Development of an algorithm for intraspecific typing of lyssavirus rabies strains based on N gene polymorphism

Gerasimenko A.A., Gorokh A.M., Pisanov R.V., Vodopyanov A.S.

Rostov-on-Don Antiplague Scientific Research Institute of Rospotrebnadzor, Rostov-on-Don, Russia

Several rabies virus classifications are known, but all of them imply phylogenetic trees construction. This makes it difficult for other authors to study newly isolated viruses, since it requires repeated construction of dendrograms. The aim of the study was to develop an algorithm for typing and dividing rabies virus strains based on N gene structure, finding marker mutations for clustered strains and automatically determining the group affiliation of the analyzed sample using computer software.
For these purposes the genomes were downloaded from the NCBI database. N genes were isolated using the author's program written in Java. Next, sequence alignment and phylogenetic analysis were performed with visualization of the resulting tree. Clusters of strains have been identified by geographical reference and mutation threshold. Marker mutations in the discovered clusters were also found using Python and tabular editors. Then, a Pythong script was developed to automatically analyze the resulting virus genomes.
In conclusion, the algorithm for intraspecific typing of rabies virus strains based on the polymorphism of N gene has been developed; marker mutations for typed groups of strains have been found; a program for identification a group of studied strains has been created.