TamiFlu Resistance #13 from Italy: Novel with Swine Inclusion plus 4 Rare PF11 Amendments

The thirteenth TamiFlu Resistant specimen with a publicly available sequence, A/Pavia/21, was deposited Friday at GenBank with only Segment 6 (NA).  The sample is contemporary and was taken 2009-11-16 on a nasal swab from a host with no gender or age identification in Pavia, a city of 71,000  in the Lombardy region of north central Italy.  This Neuraminidase is remarkable due to the number and range of polymorphisms though the sequence is truncated 35 bases from the end.

The NA of Pavia21 is novel at the amino acid and the nucleotide level with no peer within ΣPF11, nor in the TamiFlu Resistant subset.  The 5 polymorphisms on this sequence, if acquired via recombination, require a wide set of donors or more likely coincident recombination and adaptation events.  Inclusions are noted that previously appear on Swine H1N1 (recent and 1931), Avian H1N1, Seasonal H1N1, Avian H5N1, Avian H6N1, Avian H10N1, Avian H11N1 and on very small and diverse sets of European PF11 sequences. 

Three of the polymorphisms are silent.  No combination of any 2 of the 5 signals seems to appear on documented public sequences.  None of the signals other than 275Y appear on any previous PF11 TamiFlu-Resistant sequence.

NA Amino Acid Codings to 1 Novel Polymorphism and 4 Rare Signals
  • syn70S
  • 275Y
  • 332K
  • syn360G
  • syn398E

encoded from C210T, AGc->AGt 
A/Catalonia/NS675 (2009-06-08) is the singular ΣPF11 peer.

Novel to ΣPF11.
Progenitors may include:
H5N1 Avian Asia 2005, 2006, 2007, 2008
H6N1 Avian Europe 2005
H1N1 Swine 1977, 2002
H1N1 Seasonal 2007 (230I)
NCsw36883 (212E)
Iowa human swine worker 2005 H1N1 (IA/CEID23/2005)

encoded from G1080A, GGg->GGa 
Rare to ΣPF11 with 4 French instances in early pandemic.
Paris2591 (HA:225E)
Progenitors may include:
H1N1 Human North America 2007, Middle East 2006, 2007
H1N1 Avian North America 2006, 2007, 2008
H1N1 Avian Asia 2006
H1N1 Swine North America 1931, 2003, 2004, 2005, 2006
H1N1 Swine US 1931 
H1N1 Swine Asia 1993, 2001, Europe 2001
H5N1 Avian North America 2005
H6N1 Avian North America 2007, Asia 2006
H10N1 Avian North America 2007
H11N1 Avian North America 2002

encoded from G1194A, GAg->GAa 
Rare to ΣPF11 with 7 instances.
Italy160 (July from Veneto)
Spain with 5 sequences as recently as 2009-10-28
Canada (May)
Progenitors unknown; however, a 12 residue span in this area, including residue 398, revises for WSN33 and H5N1 Human.

On Pavia21 TamiFlu Resistance is indicated in typical PF11 fashion via a Single Nucleotide Polymorphism coding for 275Y on the Neuraminidase. The sequence displays the following NA Quadruple Combination:

106I, 248D, 275Y, 286S

The following permutations are now represented on the thirteen PF11 anti-viral resistant sequences:

106V, 248N, 275Y, 286S = WA28, WA29, TX47
106I, 248N, 275Y, 286S = Osaka180
106I, 248D, 275Y, 286S = HK2369, Yamaguchi22, Denmark528, Hunan SWL3, Singapore57, Tokushima2, Iwate3, Quebec147365, Pavia21

Until the 2009-08-21 deposit of the two Washington sequences, all 275Y TamiFlu-Resistant specimens on PF11 backgrounds were paired with 106I.  We continue to see only 3 of the 13 with 106V.  The addition of Pavia21 heavily leverages position 248 toward Aspartate (D) with 9 specimens versus 4 with Asparagine (N). No TamiFlu Resistant specimen on file displays 286G as yet.

Pavia21 is the most hypermorphic TamiFlu-Resistant PF11 strain seen since the oddities from the immuno-compromised patients in Washington.  Four changes other than H275Y is unusual in a single sequence. 

We are quite impressed with the Influenza reservoir's ability to recycle data between serotypes without reassortment.  Unless this sample were exposed to low level radiation during incubation, a series of accumulative recombinations have occurred over a very short time period or a triple co-infection enlisted all variants to build Pavia21 within a single host using an adaptation event to smooth the topping. 

The most probable explanation is an accumulation of recombinations across the hypermorphic Catalonia region then exporting data to Italy via wild birds with a single co-incident adaptation event within the eventual host.  Additionally, our team would not be at all surprised to find 225E on the HA of this patient's virus if the data is eventually published.

At any measure, another new background is now carrying TamiFlu Resistance in a central flyway for Influenza's primary transportation vector, wild birds.

Please visit GeneWurx.com for insight into the latest published studies.