An outbreak of viral encephalitis caused by a Japanese encephalitis virus (JEV) genotype IV infection occurred in Australia between 2021 and 2022. A total of 47 cases and seven deaths were reported as of November 2022. This is the first outbreak of human viral encephalitis caused by JEV GIV since it was first isolated in Indonesia in the late 1970s. Here, a comprehensive phylogenetic analysis based on the whole genome sequences of JEVs revealed it emerged 1037 years ago (95% HPD: 463 to 2100 years). The evolutionary order of JEV genotypes is as follows: GV, GIII, GII, GI, and GIV. The JEV GIV emerged 122 years ago (95% HPD: 57–233) and is the youngest viral lineage. The mean substitution rate of the JEV GIV lineage was 1.145 × 10⁻³ (95% HPD values, 9.55 × 10⁻⁴, 1.35 × 10⁻³), belonging to rapidly evolving viruses. A series of amino acid mutations with the changes of physico-chemical properties located in the functional important domains within the core and E proteins distinguished emerging GIV isolates from old ones. These results demonstrate the JEV GIV is the youngest JEV genotype at a rapid evolution stage and has good host/vector adaptability for introduction to non-endemic areas. Thus, surveillance of JEVs is highly recommended.

Arboviruses, transmitted by blood-sucking arthropods, are responsible for significant human and animal diseases, including fever, hemorrhagic fever, and encephalitis, posing a serious threat to global public health. Nevertheless, research on the mechanisms of arbovirus infection and the development of therapeutic interventions has been impeded. This delay is primarily due to the limitations inherent in current in vitro research models, including cell cultures and animal models. The simplicity of cell types and interspecies differences present significant obstacles to advancing our understanding of arbovirus infection mechanisms and the development of effective drugs. Human brain organoids, derived from human pluripotent stem cells or human embryonic stem cells and cultured in three-dimensional systems, more accurately replicate the extensive neuronal cellular diversity and key characteristics of human neurodevelopment. These organoids serve as an ideal model for investigating the intricate interactions between viruses and human hosts, and providing a novel platform for the development of antiviral drugs. In this review, we summarize how brain organoid models complement classical approaches to accelerate research into the infection mechanisms of arboviruses, with a particular focus on the types of neural cells, key factors, and cellular signaling pathways involved in the arbovirus infection of brain organoids that have been reported. Furthermore, we examine the development of brain organoids, address their current limitations, and propose future directions to enhance the application of brain organoids in the study of arboviral infectious diseases.

Numerous studies have demonstrated that the Japanese encephalitis virus (JEV) is classified into five genotypes. Historically, JEV GIII and GI were the dominant strains before and after the 1990s, respectively. Recently, the non-dominant genotypes have been implicated in numerous JE outbreaks, posing significant public health challenges. This study conducted a comprehensive phylogenetic analysis of 126 JEVs covering five genotypes from 1938 to 2025 globally. Notably, it is the first study to conduct a time to most recent common ancestor (tMRCA) analysis of JEV GII. The findings indicate the common ancestor of JEV emerged approximately 1081 years ago, followed by the sequential evolution of GV, GIII, GI, GII, and GIV, which are estimated to have originated approximately 237, 184, 138, 130, and 113 years ago, respectively. The overall evolutionary rate of JEV was 3.3 × 10⁻⁴ substitutions/site/year, with genotype specific rates as follows: GI at 7.3 × 10⁻⁴, GII at 8.2 × 10⁻⁴, GIII at 4.4 × 10⁻⁵, GIV at 1.7 × 10⁻³, and GV at 2.2 × 10⁻³. Significant differences were found between the E protein of recent human-derived JEV strains across five genotypes and the vaccine strain. This aligns with evidence of the current JE vaccine’s reduced efficacy against new strains, underscoring the urgent need for broadly protective JE vaccines.