Table 3.
Viruses recovered during this study that share differing degrees of nucleotide (nt) identity within each gene segment. Viruses with the same color code within a given gene segment share >99.0% nt identity. The HA and NA of the first H5N9 (AI12-1161) and H6N1 (AI12-1541) viruses isolated are the reference sequences within those respective gene segments.
| Virus | Percent Nucleotide Similarity to Reference Sequence 3 | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| PB2 | PB1 | PA | NP | MA | NS | HA | NA | ||
| A/Ruddy turnstone/NJ 1/AI11-1678/2011(H7N7) | ref | ref | ref | ref | ref | ref | N/A (H7) | N/A (N7) | Reference 4 |
| A/Ruddy turnstone/FL 2/AI12-1161/2012/H5N9 | 92.0 | 99.6 | 99.6 | 91.9 | 96.9 | 95.1 | ref | ref | Southeastern viruses —this study |
| A/Ruddy turnstone/FL/AI12-1244/2012/H5N9 | 92.0 | 99.6 | 99.6 | 91.9 | 96.9 | 95.1 | 99.9 | 100.0 | |
| A/Ruddy turnstone/FL/AI12-1476/2012/H5N9 | 91.9 | 99.6 | 99.6 | 91.9 | 96.9 | 95.2 | 99.8 | 100.0 | |
| A/Ruddy turnstone/FL/AI12-1541/2012/H6N1 | 91.9 | 99.3 | 99.4 | 91.7 | 99.1 | 95.2 | ref | ref | |
| A/Ruddy turnstone/FL/AI12-1590/2012/H6N1 | 91.7 | 99.3 | 99.4 | 91.7 | 99.1 | 95.2 | 100.0 | 100.0 | |
| A/Ruddy turnstone/FL/AI12-1591/2012/H6N1 | 91.9 | 99.2 | 99.4 | 91.7 | 99.1 | 95.2 | 99.9 | 100.0 | |
| A/Ruddy turnstone/FL/AI12-1592/2012/H6N1 | 91.9 | 99.2 | 99.4 | 91.7 | 99.1 | 95.2 | 99.9 | 100.0 | |
| A/Ruddy turnstone/FL/AI12-1593/2012/H6N1 | 91.9 | 99.3 | 99.4 | 91.7 | 99.1 | 95.2 | 100.0 | 100.0 | |
| A/Ruddy turnstone/FL/AI12-1683/2012/H6N1 | 91.9 | 99.3 | 99.4 | 91.7 | 99.1 | 95.2 | 99.9 | 100.0 | |
| A/Ruddy turnstone/FL/AI12-1638/2012/H6N1 | 91.9 | 99.3 | 99.4 | 91.7 | 99.1 | 95.2 | 99.9 | 99.9 | |
| A/Ruddy turnstone/FL/AI12-1340/2012/H6N1 | 91.9 | 99.3 | 99.4 | 91.7 | 99.1 | 95.2 | 100.0 | 100.0 | |
| A/Ruddy turnstone/FL/AI12-1368/2012/H6N1 | 92.0 | 99.3 | 99.5 | 93.7 | 99.1 | 95.1 | 99.9 | 99.9 | |
| A/Ruddy turnstone/NJ/AI12-2120/2012/H6N1 | 99.6 | 99.5 | 87.4 | 91.7 | 99.7 | 98.0 | 99.6 | 99.6 | DE Bay viruses —this study |
| A/Ruddy turnstone/NJ/AI12-2279/2012/H5N9 | 99.6 | 99.5 | 87.4 | 91.7 | 99.5 | 95.3 | 99.4 | 99.3 | |
| A/Ruddy turnstone/NJ/AI12-2166/2012/H6N1 | 99.6 | 96.1 | 87.4 | 91.7 | 96.7 | 98.2 | 99.5 | 99.5 | |
| A/Ruddy turnstone/NJ/AI12-2356/2012/H6N1 | 99.6 | 99.4 | 87.5 | 91.7 | 99.7 | 98.2 | 99.6 | 99.6 | |
| A/Ruddy turnstone/NJ/AI12-2375/2012/H6N1 | 91.8 | 93.5 | 99.4 | 93.8 | 96.8 | 95.1 | 99.2 | 93.0 | |
| A/Ruddy turnstone/NJ/AI12-2871/2012/H5N3 | 96.8 | 94.1 | 87.4 | 91.6 | 96.9 | 97.8 | 97.7 | N/A | |
| A/Ruddy turnstone/NJ/AI12-2010/2012/H6N1 | 99.6 | 99.4 | 87.4 | 91.7 | 99.6 | 98.2 | 99.6 | 99.6 | |
| A/Ruddy turnstone/NJ/AI12-2210/2012/H6N1 | 99.6 | 96.2 | 87.4 | 91.7 | 96.9 | 98.3 | 99.5 | 99.6 | |
| A/gull/MA 3/13JR00943/2013(H9N1) | 91.9 | 96.0 | 87.7 | 93.7 | 97.5 | 97.0 | N/A (H9) | 93.0 | Reference 5 |
1 New Jersey (NJ); 2 Florida (FL); 3 Massachusetts (MA) 4 Virus A/Ruddy turnstone/NJ/AI11-1678/2011/H7N7 was used as a “contributing” reference virus for internal genes; 5 Virus A/gull/MA/13JR00943/2013/H9N1 was used as a “receiving” reference sequence for internal genes and NA1.