Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

[Mamabird]

Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

The Tamiflu resistant precursor is spreading in Spain. The most recent additions were collected this month (July 3), yet the number of recent sequences (since April) in the US remains at ZERO.
HA sequence hasn't been released, but it likely has D225E.

Catalonia/378 HA (Spain) is actually closer match to Hong Kong Tamiflu resistant strain than Sapporo/1. Has your D225E, plus S206T and P300S.

Italy/172 also has these unique HA markers, but no NA available yet.

Point is, these precursers are circulating widely and must be monitored.

[HenryN]

Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

The two Ohio human isolates closely match the Ohio source swine isolate.

Not so with the swine isolates in Alberta, Canada. They do not closely match the human Swine Flu virus H1N1.

It makes one wonder how long the Canadian pig herd had been infected to accumulate that many changes? Probably not a recent human infection being passed on as had been speculated.

Correct. The swine were not very sick (no fatalities and just a cough) and surveillance (as well as relase of sequences) is/was poor.

[Mamabird]

Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

Perhaps we will have a better understanding of just how quickly this pandemic virus changes when a human infects a pig once the Argentina swine isolates are released to the public.

If we do not see changes, especially in the more highly conserved gene segments, then we should revisit the Canadian event.

[Mamabird]

Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

The two Ohio human isolates are swine triple reassortants.

The two Ohio human isolates closely match the Ohio source swine isolate.

Not so with the swine isolates in Alberta, Canada. They do not closely match the human Swine Flu virus H1N1.

It makes one wonder how long the Canadian pig herd had been infected to accumulate that many changes? Probably not a recent human infection being passed on as had been speculated.

[HenryN]

Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

The two Ohio human isolates are swine triple reassortants.

[HenryN]

Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

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).

Another HA travel log for Sapporro/1

gb|GQ365446.1| Influenza A virus (A/Sapporo/1/2009(H1N1)) seg... 34.2 2.9
gb|CY040594.1| Influenza A virus (A/swine/North Carolina/4511... 34.2 2.9
gb|CY040543.1| Influenza A virus (A/swine/North Carolina/7386... 34.2 2.9
gb|CY040510.1| Influenza A virus (A/swine/Ohio/63607-32/2008(... 34.2 2.9
gb|CY040509.1| Influenza A virus (A/swine/North Carolina/6360... 34.2 2.9
gb|CY040508.1| Influenza A virus (A/swine/North Carolina/6360... 34.2 2.9
gb|CY040504.1| Influenza A virus (A/swine/North Carolina/6360... 34.2 2.9
gb|CY040503.1| Influenza A virus (A/swine/North Carolina/6360... 34.2 2.9
gb|CY040502.1| Influenza A virus (A/swine/North Carolina/6360... 34.2 2.9
gb|CY040501.1| Influenza A virus (A/swine/North Carolina/6360... 34.2 2.9
gb|CY040500.1| Influenza A virus (A/swine/North Carolina/6360... 34.2 2.9
gb|CY040497.1| Influenza A virus (A/swine/North Carolina/225-... 34.2 2.9
gb|CY040496.1| Influenza A virus (A/swine/North Carolina/225-... 34.2 2.9
gb|CY040495.1| Influenza A virus (A/swine/North Carolina/225-... 34.2 2.9
gb|CY040494.1| Influenza A virus (A/swine/North Carolina/225-... 34.2 2.9
gb|CY040493.1| Influenza A virus (A/swine/Missouri/63607-16/2... 34.2 2.9
gb|CY040490.1| Influenza A virus (A/swine/Minnesota/63607-40/... 34.2 2.9
gb|CY040486.1| Influenza A virus (A/swine/Minnesota/63607-31/... 34.2 2.9
gb|CY040485.1| Influenza A virus (A/swine/Minnesota/63607-30/... 34.2 2.9
gb|CY040483.1| Influenza A virus (A/swine/Minnesota/63607-26/... 34.2 2.9
gb|CY040480.1| Influenza A virus (A/swine/Minnesota/63607-15/... 34.2 2.9
gb|CY040479.1| Influenza A virus (A/swine/Minnesota/63607-12/... 34.2 2.9
gb|CY040477.1| Influenza A virus (A/swine/Minnesota/225-5/200... 34.2 2.9
gb|CY040476.1| Influenza A virus (A/swine/Minnesota/225-4/200... 34.2 2.9
gb|CY040475.1| Influenza A virus (A/swine/Minnesota/225-3/200... 34.2 2.9
gb|CY040471.1| Influenza A virus (A/swine/Iowa/63607-23/2008(... 34.2 2.9
gb|CY040468.1| Influenza A virus (A/swine/Iowa/63607-1/2008 (... 34.2 2.9
gb|CY040466.1| Influenza A virus (A/swine/Iowa/225-8/2008(H1N... 34.2 2.9
gb|CY040461.1| Influenza A virus (A/swine/Illinois/225-1/2008... 34.2 2.9
gb|FJ986621.1| Influenza A virus (A/Ohio/02/2007(H1N1)) segme... 34.2 2.9
gb|FJ986620.1| Influenza A virus (A/Ohio/01/2007(H1N1)) segme... 34.2 2.9
gb|EU604689.1| Influenza A virus (A/swine/OH/511445/2007(H1N1... 34.2 2.9
gb|EU409960.1| Influenza A virus (A/swine/Ohio/C62006/06(H1N1... 34.2 2.9
gb|EU409948.1| Influenza A virus (A/swine/Ohio/24366/07(H1N1)... 34.2 2.9
gb|AY060052.1| Influenza A virus (A/SW/MN/17138/01(H1N2)) hem... 34.2 2.9

