UC Santa Barbara

In virology, the emergence of sequencing technologies has revolutionized our understanding of viral genetics and epidemiology, marking a significant advancement over traditional methods. These techniques provide deep insights into virus genetics, crucial in addressing the challenges of pathogen detection in public health, such as identifying novel pathogens and monitoring rapid viral mutations that can evade current treatments.This work highlights the crucial role of sequencing as a tool for studying virology, demonstrated through two distinct research approaches. Firstly, we address the challenge posed by the emergence of the SARS-CoV-2 Omicron variant in 2021, which led to a global surge of cases. To identify the introduction of novel SARS-CoV-2 variants in Santa Barbara County, sequencing data was utilized to develop a quantitative reverse transcription PCR-based assay (RT-qPCR), targeting unique mutations in the Omicron BA.1/BA1.1 and BA.2 genomes. This assay, tested on 270 clinical samples from Santa Barbara County, accurately and quickly detected the presence of Omicron variants, showing complete concordance with whole viral genome sequencing. The study demonstrates that by utilizing sequencing data to develop RT-qPCR assays offer a rapid and cost-effective solution for virus variant-specific detection, streamlining the identification of Omicron variants in clinical samples. Secondly, the thesis explores the retinal impact of viral infections, focusing on Zika Virus (ZIKV) and Herpes Simplex Virus 1 (HSV1) interactions with human retinal organoids (ROs) using single-cell RNA sequencing (scRNA-seq). The research reveals that early-stage ROs are broadly susceptible to ZIKV, with a robust upregulation of interferon-stimulated genes and the unfolded protein response, suggesting a dynamic cellular defense. In contrast, HSV1 infection in mature ROs suppresses innate immune responses and reduces transcriptomic diversity, indicating distinct viral pathogenesis mechanisms. These findings, unveiled through scRNA-seq, provide crucial insights into the unique mechanisms of ZIKV and HSV1 in the retina, highlighting the value of retinal organoids in ocular virology research and advancing our understanding of viral pathogenesis in sensory organs. Together, these studies underscore the versatility and efficacy of sequencing technologies in virological research, from rapid pathogen detection and variant identification to understanding complex interactions in viral pathogenesis, thereby informing public health strategies and potential therapeutic interventions.