The Lim lab studies interactions and evolution
of the human virome in development and immunity.
This research is being used in precision medicine that personalizes the prevention and treatment of diseases to individuals.
We are particularly interested in understanding
How the virome shapes the trajectory of infant development
SARS-CoV-2 mutations and their functional consequences
Genomic epidemiology and public health surveillance
Mother-Infant
We study the role of the virome and microbiome on mother-infant health. While most microbiome studies focus on bacteria, we shed light on how viruses shape host-microbiome interactions.
Our focus is on early life events that shape healthy infant development, transmission of the virome and bacterial microbiome from mother to infant, and the impact of HIV disease.
Microbiome interactions in Disease
Given the fundamental role of the microbiome in our health, we reason that the microbiome may be involved in other human diseases. This includes virome modulation in Gulf War Illness -
a chronic disorder that affects many Gulf War veterans, and immune mechanisms mediated by the microbiome in viral disease.
This research will be used to develop new microbiome modalities to treat patients.
In response to the COVID-19 pandemic, we have initiated research efforts to understand and prevent COVID-19 transmission. This includes:
SARS-CoV-2 sequencing surveillance in real-time for the state of Arizona. We have sequenced more than 100,000 COVID-19 cases to date, and are among the fastest sequencing labs in the world in turnaround time – from sample collection to genome sequenced. This information is used to inform public health responses and policies.
Comprehensive state-wide surveillance framework through clinical, community and wastewater sequencing.
Mutations that affect clinical diagnostic assays, so that we can ensure that all positive case are being detected.
Genomic sequencing surveillance led to the identification of a new E484K variant of interest in Arizona called B.1.243.1.
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.
Next-generation sequencing characterization of SARS-CoV-2 genomes from sentinel surveillance in Tempe, Arizona early in the pandemic (Jan-Mar 2020).
Efrem Lim, PhD
Associate Professor
Arizona State University
School of Life Sciences
Biodesign Institute
Center for Fundamental and Applied Microbiomics
Email: Efrem.Lim[at]asu.edu