Volume 12, Number 4—April 2006
Research
Identifying Influenza Viruses with Resequencing Microarrays
Zheng Wang*†, Luke T. Daum‡, Gary J. Vora*, David Metzgar§, Elizabeth A. Walter¶, Linda C. Canas‡, Anthony P. Malanoski*, Baochuan Lin*, and David A. Stenger*
Table 2
Influenza strain identification with respiratory pathogen microarray (RPM) version 1 versus conventional sequencing*
| Sample name | Base call rate† (%) |
||||||
|---|---|---|---|---|---|---|---|
| HA | NA | M | Strain identification from HA | GenBank accession no. | M1‡ | M2§ | |
| A/Colorado/360/05 | 84.4 | 72.7 | 63.2 | A/Nepal/1679/2004 (H3N2) | AY945284 | 0 | 8 |
| A/Qater/2039/05 | 88.4 | 74.0 | 68.5 | A/Nepal/1727/2004 (H3N2) | AY945272 | 0 | 8 |
| A/Guam/362/05 | 87.3 | 75.8 | 63.3 | A/Nepal/1679/2004 (H3N2) | AY945264 | 2 | 10 |
| A/Italy/384/05 | 83.3 | 69.6 | 63.5 | /Nepal/1727/2004 (H3N2) | AY945272 | 2 | 9 |
| A/Turkey/2108/05 | 77.9 | 67.6 | 59.2 | A/Nepal/1664/2004 (H3N2) | AY945265 | 2 | 12 |
| A/Korea/298/05 | 82.7 | 70.5 | 61.7 | A/Nepal/1727/2004 (H3N2) | AY945273 | 4 | 11 |
| A/Japan/1337/05 | 87.5 | 76.7 | 67.4 | A/Malaysia/2256/2004 (H3N2) | ISDN110616 | 4 | 14 |
| A/Japan/1383/05 | 92.1 | 84.9 | 74.8 | A/Malaysia/2256/2004 (H3N2) | ISDN110616 | 4 | 14 |
| A/Ecuador/1968/04 | 87.7 | 75.2 | 58.3 | A/New York/17/2003 (H3N2) | CY001053 | 0 | 4 |
| A/Iraq/34/05 | 84.4 | 72.7 | 65.6 | A/Christchurch/178/2004 (H3N2) | ISDN110530 | 1 | 9 |
| A/Peru/166/05 | 86.9 | 79.0 | 65.9 | A/Macau/103/2004 (H3N2) | ISDN64772 | 6 | 10 |
| A/New York/2782/04 | 82.7 | 68.0 | 63.1 | A/New York/391/2005 (H3N2) | CY002056 | 1 | 9 |
| A/England/400/05 | 88.3 | 55.3 | 61.1 | A/New York/227/2003 (H1N1) | CY002536 | 1 | 10 |
| B/Peru/1324/04 | 75.2 | 83.4 | 89.4 | B/Milano/66/04 | AJ842082 | 1 | 25 |
| B/Peru/1364/04 | 71.1 | 74.5 | 77.5 | B/Milano/66/04 | AJ842082 | 1 | 25 |
| B/Colorado/2597/04 | 81.1 | 84.3 | 85.8 | B/Texas/3/2002 | AY139049 | 4 | 27 |
| B/Japan/1905/05 | 76.2 | 76.5 | 76.6 | B/Texas/3/2002 | AY139049 | 2 | 25 |
| B/Japan/1224/05 | 80.0 | 78.2 | 83.7 | B/Texas/3/2002 | AY139049 | 2 | 25 |
| B/Alaska/1777/05 | 75.0 | 75.9 | 78.1 | B/Texas/3/2002 | AY139049 | 4 | 27 |
| B/England/1716/05 | 80.5 | 81.4 | 85.2 | B/Texas/3/2002 | AY139049 | 2 | 25 |
| B/England/2054 /05 | 81.1 | 80.1 | 78.7 | B/Texas/3/2002 | AY139049 | 1 | 24 |
| B/Hawaii/1990/04 | 51.7 | 82.9 | 83.7 | B/Tehran/80/02¶ | AJ784042 | 4 | 68 |
| B/Hawaii/1993/04 | 47.4 | 79.7 | 83.7 | B/Tehran/80/02¶ | AJ784042 | 4 | 69 |
| B/Arizona/148/04 | 42.4 | 78.2 | 82.5 | B/Tehran/80/02¶ | AJ784042 | 6 | 69 |
| B/Arizona/146/04 | 49.1 | 79.1 | 86.7 | B/Tehran/80/02¶ | AJ784042 | 6 | 69 |
*HA, hemagglutinin; NA, neuraminidase; M, matrix.
†No. of base calls generated from the RPM version 1 divided by the length of the tiled probe sequence.
‡No. of mismatches between the actual sequence and the sequence of the top BLAST search hit.
§No. of mismatches between the actual sequence and the tiled prototype probe sequence.
¶Influenza B group 2 isolates were identified as B/New York/1/2002 strain (accession no. AF532565) by the conventional sequencing method.
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