New Bolton Center Kennett Square, PA
Emergencies & Appointments:
Ryan Hospital Philadelphia, PA


Assistant Professor of Pathobiology, University of Pennsylvania School of Veterinary Medicine
Contact Information:

In the Moncla lab, we are interested in how viruses emerge in human populations, and transmit between them. We draw on tools from phylodynamics, virology, and population genetics to understand how viruses evolve within individuals, between populations, and across continents. The ultimate goal of our work is to better understand viral evolution and transmission so that we can prevent new outbreaks from occurring and mitigate the toll of endemic viral transmission. Although our lab primarily uses computational methods, we also generate new genomic data and draw on tools from basic virology to validate our computational findings.

Viral emergence and cross-species transmission

Viruses are constantly crossing species barriers and causing outbreaks in humans. Many new viral pathogens are zoonotic, meaning that they come from animal reservoirs. Most animal viruses are poorly adapted to humans, and must evolve the ability to replicate and transmit among humans. Simultaneously, environmental and epidemiologic factors that habitat encroachment, husbandry practices, and climate can facilitate opportunities for cross-species tranmission by bringing host species together. We are interested in defining the genetic, epidemiologic, and ecological factors that contribute to cross-species transmission of novel, zoonotic viruses. We are particularly interested in avian influenza viruses, which have repeatedly crossed species barriers and infected humans. By defining the evolutionary pathways by which these viruses adapt to new hosts, we can improve surveillance and vaccine design and improve human health.

Within-host diversity and adaptation

RNA viruses rapidly generate diversity because of their high mutation rates and quick generation times. Because of this, infections with RNA viruses are comprised of a population of viruses that harbors genetic diversity. The diversity that is generated within individuals is then modulated by the process of transmission, during which "transmission bottlenecks" can drastically alter the diversity and makeup of viral populations. By characterizing how viruses acquire mutations during infection, and how the fate of those mutations are shaped by transmission, we can better understand how novel variants arise and spread.

Phylodynamics of endemic human respiratory viruses

In recent years, viruses that have been previously well-controlled by vaccination have made a resurgence. For endemic human viruses, transmission intensity is impacted by the interplay between population immunity, vaccination campaigns, and human travel, movement, and interaction patterns. We are interested in how endemic RNA viruses move across time, space, and population groups, and how viral transmission is impacted by factors like geography, host immunity, and human contact networks.

Braun, K. M., Moreno, G. K., Wagner, C., Accola, M. A., Rehrauer, W. M., Baker, D. A., Koelle, K., O'Connor, D. H., Bedford, T., Friedrich, T. C., Moncla, L. H. Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks PLoS Pathogens 17: e1009849, 2021.

Moncla, L. H., Black, A., DeBolt, C., Lang, M., Graff, N. R., Perez-Osorio, A. C., Muller, N. F., Haselow, D., Lindquist, S., Bedford, T. Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State Elife 10: , 2021.

Bedford, T., Greninger, A. L., Roychoudhury, P., Starita, L. M., Famulare, M., Huang, M. L., Nalla, A., Pepper, G., Reinhardt, A., Xie, H., Shrestha, L., Nguyen, T. N., Adler, A., Brandstetter, E., Cho, S., Giroux, D., Han, P. D., Fay, K., Frazar, C. D., Ilcisin, M., Lacombe, K., Lee, J., Kiavand, A., Richardson, M., Sibley, T. R., Truong, M., Wolf, C. R., Nickerson, D. A., Rieder, M. J., Englund, J. A., Seattle Flu Study, Investigators, Hadfield, J., Hodcroft, E. B., Huddleston, J., Moncla, L. H., Muller, N. F., Neher, R. A., Deng, X., Gu, W., Federman, S., Chiu, C., Duchin, J. S., Gautom, R., Melly, G., Hiatt, B., Dykema, P., Lindquist, S., Queen, K., Tao, Y., Uehara, A., Tong, S., MacCannell, D., Armstrong, G. L., Baird, G. S., Chu, H. Y., Shendure, J., Jerome, K. R. Cryptic transmission of SARS-CoV-2 in Washington state Science 370: 571-575, 2020.

Moncla, L. H., Bedford, T., Dussart, P., Horm, S. V., Rith, S., Buchy, P., Karlsson, E. A., Li, L., Liu, Y., Zhu, H., Guan, Y., Friedrich, T. C., Horwood, P. F. Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia PLoS Pathogens 16: e1008191, 2020.

Muller, N. F., Wagner, C., Frazar, C. D., Roychoudhury, P., Lee, J., Moncla, L. H., Pelle, B., Richardson, M., Ryke, E., Xie, H., Shrestha, L., Addetia, A., Rachleff, V. M., Lieberman, N. A. P., Huang, M. L., Gautom, R., Melly, G., Hiatt, B., Dykema, P., Adler, A., Brandstetter, E., Han, P. D., Fay, K., Llcisin, M., Lacombe, K., Sibley, T. R., Truong, M., Wolf, C. R., Boeckh, M., Englund, J. A., Famulare, M., Lutz, B. R., Rieder, M. J., Thompson, M., Duchin, J. S., Starita, L. M., Chu, H. Y., Shendure, J., Jerome, K. R., Lindquist, S., Greninger, A. L., Nickerson, D. A., Bedford, T. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State medRxiv : , 2020.

Black, A., Moncla, L. H., Laiton-Donato, K., Potter, B., Pardo, L., Rico, A., Tovar, C., Rojas, D. P., Longini, I. M., Halloran, M. E., Pelaez-Carvajal, D., Ramirez, J. D., Mercado-Reyes, M., Bedford, T. Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia BMC Infectious Diseases 19: 963, 2019.

Salvo, M. A., Aliota, M. T., Moncla, L. H., Velez, I. D., Trujillo, A. I., Friedrich, T. C., Osorio, J. E. Tracking dengue virus type 1 genetic diversity during lineage replacement in an hyperendemic area in Colombia PloS One 14: e0212947, 2019.

Soh, Y. S., Moncla, L. H., Eguia, R., Bedford, T., Bloom, J. D. Comprehensive mapping of adaptation of the avian influenza polymerase protein PB2 to humans Elife 8: , 2019.

Imai, H., Dinis, J. M., Zhong, G., Moncla, L. H., Lopes, T. J. S., McBride, R., Thompson, A. J., Peng, W., Le, M. T. Q., Hanson, A., Lauck, M., Sakai-Tagawa, Y., Yamada, S., Eggenberger, J., O'Connor, D. H., Suzuki, Y., Hatta, M., Paulson, J. C., Neumann, G., Friedrich, T. C., Kawaoka, Y. Diversity of influenza A(H5N1) viruses in infected humans, Northern Vietnam, 2004-2010 Emerging Infectious Diseases 24: 1128-1238, 2018.

Xue, K. S., Moncla, L. H., Bedford, T., Bloom, J. D. Within-host evolution of human influenza virus Trends in Microbiology 26: 781-793, 2018.

BS (Biology ) The Pennsylvania State University, 2012

PhD (Microbiology) University of Wisconsin-Madison, 2017

Fred Hutchinson Cancer Center (2017 to 2022)
Post-doctoral Research Fellow