Figure 1

A schematic diagram illustrating the concept of classification of a viral sequence. The filled spheres represent known sequences that have been clustered into four groups, a through d, the boundaries of which are depicted by black circles. Suppose the dark spheres in each cluster represent the respective reference sequences and the red asterisk denotes a query sequence. Since the query is located at the interface of b and d clusters, its genotype (or subtype) is elusive. On the other hand, a nearest neighbour method may assign it to the nearest reference sequence, which happens to be d in this example. If the classification method does not take into account the clustering patterns of the known sequences and relies on the distances to the nearest reference sequences, its result may not be robust to the choice of references.