Recombinomics | Elegant Evolution

Home Founder What's New In The News Consulting

H1N1 Consulting

Paradigm Shift

Viral Evolution

Intervention Monitoring

Vaccine Screening

Vaccine Development

Expression Profiling

Drug Discovery

Custom Therapies


Audio:Nov18 Dec16 Jan4 Jan20  RSS Feed twitter News Now                         


H1N1 RBD Changes S188R and D190Y in Costa Rica Swine
Recombinomics Commentary 16:40
February 10, 2011

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 the 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.

Media link

Recombinomics Presentations

Recombinomics Publications

Recombinomics Paper at Nature Precedings

Home | Founder | What's New | In The News | Contact Us

© 2011 Recombinomics.  All rights reserved.