David Bacsik, MD, PhD
Nominated From: University of Washington
Research Site: Universidad Peruana Cayetano Heredia
Research Area: Genomic epidemiology, respiratory viruses, influenza, RSV, sequencing, phylogenetics
Primary Mentor: Dr. Alex Greninger
Research Project
Genomic surveillance of respiratory viruses in the Andes Region
In response to the COVID-19 pandemic, experts around the world rapidly developed genomic surveillance programs to track the spread of the SARS-CoV-2 virus. Viral samples were sequenced in nearly every country, including low and middle-income countries. The data generated by this global community of scientists have enabled continuous monitoring of SARS-CoV-2’s transmission and evolution over the last four years.
However, in many places, this successful model has not yet been applied to other pathogens and regular sequencing remains limited to SARS-CoV-2. To develop genomic surveillance capacity in the Andes Region further, we will sequence the diverse viral pathogens causing severe respiratory illness–including influenza virus, respiratory syncytial virus, and human metapneumovirus.
Our team includes Dr. Pablo Tsukayama at la Universidad Peruana Cayetano Heredia and Dr. Alex Greninger at the University of Washington. Building upon the region’s established surveillance capacity, we will collaborate with the Project of Febrile Illness Surveillance in the Andean and Amazon Countries (PISAAC).
We will test respiratory swab specimens using a high-throughput molecular panel. We will quantify the causes of respiratory illness in the PISAAC cohort and generate whole-genome viral sequences. We will then perform phylogenetic analysis to understand patterns of transmission in Peru and neighboring countries. Using this data, we will identify viral introductions, monitor local evolution, and assess persistence between respiratory virus seasons.
Research Significance
The COVID-19 pandemic has proven the value and feasibility of conducting genomic surveillance in middle-income countries. Now, there is an unprecedented opportunity to expand genomic surveillance to other important respiratory pathogens. In this project, we will develop long-term infrastructure needed for genomic surveillance in Peru and across the Andes Region. Our work will complement classical epidemiology to bolster local public health interventions within Peru and its neighbors. Furthermore, our results will be shared publicly, providing high-quality viral genomes from this undersampled region of the world.
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