부산대학교 도서관

Background: A fatal case of Japanese encephalitis (JE) occurred in a resident of the Tiwi Islands, in the Northern Territory of Australia in February 2021, preceding the large JE outbreak in south-eastern Australia in 2022. This study reports the detection, whole genome sequencing and analysis of the virus responsible (designated JEV/Australia/NT_Tiwi Islands/2021). Methods: Reverse transcription quantitative PCR (RT-qPCR) testing was performed on post-mortem brain specimens using a range of JE virus (JEV)-specific assays. Virus isolation from brain specimens was attempted by inoculation of mosquito and mammalian cells or embryonated chicken eggs. Whole genome sequencing was undertaken using a combination of Illumina next generation sequencing methodologies, including a tiling amplicon approach. Phylogenetic and selection analyses were performed using alignments of the Tiwi Islands JEV genome and envelope (E) protein gene sequences and publicly available JEV sequences. Results: Virus isolation was unsuccessful and JEV RNA was detected only by RT-qPCR assays capable of detecting all JEV genotypes. Phylogenetic analysis revealed that the Tiwi Islands strain is a divergent member of genotype IV (GIV) and is closely related to the 2022 Australian outbreak virus (99.8% nucleotide identity). The Australian strains share highest levels of nucleotide identity with Indonesian viruses from 2017 and 2019 (96.7–96.8%). The most recent common ancestor of this Australian-Indonesian clade was estimated to have emerged in 2007 (95% HPD range: 1998–2014). Positive selection was detected using two methods (MEME and FEL) at several sites in the E and non-structural protein genes, including a single site in the E protein (S194N) unique to the Australian GIV strains. Conclusion: This case represents the first detection of GIV JEV acquired in Australia, and only the second confirmed fatal human infection with a GIV JEV strain. The close phylogenetic relationship between the Tiwi Islands strain and recent Indonesian viruses is indicative of the origin of this novel GIV lineage, which we estimate has circulated in the region for several years prior to the Tiwi Islands case. Author summary: A fatal human case of Japanese encephalitis (JE) occurred in a patient from the Tiwi Islands of northern Australia in February 2021. The Tiwi Islands are 80km north of Darwin in the Timor Sea. Attempts to culture the virus from post-mortem brain tissue were unsuccessful. However, the whole genome was successfully sequenced and compared phylogenetically to other JE viruses. The Tiwi Islands strain was shown to belong to the rarely detected genotype IV (GIV) of the JE virus (JEV), together with the Australian 2022 outbreak strain, and is only the second fatal case of JE associated with a GIV virus. JEV strains isolated from Indonesia in 2017 and 2019 were shown to be the most-closely-related to the Australian GIV strain providing evidence for the geographic origins of the emergent Australian virus. From evolutionary analysis, the clade containing the Australian and recent Indonesian viruses was estimated to have emerged between 1998 and 2014, suggesting that this lineage of GIV viruses has been circulating for several years before the Tiwi Islands case. This is the third JE virus genotype to be detected in Australia and demonstrates the ease with which new genotypes can spread and unexpectedly cause disease in new areas. The possible origin and risks of further incursions into Australia are discussed. [ABSTRACT FROM AUTHOR]