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RBD Driven H1N1 Immunological Escape In UK
Recombinomics Commentary 12:20
January 18, 2011

The US CDC has released a series of recent H1N1 sequences at GISAID and declared three of the isolates as “low reactors” signaling a titer reduction of four fold or higher when tested against anti-sera directed against the current pandemic H1N1 target, A/California/7/2009. 

Two of the low reactors were from Costa Rica and had changes among positions 156-159 (one, A/Costa Rica/5458/2010, had a K156E mixture, while the other, A/Costa Rica/5529/2010, had G158E).  All prior pH1N1 low reactors identified the CDC had a least one change in this region. 

However, the third “low reactor”, A/India/5103/2010,was wild type at positions 156-159, but it had S186P and S188T.  These two changes dominate recent sequences from the UK, with 36/41 HA sequences having at least one of these two receptor binding domain changes, signaling immunological escape.

Changes in these regions mimic escape for seasonal H1N1 in 2007-2009.  In the summer of 2008 H274Y became fixed by hitchhiking with receptor binding domain changes flaking position 190.  In South Africa H274Y levels rose to 100% and the dominant sub-clade had A193T.  Sequences also had additional changes in this region, with at least one change at positions 186, 188, or 196.  Moreover, seasonal H1N1 sequences targeted these positions, which led to a database with multiple versions of each position (N187S, N187D, G189A, G189N, G189S, G189V, H196R, H196N).

The sequences from the UK mimic this strategy, with 36/41 sequences having either S186P or S188T.  However, a small subset of sequences has additional changes in this region. A/England/4640543/2010 has S188T and D190G, while A/England/4500186/2010 has S186P and D190Y.  Similarly, A/England/119/2010 has S186P and D188N.  Thus, multiple changes at the same position (S188T, S188N, D190G, D190Y) co-circulating in the UK suggest more combinations will appear via recombination, signaling additional immunological escape.
This escape is supported by the high frequency of these changes in UK isolates, as well as an antigenic characterization assays with a checkered past.  Although these assays have been in place for decades, the sensitivity and reproducibility issues has plagued analysis, especially for H1N1 isolates.  For pH1N1, G158E has implicated in the generation of “low reactors” by multiple labs, including the US CDC.  An early pH1N1 sequences from Germany had G158E and was designated as a low reactor.  Similarly, another isolate from Germany with G158E was also designated as a low reactor by Mill Hill.  This change was also cited by MedImmune when characterizing California/7 clones.  One clone with G158E grew well in eggs but was not selected because of low reactivity with California/7 anti-sera.  In addition analysis of escape mutants identified G158E.

However, when sequences with G158E began to appear in US pH1N1 isolates, they were not designated as low reactors by the CDC, even though the earlier sequence from Germany was, which is alos true for the recent 2010 isolate from Costa Rica, signaling intra-lab variation.  This type of sensitivity, reproducibility issues also arose for a sequence from Ukraine.  A/Lviv/N6/2009, which had D225G, was designated a s low reactor by Mill Hill.  However, all CDC low reactors were limited to changes between positions 156-159, and all low reactors from the US had changes at position 159.  Moreover, when the CDC published a sequence from the above sample from Ukraine, their sequence had G158E and D225G, but was not designated a s low reactor.  The WHO regional center in Australia published ferret anti-sera data and A/Lviv/N6/2009 had a striking reduction in titer against a variety of antisera, demonstrating inter-lab variation.

This type of variation in WHO regional centers was also seen in the 2007/2008 season, which had A/Solomon Islands/3/2006 (clade 2A) as the seasonal H1N1 vaccine target, which represented a change from New Caledonia/20/1999, and New Caledonia (clade 1) was clearly declining.  However, Solomon Islands/3 was also declining and was being replaced by clade 2B (A/Brisbane/59/2007) and clade 2C (A/Hong Kong/2562/2006).  The CDC used anti-sera which could distinguish clade 1 from clade 2, but not the three clade 2 sub-types from each other.  Consequently the clade 2B and clade 2C where designated as Solomon Island-like and a “match” for the vaccine.  However, the WHO regional center in Australia developed anti-sera against Brisbane/59 grown in mammalian cells and that anti-sera could clearly distinguish between the three clade 2 sub-clades, and the target for the 2008/2009 was changed to A/Brisbane/59/2007. 

However, the mismatch with Solomon Island/3 aided immunological escape, and when Brisbane/59 was introduced, Brisbane/59 was dominant, but had the receptor binding domain changes flanking position 190, leading to many reports of vaccine breakthroughs in the 2008/2009 and the fixing of H274Y worldwide.

This season, the same paradigm is being employed against the outdated pH1N1 vaccine target, A/California/7/2009.  Vaccine breakthrough was reported in Australia, and now the designation of India/5103 with S186P and S188T supports escape by isolates with one or more of these changes and subsequent dominance as seen in the recent sequences from the UK.

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