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New H3N2 New York Complete Sequences at GenBank

Recombinomics Commentary
February 20, 2005

A new set of H3N2 sequences from the New York area  have been made available at GenBank.  These are complete sequences for all 8 genes generated by the NIAID Influenza Genome Sequence.  This set was deposited by TIGR/Wadsworth-NYSDOH/NCBI, National Center for Biotechnology Information.  In addition to the complete sequences, the age gender and location of the patient is given.  This is a welcome addition and will help considerably in the analysis.

Remarkably, the data base is lacking complete sequences for some of the most important current H3N2 isolates including A/Fujian/411/2003, A/Wyoming/3/2004, A/Kumamota/102/02, A/Wellington/1/2004, and A/California/7/2004.  Most only have sequence data for 1 or 2 genes (HA and NA), and even those sequences are frequently partial. The most information available is for Panama/411, which was used for 5 years as the H3N2 component in the trivalent human vaccine. Public data is only available for HA and NA as well as partial sequences for NP and NS.

This New York data set is an excellent example of putting resources to good work and these full sequences for all 8 genes should further the understanding on how influenza emerges and evolves, which is via recombination, although the many gaps in the current data base make such changes more difficult to see.

A complete data set on A/California/7/2004 will also help determine the reasons for its remarkable virulence.

The latest isolates are from

81M, Montgomery County, NY (A/New York/121/2002(H3N2))

11F, Lawrence County, NY (A/New York/113/2002(H3N2))

21F, Madison County, NY (A/New York/100/2002(H3N2))

5mF, Suffolk County, NY (A/New York/95/2002(H3N2))

21F Rensselaer County, NY (A/New York/91/2002(H3N2))

28M Delaware County, NY (A/New York/84/2001(H3N2))

21F Ontario County, NY (A/New York/40/2003(H3N2))

71F Dutchess County, NY (A/New York/23/2003(H3N2))

20M Suffolk County, NY (A/New York/12/2003(H3N2))

24M Columbia County, NY (A/New York/110/2002(H3N2))

16M Clinton County, NY (A/New York/83/2001(H3N2))

4M Yates County, NY (A/New York/60A/2003(H3N2))

1mM Cataraugus County, NY (A/New York/54/2003(H3N2))

15M Otsego County, NY (A/New York/50/2003(H3N2))

3M Allegany County, NY (A/New York/48/2003(H3N2))

33M Schenectady, NY (A/New York/47/2003(H3N2))

16F Greene County, NY (A/New York/45/2003(H3N2))

9M St. Lawrence County, NY (A/New York/44/2003(H3N2))

11M Chautauqua County, NY (A/New York/43/2002(H3N2))

22F Chautauqua County, NY (A/New York/42/2003(H3N2))

19F Ontario County, NY (A/New York/41/2002(H3N2))

18F Cortland County, NY (A/New York/36/2003(H3N2))

24F Ulaster County, NY (A/New York/43/2002(H3N2))

91F Monroe County, NY (A/New

52F Albany County, NY (A/New York/30/2002(H3N2))

3F Onondaga County, NY (A/New York/28/2003(H3N2))

22M Madison County, NY (A/New York/16/2003(H3N2))

57M Herkimer County, NY (A/New York/61A/2003(H3N2))

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