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Paradigm Shift Intervention Monitoring
The USDA has released six HA
sequences from Costa Rica swine collected in November, 2010. These
sequences are closely related to each other, and quite distinct from
pH1N1 sub-clades dominant
in November/December human
isolates in the United
States and Canada., which have S186P or S188T.
One of the isolates, A/swine/Costa Rica/000125-15/2010, has a cluster of RBD changes (H184D, S188R, D190Y, Q192H, D199Y). Two of these changes (H184D and D190Y) are also in another isolate, A/swine/Costa Rica/000125-3/2010.
Other non-synonymous changes in this series are N34D, K57R, K122N, P162L, S165I, E238K, K286R, A318V, I375V, R549K. Most of these changes are in most of these Costa Rica swine isolates.
This genetic diversity can serve as a reservoir for rapid change in pH1N1 in humans. This virus can readily jump back to humans from swine to introduce these changes into the human population. Most of these changes are already circulating in human isolates (see list here here here).
D190Y has been seen previous in a 2009 sequence in Brazil, A/Brazil/7450/2009, as well as a recent isolate in England, A/England/4500186/2010.
The large number of changes flanking this change is similar to changes associated with the fixing of H274Y in 2009. Virtually all seasonal H1N1 isolates emerging in the fall of 2009 had A193T which was coupled to one or more changes at positions 187, 189, or 196. These changes allowed for immunological escape and rapid spread throughout the northern hemisphere, including countries where the Brisbane/59 sub-clade was circulating in the prior season.
Recently released pH1N1 sequences from the northern hemisphere are sioalted by sub-clades with S186P or S188T, with the latter becoming more dominant. Acquisitions of additional changes via recombination will likely increase spread and virulence.
H1N1 is now becoming dominant in many countries in the northern hemisphere as levels of H3N2 decline. These changes will lead to increases in deaths in pediatric and young adult cases and increase pandemic concerns.