Phylogenetic analysis of rabies virus isolates recovered in the Novosibirsk Oblast (the Russian Federation)

Introduction. The Novosibirsk Oblast is classified as a rabies-endemic region within the Siberian Federal District of the Russian Federation, ranking first in the number of reported cases among all constituent territories of the district. However, there is a notable lack of research on the genetic properties of the rabies virus field isolates.

Objective. This study seeks to assess how rabies outbreaks in the rabies endemic Novosibirsk Oblast are connected with those in the neighbouring regions, by analyzing genetic diversity of rabies virus variants and their spatial distribution.

Materials and methods. Two overlapping genome fragments containing full-size nucleoprotein (N) gene of rabies virus were Sanger-sequenced following purification, using a previously established procedure. Phylogenetic analysis was performed using a Bayesian approach as implemented in the Bayesian Evolutionary Analysis Sampling Trees (BEAST Х) software package.

Results. The number of registered animal rabies cases after 2012 declined markedly and has not exceeded 60 cases per year. All the studied isolates belong to genetic group C. The isolates are classified into two genetic clusters – C2c (35 isolates) and C2b (18 isolates). One of the rabies virus isolates was recovered in mouse neuroblastoma cell culture. All group C clusters found in the Novosibirsk Oblast have previously been reported in Kazakhstan as well. The most stable connections are observed within the East Kazakhstan (Сlusters C2c, C1b) and North Kazakhstan (Сlusters C2c, C2b) Oblasts. Results of the phylogenetic analysis are consistent with earlier descriptions of “fox” rabies and with the findings of epizootiological monitoring in adjacent territories of Western Siberia and Kazakhstan.

Conclusion. At present, two independently derived virus clusters – C2b and C2c – are circulating in the Novosibirsk Oblast.

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