Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

[HenryN]

Originally Posted by English Teacher

I know that this isn't a discussion board, so I'd like to ask Dr. Niman if he will start a thread over there to explain this to the laymen like me. It seems very important, but I don't understand anything except that the H1N1 has developed a resistance to Tamiflu? Thanks.

Here is the key travel log for H274Y

gb|GQ351316.1| Influenza A virus (A/Hong Kong/2369/2009(H1N1)... 36.2 0.73
gb|EU567011.1| Influenza A virus (A/Indiana/01/2008(H1N1)) se... 36.2 0.73
gb|DQ493078.1| Influenza A virus (A/Vietnam/CL2009/2005(H5N1)... 36.2 0.73
gb|DQ250165.1| Influenza A virus (A/Vietnam/CL2009/2005(H5N1)... 36.2 0.73

[Toaster2]

Originally Posted by niman

Pandemic H1N1 can also get H274Y from H5N1 and some of the new polymorphisms on H1N1 link back to H5N1, which is why pandmeic H1N1 in countries like Egypt, Indonesia, Vietnam, and India may be major problems.

Can you elaborate on this ? None of these sequences are from geographic areas where H5N1 is in humans (recently) so I do not understand your comment.

[HenryN]

For those interested in the historic nature of the Hong Kong sequence, this is the NBCI pandemic H1N1 front page yesterday afternoon:

July 06, 2009, 8 submitted by Beijing Institute of Microbiology and Epidemiology, China; 8 by University of Padova, Italy; 3 by Centre for Health Protection, Hong Kong; 2 by University of Florence, Italy; 8 by WRAIR:

	PB2	PB1	PA	HA	NP	NA	MP	NS
Influenza A virus (A/Beijing/502/2009(H1N1))	GQ290112	GQ290111	GQ290105	GQ290106	GQ290109	GQ290107	GQ290108	GQ290110
Influenza A virus (A/Firenze/10/2009(H1N1))				GQ351319		GQ351320
Influenza A virus (A/Hong Kong/2369/2009(H1N1))				GQ351314		GQ351316*	GQ351315
Influenza A virus (A/Italy/85/2009(H1N1))	GQ351287	GQ351288	GQ351289	GQ351290	GQ351291	GQ351292	GQ351293	GQ351294
Influenza A virus (A/Santo Domingo/572N/2009(H1N1))	CY041957	CY041958	CY041959	CY041960	CY041961	CY041962	CY041963	CY041964

* This sequence has the H274Y mutation that might confer resistance to Oseltamivir.

[HenryN]

Kudos to the Health Protection Agency in Hong Kong for the prompt release of the NA sequence with H274Y.

It is of note that neither Denmark nor Japan have released the sequences (apologies from Japan on withholding data for publication notwithstanding).

Journalists should hold their feet to the fire and ask WHY are the NA sequences with H274Y NOT public.

[HenryN]

Originally Posted by Toaster2

Can you elaborate on this ? None of these sequences are from geographic areas where H5N1 is in humans (recently) so I do not understand your comment.

All of the sequences in the travel log have H274Y and downstream matches (and all are from humans, including the two H5N1 sequences from Vietnam).

[AlaskaDenise]

When I looked up the 3 different NAs, I found an "F" for Indiana, while there is a "Y" for Vietnam and HK. What's the "F"?

ABB76122 A/Vietnam/CL2009/2005(H5N1)
ACB11804 A/Indiana/01/2008(H1N1)
ACT10319 A/Hong Kong/2369/2009(H1N1)

If I'm reading it right, concensus is the top line below, then the 3 above:

YYY
. . .
F . .
. . .

(added: starting in position 274)

.

[HenryN]

Originally Posted by AlaskaDenise

When I looked up the 3 different NAs, I found an "F" for Indiana, while there is a "Y" for Vietnam and HK. What's the "F"?



If I'm reading it right, concensus is the top line below, then the 3 above:

YYY
. . .
F . .
. . .

(added: starting in position 274)

.

F is phenylalanine, is upstream, and is in H1 seasonal flu.

[AlaskaDenise]

Originally Posted by niman

The real gateway between H274Y on H1N1 seasonal flu and moving it to H1N1 pandmeic flu is the sequence seen in Indiana last year. It had the key change that allowed H274Y to go from H5N1 to H1N1, and that same change allows for H274Y to go from seasonal H1N1 to pandemic H1N1...........

