Rhiza Labs FluTracker Forum

CDC has released a Maryland H3 sequence at GISAID collected on March 5, which is presumably from the death cluster.

_________________
www.twitter.com/hniman

As expected, it is an H3 variant (with S199A and closely related to Brisbane/299/2011).

_________________
www.twitter.com/hniman

Above sequence is from A/Maryland/05/2012. CDC also released fuller sequences from A/Maryland/04/2012 and A/Maryland/06/2012. All three sets of sequences were collected March 5, presumably from the three children of the index case.
Additional sequences were from samples collected on February 20 and 21, which may represent the index case. All five H3 sequences are virtually identical.

_________________
www.twitter.com/hniman

Top 100 H3 matches (all five sequences from Maryland virtually identical)

EPI359098 A/Maryland/04/2012 (A/H3N2) segment 4 (HA) 3142.3 0.000000e+00 1701/1701 (100%)
EPI359623 A/Maryland/05/2012 (A/H3N2) segment 4 (HA) 3136.7 0.000000e+00 1700/1701 (99%)
EPI359569 A/Maryland/08/2012 (A/H3N2) segment 4 (HA) 3136.7 0.000000e+00 1700/1701 (99%)
EPI359564 A/Maryland/06/2012 (A/H3N2) segment 4 (HA) 3136.7 0.000000e+00 1700/1701 (99%)
EPI359571 A/Maryland/09/2012 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI359211 A/Umea/7/2011 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI359209 A/Umea/6/2011 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI359019 A/Stockholm/12-00979/2012 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI357044 A/Stockholm/6/20112 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI354203 A/Netherlands/001/2012 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI353940 A/Stockholm/38/2011 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI353603 A/Malmoe/1/2012 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI353557 A/Stockholm/3/2012 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI353473 A/Texas/06/2012 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI351725 A/Stockholm/44/2011 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI351627 A/Stockholm/41/2011 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI351557 A/Stockholm/45/2011 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI351413 A/Uppsala/10/2011 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI351292 A/Texas/14/2011 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI351282 A/Florida/42/2011 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI351216 A/Uppsala/9/2011 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI347594 A/Vaxjo/1/2011 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI347591 A/Stockholm/31/2011 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI346408 A/Stockholm/28/2011 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI353448 A/Florida/02/2012 (A/H3N2) segment 4 (HA) 3127.5 0.000000e+00 1698/1701 (99%)
EPI352683 A/Netherlands/702/2011 (A/H3N2) segment 4 (HA) 3127.5 0.000000e+00 1698/1701 (99%)
EPI351632 A/Uppsala/11/2011 (A/H3N2) segment 4 (HA) 3127.5 0.000000e+00 1698/1701 (99%)
EPI357008 A/Stockholm/11/2012 (A/H3N2) segment 4 (HA) 3125.7 0.000000e+00 1698/1701 (99%)
EPI354199 A/Netherlands/710/2011 (A/H3N2) segment 4 (HA) 3125.7 0.000000e+00 1698/1701 (99%)
EPI353566 A/Vaxjo/2/2012 (A/H3N2) segment 4 (HA) 3125.7 0.000000e+00 1698/1701 (99%)
EPI353563 A/Vaxjo/1/2012 (A/H3N2) segment 4 (HA) 3125.7 0.000000e+00 1698/1701 (99%)
EPI352218 A/New York/20/2011 (A/H3N2) segment 4 (HA) 3125.7 0.000000e+00 1698/1701 (99%)
EPI347509 A/Massachusetts/11/2011 (A/H3N2) segment 4 (HA) 3125.7 0.000000e+00 1698/1701 (99%)
EPI358025 A/New Jersey/01/2012 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI352833 A/Catalonia/S4477/2012 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI352765 A/Porto/EuroEva69/2012 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI351644 A/Stockholm/42/2011 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI342205 A/Barbados/170/2010 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI342203 A/Barbados/170/2010 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI342197 A/Pennsylvania/08/2010 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI342195 A/Pennsylvania/08/2010 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI309405 A/Costa Rica/0096/2001 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI301111 A/California/27/2010 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI301018 A/Florida/27/2010 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI295199 A/Belize/3715/2010 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI291556 A/Costa Rica/6696/2010 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI287082 A/Panama/307149/2010 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI279988 A/Mexico/4056/2010 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI279979 A/Barbados/170/2010 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI279967 A/Pennsylvania/08/2010 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI279961 A/Florida/11/2010 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI278766 A/Dominican Republic/4319/2010 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI278760 A/Panama/307149/2010 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI295054 A/California/18/2010 (A/H3N2) segment 4 (HA) 3116.4 0.000000e+00 1696/1701 (99%)
EPI359476 A/Boston/DOA75/2011 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI359013 A/Stockholm/42/2011 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI340936 A/Paraguay/210/2011 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI335948 A/Santiago/18454/2011 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI335931 A/Paraguay/210/2011 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI335923 A/Iowa/19/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI335861 A/Argentina/676/2011 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI325977 A/Mexico City/WRAIR3580T/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI325969 A/Mexico City/WRAIR3579T/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI325953 A/Mexico City/WRAIR3578T/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI325945 A/Mexico City/WRAIR3578N/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI319844 A/Wisconsin/20/2011 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI319740 A/Minnesota/09/2011 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI319128 A/Illinois/NHRC0002/2011 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI316888 A/Uppsala/3/2011 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI316871 A/Uppsala/2/2011 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI316173 A/Peru/8410/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI316114 A/Mississippi/03/2011 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI316091 A/Louisiana/01/2011 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI309578 A/Argentina/8409/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI309481 A/South Carolina/01/2011 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI309464 A/Wyoming/04/2011 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI309438 A/Guadeloupe/129/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI302319 A/Iowa/12/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI302304 A/Iowa/11/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI302268 A/British Columbia/RV29/2011 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI302233 A/Rheinland-Pfalz/7/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI301753 A/North Carolina/13/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI301737 A/Arkansas/03/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI301360 A/England/3940462/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI301354 A/Argentina/28378/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI301125 A/Nebraska/03/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI301121 A/Arkansas/05/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI301101 A/Texas/12/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI301010 A/Alabama/07/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI295071 A/Mississippi/05/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI294010 A/Argentina/27891/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI286713 A/Gothenburg/1/2010 (A/H3N2) segment 4 (HA) 3112.7 0.000000e+00 1695/1700 (99%)
EPI278815 A/Panama/307149/2010 (A/H3N2) segment 4 (HA) 3112.7 0.000000e+00 1695/1701 (99%)
EPI319656 A/California/22/2011 (A/H3N2) segment 4 (HA) 3110.9 0.000000e+00 1695/1701 (99%)
EPI316236 A/Washington/06/2011 (A/H3N2) segment 4 (HA) 3110.9 0.000000e+00 1695/1701 (99%)
EPI316181 A/Rhode Island/04/2011 (A/H3N2) segment 4 (HA) 3110.9 0.000000e+00 1695/1701 (99%)
EPI316082 A/Kansas/03/2011 (A/H3N2) segment 4 (HA) 3110.9 0.000000e+00 1695/1701 (99%)
EPI309581 A/Georgia/01/2011 (A/H3N2) segment 4 (HA) 3110.9 0.000000e+00 1695/1701 (99%)
EPI309563 A/Delaware/02/2011 (A/H3N2) segment 4 (HA) 3110.9 0.000000e+00 1695/1701 (99%)
EPI309387 A/Mexico/6605/2010 (A/H3N2) segment 4 (HA) 3110.9 0.000000e+00 1695/1701 (99%)

