Rhiza Labs FluTracker Forum

The CDC released a series of recent H3N2 sequences, including February 15 samples from Minnesota and Delaware, but no sequences from Maryland were released, adding to concerns that these were drift variants, CDC denials notwithstanding.

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February 2012 CDC sequences:

A/Minnesota/04/2012 EPI_ISL_107920 H3N2 C2 --- --- --- 1701 --- 1410 982 --- --- --- 2012-02-15
A/Delaware/02/2012 EPI_ISL_107918 H3N2 C2 --- --- --- 1701 --- 1410 982 --- --- --- 2012-02-15
A/Nebraska/07/2012 EPI_ISL_107914 H3N2 C2 --- --- --- 1701 --- 1410 982 --- --- --- 2012-02-06
A/Texas/20/2012 EPI_ISL_107039 H3N2 C1 --- --- --- 1701 --- 1410 982 --- --- --- 2012-02-06
A/Wisconsin/07/2012 EPI_ISL_107917 H3N2 C2 --- --- --- 1701 --- 1410 982 --- --- --- 2012-02-03
A/Maine/02/2012 EPI_ISL_107915 H3N2 C2 --- --- --- 1701 --- 1410 982 --- --- --- 2012-02-03
A/New Jersey/01/2012 EPI_ISL_107035 H3N2 C1 --- --- --- 1701 --- 1410 982 --- --- --- 2012-02-03
A/Vermont/04/2012 EPI_ISL_107919 H3N2 M1/C2 --- --- --- 1701 --- 1410 982 --- --- --- 2012-02-02
A/Kansas/03/2012 EPI_ISL_107913 H3N2 C2/C2 --- --- --- 1701 --- 1410 982 --- --- --- 2012-02-01
A/Indiana/01/2012 EPI_ISL_107037 H3N2 M1/C1 --- --- --- 1701 --- 1300 982 --- --- --- 2012-02-01
A/Virginia/04/2012 EPI_ISL_107031 H3N2 C1 --- --- --- 1701 --- 1410 982 --- --- --- 2012-02-01

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January 2012 H3N2 CDC sequences

