Table 1.
Nucleotide and amino acid similarity comparisons among type 2 lineagesa
| Strain (accession no.) | Region | % of similarity to strain (accession no.) shown |
Region | ||||||
|---|---|---|---|---|---|---|---|---|---|
| GBR/1993/Oxford-H2/2b (L13745) | GBR/Oxford-S2/2b (AB000288) | NOR/1993/NORAS1128/r(AB000290) | ITA/2002/PA65R/2c (JX087963) | USA/1999/1299-CA/2c (EF138827) | ITA/2009/PR5142/2d (JX087964) | GBR/1993/Oxford-AS8811/2a (AB000289) | |||
| GBR/1993/Oxford-H2/2b (L13745) | 96.4 | 95.9 | 98.6 | 97.8 | 97.6 | 95.7 | N | ||
| 90.0 | 95.2 | 90.9 | 94.4 | 92.6 | 70.2 | HVR | |||
| 94.6 | 96.4 | 94.6 | 95.9 | 93.8 | 85.3 | Cap | |||
| GBR/Oxford-S2/2b (AB000288) | D5′ | 99.5 | 94.2 | 95.4 | 94.9 | 94.4 | 93.2 | N | |
| D3′ | 100 | 88.7 | 85.7 | 88.3 | 87.4 | 66.0 | HVR | ||
| Cap | 97.5 | 93.0 | 91.4 | 92.5 | 90.5 | 82.7 | Cap | ||
| NOR/1993/NORAS1128/r (AB000290) | D5′ | 94.3 | 94.3 | 97.1 | 96.6 | 94.9 | 94.2 | N | |
| D3′ | 100 | 100 | 88.7 | 91.3 | 88.7 | 67.7 | HVR | ||
| Cap | 95.0 | 93.8 | 93.1 | 94.3 | 91.1 | 83.7 | Cap | ||
| ITA/2002/PA65R/2c (JX087963) | D5′ | 94.9 | 94.8 | 96.8 | 99.3 | 97.8 | 95.9 | N | |
| D3′ | 94.0 | 94.0 | 94.0 | 95.7 | 93.1 | 68.9 | HVR | ||
| Cap | 92.7 | 91.1 | 93.7 | 97.3 | 94.4 | 84.5 | Cap | ||
| USA/1999/1299-CA/2c (EF138827) | D5′ | 95.0 | 94.5 | 97.5 | 98.0 | 97.6 | 95.9 | N | |
| D3′ | 94.5 | 94.5 | 94.5 | 97.5 | 95.7 | 71.5 | HVR | ||
| Cap | 93.1 | 91.4 | 94.6 | 96.0 | 95.6 | 85.7 | Cap | ||
| ITA/2009/PR5142/2d (JX087964) | D5′ | 93.8 | 93.3 | 92.5 | 93.3 | 92.8 | 95.4 | N | |
| D3′ | 93.5 | 93.5 | 93.5 | 93.5 | 94.0 | 70.6 | HVR | ||
| Cap | 92.0 | 90.6 | 90.1 | 90.8 | 91.3 | 84.3 | Cap | ||
| GBR/1993/Oxford-AS8811/2a (AB000289) | D5′ | 88.3 | 87.8 | 87.1 | 87.1 | 86.3 | 87.8 | ||
| D3′ | 91.0 | 91.0 | 91.0 | 88.5 | 89.5 | 88.5 | |||
| Cap | 83.5 | 82.0 | 81.9 | 81.6 | 81.9 | 81.8 | |||
The values in the bottom left portion of the table represent the nucleotide comparisons in the 449-bp region (D5′) targeted by diagnostic primers Mon269/Mon270 at the 5′ end of ORF2 (nt 4526 to 4974 of accession no. L13745), in the 239-bp region (D3′) targeted by primers prBEG/Mon2 at the 3′ end of ORF2 (nt 6477 to 6715 of accession no. L13745), and in the full-length (2.4-kb) ORF2 protein (Cap). The values in the top right portion of the table represent the amino acid comparisons among the type 2 lineages in the conserved N terminus (N) (aa 1 to 415), in the hypervariable region (HVR) (aa 416 to 650), and in the full-length capsid protein (Cap). The recombinant (r) strain 2c/2b is also included. The sequence of strain GBR/1993/Oxford-ref/2b (L06802) showed 99.9% nucleotide and amino acid similarity to that of strain GBR/1993/Oxford-H2 and was not included in the table.