About

Bonmyong (Bora) Lee, MD, is an Assistant Professor of Clinical Radiology at the University of Pennsylvania's Perelman School of Medicine. He is an active member of the medical staff serving as a radiologist at Penn Presbyterian Medical Center, Chester County Hospital, and Pennsylvania Hospital, and is an attending radiologist at the Hospital of the University of Pennsylvania. Dr. Lee specializes in radiology with a focus on breast imaging, as indicated by his division affiliation. His educational background includes a B.S. in Biology from Duke University and an M.D. from the University of Virginia School of Medicine. His research contributions include work on BI-RADS report usage, breast MRI lesion characteristics, and radiology communication practices, with multiple publications in radiology and medical journals.

Research topics

• Biology
• Virology
• Political Science
• Genetics
• Medicine
• Immunology
• Pathology
• Ecology
• Zoology
• Law
• Molecular biology
• Biochemistry
• Cell biology
• Internal medicine

Selected publications

• Evolutionary and structural basis of SLAMF1 utilization in morbilliviruses—Implications for host range and cross-species transmission

  PLoS Pathogens · 2025-06-10 · 3 citations

  articleOpen access

  Morbilliviruses, including measles virus (MV), canine distemper virus (CDV), peste des petits ruminants virus, and cetacean morbillivirus pose a significant threat to humans and animals. While the host range of morbilliviruses is generally well-defined, cross-species transmission events with significant mortality have also been reported. Their entry into immune cells, the primary targets of morbilliviruses, relies on the signaling lymphocytic activation molecule (SLAM), also known as SLAMF1 or CD150. In this study, we hypothesize that the ability of morbilliviruses to utilize heterologous SLAM receptors stems from evolutionarily conserved structural determinants within the SLAM protein and that minimal genetic changes in the viral receptor-binding H protein can enable adaptation to novel hosts. To test this, we systematically assessed SLAM utilization and adaptation by diverse morbilliviruses. We found that most morbilliviruses efficiently utilize SLAM from multiple host species, including Myotis bat SLAM, but not human SLAM. Only MV could efficiently utilize human SLAM. Additionally, unlike other morbilliviruses, MV utilized Myotis bat SLAM inefficiently. As an example of morbillivirus adaptation to non-host animal SLAM, we conducted an MV adaptation experiment with Myotis bat SLAM. We demonstrated that MV readily adapted to utilize Myotis bat SLAM by acquiring a single N187Y mutation in its hemagglutinin protein. Notably, hypothetical ancestral SLAMs acted as universal receptors for all morbilliviruses. These results reinforced that morbillivirus receptor usage is primarily supported by evolutionarily conserved structural features of SLAM, highlighting a molecular basis that enables morbilliviruses to rapidly adapt to diverse animal SLAMs.

  PublisherDOI

• De novo rescue of new henipaviruses under BSL-4 conditions – From sequence to pathogen

  Advances in virus research · 2025-01-01

  reviewSenior authorCorresponding
  PublisherDOI

• Annual (2024) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)

  Journal of General Virology · 2025-06-13 · 6 citations

  articleOpen access

  In April 2024, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was expanded by 1 new order, 1 new family, 6 new subfamilies, 34 new genera and 270 new species. One class, two orders and six species were renamed. Seven families and 12 genera were moved; ten species were renamed and moved; and nine species were abolished. This article presents the updated taxonomy of Negarnaviricota as currently accepted by the ICTV, providing an essential annual update on the classification of members of this phylum that deepen understandings of their evolution, and supports critical public health measures for virus identification and tracking.

  PublisherDOI

• Precision engineering of human cytomegalovirus without BAC constraints: a Sendai virus-delivered CRISPR/Cas9 approach

  Journal of General Virology · 2025-07-15

  articleOpen accessSenior author

  Human cytomegalovirus (HCMV) genetic manipulation traditionally relies on bacterial artificial chromosome (BAC) recombineering, necessitated by its large ~236 kb genome. This approach is limited by the scarcity of HCMV strains engineered into BACs and often requires the deletion of 'non-essential' genes to accommodate the BAC cassette. We developed a novel approach using temperature-sensitive Sendai virus (SeV) vectors to deliver CRISPR/Cas9 for targeted HCMV genome editing without these constraints. This system achieves high editing efficiency (80-90%) in fibroblasts, epithelial cells and endothelial cells without BAC intermediates. As proof of principle, we targeted the HCMV (TB40/E strain) pentamer complex (PC) genes UL128 and UL130, crucial for viral entry into non-fibroblast cells. Edited viruses showed significantly reduced infectivity in epithelial cells, confirming functional disruption of the PC. Plaque purification yielded isogenic clones with phenotypes comparable to AD169, a naturally PC-deficient strain. Furthermore, multiplexed editing created precise 663 bp deletions in over 60% of viral genomes. Importantly, this method enables HCMV editing in physiologically relevant cell types without fibroblast passaging, which typically introduces mutations. This SeV-Cas9 system represents a significant advancement for studying HCMV biology in diverse cell types.

