Table 3.
| A. Sub-genotypes within genotype 1 of class I | B. Sub-genotypes within genotype I of class II | C. Sub-genotypes within genotype V of class II | D. Sub-genotypes within genotype VII of class II | ||||
|---|---|---|---|---|---|---|---|
| 1.1 (1a + 1b) | I.1 (a + c + d) | V.1 (b) | VII.1 (b + d + e + j + f + l) | ||||
| 1.2 (1c + 1d)d | 7.27 | I.2 (b) | 8.58 | V.2 (c) | 5.86 | VII.2 (h + i + k) | 9.91 |
| 1.1.1 (1a) | I.1.1 (a) | VII.1.1 (b + d + e + j + l) | |||||
| 1.1.2 (1b) | 7.99 | I.1.2 (c + d) | 8.52 | VII.1.2 (VIIf) | 5.58 | ||
| I.1.2.1 (c) | |||||||
| I.1.2.2 (d) | 10.96 | ||||||
| E. Sub-genotypes within genotype VI of class II | |||||||
| VI.1 (b) | VI.2.1 (a + h + j + k + n) | VI.2.2.1 (e) | VI.2.1.1 (a + j + k + n) | ||||
| VI.2 (a + e + f + h + j + k + n) | 8.05 | VI.2.2 (f + e) | 8.55 | VI.2.2.2 (f) | 6.14 | VI.2.1.2 (h) | 8.12 |
| VI.2.1.1.1 (a + n) | VI.2.1.1.2.1 (j) | ||||||
| VI.2.1.1.2 (j + k) | 6.59 | VI.2.1.1.2.2 (k) | 5.15 | ||||
| F. Sub-genotypes within genotype XII of class II | G. Sub-genotypes within genotype XIII of class II | H. Sub-genotypes within genotype XIV of class II | I. Sub-genotypes within genotype XVIII of class II | ||||
|---|---|---|---|---|---|---|---|
| XII.1 (a) | XIII.1 (a) | XIV.1 (a) | XVIII.1 (a) | ||||
| XII.2 (b) | 8.86 | XIII.2 (b) | 9.32 | XIV.2 (b) | 7.55 | XVIII.2 (b) | 6.46 |
| XIII.1.1 (a) | |||||||
| XIII.1.2 (a) | 5.41 | ||||||
| XIII.2.1 (b) | |||||||
| XIII.2.2 (b) | 6.64 | ||||||
| J. Sub-genotypes within genotype XXI of class II | |||||||
| XXI.2.1 (VIg + VIm) | XXI.2.1.1 (VIg) | ||||||
| XXI.2.2 (VIi) | 11.03 | XXI.2.1.2 (VIm) | 9.19 | ||||
Inferred from the complete nucleotide F gene sequences.
The nucleotide distances were calculated at every defining node.
The number of base substitutions per site from averaging all sequence pairs between class I and class II sub-genotypes is shown. Analysis was conducted using the Maximum Composite Likelihood model (Tamura et al., 2004). The rate variation among sites was modeled with a gamma distribution (shape parameter = 1). The number of nucleotide sequences in each sub-genotypes is shown in parenthesis. Codon positions included were 1st, 2nd, 3rd and noncoding. All positions containing gaps and missing data were eliminated. Evolutionary analyses were conducted in MEGA6 (Tamura et al., 2013).
For easier comparison, the former sub-genotype names are provided in parentheses.