I understood the above statement to mean that Indiana/01/2008 had 274Y, which is why I was surprised to see an "F". I'm still not understanding how the "F" can create a "Y", but then I'm not a sequences-guru.

.

[HenryN]

Originally Posted by AlaskaDenise

I understood the above statement to mean that Indiana/01/2008 had 274Y, which is why I was surprised to see an "F". I'm still not understanding how the "F" can create a "Y", but then I'm not a sequences-guru.

.

F is at position 273. Tamiflu resistance is at position 274 (where all have Y as in H274Y).
For H1 seasonal flu sensitive is FHY, resistant is FYY.

[HenryN]

Commentary

[HenryN]

Tamiflu-resistant swine flu strain emerges


NZPA July 9, 2009, 6:32 am

New Zealand health officials hope the diagnosis of a San Francisco teenager with a Tamiflu-resistant strain of swine flu is a random mutation of the virus.

"We will be asking the Pandemic Influenza Technical Advisory Group (PITAG) to have a look at this," deputy director of public health Fran McGrath told NZPA.
She hoped it would turn out to be a "point mutation" of the virus -- which can occur in a patient even if they are not taking the anti-viral drug.
The Health Ministry would ask its technical experts to talk to virologists and other specialists at the Centres for Disease Control, in the United States, "about any evidence of the sort that we're going to be worried about", she said.
There were two main possibilities: either the case in the 16-year-old American girl showed swine flu was capable of not only developing drug resistance but also spreading between humans in that resistant form, or it was a one-off point mutation.
Two other cases of swine flu resistant to Tamiflu had occurred in patients taking the drug in Japan and Denmark, but Dr McGrath said it would be good if the virus had not yet mutated to a form which could spread carrying the mutation.
"So far, these are looking like point mutations, which is good news," she said.
Arthur Reingold, a professor at the University of California's school of public health, told the San Francisco Chronicle the fact the teenager was not taking Tamiflu suggested she may have caught the resistant variant from somebody else.
But Dr McGrath said it was important to remember that the virus spreading in New Zealand was still capable of being treated with Tamiflu.
Since January 2008 seasonal A (H1N1) flu viruses have become resistant to Tamiflu.
So far, six samples of the swine flu A (H1N1) viruses have also been tested, and none had the mutation, which indicated they were still sensitive to the drug.
New Zealand had a fair way to go before having to deal with a resistant form with good transmissibility, but when that happened the next step would be to switch to another anti-viral, such as Relenza.
Dr McGrath said the factor which would influence any use of swine flu vaccine in NZ would be the pattern of infections and their severity.
"Right at the moment, there isn't a lot of reason why we'd want to short-circuit the normal licensing process," she said.
"Severity would be the key factor."
Two New Zealand scientists have said in a study published in the journal Eurosurveillance that the present form of swine flu may be at least 40 times less lethal than originally estimated.
Probably no more than one in 10,000 patients might die, and the toll might be as low as one in 1 in 100,000 patients, according to Nick Wilson and Michael Baker.
Prime Minister John Key said this week that the Government had ordered a stockpile of a new swine flu vaccine for healthcare staff and other emergency workers.
The Government has ordered 300,000 doses of a vaccine from Baxter Healthcare -- enough to give 150,000 people the required two doses -- and it will be delivered within a month.
But the licensing of the vaccine is likely to take until December.
The death of a Christchurch man yesterday took the total number of swine flu deaths in New Zealand to five.
Chief Coroner Neil MacLean said the 49-year-old victim, who was thought to have underlying respiratory problems, died at the weekend.
A 46-year-old Blenheim man who died at his home a week ago was the country's fourth linked death, said Dr McGrath.
"While he has tested positive for novel influenza A, he had pre-existing medical conditions," she said.
The number of confirmed cases of swine flu yesterday was 1272, but Dr McGrath said this was only a small sampling of the actual number of cases.

http://nz.news.yahoo.com/a/-/top-sto...train-emerges/

[HenryN]

NA sequence of Osaka/1 matches New Jersey/1 (which matches Hong Kong prior to acquistion of H274Y).

[gsgs]

add 1 for normal numbering, so it's H275Y

[HenryN]

Originally Posted by gsgs

add 1 for normal numbering, so it's H275Y

Just about everyone uses H274Y except Japan. Its the same change as H5N1, where it is also called H274Y.

