A new subtype of eastern tick-borne encephalitis virus discovered in Qinghai-Tibet Plateau, China

Abstract

Tick-borne encephalitis virus (TBEV) has been classified into three subtypes, namely the European (Eu-TBEV), Far Eastern (FE-TBEV), and Siberian (Sib-TBEV). In this study, we discovered a new subtype of TBEV in wild rodent Marmota himalayana in Qinghai-Tibet Plateau in China, proposed as subtype Himalayan (Him-TBEV). Two complete genomes of TBEV were obtained from respiratory samples of 200 marmots. The phylogenetic analysis using the E protein and polyprotein demonstrated that the two strains of Him-TBEV formed an independent branch, separated from Eu-TBEV, Sib-TBEV, and FE-TBEV. The nomenclature of Him-TBEV as a new subtype was also supported by comparative analysis using nucleotide and amino acid sequences of E protein and polyprotein. For E protein, The Him-TBEV showed 82.6-84.6% nucleotide identities and 92.7-95.0% amino acid identities with other three subtypes. For polyprotein, the Him-TBEV showed 83.5-85.2% nucleotide identities and 92.6-94.2% amino acids identities with other three subtypes. Furthermore, of 69 amino acid substitutions profiles detected in complete polyprotein of 112 strains of TBEV, Him-TBEV subtype displayed unique amino acids in the 36 positions. Notably, for the subtype-specific amino acid position 206 of E protein, Him-TBEV shared the Val with Eu-TBEV, but differed from FE-TBEV and Sib-TBEV. The evolutionary analysis with BEAST suggested that Him-TBEV diverged from other subtypes of eastern TBEV group about 2469 years ago. It should be mentioned that Qinghai-Tibet Plateau in China is the plague endemic region where Marmota himalayana is the primary host. The public health significance of discovery of Him-TBEV in Marmota himalayana must be carefully evaluated.

Fig. 1. Phylogenetic relationship of Himalayan subtype with other subtypes of TBEV.

a The phylogenetic tree of E protein. b The phylogenetic tree of polyprotein. Strains of Him-TBEV were indicated in boldface. Phylogenetic trees were constructed using MEGA 6.0 with neighbor-joining method (1000 bootstrap replications). Bootstrap values (>70%) are shown at the branches. Scale bar below indicates the nucleotide substitutions per site

Fig. 2. The Bayesian maximum clade credibility tree based on nucleotide sequences of E protein.

The year of sampling, strain name and accession number are on the tip labels. Node labels indicate the most recent common ancestor (tMRCA) and the posterior probabilities. Strains of Him-TBEV were indicated in boldface. The TBEV strains detected in China were marked with black triangle

Fig. 3. A possible model of TBEV dispersal.

The maximum clade credibility tree is plotted onto geographic location. The time of estimated tMRCA of each phylogenetic linage are indicated at the major nodes in the tree