Friday, 14 February 2014

H7N9 keeps changing and mingling and mixing...

A new report in Eurosurveillance out today has once again raised the spectre of a pandemic H7N9 spread. 

Not just for what the Meng and colleagues from China and the United States have shown in their detailed analysis of the PB1 gene segment of (mostly) avian influenza A(H7N9) viruses from humans birds and the environment in 2013, but also for what they have indirectly highlighted: a massive absence of 2014 H7N9 sequence data on GISAID or GenBank sequence databases. 

Being asked for comment, which I provided in 2 stories linked below (2 and 3), I dug into the sequence databases and was stunned (yes, really!) to find that there are hardly any sequences available from H7N9 gene segments or genomes this year.
Given that this year's human case tally of H7N9 infections has surpassed that of 2013's 1st wave, I find that really surprising, and confusing. Also given a few subtle pattern changes that I've been writing about of late including the shifting age balances, sex ratios, fewer farmers, more family clusters, apparently limited impact on human case numbers from market closures >2-weeks ago...I would have said keeping our eye on the genetic ball was more important right now than ever.

What's going on?

Meng and colleagues use the PB1 gene to highlight changes to H7N9 resulting in 4 genetically distinct clusters with links through time and geography. 

There seems to be continued and active change in H7N9 based on analysis of this 1 segment. Not surprising for a virus whose genes exist as a deck of 8 cards, each capable of its own drift changes, just waiting to be shuffled but the next already-occupied host it enters.

I really wonder how much of the virus we knew of as H7N9 in 2013 has changed and what the virus we know in 2014 is like by comparison. 

The only way to answer that will be to see and analyse the sequences from 2014. And hopefully, do that soon. 

These bits of viral genetic material don't just make pretty trees (or hard to see ones like in he Eurosurveillance article), they identify significant changes to the virus that signal potential for, or real, change in transmission, disease type and severity, site of preferred replication and our likelihood of successfully detecting the virus using sequence-dependent, PCR-based diagnostics.

Sources...

  1. Eurosurveillance article.
    http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=20699
  2. CIDRAP story
    http://www.cidrap.umn.edu/news-perspective/2014/02/h7n9-cases-pause-new-report-details-reassortants
  3. Bloomberg News story
    http://www.bloomberg.com/news/2014-02-13/pandemic-potential-seen-in-gene-changes-of-bird-flu.html