[HenryN]

HA travel log for Sapporo/1

gb|GQ365446.1| Influenza A virus (A/Sapporo/1/2009(H1N1)) seg... 40.1 0.047
gb|FJ231773.1| Influenza A virus (A/Rheinland-Pfalz/58/2005(H... 40.1 0.047
gb|CY040170.1| Influenza A virus (A/Puerto Rico/8-SV14/1934(H... 40.1 0.047
gb|CY038903.1| Influenza A virus (A/Puerto Rico/8-SV3/1934(H1... 40.1 0.047
gb|CY038895.1| Influenza A virus (A/Puerto Rico/8-SV1/1934(H1... 40.1 0.047
gb|CY034132.1| Influenza A virus (A/WSN/1933(H1N1)) segment 4... 40.1 0.047
gb|CY033577.1| Influenza A virus (A/Puerto Rico/8/1934(H1N1))... 40.1 0.047
gb|CY032213.1| Influenza A virus (A/swine/Wisconsin/1/1961(H1... 40.1 0.047
gb|EF190982.1| Influenza A virus (A/lvPR8/34(H1N1)) segment 4... 40.1 0.047
gb|EF190974.1| Influenza A virus (A/hvPR8/34(H1N1)) segment 4... 40.1 0.047
gb|CY020469.1| Influenza A virus (A/Phila/1935(H1N1)) segment... 40.1 0.047
gb|CY020445.1| Influenza A virus (A/Henry/1936(H1N1)) segment... 40.1 0.047
gb|EF467821.1| Influenza A virus (A/Puerto Rico/8/34(H1N1)) s... 40.1 0.047
gb|CY019955.1| Influenza A virus (A/Alaska/1935(H1N1)) segmen... 40.1 0.047
gb|CY010788.1| Influenza A virus (A/WSN/1933 TS61(H1N1)) segm... 40.1 0.047
gb|DQ508905.1| Influenza A virus (A/Wilson-Smith/1933(H1N1)) ... 40.1 0.047
gb|CY009604.1| Influenza A virus (A/Wilson-Smith/33(H1N1)) se... 40.1 0.047
gb|CY009444.1| Influenza A virus (A/Puerto Rico/8/34(H1N1)) s... 40.1 0.047
gb|J02176.1|FLAHAMY Influenza A virus (A/WSN/33) hemagglutini... 40.1 0.047
gb|CY009324.1| Influenza A virus (A/Melbourne/35(H1N1)) segme... 40.1 0.047
gb|AF389118.1| Influenza A virus (A/Puerto Rico/8/34/Mount Si... 40.1 0.047
gb|AF408861.1|AF408861 Influenza A virus (A/NWS-Mvi(H1N2)) he... 40.1 0.047
gb|AF408860.1|AF408860 Influenza A virus (A/NWS-Tokyo(H1N2)) ... 40.1 0.047
gb|AF408859.1|AF408859 Influenza A virus (A/NWS-G70c(H1N9)) h... 40.1 0.047
emb|Z54287.1| Influenza A virus (Mongolia/153/88 (H1N1)) RNA ... 40.1 0.047
emb|Z54288.1| Influenza A virus (A/Mongolia/111/91 (H1N1)) RN... 40.1 0.047
emb|X57493.1| Influenza A virus (A/swine/Illinois/63(H1N1)) H... 40.1 0.047
emb|V01088.1| Influenza A virus (A/PR/8/34(HON1)) hemagglutin... 40.1 0.047
gb|AF091307.1|AF091307 Influenza A virus (A/swine/Wisconsin/1... 40.1 0.047
gb|U38242.1|IAU38242 Influenza A virus (A/Tokyo/3/1967(H1)) h... 40.1 0.047
gb|U37727.1|IAU37727 Influenza A virus (A/NWS/G70C(H1N9)) hem... 40.1 0.047
gb|U08904.1|IVU08904 Influenza virus A/WS/33 (H1N1) haemagglu... 40.1 0.047
gb|U08903.1|IVU08903 Influenza virus A/NWS/33 (H1N1) haemaggl... 40.1 0.047

[HenryN]

gb|GQ365446.1| Influenza A virus (A/Sapporo/1/2009(H1N1)) seg... 36.2 0.73
dbj|AB434384.1| Influenza A virus (A/swine/Kyoto/3/1979(H1N1)... 36.2 0.73
gb|CY028179.1| Influenza A virus (A/swine/Tennessee/3/1978(H1... 36.2 0.73
gb|CY027291.1| Influenza A virus (A/swine/Ohio/23/1935(H1N1))... 36.2 0.73
gb|EU139823.1| Influenza A virus (A/swine/Iowa/15/1930(H1N1))... 36.2 0.73
gb|CY009628.1| Influenza A virus (A/swine/1931(H1N1)) segment...
gb|AF091308.1|AF091308 Influenza A virus (A/swine/Iowa/15/30 ... 36.2 0.73
gb|U11703.1|IAU11703 Influenza A virus (A/swine/St-Hyacinthe/... 36.2 0.73

[HenryN]

It is worth noting that 1918 was a recombinant between human A/WSN/33 and swine A/swine/Iowa/15/1930.

