PurposeSeasonal Hyperacute Panuveitis (SHAPU) is an ocular emergency where the genesis between infective and immunological is under investigation. This is the first report in the literature that attempts to explore the unidentified cause using next-generation metagenomic sequencing and immunomarker analysis. DesignCross-sectional quantitative study. MethodsIn this study, vitreous samples were collected from the SHAPU cases during the outbreak of 2019/2020. The vitreous samples of 10 random cases got selected for metagenomic next-generation sequencing. And 5 vitreous samples ran for immune analysis of levels of interleukin (IL) 6 and 10 using the ELISA technique. The ocular samples were extracted and sequenced on Illumina iSeq100 and analyzed through CZ ID platform. The true hits, for the suspected causative organisms were confirmed using qPCR through designed primers specific for that particular organism. ResultsA total of 30 eyes of 30 patients were included. Upon sequencing the DNA libraries, hits were observed for Streptococcus pneumoniae in 2/10 cases, confirmed by qPCR. IL-6 level was increased in 5/5 cases with IL-6/IL-10 greater than 1. ConclusionWe report the presence of S. pneumoniae for the first time using a metagenomics analysis and increased IL-6 to IL-10 ratio via immune-analysis, indicating that SHAPU could have both infective and immunological facets on its causation.