Targeted Metagenomics Reveals Hidden Chickenpox Epidemic Amid Mpox Surveillance in Uganda
In this study, we investigated clinically suspected Mpox cases that tested negative for MPXV by PCR. Using metagenomic sequencing, we identified VZV as the predominant pathogen among these cases. To facilitate detailed genomic characterization of VZV, we developed a custom analysis pipeline, VaricellaGen (https://github.com/MicroBioGenoHub/VaricellaGen), an automated pipeline that integrates multiple bioinformatics tools for quality control, variant calling, consensus genome generation, clade typing, and phylogenetic analysis.