Exploration of viral diversity in Aedes mosquitoes employing different shotgun metagenomic data analysis pipeline.

In this study, shotgun metagenomic methodology using ION Torrent platform was optimized for exploration of viral diversity. A total of 1913 Aedes larvae were collected from Central India during post monsoon season in 2024. Aedes larvae reared to adult and processed through ION Torrent sequencing. Computational analysis was performed using three different pipelines: CHAN ZUCKERBERG ID (czid.org), Genome Detective Platform and Galaxy tool. A mock database of 11 known viruses was created to validate all three pipelines. In terms of accuracy, genome detective and CZID performed exceptionally well in detection and hence can be used in future studies. We found presence of viruses viz Alphamesonivirus cavallynese and Phasivirus phasinese dominating in all samples. Dengue virus detected in one sample by CZID, where as Wenhzou sobemo-like virus, Hubei mosquito virus 2, Cell fusing agent virus, found most commonly among samples. Other viruses found like Gylbovirus aagae (Aedes anphevirus), Aedes totivirus, Verdadero virus, Chaq-like virus etc. The variation in the result in different pipeline is due incorporation of different databases, algorithms, metrics and parameters.