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