SARS-CoV-2 Evolution and Genetics with Dr. Niema Moshiri

In this video interview, we are joined by Dr. Niema Moshiri, assistant teaching professor of computer science & engineering at the University of California, San Diego (UCSD). He discusses how scientists are using the genetic sequences of SARS-CoV-2 to study viral transmission patterns and the evolution of the SARS-CoV-2 virus. He currently holds a grant from the National Science Foundation to develop novel software and hardware systems that can quickly analyze massive amounts of genetic data from COVID-19 labs around the world. 

Key Points

• By looking at differences between SARS-CoV-2 genetic sequences obtained from different people in a given population, we can infer how SARS-CoV-2 spread within that population
  • Example: if SARS-CoV-2 is spreading via community transmission, perhaps public health policies should emphasize masking and social distancing
  • Example: if SARS-CoV-2 is spread via “seeding” from an outsider to the community, perhaps public health policies should emphasize travel restrictions and quarantine for travelers
• The mutation rate in the region of the spike protein is generally slower than the rest of the viral genome because the spike protein is integral to the viral lifecycle
• Sharing of data with preprint servers and public databases has been critical to scientific research during the COVID-19 pandemic

Time Stamps

• 0:00 Introduction
• 0:40 Viral transmission patterns of SARS-CoV-2 and its “evolutionary tree” (AKA phylogeny)
• 1:30 Studying viral transmission patterns with databases of SARS-CoV-2 genetic sequences
• 2:24 GISAID, a database of SARS-CoV-2 genetic sequences
• 4:40 The reference genome for SARS-CoV-2
• 7:45 SARS-CoV-2 consumer testing vs. SARS-CoV-2 genetic sequencing for scientific research
• 10:09 How can we use SARS-CoV-2 phylogenetics to answer questions that are relevant & actionable for public health policies?
• 11:17 NextStrain and the global evolutionary tree for SARS-CoV-21
• 3:33 Viral transmission dynamics in Europe
• 15:34 Calculating the mutation rate of SARS-CoV-2
• 19:57 Conserved regions of the SARS-CoV-2 genome
• 21:34 The value of data sharing and international collaboration in SARS-CoV-2 research