A/Minnesota/03/2012 EPI_ISL_107032 H3N2 C2 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-30
A/Pennsylvania/04/2012 EPI_ISL_107030 H3N2 C2 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-25
A/Massachusetts/02/2012 EPI_ISL_105768 H3N2 M1/C1 --- --- --- 1701 --- 1410 984 --- --- --- 2012-01-23
A/Virginia/03/2012 EPI_ISL_105762 H3N2 M1/C1 --- --- --- 1701 --- 1410 984 --- --- --- 2012-01-23
A/Connecticut/02/2012 EPI_ISL_107034 H3N2 C2 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-22
A/Alabama/02/2012 EPI_ISL_106107 H3N2 X/C2 --- --- --- 1701 --- 1410 984 --- --- --- 2012-01-21
A/Kyrgyzstan/119/2012 EPI_ISL_107036 H3N2 X/C1 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-20
A/North Carolina/01/2012 EPI_ISL_106106 H3N2 C2 --- --- --- 1701 --- 1410 984 --- --- --- 2012-01-19
A/Montana/01/2012 EPI_ISL_105800 H3N2 M1/C1 --- --- --- 1701 --- 1410 984 --- --- --- 2012-01-17
A/Missouri/02/2012 EPI_ISL_105759 H3N2 C1 --- --- --- 1701 --- 1410 984 --- --- --- 2012-01-17
A/Virginia/01/2012 EPI_ISL_103756 H3N2 C1 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-17
A/Texas/10/2012 EPI_ISL_105770 H3N2 C2 --- --- --- 1701 --- 1410 984 --- --- --- 2012-01-16
A/Idaho/02/2012 EPI_ISL_105764 H3N2 M1/C1 --- --- --- 1701 --- 1410 984 --- --- --- 2012-01-16
A/Vermont/01/2012 EPI_ISL_103750 H3N2 M1/C1 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-16
A/New York/01/2012 EPI_ISL_107042 H3N2 M1/C1 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-15
A/Georgia/01/2012 EPI_ISL_105760 H3N2 M1/C1 --- --- --- 1701 --- 1410 984 --- --- --- 2012-01-15
A/Guam/402/2012 EPI_ISL_107038 H3N2 C1 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-14
A/Minnesota/02/2012 EPI_ISL_107028 H3N2 C2 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-14
A/Nebraska/01/2012 EPI_ISL_103752 H3N2 C1 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-14
A/Mississippi/01/2012 EPI_ISL_106103 H3N2 C1 --- --- --- 1701 --- 1410 984 --- --- --- 2012-01-12
A/Colorado/05/2012 EPI_ISL_106111 H3N2 C1 --- --- --- 1701 --- 1410 984 --- --- --- 2012-01-11
A/South Carolina/03/2012 EPI_ISL_106105 H3N2 X1/C2 --- --- --- 1701 --- 1410 984 --- --- --- 2012-01-11
A/Kansas/01/2012 EPI_ISL_105766 H3N2 C2 --- --- --- 1701 --- 1410 984 --- --- --- 2012-01-11
A/Arkansas/01/2012 EPI_ISL_103758 H3N2 C2 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-11
A/Washington/01/2012 EPI_ISL_103751 H3N2 C1 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-11
A/California/07/2012 EPI_ISL_106113 H3N2 C2 --- --- --- 1701 --- 1410 984 --- --- --- 2012-01-10
A/Wyoming/01/2012 EPI_ISL_105763 H3N2 C2 --- --- --- 1701 --- 1410 984 --- --- --- 2012-01-10
A/Nevada/01/2012 EPI_ISL_103754 H3N2 M1/C1 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-10
A/Tennessee/01/2012 EPI_ISL_107025 H3N2 C1 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-09
A/Florida/02/2012 EPI_ISL_103742 H3N2 C1 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-09
A/Texas/06/2012 EPI_ISL_103749 H3N2 M1/C1 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-05
A/Oregon/01/2012 EPI_ISL_106112 H3N2 M1/C2 --- --- --- 1701 --- 1410 984 --- --- --- 2012-01-04
A/California/01/2012 EPI_ISL_103747 H3N2 C2 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-04
A/South Carolina/01/2012 EPI_ISL_103141 H3N2 X1/C2 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-04
A/South Dakota/02/2012 EPI_ISL_106109 H3N2 M2/C2 --- --- --- 1701 --- 1410 984 --- --- --- 2012-01-03
A/Iowa/01/2012 EPI_ISL_103746 H3N2 C2 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-03
A/Wisconsin/01/2012 EPI_ISL_102984 H3N2 C2 --- --- --- 1701 --- 1410 982 --- --- --- 2012-01-02
A/Utah/04/2012 EPI_ISL_105767 H3N2 C2 --- --- --- 1701 --- 1410 984 --- --- --- 2012-01-01

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V223I includes:
EPI359088 A/Minnesota/04/2012 (A/H3N2) segment 4 (HA) 27.0 7.775615e+00 14/14 (100%)
EPI359085 A/Vermont/04/2012 (A/H3N2) segment 4 (HA) 27.0 7.775615e+00 14/14 (100%)
EPI359082 A/Delaware/02/2012 (A/H3N2) segment 4 (HA) 27.0 7.775615e+00 14/14 (100%)
EPI359079 A/Wisconsin/07/2012 (A/H3N2) segment 4 (HA) 27.0 7.775615e+00 14/14 (100%)
EPI359070 A/Nebraska/07/2012 (A/H3N2) segment 4 (HA) 27.0 7.775615e+00 14/14 (100%)
EPI358031 A/Indiana/01/2012 (A/H3N2) segment 4 (HA) 27.0 7.775615e+00 14/14 (100%)
EPI358022 A/Connecticut/02/2012 (A/H3N2) segment 4 (HA) 27.0 7.775615e+00 14/14 (100%)
EPI358015 A/Minnesota/03/2012 (A/H3N2) segment 4 (HA) 27.0 7.775615e+00 14/14 (100%)
EPI358012 A/Virginia/04/2012 (A/H3N2) segment 4 (HA) 27.0 7.775615e+00 14/14 (100%)
EPI358010 A/Pennsylvania/04/2012 (A/H3N2) segment 4 (HA) 27.0 7.775615e+00 14/14 (100%)
EPI357998 A/Arizona/06/2011 (A/H3N2) segment 4 (HA) 27.0 7.775615e+00 14/14 (100%)
EPI357995 A/Tennessee/01/2012 (A/H3N2) segment 4 (HA) 27.0 7.775615e+00 14/14 (100%)

