Low Reactors Thread

[sharon sanders]

Re: Mutations in A/H1N1 Not Confirmed to Affect Effectiveness of Current Vaccine

more from that article:

snip


?Every year there are a certain percentage of people who are vaccinated and just don?t respond to it,? said Dr. Tracy Murphy, state epidemiologist.

Murphy said that although it can happen to anyone, people older than 65, children and people with chronic diseases are less likely to ?have a protective response to the vaccine.?

Murphy said he has not seen any reason to believe the H1N1 vaccine is inferior or flawed when compared with other vaccines.

?It?s certainly still a good protective measure, but it falls short of being 100 percent effective,? Murphy said. ?That?s why, during the flu season, we encourage everyone, whether they?ve been vaccinated or not, to take precaution.?

Murphy said that although flu strains can mutate and evade vaccines, he does not believe that is the case with the current strain of H1N1.


snip

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I think the current vaccine ONE of several tools to be used against A/H1N1. It is not a 100% guarantee.

[JJackson]

Re: Mutations in A/H1N1 Not Confirmed to Affect Effectiveness of Current Vaccine

but it should raise some eyebrows.

Why?

That someone who had had a flu jab subsequently caught flu is hardly news worthy. No one has ever claimed the vaccine had a 100% protection rate - or anything close. The effectiveness of the seasonal flu vaccine, in the elderly who make up the bulk of those injected, has always been suspect.

Again, I do not see how mutations at 225 come into this. Protection is not a binary state it is conferred as the accumulated benefit of the innate immune response plus any antibodies the host has to antigenic sites on the infectious agent. In flu's case there are several primary antigenic sites, mainly on HA and NA, and a change of one SNP that happens to fall in one site might render that one antibody ineffective, or only partially effective. It can not, however, prevent the other antibodies from doing their job or have any effect on all the components of the innate immune system.

[ms4920]

Re: Mutations in A/H1N1 Not Confirmed to Affect Effectiveness of Current Vaccine

Niman is stating that this is due to vaccine failure and 225g mutation? He wrote a commentary on it.

I am confused. Some of you state different

I am going with that the vaccine is not 100% effective, just like any other seasonal flu vaccine or any other vaccine.

[alert]

Re: Mutations in A/H1N1 Not Confirmed to Affect Effectiveness of Current Vaccine

Thanks for the explanation.

Before we jump the 225G/vaccine escape bandwagon, we should remember (quote from your article)

Have we ever seen an estimate of the % of those vaccinated against panflu who will fail to respond?

I remember reading somewhere that the childhood vaccines, such as mumps and measles, are only 95% effective in that sense. If the seasonal or pandemic flu vaccines are that effective, then the chance of the vaccine just not working in a given individual far exceeds the chance of encountering a "low reactor".

This would not be the first H1N1 infection in a vaccinated individual.

Assuming that they are actually able to isolate the virus from this individual, I would like them to test to see whether it was a low reactor, or whether the vaccine just did not give the individual any immunity.

[ms4920]

Re: Mutations in A/H1N1 Not Confirmed to Affect Effectiveness of Current Vaccine

This article was very poorly written. We do not when she got vaccinated and was it H1N1 vaccines. We are assuming it was h1n1 vaccine, but the writer of this article is not giving much info., so there is much to be desired from this and what is really going on.

[JJackson]

Re: Mutations in A/H1N1 Not Confirmed to Affect Effectiveness of Current Vaccine

I had rather hoped this thread would die a natural death and the question of whether or not single nucleotide change - regardless of where it occurred - could cause an otherwise well matched vaccine to stop working had been resolved. It could be 'the straw that broke the camels back' in if a vaccine was already a poor match and yet another change occurred it could cause an even worse match and a higher percentage of tests returning 'low reactor' status. In such a case I would expect this to be seen as an increase in the percentage of test failures from an already significant base.
I thought one or two links might be helpful for any one trying to understand some of the background to this debate.

The first is to The epitope regions of H1-subtype influenza A, with application to vaccine efficacy which includes this table showing the 5 primary antigenic sites (A to E) on HA (which is the most antigenically significant flu protien) and exactly which residues fall within them. (You will find 225 in site D)


Table I.

