V has now made appearances in China, Hong Kong, the UAE, England, Sweden, Norway and Greece with extensive penetration in Spain, Italy and neighbors of the Ukraine.  Latvia, Romania, Belarus, Moldova and Poland show the change.  Russia's Vector lab has demonstrated the polymorphism on Tomsk01 and Almati01.  Furthermore, the only two published human strains in the world with the adjacent RBD combination of 225E and 226R, Novgorod01 and StPetersburg5, also carry syn291V.

The evidence shows that this Neuraminidase revision is found on a number of unusual sequences, crosses geography easily and evidently crosses sub-clades having various RBD combinations with similar ease.

Until Dr. Ilaria Capua and her team at the Istituto Zooprofilattico Sperimentale delle Venezie published 2 sequences at GenBank on 2009-01-15, a clear progenitor candidate strain was not evident.  Avian H5N1 from Nigeria sampled in 2006 carries this NA syn291V and the RBD concern HA 225G.

  • HA and NA - A/chicken/Nigeria/08RS848-6/2006 (H5N1)
  • HA and NA - A/chicken/Nigeria/08RS848-8/2006 (H5N1)
Most importantly these two recent Avian H5N1 sequences are candidates as progenitors of the HA syn413K and NA syn407V cross segment linkage that is trending toward 100 sequences in ΣPF11 during the past two months.  These four obvious polymorphisms are only a subset of the current pandemic polymorphisms identified for which these Nigerian Avian H5N1 sequences may be contributors:
  • HA 225G
  • HA syn413K
  • NA syn291V
  • NA syn407V
Several of the polymorphisms in the recent Ancona, Italy deposit coincide with the Nigerian Avian H5N1  strains, 1918 and the Tinamou from Argentina in 2008.  We are inclined to review US sequences for introductions from the Nigerian Avian H5N1 and would be most appreciative of any hands on deck that would be willing to undertake a part of this retrospective exertion and make their results available to the general public.

A hearty show of gratitude from all genetics researchers is due today to the labs who worked on these sequences in Italy.  Thank you for publishing your data in a timely fashion.

Gather & Solve.

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