The relationship between the structure of the tick-borne encephalitis virus strains and their pathogenic properties

Abstract

Tick-borne encephalitis virus (TBEV) is transmitted to vertebrates by taiga or forest ticks through bites, inducing disease of variable severity. The reasons underlying these differences in the severity of the disease are unknown. In order to identify genetic factors affecting the pathogenicity of virus strains, we have sequenced and compared the complete genomes of 34 Far-Eastern subtype (FE) TBEV strains isolated from patients with different disease severity (Primorye, the Russian Far East). We analyzed the complete genomes of 11 human pathogenic strains isolated from the brains of dead patients with the encephalitic form of the disease (Efd), 4 strains from the blood of patients with the febrile form of TBE (Ffd), and 19 strains from patients with the subclinical form of TBE (Sfd). On the phylogenetic tree, pathogenic Efd strains formed two clusters containing the prototype strains, Senzhang and Sofjin, respectively. Sfd strains formed a third separate cluster, including the Oshima strain. The strains that caused the febrile form of the disease did not form a separate cluster. In the viral proteins, we found 198 positions with at least one amino acid residue substitution, of which only 17 amino acid residue substitutions were correlated with the variable pathogenicity of these strains in humans and they authentically differed between the groups. We considered the role of each amino acid substitution and assumed that the deletion of 111 amino acids in the capsid protein in combination with the amino acid substitutions R16K and S45F in the NS3 protease may affect the budding process of viral particles. These changes may be the major reason for the diminished pathogenicity of TBEV strains. We recommend Sfd strains for testing as attenuation vaccine candidates.

Figure 1. ML phylogenetic tree of TBEV strains.

The tree was based on the complete genomes of strains inducing diseases of different severity. Pathogenic strains Efd are shown in black, Sfd strains in green and strains with the febrile form of TBEV are shown in red. Prototype strains are shown in blue. Numbers above or below branches indicate posterior node probabilities and bootstrap values from NJ analysis.

Figure 2. Aligned nucleotide sequences of the 5′ UTR.

Pathogenic strains Efd are shown in black, Sfd strains in green and strains with the febrile form of TBEV are shown in red. Prototype strains are shown in blue. The nucleotides identical to the sequence of strain Sofjin are indicated by dots of the corresponding color.

Figure 3. Tertiary structure of NS3 protease.

The crystal structure of the West Nile protease (PDB code 3e90) was taken as a template for homology modeling. (A) The tertiary structure of NS3/NS2B for the pathogenic strain Dalnegorsk. (B) The tertiary structure of NS3/NS2B for the Sfd strain Primorye-270. The arrows indicate the replacement of key amino acids. The active center is indicated by the rectangle and its amino acid residues are shown as red atoms.

Figure 4. Tertiary structures of RNA-dependent RNA polymerase (RdRp).

(A) The tertiary structure of RdRp for the pathogenic strain Dalnegorsk. (B) The tertiary structure of RdRp for the Sfd strain Primorye-270. In both models, the various subdomains are colored as follows: blue – fingers, green – palm, and pink – thumb. The amino acid residue substitutions in both models are indicated by red atoms.

Figure 5. The scheme of the polyprotein and the position of key amino acid substitutions.