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Virtually all 2012 H3N2 sequences in US are drift variants, either A/Victoria/361/2011-like (with A198S and V223I) or A/Brisbane/299/2011-iike (with S199A).

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IVR-164(A/Brisbane/299/2011)

Isolate ID:

EPI_ISL_107044
Passage details/history:

E5E8/E1
Type:

A / H3N2
Lineage:



Sample information

Collection date:

2011 (Month and day unknown)
Host

Laboratory derived
Additional host information:


Location:

Australia
Additional location information:




Institute information

Originating lab:
WHO Collaborating Centre for Reference and Research on Influenza
Sample ID given by the sample provider:

IVR-164(A/BRISBANE/299/2011)
Address:
WHO Collaborating Centre for Reference and Research on Influenza

10 Wreckyn Street
North Melbourne, Victoria 3051
Australia


Submitting lab:
Centers for Disease Control and Prevention
Sample ID given by the submitting laboratory:

2012703507
Authors:

Address:
Centers for Disease Control and Prevention
WHO Collaborating Center for Surveillance, Epidemiology and Control of Influenza, Influenza Division
1600 Clifton Road, N.E.
Atlanta, GA 30333
United States


Publication
Publication


In vivo antiviral resistance

Unspecified Genotype Phenotype
Antiviral resistance tested by unknown method
Adamantanes:

Unknown
Oseltamivir:

Unknown
Zanamivir:

Unknown
Peramivir:

Unknown
Other:

Unknown


Antiviral resistance tested by sequence prediction
Adamantanes:

Unknown
Oseltamivir:

Unknown
Zanamivir:

Unknown
Peramivir:

Unknown
Other:

Unknown

Antiviral resistance tested by experimental procedures
Adamantanes:

Unknown
Oseltamivir:

Unknown
Zanamivir:

Unknown
Peramivir:

Unknown
Other:

Unknown

Additional information
Antigenic characterization:

REASSORTANT A/BRISBANE/299/2011-LIKE GP,INTERNAL ONLY A/PERTH/16/2009-LIKE (H3N2) GP

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Todd W.

A question I have is whether the particular variant of flu that the mother had was one of the strains included in the vaccine this year. The Maryland Department of Health and Mental Hygiene is "working with CDC" on more testing, but has not confirmed that this is the case. My guess is that this was just an instance where the vaccine did not produce a sufficient immune response, but that it did match the strain with which she was infected.

Regarding MRSA, is there any clear indication of when it first arose as a superbug? Just wondering if a related bacterium may have been involved in the deaths in the 1918 flu pandemic.

Yesterday 05:38 AM
================================================================

Maryn McKenna, Maryn McKenna is an award-winning journalist and the author of SUPERBUG and BEATING BACK THE DEVIL. She blogs for Wired.

Smart questions. The MDHMH says it was the same strain, and I know of someone who privately asked the CDC if it was a drifted variant, and was told no.

http://www.wired.com/wiredscience/2012/ ... pneumonia/

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The only H3 sequences from Maryand in the 2011/2012 season is A/Maryland/21/2011, which has A198S and V223I (as does the new H3N2 target A/Victoria/361/2011, a clear drift variant of Perth/16/2009).

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Commentary

http://www.recombinomics.com/News/03271 ... _Dual.html

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