Amino acids in epitopes A, B, C, D and E of H1 (A/California/04/2009 numbering, modified from Caton et al., 1982)

Epitope Amino acids

A 118 120 121 122 126 127 128 129 132 133 134 135 137 139 140 141 142 143 146 147 149 165 252 253

B 124 125 152 153 154 155 156 157 160 162 183 184 185 186 187 189 190 191 193 194 195 196

C 34 35 36 37 38 40 41 43 44 45 269 270 271 272 273 274 276 277 278 283 288 292 295 297 298 302 303 305 306 307 308 309 310
D 89 94 95 96 113 117 163 164 166 167 168 169 170 171 172 173 174 176 179 198 200 202 204 205 206 207 208 209 210 211 212 213 214 215 216 222 223 224 225 226 227 235 237 239 241 243 244 245
E 47 48 50 51 53 54 56 57 58 66 68 69 70 71 72 73 74 75 78 79 80 82 83 84 85 86 102 257 258 259 260 261 263 267

For A/PR/8/1934 numbering, amino acid numbers above 130 would have 1 subtracted from them.

The next link is to a description of the Influenza hemagglutination inhibition assay which is the test used to see if a sample reacts well, or poorly, to anti-sera for a given strain. I don't think those who do not share my views on this issue, and I, have a problem on the definition of the test used to generate the LR status, just on the significance of a particular sample rating LR. I include it for those who wish to understand what is being discussed.

One more. While I was looking for the link above I found this Being older is a good defense against 2009 H1N1 influenza virus on Vincent Racaniello's blog which might be of interest as it includes a general discussion on cross reactive immunity.

Hope it helps JJ.

[JJackson]

Re: Mutations in A/H1N1 Not Confirmed to Affect Effectiveness of Current Vaccine

This house believes

In the interests of full disclosure, and because I am not interested in winning an argument but in a fuller understanding of a problem, I will discuss below a possible argument in favour of 225 - or any other SNP - having an excessive weighting which could have been used against my position.

In order to understand we simplify. What we are really interested in is the virus/host immune system interaction but as we don't really understand this fully we make a number of assumptions and simplifications. As a crude proxy we use HA % homology as a starting point. Of the 8 flu RNA segments the one that codes for the HA protein has about 1500 residues if we compare the sequence of interest with the sequence for the strain the vaccine was based on we can get a value which is usually expressed as a %. 100% being identical at all 1500 positions 0% being all different. This is a useful first step, and not a bad guide to how effective a vaccine might be. However it has some problems firstly it only looks at HA, secondly it treats all 1500 positions as if they had equal weight and thirdly it is looking at nucleotide bases when the amino acid sequences they code for would be more useful. If we look at each in turn.
1] As mentioned in my previous post HA has five primary antigenic site but there are 3 more on NA and even this is a simplification. In a real infection other areas may act as secondary sites and even internal proteins - which would be invisible to the immune system in an intact virus - are 'displayed' to its immune system by MHC molecules on the surface of infected host cells. (Link to paper with full NA epitope positions)
2] Of the 1500ish positions not all fall within the sites A to E. We can refine the concept of % homology by calculating the number of differences divided by the number of positions for each site, which is the Pepitope (this is not usually given as a % but as a value between 0 and 1) but is really just %homology for each epitope. You will not be shocked to hear that even this is not the full story as amongst the primary sites on HA and NA some are more significant than others and this even varies depending on which two viral sequences you are comparing.
3] Blocks of 3 nucleotide sequences (called a codon) code for one amino acid, however the third 'letter' in the block is often redundant, in that if you change it you still produce the same amino acid. (Link to codon translation table)

So let us say we allowed for these and calculated an aggregate Pepitope like value which compared the protein homology across the 8 primary antigenic sites this should give us a better value. In the paper linked to in 1] above they look at the further complication of Original Antigenic Sin (OAS) which they view as being a factor which might make a vaccine be worse, than no vaccine at all, for Pepitope values between 0.23 and 0.6. (N.B. if you do read this paper I would take issue with the premise that the dominance of an antigenic site can be calculated from its rate of change as this makes no allowance for biological function constraints on the viability of changes at any given point).

