Interactions between tick-borne encephalitis virus non-structural protein 1 and blood-brain barrier tight junction proteins: potential clues to strain-specific neuropathogenicity

Tick-borne encephalitis virus (TBEV) invades the central nervous system (CNS) through strain-specific mechanisms that remain poorly understood. In mosquito-borne orthoflaviviruses such as dengue and yellow fever viruses, the non-structural protein 1 (NS1) has been shown to disrupt endothelial barrier integrity by targeting tight junction proteins (TJPs), thereby facilitating viral neuroinvasion. However, comparable mechanisms in TBEV remain largely unexplored.

Here, we investigate the potential interaction of NS1 from high (Hypr)- and low (Vs)-pathogenicity TBEV strains to different blood-brain barrier (BBB) TJPs, using AlphaFold3 (AF3) multimer modelling and in vitro binding assays. We find that NS1 from the highly pathogenic strain exhibits higher predicted interactions with multiple TJPs, including two junctional adhesion molecules (JAM-A, JAM-B) and Claudin-10, which are critical component of the paracellular barrier. In contrast, low pathogenic strain Vs interaction was limited to JAM-A and Claudin-5.

Experimental validation using recombinant NS1 proteins revealed strain-specific binding profiles: Hypr NS1 displayed high-affinity, saturable direct binding to immobilized JAM-A (KD = 0.271 µg/mL), whereas Vs NS1 showed negligible interaction (KD = 0.000023 µg/mL). No binding to ZO-1, a barrier scaffold lacking an extracellular domain, was observed for either strain. This differential interaction may be modulated by 22 specific amino acid substitutions localized to the Wing and β-ladder domains, which distinguish the highly neurovirulent Hypr strain from the avirulent Vs strain. Notably, despite its weak JAM-A interaction, the Vs strain is associated with slow-progressing infections that can culminate in chronic neurological disease, highlighting the need for further investigation into noncanonical pathways of neuroinvasion.