Cryptic Drift

Flu strains can change by “shift” or “drift”. Shift is said to occur when gene segments reassort to create a new virus. This how pandemics start. Drift is said to occur when enough small changes accumulate so that the virus can evade the immune system. This can result in a bad flu season.

We are told that neither of these events have occurred. If so, how to explain the current very bad flu outbreaks?

From KIWA radio:

Dr. Gregory Poland is a vaccine expert at the Mayo Clinic in Rochester.

“What we’re seeing unfortunately is a strain called influenza-a h3n2 and that’s an important seasonal virus because it is the one that causes the most morbidity and mortality in humans.”

He says the last time we saw a widespread outbreak of this strain was about a decade ago and it was responsible for thousands of deaths.

There are a couple of problems with this statement:

1. The CDC says the strain causing massive outbreaks this year is the same strain that caused a mild flu season last year.

2. The H3N2 strain that was so severe in 2003-2004 was a clear example of drift.

Strange how these two facts are not being mentioned by flu experts.

For reference:

From the CDC this week:

325 (99.4%) of the 327 H3N2 influenza viruses tested have been characterized as A/Victoria/361/2011-like, the influenza A (H3N2) component of the 2012-2013 Northern Hemisphere influenza vaccine.
2 (0.6%) of the 327 H3N2 viruses tested showed reduced titers with antiserum produced against A/Victoria/361/2011

From the CDC in 2004:

Of the 949 influenza A (H3N2) isolates that have been characterized, 106 (11.2%) were similar antigenically to the vaccine strain A/Panama/2007/99 (H3N2), and 843 (88.8%) were similar to the drift variant, A/Fujian/411/2002 (H3N2).

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4 thoughts on “Cryptic Drift

  1. Fujian flu drifted “suddenly” in early or mid 2002 (first::A/HK/CUHK24044/2002/06/01) in ~10 nucleotide positions in HA, That strain then started to dominate in Asia in late 2002
    and was seen in USA 2002/03, but it was not the major strain in USA that season.
    It only became the semi-pandemic virus in USA in 2003/04 after it reassorted in 2003
    and got (7 afair) other segments .
    Since 2011 we have 2 circulating H3N2s, one the “Egypt/Iowa”-strain from 2009
    and one reassortant with that. Almost all H3N2 since 2007 goes back in all segments to a common
    ancester from 2007 (“US/Index/2007”), so the 2 strains from 2011 are not that much different.
    But neither were the reassorted ones in 2003

    1. > 1. The CDC says the strain causing massive outbreaks this year
      > is the same strain that caused a mild flu season last year.

      where does the CDC say this ?

  2. The CDC has released over 50 sets of H3N2 sequences from the current 2012/2013 season (most recent collection from November 27). Included are the two LOW REACTORS cited in week 48 FluView (A/Hawaii/29/2012 and A/Iowa/14/2012). Hawaii/29 has HA L157S, a change in a region (positions 157-161) known to produce low reactors and cited by the CDC in the 2012/2013 vaccine selection meeting. The CDC is testing Hawaii/22 as a new vaccine target (and both isolates are virtually identical – sequences for all 8 gene segments of Hawaii/22 have also been released).

    The other low reactor has lost a glycosylation site at position 126 due to T128A (H3 numbering). That change and associated chnages in Iowa/14 are widespread and are found in almost half of the most recent H3N2 sequences from the US, as well as all 6 sequences from the UK. This drifted variant is driving the US numbers and is not well recognized by the curent vaccine, CDC “matches” based on insensitive antigen characterization tests notwithstanding.

    1. with “released”, you probably mean GISAID (you did it in the past), which is not public
      And reassortment cannot be determined from HA alone.
      So, what type is this season’s H3N2 ? What other public virus does it match
      in all segments closer than -say- 99%, a typical 3-years-evolution-distance ?
      Do they know it ? If no, why ? They had ample opportunity by now to test it.
      If yes, why do they not talk about it ? Why did the reporters in the
      press-briefing not ask for it ?
      Why don’t they publish the virus, e.g. by uploading it to genbank ?
      Can we require it via a FOA request ?
      Will Canada publish it first ?

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