All of the above is a little background explaining why looking at Single Point Mutations (SNPs) - which are changes of one of those 1500 HA bases - and expecting that to make a vaccine stop working is a stretch. Where a SNP could have a disproportionate effect (I hasten to add I do not think that this is happening here) is if it causes a conformational change to the protein's Tertiary structure. That may need a little further explanation.

By a process of transcription and translation the codons of genetic information in the HA gene are converted into the amino acid sequence of the HA protein. This is a string of amino acids, like links of sausages, (protein's primary structure) but it immediately forms bonds between the side chains on the amino acids so the 'sausages' form sheets or spirals or other structures, this is the protein's secondary structure. The secondary structure then forms further bonds to each other with hydrophobic bits hiding in the middle and hydrophilic bits on the outside. This final Tertiary structure is not coded for in the genetic sequence and is, infact, dependent on the environment in which it forms. It is also not fixed if you change the pH, or other properties of the medium the protein is in, it will reconfigure (or more likely just flex a bit). This can be a very important biological property, for instance the weak binding of oxygen to heamoglobin for oxygen transport uses this. IF a change at one base caused a change in an amino acid at a point which then caused a different build of the secondary, and subsequent Tertiary structure, then it COULD cause all the antigenic sites to be presented differently. It is hard to envisage a scenario in which this could occur and not have such profound affects on the proteins biological function that it rendered it non-viable but as no one knows what would or would not be viable it is THEORETICALLY possible. The point of change in this scenario need not even fall within any of the antigenic sites, it need only cause a change effecting more than one of them. If you look at the nucleotide sequences for the antigenic sites (table in previous post) you will see that they are not a contiguous block due to the folding described in the section on secondary structure.
The graphic below is taken from the paper linked to at 1] as it shows the secondary structure (twirly ribbon bits) and then for the primary antigenic sites it attempts to show the 'solid' surface (grape like clusters). The whole concept of 'solid surface' is a manifestation of our macro scale world and does not really apply on this scale. Biological molecules are more fuzzy and 'feel' each others electrical surfaces being attracted, repelled and forming bonds of different types and strengths.



The above is of NA, for a change, but there is also one for HA if you follow the link.

You will see I have underlined some terms in the text this in not for emphasis but because I am very aware that readers of this site come with very different levels of background knowledge of the biological processes being discussed and these are terms which I thought would be useful to use as search terms if you would like a bit more explanation. Also Pepitope is really printed Pepitope with an italicised P and is a variable rather than a word so may not come up as expected in searches.

[gsgs]

Re: Mutations in A/H1N1 Not Confirmed to Affect Effectiveness of Current Vaccine

antigenic sites:

Cb(78-83)
Sa(128-129,156-160,162-167)
Sb(187-198)
Ca1(169-173,206-208,238-240
Ca2(140-145,224-226)

H3-numbering , Brownlee+Fodor (2001)

In the mice study they say they found important old-vaccine-escapes
in Sa, but I can see no epitope supporting their results.

[calyx]

Re: Mutations in A/H1N1 Not Confirmed to Affect Effectiveness of Current Vaccine

Alert - that is what i was trying to get across a few posts back. That the testing standards are different which explains how the CDC can come up with different results than Mill Hill. Here is a notice discussing harmonization of the antibody standard that "hopes to be in place by November" 2009. Since the Mill Hill findings were released late in November it is possible to speculate the standards were not in place at that time and why findings are not disputed, retracted, or corrected because they are right.