[wotan]

Originally Posted by niman

It is worth noting that 1918 was a recombinant between human A/WSN/33 and swine A/swine/Iowa/15/1930.

Maybe I'm being dense, but I am lost here. Unless I am reading it wrong, the two sequences you mention are from the 1930s, so how can 1918 have been a recombinant of them?

[HenryN]

Originally Posted by wotan

Maybe I'm being dense, but I am lost here. Unless I am reading it wrong, the two sequences you mention are from the 1930s, so how can 1918 have been a recombinant of them?

Over 90% of polymorphisms in 1918 can be found in the two H1N1 viruses (human and swine) from the 1930's (the two 1930's viruses represent what was circulating prior to 1918).

[wotan]

Originally Posted by niman

Over 90% of polymorphisms in 1918 can be found in the two H1N1 viruses (human and swine) from the 1930's (the two 1930's viruses represent what was circulating prior to 1918).

Now I don't get the last statement. How do we know they represent what was in circulation prior to 1918? If there is another thread where I can read up on that please direct me to it.

[HenryN]

Commentary

[AlaskaDenise]

Originally Posted by niman

Commentary

Commentary

Hong Kong Tamiflu Resistant Pandemic Sequence Released

Recombinomics Commentary 06:57
July 7, 2009

The NA sequence from the Hong Kong teenagerwith oseltamivir Tamiflu resistance, A/Hong Kong/2369/2009, has been released. The sequence is clearly that of pandemic H1N1 and exactly matches (other than H274Y) the sequence of an earlier isolate A/New Jersey/1/2009. Similarly, the HA sequence is also swine and has two recently acquired polymorphisms, one of which is also in New Jersey/1/2009. Thus this sequence is in circulation and as was seen in the isolates in Denmark and Japan, the H274Y is appended onto a swine H1N1 background.

These results mimic that seen in seasonal flu, where H274Y was appended onto multiple seasonal flu background. The polymorphisms jumped from one background to the next, via genetic hitchhiking and recombination. Thus like seasonal flu, the pandemic H1N1 has no evidence of reassortment. The H274Y is on an evolutionarily fit H1N1 that will allow the H274Y to move about through the pandemic H1N1 gene pool. This movement will be facilitated by widespread Tamiflu usage, which will select minor populations as happened in Denmark and Japan, where H274Y was identified in patients receiving a maintenance dose of Tamiflu.

However, in Hong Kong, like the many examples of H274Y in H1N1 seasonal flu, the resistance is in patients not receiving Tamiflu. However, the lessons of H274Y in seasonal flu were not learned. Recent comments have described H274Y acquisitions through random mutation and reassortment. However, there has been no examples of recent seasonal H1N1 flu genes in the pandemic H1N1 sequences, and the H274Y in patients receiving Tamiflu likely represent selection of a minor population with H274Y that is silently spread. The release of the sequences from Denmark and Japan would be useful.

.

[AlaskaDenise]

Originally Posted by niman

Commentary

Commentary

Widespread Evolutionarily Fit Tamiflu Resistant Pandemic H1N1

Recombinomics Commentary 06:41
July 10, 2009

The NA sequence of the first pandemic isolate in Sapporo, Japan (A/Sopporo/1/2009) was released at Genbank today. Since Hokkaido's first report case was June 15, the isolate is relatively recent. It exactly matches the first isolate from New Jersey, A/New Jersey/1/2009, which was from a patient (22F) in Bergen county (see map) and collected in April. Both of these isolates match the California traveler who was tested at Hong Kong airport on June 11 and was found to be infected with oseltamivir resistant H1N1 (A/Hong Kong/2369/2009) based on H274Y, which was the only difference between the Hong Kong sequence and those form Bergen, New Jersey and Sopporo. The same sequence in these three locations indicates the evolutionarily fit H1N1 is widespread and has been circulating for months, but the number of pubic sequences remains low.