[HenryN]

Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

gb|GQ379856.1| Influenza A virus (A/Catalonia/517/2009(H1N1))... 32.2 11
gb|GQ379852.1| Influenza A virus (A/Catalonia/502/2009(H1N1))... 32.2 11
gb|GQ379840.1| Influenza A virus (A/Catalonia/476/2009(H1N1))... 32.2 11
gb|GQ379833.1| Influenza A virus (A/Catalonia/442/2009(H1N1))... 32.2 11
gb|GQ369275.1| Influenza A virus (A/Stockholm/37/2009(H1N1)) ... 32.2 11
gb|GQ365448.1| Influenza A virus (A/Sapporo/1/2009(H1N1)) seg... 32.2 11
gb|GQ355297.1| Influenza A virus (A/Catalonia/387/2009(H1N1))... 32.2 11
gb|GQ351316.1| Influenza A virus (A/Hong Kong/2369/2009(H1N1)... 32.2 11
gb|GQ338380.1| Influenza A virus (A/Oklahoma/03/2009(H1N1)) s... 32.2 11
gb|GQ160533.1| Influenza A virus (A/New Jersey/01/2009(H1N1))... 32.2 11

Same travel log (Jun 22 isolate from China)

LOCUS GQ396511 1332 bp cRNA linear VRL 22-JUL-2009
DEFINITION Influenza A virus (A/Changsha/05/2009(H1N1)) segment 6
nonfunctional neuraminidase (NA) gene, partial sequence.
ACCESSION GQ396511
VERSION GQ396511.1 GI:254575147
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/Changsha/05/2009(H1N1))
ORGANISM Influenza A virus (A/Changsha/05/2009(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1332)
AUTHORS Zhang,R.S., Su,L. and Ou,X.H.
TITLE Direct Submission
JOURNAL Submitted (21-JUL-2009) Center for Disease Control and Prevention
of Changsha, Chang Sha, Hunan 410000, China
COMMENT Swine influenza A (H1N1) virus isolated during human swine flu
outbreak of 2009.
FEATURES Location/Qualifiers
source 1..1332
/organism="Influenza A virus (A/Changsha/05/2009(H1N1))"
/mol_type="viral cRNA"
/strain="A/Changsha/05/2009"
/serotype="H1N1"
/isolation_source="nasopharyngeal"
/host="Homo sapiens"
/db_xref="taxon:660566"
/segment="6"
/country="China"
/collection_date="22-Jun-2009"
/note="lineage: swl"
gene <1..1320
/gene="NA"
misc_feature <1..1320
/gene="NA"
/note="nonfunctional neuraminidase due to mutation"
ORIGIN
1 tcaatatgga ttagccactc aattcaactt gggaatcaaa atcagattga aacatgcaat
61 caaagcgtca ttacttatga aaacaacact tgggtaaatc agacatatgt taacatcagc
121 aacaccaact ttgctgctgg acagtcagtg gtttccgtga aattagcggg caattcctct
181 ctctgccctg ttagtggatg ggctatatac agtaaagaca acagtataag aatcggttcc
241 aagggggatg tgtttgtcat aagggaacca ttcatatcat gctccccctt ggaatgcaga
301 accttcttct tgactcaagg ggccttgcta aatgacaaac attccaatgg aaccattaaa
361 gacaggagcc catatcgaac cctaatgagc tgtcctattg gtgaagttcc ctctccatac
421 aactcatgat ttgagtcagt cgcttggtca gcaagtgctt gtcatgatgg catcaattgg
481 ctaacaattg gaatttctgg cccagacaat ggggcagtgg ctgtgttaaa gtacaacggc
541 ataataacag acactatcaa gagttggaga aacaatatat tgagaacaca agagtctgaa
601 tgtgcatgtg taaatggttc ttgctttact gtaatgaccg atggaccaag tgatggacag
661 gcctcataca agatcttcag aatagaaaag ggaaagatag tcaaatcagt cgaaatgaat
721 gcccctaatt atcactatga ggaatgctcc tgttatcctg attctagtga aatcacatgt
781 gtatgcaggg ataactggca tggctcgaat cgaccgtggg tgtctttcaa ccagaatctg
841 gaatatcaga taggatacat atgcagtggg attttcggag acaatccacg ccctaatgat
901 aagacaggca gttgtggtcc agtatcgtct aatggagcaa atggagtaaa aggattttca
961 ttcaaatacg gcaatggtgt ttggataggg agaactaaaa gcattagttc aagaaacggt
1021 tttgagatga tttgggatcc gaacggatgg actgggacag acaataactt ctcaataaag
1081 caagatatcg taggaataaa tgagtggtca ggatatagcg ggagttttgt tcagcatcca
1141 gaactaacag ggctggattg tataagacct tgcttctggg ttgaactaat cagagggcga
1201 cccaaagaga acacaatctg gactagcggg agcagcatat ccttttgtgg tgtaaacagt
1261 gacactgtgg gttggtcttg gccagacggt gctgagttgc catttaccat tgacaagtaa
1321 tttgttcaaa aa