Currently pandemic A (H1N1) vaccine clinical trials are in progress in many countries and vaccine immunogenicity is being evaluated by VN and HI assays. In order to improve the comparability of results of clinical trials and other serological studies, a candidate international standard (IS) for antibody to A/California/7/2009 (H1N1)v-like viruses has been developed and is under evaluation by international collaborative studies. The candidate IS is a freeze-dried preparation of pooled human sera.

http://www.who.int/csr/resources/pub...l_standard.pdf

[Vibrant62]

Re: Mutations in A/H1N1 Not Confirmed to Affect Effectiveness of Current Vaccine

JJ - Thank you for such a coherent explanation

[sharon sanders]

Re: Mutations in A/H1N1 Not Confirmed to Affect Effectiveness of Current Vaccine

I just spoke to someone at WHO and they told me that the final California 09 (H1N1) "like" strain for vaccine production later this year has not been chosen yet.

[alert]

Re: Mutations in A/H1N1 Not Confirmed to Affect Effectiveness of Current Vaccine

Alert - that is what i was trying to get across a few posts back. That the testing standards are different which explains how the CDC can come up with different results than Mill Hill. Here is a notice discussing harmonization of the antibody standard that "hopes to be in place by November" 2009. Since the Mill Hill findings were released late in November it is possible to speculate the standards were not in place at that time and why findings are not disputed, retracted, or corrected because they are right.


http://www.who.int/csr/resources/pub...l_standard.pdf

I'm not sure I agree with your conclusion. First, I'm not sure the two viruses are completely identical. Niman calls the sequence a "clone", but I wonder if we have the complete sequence on both viruses to ensure there is absolutely no difference. Of note is that we have no clue the identity of this "clone" (when and where was it taken). Secondly, we would want to see the passage type on both viruses to rule out any changes occurring during passage. Thirdly, I'm not sure that the discrepancy you mention is significant enough to cause two competant labs to disagree on whether a single virus is a low reactor. The fact that the CDC is finding some low reactors (the R224K one you mentioned, for example), makes me think they know what a low reactor is. This is, of course, still two different viruses.

Assuming that the sequences really are complete and identical, and assuming that the passages are the same (or insgnificant), it is almost inconceivable that one could be a low reactor and the other one not. That is why I would want to see the whole sequence, as well as the methods of passage.

[calyx]

Re: Mutations in A/H1N1 Not Confirmed to Affect Effectiveness of Current Vaccine

Today the World Health Organization picked the strains to go in next fall's Northern Hemisphere flu vaccine. The ingredients: the pandemic H1N1, or swine flu, virus that now predominates almost everywhere, an H3N2 that's circulating in parts of Asia, and an influenza-B virus now causing most Chinese flu.

http://www.npr.org/blogs/health/2010...u_vaccine.html

[sharon sanders]

Re: Mutations in A/H1N1 Not Confirmed to Affect Effectiveness of Current Vaccine

http://www.npr.org/blogs/health/2010...u_vaccine.html

— an an A/California/7/2009 (H1N1)-like virus;
— an an A/Perth/16/2009 (H3N2)-like virus;*
— a B/Brisbane/60/2008-like virus.


The "like" version of A/California/7/2009 (H1N1) has not been chosen yet.

http://www.flutrackers.com/forum/showpost.php?p=342359&postcount=4

[JJackson]

Re: Mutations in A/H1N1 Not Confirmed to Affect Effectiveness of Current Vaccine

You do not have to look far for an identical HA that is not designated low reactor. Lviv N2 is the same as N6 (100% homologous at the protein level on both HA and NA) and from the same batch sequenced by Mill Hill. Niman's commentary implies that the term 'California/7-like' means not low reactor "yet designated as California/7-like, indicating the titter had not been reduced by four fold or more" but in my conversation with John McCauley (Mill Hill Director) in December (see post #68 in this thread) they labelled N6 as both 'California like' and 'low reactor' implying they were not mutually exclusive. I can not explicitly say that N2 was ever HI tested but it was certainly not designated LR and all the sequence I have seen are very 'California like' in that the % homology is still very high.

I read some of the USAF report linked to by Mixin this morning and she has now posted a detail on A/OCONUS6/18529/2009 (low reactor) which has a 98.5% homology and - as far as I can see - only one antigenically significant change (S203T) in the D epitope. The post is at this link and they have a great graphics system for visualising HA changes relative to the primary antigenic sites.