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Influenza viruses resistant to oseltamivir, news and updates
Knowing Gs as you do, that was almost funny.
To the comedy room you shall go with remarks like that.
I was going to post an alternative methodology involving 100 pieces of paper numbered 1-100 and throwing them in the air, while closing my eyes and clicking my heals, but I excercised restraint.
Update through June 2 shows a major increase (doubling the total number of positives) in resistance in Japan (20 new positives in the most 184 most recent H1N1 cases):
SEARO Total 13 1 (8%)
WPRO Australia 83 3 (4%)
China 1 0
China, Hong Kong SAR 581 68 (12%)
Guam 15 0 Japan 1544 42 (3%)
Malaysia 13 0
Mongolia 4 0
New Zealand 88 0
Philippines 37 0
Republic of Korea 99 0
Singapore 7 0
I agree although I am not surely a specialist in this field...
I think the single viral isolation in Italy may be taken with caution...
It is hard to understand for me. Thus, I hope someone among the experts at Ft may clarified a bit this strange situation, also for people like me that cannot share the same level of knowledge.
Italy appears to be low due to a lag in sampling. Most countries that had low values in 2007 saw higher levels in 2008. In Japan, there was only 1 positive in late 2007 (out of 279). The numbers increased in 2008. In March, the postives were 3 out of 45 and more recently the numbers were 20 out of the last 186 so the recent frequency was 30 fold higher than late 2007.
In Italy there were 0 positives out of 94 tested in Dec 2007 or Jan 2008. In Feb the number was 1 in 12 and there was no testing after that, so Italy could easily have frequencies above 10% for the Feb-Apr months, but really has only tested 12 samples collected in that period (and 1 was positive).
I was going to post an alternative methodology involving 100 pieces of paper numbered 1-100 and throwing them in the air, while closing my eyes and clicking my heals, but I excercised restraint.
Ohhh, the mental image!!
So based on your analysis, what is your estimate of probability in the next 12 months?
The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918
The numbers in the US are also heavily skewed. So far all positive public sequences in the 2007/2008 season have been clade 2B (Brisbane/59 - like). The recent MMWR report on influenza in the US indicates 3/4 of the H1N1 isolates have been Solomon Island (clade 2A) and there were only 70 Brisbane. However, under the resistant section the number of H274Y positives is 84 (out of 824), which means that many more were tested (sequenced?) for resistance than reported as Brisbane.
I have been mapping the positives based on sequence and this season there are 24 (11 in 2007) that have been made public so far and I have about 80 something Clade 2B isolates on my tree (but I think it has holes), so of the public sequences H274Y is in more than 30% on my tree (but the % with H274Y is probably a bit lower because I haven't filled in the holes which are from H274Y negative sequences).
In the US, the H1N1 frequency overall went down in 2008, so the total numbers are low in the US because of more Solomon Island at the beginning of the season, and more H3N2 at the end of the season.
Thus, for the US the frequency may have bene closer to 30% of Brisbane isolates, but largely limited to Dec 2007 and Jan 2008. Moreover, most of the H1N1 was said to be in western states, which isn't all that obvious from the public sequences, which clearly respresent a subset of the total (and the representation may be heavily biased because there also are not that many US public Solomon Island isolates from the 2007/2008 season).
> WHO collaborating laboratories had characterized 290 H1N1 :
> 200 were Solomon and 70 Brisbane
> 84 from 824 tested H1N1 had H274Y
[by any lab, not necessarily WHO-collaborating ?]
> 4 from 588 had H274Y in 2006/7
if all the resistant viruses were Brisbane, then we had
42% resistance in Brisbane !
I assume there was almost no Solomon in Europe,
all Brisbane
The numbers from the MMWR really don't add up. The above data would be CDC data. In 2006/2007 there were five positives - four by CDC and one by SDI under NIAID.
All of the MMWR data would be by the CDC. If the ratio of 3/1 of Solomon to Brisbane held, then about 40% of the Brisbane isolate would have had H274Y as indicated earlier
So far there have only been 23 positive in the public sequences from the US this season and all are Brisbane. The percentage on released sequences is closer to 30%.
It is likely that the H274Y frequency in the US is 30-40% and all will be Brisbane (and I suspect the number of independent introductions will be markedly higher that the 3 seen for the first 23 - which I think will be true for other countries). Many will start with "Northern EU" and then spread to other clade 2B isolates that map to additional branches which contain isolates without H274Y.
Of course the more data that is released, the more problems for a "random mutation" explanation (which is why it is headed for the circular file).
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