_________________
www.twitter.com/hniman

Isolate name:

A/Brisbane/299/2011 X-215

Isolate ID:

EPI_ISL_107921
Passage details/history:

EX/E2
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:
New York Medical College
Sample ID given by the sample provider:

A/BRISBANE/299/2011 X-215
Address:
New York Medical College

Valhalla, New York 10595
United States


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

2012703808
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

_________________
www.twitter.com/hniman

S199A Emergence and Spread in H3N2 Variants
Recombinomics Commentary 22:40
September 23, 2010

In August the US CDC issued an H3N2 health alert linked to two small outbreaks in eastern Iowa. The level of H3N2 in the US last season was very low, due largely to the spread of pandemic H1N1. However, H3N2 began to rebound in several Asian countries, and labs worldwide have been releasing H3N2 sequences.

The CDC released the sequence from Iowa. It was the Perth/16 strain, but like most of the H3N2 circulating in late 2009, early 2010 it had evolved away from the Perth target, which had been isolated in April, 2009.......

http://www.recombinomics.com/News/09231 ... S199A.html

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Commentary

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

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www.twitter.com/hniman

Note that the selection of Brisbane/299/2011 as a potential vaccine target clearly demonstrates CDC's knowldege that S199A in the above target as well as the Maryland cluster signaled a significant vaccine problem.

_________________
www.twitter.com/hniman

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

_________________
www.twitter.com/hniman

Isolate name:

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

Isolate ID:

EPI_ISL_107043
Passage details/history:

E5E8/E3
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

_________________
www.twitter.com/hniman