Delving into Viruses and Immune System Dynamics with Shiraz Shah

Returning guest Shiraz Shah specializes in bioinformatics. He uses microbial data analysis to uncover the complex and fascinating relationships between viruses, bacteria, and chronic conditions like childhood asthma. This conversation serves as part of a series in preparation for Richard's upcoming book on viruses, and Shiraz Shah shares his unique and valuable perspective on viral structure and functions gleaned from years of cutting-edge analysis. Topics include

• How CRISPR research and techniques are derived from bacteria snipping and retaining parts of viruses that infected the bacteria,
• How human DNA is part of the evolution arms race between bacteria and viruses, and
• How the presence of a type of prophage in a person's gut can make the difference in immune therapy cancer treatment and what this implies about the complex influence of viruses.

Shiraz Shah is a senior researcher at the Copenhagen Prospective Studies on Asthma in Childhood (COPSAC). Much of his graduate work focused on CRISPR-Cas9 bioinformatics. His current work involves analysis of data regarding bacteria hosts and viruses in the gut microbiome in particular. He explains how this analysis works at the level of genomics; for example, a virome sequencing might be compared to numerous other protein sequences in a search for significant patterns. COPSAC plans to take this collection of virus and bacteria data and follow the cohort of children for any corresponding organisms that might indicate causes or preventions of childhood asthma.

This opens up into an enlightening conversation about the complex role of phages, which are viruses that use bacteria as their host cell. Viruses are everywhere, Dr. Shah asserts, and he believes our old view that viruses are predominantly dangerous, mostly causing sickness, is outdated. Most of us and the kids COPSAC studies are full of viruses without any sickness. So, what are those viruses up to? Replicating. And that effort makes for a sometimes commensal or mutualistic host relationship. Dr. Shah explains that scientists see a lot of prophages that are maintained over several generations and kept by bacteria because they help the host bacteria. He and Richard bring up examples involving cancer and cholera, where a phage's presence changes the bacterial response in a human body in numerous ways, sometimes beneficial or commensal, and sometimes towards more virulent behaviors. Dr. Shah and Richard also debate the level of intent, signaling, and quorum-sensing abilities of viruses. Near the end of their conversation, Dr. Shah explains that his present work, called viromics, may have as a significant impact as metagenomics. In a few years, scientists may therefore have a completely different and exciting view of viruses. Listen in for an expert's view of this new type of foundational research.

For more about Shiraz Shah, see his page at COPSAC: copsac.com/home/about/staff/shiraz-shah/. Available on Apple Podcasts: apple.co/2Os0myK