PhD, University of Washington
Virome, Microbiome, SARS-CoV-2
Efrem Lim is a virologist who studies the human virome in health and disease. The virome is the diverse community of viruses harbored in and on humans, some of which cause disease while others are commensal. The Lim lab is particularly interested in understanding the interactions of the human virome in development and immunity. While most microbiome studies focus on bacteria, his interdisciplinary group sheds light on how viruses shape host-microbiome interactions.
The Lim lab integrates molecular virology and bioinformatics approaches in clinical cohorts to understand:
- how the virome impacts the trajectory of infant development
- the role of microbiome interactions in disease
Their research is being used in precision medicine that personalizes the prevention and treatment of diseases to individuals.
In response to the COVID-19 pandemic, the Lim lab has led research efforts to understand and prevent SARS-CoV-2 transmission. This includes next-generation sequencing studies of SARS-CoV-2 to identify transmission patterns and functional studies to characterize virus mutations in clinical isolates.
- Next-generation sequencing characterization of SARS-CoV-2 genomes from sentinel surveillance in Tempe, Arizona early in the pandemic (Jan-Mar 2020).
- Phylodynamic tracing to provide unique epidemiological insights into the origins and transmission of SARS-CoV-2 in Arizona, in a joint state-wide effort called the Arizona COVID-19 Genomics Union (ACGU).
- Confirmation of the first B.1.1.7/UK variant cases in Arizona. The 3 genome sequences clade within 20I/501Y.V1, also known as B.1.1.7 lineage or the UK variant. Samples were sequenced twice, independently.
- Genomic sequencing surveillance identification of a new E484K variant of interest in Arizona called B.1.243.1. This variant is being established in Arizona, but there is now evidence of transmission to other states in the US. 21 out of 24 cases of B.1.243.1 are from Arizona beginning in early February. The other 3 cases have been reported in Texas and New Mexico.
- Establishment of the ASU COVID-19 Sequencing Center. We continue to track variants of concern in real-time using next-generation sequencing. This information is used to inform public health responses and policies. We have sequenced more than 4,000 COVID-19 cases.