UF Researcher Dr. Marco Salemi Utilizes UF | ICBR to Understand COVID19 Epidemiology.

Overview: As the SARS 2 virus has grown into a pandemic infection, the rise of mutated viral variants has occurred within certain geographical locations. Using genome sequencing from isolated viral RNA, it is possible to detect and quantify circulating viral lineages (including novel, potentially more transmissible and/or pathogenic) in the human population. In collaboration with virologist Dr. Marco Salemi, Professor in the UF Department of Pathology, the UF | ICBR has begun to use high throughput DNA sequencing technology to help identify COVID19 variant spread within the state of Florida. 

Gene Expression & Genotyping

NextGen DNA Sequencing

Bioinformatics

Our Role: Dr. Yanping Zhang and her team in the ICBR Gene Expression & Genotyping core developed an automated procedure using a robotic liquid handler that automates the conversion of viral RNA into DNA. In response to the very large sample volume, Dr. Zhang modified a standard protocol that uses single test tube for each sample into a 384-well format. All 384 samples were then combined into a “library” and sent to the ICBR NextGen DNA Sequencing core led by Dr. David Moraga. Using the Illumina NovaSeq6000 instrument, Dr. Moraga sequenced 768 patient samples overnight – generating millions of short DNA “reads”. Using HiPerGATOR the “raw” DNA reads were then analyzed by Dr. Alberto Riva, Scientific Director of the ICBR Bioinformatics Core. Complete viral genomes were assembled from the millions of short DNA reads using the unique molecular bar code to identify which sequences were associated with each sample.