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pH1N1: Arizona 2011 on a Pandemic Background with an Observed 5% Case Fatality Rate

 

pH1N1: Arizona 2011 on a Pandemic Background with an Observed 5% Case Fatality Rate

Posted by labvirus on July 22, 2011

Arizona 2011 on a Pandemic Background with an Observed 5% Case Fatality Rate

Last Update
2011-07-20

On 2011-06-21, the lead public health agency from the United States released 50 sequences at GISAID containing a subset from a heavily zoonotic sub-clade that is circulating across a worldwide geography in Americans and in individuals of at least 11 other nationalities.  Eight matched pairs (HA and NA segments) from the emergent sub-clade are found in this deposit.

This Pandemic H1N1 Upsilon Sub-Clade is termed as pH1N1υ for reference brevity and encompasses the 230I-Permissive, 189T-Bearing Hydra that has emerged from January 2010 to April 2011 across 62 HA and 53 NA sequences defining a clinical subset of 58 cases, including fatalities, vaccine escape situations and TamiFlu resistance.  Across the HA segments (19 Fragments), 745 polymorphisms are found (93 distinct).  The NA is less volatile, but does lead other sub-clades with 251 polymorphisms spread over 68 distinct codons.

Although complete clinical outcomes are not forthcoming, the Case Fatality Rate for pH1N1υ cases remains at or above 5% for a number of reasons, including very high Zoonotic Potential scores indicating rapid acquisition of genetic material from animal reservoirs.  This sub-clade displays hypermorphic behaviour, carrying an average of 12 changes per HA and 4.7 per NA.  At this analysis, GeneWurx investigates the potential donor reservoirs for the late season 2011 sequence that bears the highest count of pH1N1υ HA polymorphisms, Arizona02_43F_2011_03_08.  The HA polymorphism count of 19 (7 Amino and 12 Silent) and 6 for the NA (0 Amino and 6 Silent) ranks this sequence within the ultimate decile of cladded pH1N1 sequences.

Four HA revisions novel to pH1N1υ demonstrate a continued genetic re-seeding though the base of this sub-clade is founded on a significant immune escape charge.  A triad of novelties (210N, syn334G, syn337A) are found individually and grouped on various animal reservoirs closely related to the change pattern for pH1N1υ, H2N2 and H6N1.  The fourth novelty, 516V, appears within H2N2. The 210N and syn337A have recently appeared on pH1N1 Clade 2: 188T.

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22/07/2011

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