The comparative genomic analysis provides insights into the phylogeny and virulence of tick-borne encephalitis virus vaccine strain Senzhang

Abstract

Tick-borne encephalitis virus (TBEV) is one of the most dangerous tick-borne viral pathogens for humans. It can cause severe tick-borne encephalitis (TBE), multiple neurological complications, and death. The European subtype (TBEV-Eu), Siberian subtype (TBEV-Sib), and Far-Eastern subtype (TBEV-FE) are three main TBEV subtypes, causing varying clinical manifestations. Though TBEV-FE is the most virulent TBEV subtype, the degree of variation in the amino acid sequence of TBEV polyprotein is not high, leaving an issue without proper explanation. We performed phylogenic analysis on 243 TBEV strains and then took Senzhang strain as a query strain and representative strains of three major TBEV subtypes as reference strains to perform the comparative genomic analysis, including synteny analysis, SNP analysis, InDel analysis, and multiple sequence alignment of their envelope (E) proteins. The results demonstrated that insertions or deletions of large fragments occurred at the 3' end but not at the 5' end or in the CDS region of TBEV Senzhang strain. In addition, SNP sites are mainly located in the CDS region, with few SNP sites in the non-coding region. Our data highlighted the insertions or deletions of large fragments at the 3' end and SNP sites in the CDS region as genomic properties of the TBEV Senzhang strain compared to representative strains with the main subtypes. These features are probably related to the virulence of the TBEV Senzhang strain and could be considered in future vaccine development and drug target screening for TBEV.

Fig 1. The phylogenic tree of 243 TBEV strains.

The red triangle indicates the Senzhang strain; the orange triangles indicate three strains with subtypes inconsistent with the retrieved information, and the blue triangles indicate 17 strains without recorded subtypes but subtyped by the phylogenic analysis.

Fig 2. TBEV genome-wide synteny analysis.

A: Comparison of Senzhang strain and Neudoerfl strain; B: Comparison of Senzhang strain and 205 strain; C: Comparison of Senzhang and Vasilchenko strain. Query sequence: Senzhang strain, JQ650523; reference sequences: Neudoerfl strain, U27495; 205 strain, JX498939; Vasilchenko strain, L40361.

Fig 3. SNPs of Senzhang strain compared to reference strains.

A: Distribution of SNP types of Senzhang strain compared to Neudoerfl strain. B: Distribution of SNP types of Senzhang strain compared to Vasilchenko strain. C: Distribution of SNP types of Senzhang strain compared to 205 strain. For A to C graph, the amount of SNPs was marked in the corresponding part of the pie diagram. D: Relative percentage of specific base substitution for SNPs of Senzhang strain compared to reference strains. Syn: Synonymous; Nonsyn: Nonsynonymous.

Fig 4. Physicochemical properties and structural features of E protein of Senzhang strain.

A: Schematic diagram of E protein structural domains. B: Hydrophobicity evaluation of E protein. C: Predicted transmembrane region of E protein. D: Predicted secondary structure of E protein. E: A tertiary structural model of E protein.

Fig 5. Multiple AA sequence alignment of TBEV E proteins.