Recent Research Themes, 2019–2026

​

• Dynamic risk at wildlife–livestock–human interfaces: Recent publications reinforce a sustained focus on how ecological context structures pathogen emergence, including avian influenza circulation in wild reservoirs, domestic ducks, agricultural landscapes, and North American wild bird systems.

• Respiratory-virus interaction and co-circulation: Recent work on RSV and seasonal influenza suggests a growing theme around multi-pathogen respiratory ecology, including how co-circulating viruses may interact across regions, seasons, and epidemic cycles.

• Antigenic novelty, vaccine relevance, and immune escape: Publications on antigenically novel influenza A viruses, repeated influenza vaccination, heterologous antibody responses, and RSV T-cell epitope evolution highlight an emerging emphasis on linking sequence evolution to immune recognition and vaccine preparedness.

• Multilayer epidemic modeling: Recent COVID-19 and HIV-related publications demonstrate a developing program around multilayer networks, molecular clusters, local social structure, and socioecological drivers of transmission.

• Surveillance system design and diagnostic genomics: Work on respiratory viral sequencing panels and genomic surveillance emphasizes practical translation of pathogen genomics into public health systems capable of detecting variants and co-circulating pathogens.

• Cross-pathogen comparative phylodynamics: Our research spans across influenza, RSV, SARS-CoV-2, EV-D68, rabies, HIV, and negative-sense RNA virus taxonomy, reflecting a cross-pathogen framework for studying emergence, persistence, spread, and public health relevance.

• Pandemic control, preparedness, and collateral effects: Recent Science commentary and pandemic-related publications show a broader systems perspective on pandemic control, surveillance, population response, and the unintended consequences of intervention strategies. Most recent work takes a computational approach to link sequence-structure-functional phenotype predictions to population processes, including fundamental biological, demographic, and environmental mechanisms that determine pathogen diversity the pandemic potential of circulating viruses

 

Active Research Areas

​

Genomic Epidemiology and Phylodynamics
The Bahl Lab has advanced the use of pathogen genome sequencing and evolutionary analysis to reconstruct transmission dynamics, characterize epidemic spread, and identify mechanisms of viral emergence and adaptation. His work applies phylogenetic, phylodynamic, and molecular epidemiological methods across influenza, SARS-CoV-2, RSV, rabies, enterovirus D68, HIV, and other RNA viruses.

​

Influenza Ecology, Evolution, and One Health Emergence
A central contribution of Dr. Bahl’s research is the integration of viral genomics with host ecology, geography, agriculture, and wildlife movement to explain influenza emergence and persistence. His studies of avian influenza have shown how host diversity, animal behavior, geographic structure, agricultural systems, and wild-domestic interfaces shape interspecies transmission and viral diffusion.

​

Respiratory Virus Evolution, Immunity, and Antigenic Risk
Recent work extends this program beyond classical phylodynamics into respiratory-virus immunology and antigenic preparedness. This includes work on RSV genome classification and T-cell epitope evolution, repeated influenza vaccination, heterologous antibody responses, swine influenza pandemic risk, and sequence-based detection of antigenically novel influenza A viruses.

​

Molecular Transmission Networks and Socioecological Epidemic Dynamics
Our work increasingly integrates pathogen genomics with social, spatial, and network data to understand how transmission unfolds in real populations. This includes methodological synthesis across Bayesian phylodynamics, multilayer social networks, and molecular clusters identification for local SARS-CoV-2 spread.

​

Operational Genomic Surveillance and Public Health Preparedness
Our research emphasizes genomic surveillance as a public health decision-support system rather than a purely retrospective research tool. Publications on respiratory viral sequencing panels, SARS-CoV-2 variants, co-circulating viruses, and pathogen genomic systems support scalable surveillance for outbreak detection, variant tracking, and population-level monitoring.

​

Virus Classification, Nomenclature, and Comparative Evolution
The Bahl Lab has contributed to international efforts to standardize viral classification and nomenclature, including work on Newcastle disease virus, A/H9 influenza viruses, RSV, and negative-sense RNA viruses. These contributions support comparative virology, surveillance interoperability, and clearer communication across global research and public health communities.