The Hong Kong, ex-San Francisco case was mild. The patient recovered without taking any antivirals, raising concerns that the resistance is circulating worldwide. The same genetic change, H274Y, has also been reported in patients receiving prophylactic levels of Tamiflu in Denmark and Osaka, Japan. The Osaka sequence, other than H274Y, matches multiple isolates from Japan, and is distinct from the Hong Kong/San Francisco/Sapporo/Bergen sub-clade. The sequence from Denmark has not been made public.

However, other countries are reporting suspect Tamiflu resistance in patients who have been treated for at least a month and are symptom free, but shed detectable H1N1. These reports raise concerns that H274Y is more widespread than the 3 confirmed cases and one presumed case in San Francisco.

The finding of H274Y in all confirmed cases raises concerns that the pattern in pandemic H1N1 will follow the pattern seen for seasonal flu, where H274Y increased to almost 100% in the Brisbane/59 strain of seasonal flu. The spread of H274Y in the Brisbane strain was facilitated by the acquisition of key polymorphisms from the Hong Kong (clade 2C) strain of H1N1. However, H274Y had also been reported in clade 1 and clade 2c isolates from patients who were not receiving Tamiflu, and in countries where Tamiflu usage was low. The H274Y jumped from one sub-clade to another via genetic hitchhiking and recombination explained the pattern of acquisitions.'

The spread of H274Y in pandemic flu may be accelerated by widespread Tamiflu usage, levels approaching 100% in H1N1 seasonal flu, and the novel H1N1 reported in Canadian farm workers infected with an H3N2 triple reassortant that has acquired Brisbane/59 H1 and N1, with H274Y.

Thus, the detection of H274Y in pandemic H1N1 from patients who were and were not taking Tamiflu, as well as Brisbane N1 in H1N1 seasonal flu and H1N1 novel flu raises concerns that the levels of H274Y will markedly increase in the near term.

.

[HenryN]

Originally Posted by wotan

Now I don't get the last statement. How do we know they represent what was in circulation prior to 1918? If there is another thread where I can read up on that please direct me to it.

There is any sequence data prior to 1918 and the first H1 sequences are the ones I mentioned. On a phylogenetic tree, 1918 falls between the 1930 human and swine sequences. There was a Scientific American article on the 1918 virus several years ago, but I don't have the reference handy.

[HenryN]

Originally Posted by niman

There is any sequence data prior to 1918 and the first H1 sequences are the ones I mentioned. On a phylogenetic tree, 1918 falls between the 1930 human and swine sequences. There was a Scientific American article on the 1918 viruse several years ago, but I don't have the reference handy.

January, 2005

Commentary

[AlaskaDenise]

Originally Posted by niman

It is worth noting that 1918 was a recombinant between human A/WSN/33 and swine A/swine/Iowa/15/1930.

When looking at the A/H1N1 HAs from 1918 to 1939, one thing that jumps out in an alignment is that the WSN and W-S are so different than 1918 and from 1934 onward. What was so different about 1933?

added: I was just looking at human

.

[HenryN]

Originally Posted by AlaskaDenise

When looking at the A/H1N1 HAs from 1918 to 1939, one thing that jumps out in an alignment is that the WSN and W-S are so different than 1918 and from 1934 onward. What was so different about 1933?

.

WS/33 was the first human influenza isolated (isolated in William Smith's lab in 1933). WSN/33 was passed through mice and isolated from mouse brain (N stands for neurological).

1918 was associated with neurological problems, including long term in 1918 survivors.

[AlaskaDenise]

Originally Posted by niman

It is worth noting that 1918 was a recombinant between human A/WSN/33 and swine A/swine/Iowa/15/1930.

I just redid that alignment to include swine - what you say just jumps right out at you. Amazing. Obviously those swine sequences must have existed prior to 1918.

.

[AlaskaDenise]

Originally Posted by niman

WS/33 was the first human influenza isolated (isolated in William Smith's lab in 1933). WSN/33 was passed through mice and isolated from mouse brain (N stands for neurological).

1918 was associated with neurological problems, including long term in 1918 survivors.

That answers a long standing question - that WSN is lab created and only W-S is natural. Thanks.

Very scarey genes there.

.

[wotan]

Originally Posted by niman

January, 2005

Commentary

Thanks, gives me a lot to think about for awhile.