  PublisherDOI

• The IFIT2–IFIT3 antiviral complex targets short 5’ untranslated regions on viral mRNAs for translation inhibition

  Nature Microbiology · 2025-10-15 · 6 citations

  articleOpen access

  Recognition of foreign RNA is critical for the innate immune response to viruses. Interferon (IFN)-induced proteins with tetratricopeptide repeats (IFIT) 2 and 3 are highly upregulated following viral infection, but mechanistic insight into their antiviral role is lacking. Here we demonstrate that short 5' untranslated regions (UTRs), a characteristic of many viral mRNAs, can serve as a molecular pattern for innate immune recognition via IFIT2 and IFIT3. Structure determination of the IFIT2-IFIT3 complex at 3.2 Å using cryo-EM reveals a domain-swapped heterodimer that is required for recognition of the viral mRNA 5' end, translation inhibition and antiviral activity. Critically, viral or host 5' UTR lengths less than 50 nucleotides are necessary and sufficient to enable translation inhibition by the IFIT2-IFIT3 complex. Accordingly, diverse viruses whose mRNAs contain short 5' UTRs, such as vesicular stomatitis virus and parainfluenza virus 3, are sensitive to IFIT2-IFIT3-mediated antiviral activity. Our work thus reveals a pattern of antiviral nucleic acid immune recognition that takes advantage of the inherent constraints on viral genome size.

  PublisherOA PDFDOI

• <i>De novo</i> recovery of Ghana virus, an African bat Henipavirus, reveals differential tropism and attenuated pathogenicity compared to Nipah virus

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-08 · 1 citations

  preprintOpen accessSenior authorCorresponding

  Summary Henipaviruses (HNVs) like Nipah (NiV) and Hendra (HeV) viruses represent severe zoonotic threats. Ghana virus (GhV), identified in 2012, is the only African bat henipavirus with a near-complete genome assembly. However, without isolates in culture, GhV biology, pathogenicity, and zoonotic potential remain poorly understood. Using reverse genetics, we recovered a full-length infectious clone of GhV at BSL-4 following rational reconstruction of its incomplete 3′ leader and modification of a non-canonical transcriptional initiation site. GhV demonstrated restricted receptor tropism (ephrin-B2 but not ephrin-B3) and distinct innate immune antagonism. Replication was attenuated in primary human cells, but was enhanced in bat cells. In Syrian golden hamsters, GhV infection caused no disease or mortality. Furthermore, a chimeric NiV encoding the GhV receptor-binding protein was completely attenuated in vivo , implicating ephrin-B3 receptor usage as a critical determinant of HNV pathogenesis. These findings elucidate GhV zoonotic potential and inform strategies for virus surveillance and control. Abstract Figure

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• Immunogenicity, security and protection against small ruminant lentivirus (SRLV) challenge in sheep, induced by intranasal immunization with a recombinant Sendai virus vector expressing SRLV gag-P25

  Veterinary Quarterly · 2025-09-17 · 1 citations

  articleOpen access

  -P25 (rSeV-GFP-P25) in lambs. Twenty-one SRLV-negative lambs were divided into three groups and inoculated intranasally thrice with culture medium (group 1); SeV-GFP (group 2) or rSeV-GFP-P25 (group 3). Lambs were challenged with homologous SRLV at 16 weeks post-first immunization. Clinical and hematological parameters, antibody responses, SRLV viral loads in peripheral blood mononuclear cells (PBMCs) and target tissues, histopathological and histomorphometric analyses, assisted with artificial intelligence, of interstitial pneumonia were assessed. No clinicopathological alterations were observed, except for a transient temperature increase in group 3 post-first immunization. Group 2 showed mild SeV-neutralizing antibodies, while rSeV-GFP-P25 (group 3) induced negligible SRLV-specific antibody responses. Group 3 exhibited higher SRLV DNA copies in PBMCs but lower in most SRLV target tissues compared to control groups, with no SRLV DNA detected in spleen and bone marrow. Histomorphometry revealed reduced alveolar septal thickening in group 3, indicating partial protection against early SRLV-associated interstitial pneumonia. These results warrant further investigation into cellular immunity and long-term protection.

