Table 1.
Criteria for classification of NDV isolates.
| Criterion | Description |
|---|---|
| 1 | Assignment of viruses into new genotypes and sub-genotypes is done based on complete fusion gene phylogenetic analysis (sequences of at least 1645 nucleotides or longer). |
| 2 | Assignment of viruses into new genotypes and sub-genotypes is done only utilizing a complete dataset of sequences from all existing genotypes. All classification criteria listed below need to be fulfilled for naming new genotypes and sub-genotypes. |
| 3 | Sub-trees and pilot tree can be used for assigning new isolates to existing sub/genotypes. |
| 4a | New genotypes or sub-genotypes are created only when four or more independent isolates, without a direct epidemiologic link (i.e. distinct outbreaks), are available. |
| 5 | New genotypes and sub-genotypes are created based on the phylogenetic tree topology (need to cluster into monophyletic branches) using the Maximum Likelihood method and the general time-reversible (GTR) model with gamma distribution (Γ) utilizing RaxML or a comparable tool. |
| 6a | The mean nucleotide distance (evolutionary distances) between groups is inferred as the number of base substitutions per site from averaging over all sequence pairs between groups using MEGA v. 5/6/7 software (or a comparable tool) and utilizing the Maximum Composite Likelihood model with rate variation among sites that was modeled with a gamma distribution (shape parameter = 1). |
| 7a | Different genotypes have an average distance per site above 10% (0.1). |
| 8 | Different sub-genotypes have an average distance per site above 5% (0.05). |
| 9 | The bootstrap value at the genotype and sub-genotype defining node is 70% or above (≥70%). |
| 10 | Viruses that do not fulfill all classification criteria are assigned to the lower order (closer to the root) sub/genotype (see Table 2 for nomenclature criteria). |
a
Criteria that were adopted from the Diel et al. (2012a) classification system.