[Giuseppe]

Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

Another possible case of oseltamivir-resistant pandemic H1N1 2009 virus infection in Belgium: http://www.eurosurveillance.org/View...rticleId=19270

(...)
No complications have been detected so far.

One confirmed case, already under treatment with oseltamivir, was hospitalised because influenza symptoms persisted and the patient had asthma as underlying condition.

Respiratory samples from this patient are currently being cultured and tested for resistance against oseltamivir.

One pregnant woman was confirmed to be infected with influenza A(H1N1)v.

Information on underlying factors for the other 41 patients was not available.
(...)
-
------

[Mamabird]

Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

The Tamiflu resistant precursor is spreading in Spain. The most recent additions were collected this month (July 3), yet the number of recent sequences (since April) in the US remains at ZERO.
HA sequence hasn't been released, but it likely has D225E.

Agreed, and S206T as well.

[HenryN]

Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

The Tamiflu resistant precursor is spreading in Spain. The most recent additions were collected this month (July 3), yet the number of recent sequences (since April) in the US remains at ZERO.
HA sequence hasn't been released, but it likely has D225E.

[HenryN]

Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

More NA matches

gb|GQ369275.1| Influenza A virus (A/Stockholm/37/2009(H1N1)) ... 2224 0.0
gb|GQ365448.1| Influenza A virus (A/Sapporo/1/2009(H1N1)) seg... 2224 0.0
gb|GQ355297.1| Influenza A virus (A/Catalonia/387/2009(H1N1))... 2224 0.0
gb|GQ160533.1| Influenza A virus (A/New Jersey/01/2009(H1N1))... 2224 0.0

gb|GQ379856.1| Influenza A virus (A/Catalonia/517/2009(H1N1))... 32.2 11
gb|GQ379852.1| Influenza A virus (A/Catalonia/502/2009(H1N1))... 32.2 11
gb|GQ379840.1| Influenza A virus (A/Catalonia/476/2009(H1N1))... 32.2 11
gb|GQ379833.1| Influenza A virus (A/Catalonia/442/2009(H1N1))... 32.2 11
gb|GQ369275.1| Influenza A virus (A/Stockholm/37/2009(H1N1)) ... 32.2 11
gb|GQ365448.1| Influenza A virus (A/Sapporo/1/2009(H1N1)) seg... 32.2 11
gb|GQ355297.1| Influenza A virus (A/Catalonia/387/2009(H1N1))... 32.2 11
gb|GQ351316.1| Influenza A virus (A/Hong Kong/2369/2009(H1N1)... 32.2 11
gb|GQ338380.1| Influenza A virus (A/Oklahoma/03/2009(H1N1)) s... 32.2 11
gb|GQ160533.1| Influenza A virus (A/New Jersey/01/2009(H1N1))... 32.2 11

[HenryN]

Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

Note from HK SAR:

A resistant strain?

(...)
[On the Filipino patient in critical conditions]

Secretary for Food and Health:
I do not have the detailed information regarding this particular patient, but I think she is still in a critical condition in the intensive care unit of the United Christian Hospital. Whether Hong Kong has a fatal case or not will not affect our emergency measures at the moment. Of course, we will investigate the nature of the virus. We are doing genetic sequencing to see whether there is any significant change of the virus.
(...)

From: http://www.info.gov.hk/gia/general/2...0907130139.htm

Yes, they switched from Tamiflu to Relenza and by now that should have a sequence (at least in the region encompassing H274Y).

[Giuseppe]

Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

Note from HK SAR:

A resistant strain?

(...)
[On the Filipino patient in critical conditions]

Secretary for Food and Health:
I do not have the detailed information regarding this particular patient, but I think she is still in a critical condition in the intensive care unit of the United Christian Hospital. Whether Hong Kong has a fatal case or not will not affect our emergency measures at the moment. Of course, we will investigate the nature of the virus. We are doing genetic sequencing to see whether there is any significant change of the virus.
(...)

From: http://www.info.gov.hk/gia/general/2...0907130139.htm

[HenryN]

Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

Are the viruses from the more severe or fatal cases in the US (and elsewhere) being sequenced? From what I've seen in the news, it appears that few are being sequenced. Have any of the viruses responsible for the fatalities in Argentina been sequenced?

There are no recent public sequences from Argentina.

[Zac]

Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

Are the viruses from the more severe or fatal cases in the US (and elsewhere) being sequenced? From what I've seen in the news, it appears that few are being sequenced. Have any of the viruses responsible for the fatalities in Argentina been sequenced?