  PublisherDOI

• T cell epitope mapping reveals immunodominance of evolutionarily conserved regions within SARS-CoV-2 proteome

  iScience · 2025-07-02 · 2 citations

  articleOpen access

  alanine scanning highlighted the functional importance of mutationally constrained immunodominant regions. Collectively, these findings identify immunodominant T cell epitopes across the SARS-CoV-2 proteome that may enhance immune surveillance against emerging variants and inform next-generation vaccine designs providing broader and more durable protection.

  PublisherDOI

• De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies

  Genome Research · 2025-03-21 · 3 citations

  articleOpen accessSenior author

  Immunoglobulin ( IGH , IGK , IGL ) loci in the human genome are highly polymorphic regions that encode the building blocks of the light and heavy chain IG proteins that dimerize to form antibodies. The processes of V(D)J recombination and somatic hypermutation in B cells are responsible for creating an enormous reservoir of highly specific antibodies capable of binding a vast array of possible antigens. However, the antibody repertoire is fundamentally limited by the set of variable (V), diversity (D), and joining (J) alleles present in the germline IG loci. To better understand how the germline IG haplotypes contribute to the expressed antibody repertoire, we combined genome sequencing of the germline IG loci with single-cell transcriptome sequencing of B cells from the same donor. Sequencing and assembly of the germline IG loci captured the IGH locus in a single fully phased contig where the maternal and paternal contributions to the germline V, D, and J repertoire can be fully resolved. The B cells were collected following a measles, mumps, and rubella (MMR) vaccination, resulting in a population of cells that were activated in response to this specific immune challenge. Single-cell, full-length transcriptome sequencing of these B cells results in whole transcriptome characterization of each cell, as well as highly accurate consensus sequences for the somatically rearranged and hypermutated light and heavy chain IG transcripts. A subset of antibodies synthesized based on their consensus heavy and light chain transcript sequences demonstrate binding to measles antigens and neutralization of authentic measles virus.

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• The exon junction complex coordinates the cotranscriptional inclusion of blocks of neighboring exons

  Genes & Development · 2025-10-16 · 1 citations

  articleOpen access

  The exon junction complex (EJC) has roles in mRNA export and cytoplasmic quality control. However, the EJC is recruited to pre-mRNA by the spliceosome prior to the completion of splicing. When splicing is cotranscriptional, the EJC is deposited on nascent RNA early during synthesis, raising the question of whether the EJC regulates downstream RNA processing. Here we show, using long-read sequencing, that degron-mediated depletion of EJC component EIF4A3 leads to skipping of neighboring pairs of two or more exons on the same mRNA molecule. These data suggest that the entire “exon block” requires the EJC for inclusion. Introns flanking EJC-dependent exon blocks were longer and spliced after internal introns. In our working model, block exons are first spliced together to form a larger EJC-marked exon that promotes surrounding splicing events. Strikingly, analysis of 480 RNA binding protein knockdowns across two different human cell lines revealed block exons that are dependent on other splicing factors, indicating that coordinated splicing of adjacent exons is a general mechanism, of which the EJC is the dominant regulator. Cell type-specific coordinated splicing of adjacent exon pairs has been observed before. Here we identify the EJC as the main protein factor massively regulating this novel splicing mechanism in trans .

  PublisherOA PDFDOI

Recent grants

• Tropism, pathogenicity, and potential for zoonotic spillover of emergent henipa- and henipa-like viruses

  NIH · $2.7M · 2016–2021

• SUMO and ubiquitin modifications in henipavirus matrix trafficking and function

  NIH · $2.1M · 2016–2021

• NIH Grant U01AI082100

  NIH · $3.0M · 2014

• NIH Grant R21AI115226

  NIH · $460k · 2016

• NIH Grant K08HL003923

  NIH · $570k · 2003

Frequent coauthors

• Robert W. Doms

  University of Pennsylvania

  89 shared

• Tao Wang

  Northwest A&F University

  64 shared

• Peng Li

  Shenzhen Polytechnic

  64 shared

• Jaspreet Kaur

  University of Regensburg

  64 shared

• Mickey Koh

  University of London

  64 shared

• Hui Xu

  64 shared

• Xing Zhang

  University of Chinese Academy of Sciences

  64 shared

• Yong Kang

  Wuhan University

  64 shared

Labs

• Bonmyong (Bora) Lee LaboratoryPI

Education

• Residency/Post-doc, Pathology & Laboratory Medicine

  Hospital of the University of Pennsylvania

  2001

• M.D.

  Yale University School of Medicine

  1995