Publications

2024

Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance
Bernadeta Dadonaite, Jenny J Ahn, Jordan T Ort, Jin Yu, Colleen Furey, Annie Dosey, William W Hannon, Amy Vincent Baker, Richard J Webby, Neil P King, Yan Liu, Scott E Hensley, Thomas P Peacock, Louise H Moncla, Jesse D Bloom‡. bioRxiv, May 24, 2024, DOI:10.1101/2024.05.23.595634

Within-host influenza viral diversity in the pediatric population as a function of age, vaccine, and health status
Ashley Sobel Leonard, Lydia Mendoza, Alexander G McFarland, Andrew D Marques, John K Everett, Louise Moncla, Frederic D Bushman, Audrey R Odom John, Scott E Hensley‡, May 28, 2024, Virus Evolution, DOI:Volume 10, Issue 1, 2024, veae034, https://doi.org/10.1093/ve/veae034

Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county
Miguel I Paredes‡, Amanda C Perofsky, Lauren Frisbie, Louise H Moncla, Pavitra Roychoudhury, Hong Xie, Shah A Mohamed Bakhash, Kevin Kong, Isabel Arnould, Tien V Nguyen, Seffir T Wendm, Pooneh Hajian, Sean Ellis, Patrick C Mathias, Alexander L Greninger, Lea M Starita, Chris D Frazar, Erica Ryke, Weizhi Zhong, Luis Gamboa, Machiko Threlkeld, Jover Lee, Jeremy Stone, Evan McDermot, Melissa Truong, Jay Shendure, Hanna N Oltean, Cécile Viboud, Helen Chu, Nicola F Müller, Trevor Bedford‡, March 26, 2024, PLoS Pathogens, DOI:10.1371/journal.ppat.1012117

SARS-CoV-2 evolution during prolonged infection in immunocompromised patients
Andrew D Marques, Jevon Graham-Wooten, Ayannah S Fitzgerald, Ashley Sobel Leonard, Emma J Cook, John K Everett, Kyle G Rodino, Louise H Moncla, Brendan J Kelly, Ronald G Collman, Frederic D Bushman. MBio, March 13, 2024, DOI:10.1128/mbio.00110-24

2023

Avian H7N9 influenza viruses are evolutionarily constrained by stochastic processes during replication and transmission in mammals
Katarina M Braun, Luis A Haddock III, Chelsea M Crooks, Gabrielle L Barry, Joseph Lalli, Gabriele Neumann, Tokiko Watanabe, Masaki Imai, Seiya Yamayoshi, Mutsumi Ito, Louise H Moncla, Katia Koelle, Yoshihiro Kawaoka, Thomas C Friedrich‡. Virus Evolution, January 19, 2023, DOI:10.1093/ve/vead004

2022

A multivalent nucleoside-modified mRNA vaccine against all known influenza virus subtypes
Claudia P Arevalo, Marcus J Bolton, Valerie Le Sage, Naiqing Ye, Colleen Furey, Hiromi Muramatsu, Mohamad-Gabriel Alameh, Norbert Pardi, Elizabeth M Drapeau, Kaela Parkhouse, Tyler Garretson, Jeffrey S Morris, Louise H Moncla, Ying K Tam, Steven HY Fan, Seema S Lakdawala, Drew Weissman, Scott E Hensley‡. Science, November 24, 2022, DOI: 10.1126/science.abm0271

2021

Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks
Katarina Braun, Gage Moreno, Cassia Wagner, Molly A. Accola, William M. Rehrauer, David Baker, Katia Koelle, David H. O’Connor, Trevor Bedford, Thomas C. Friedrich‡, Louise H. Moncla‡. PLOS Pathogens, August 23, 2021, DOI: 10.1371/journal.ppat.1009849

Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State
Louise H. Moncla‡, Allison Black, Chas DeBolt, Misty Lang, Nicholas R. Graff, Ailyn C. Pérez-Osorio, Nicola F. Müller, Dirk Haselow, Scott Lindquist, Trevor Bedford‡. eLife, April 19, 2021, DOI: 10.7554/eLife.66448

Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State
Nicola F. Müller‡, Cassia Wagner, Chris D. Frazar, Pavitra Roychoudhury, Jover Lee, Louise H. Moncla, Benjamin Pelle, Matthew Richardson, Erica Ryke, Hong Xie, Lasata Shrestha, Amin Addetia, Victoria M. Rachleff, Nicole A. P. Lieberman, Meei-Li Huang, Romesh Gautom, Geoff Melly, Brian Hiatt, Philip Dykema, Amanda Adler, Elisabeth Brandstetter, Peter D. Han, Kairsten Fay, Misja Ilcisin, Kirsten Lacombe, Thomas R. Sibley, Melissa Truong, Caitlin R. Wolf, Michael Boeckh, Janet A. Englund, Michael Famulare, Barry R. Lutz, Mark J. Rieder, Matthew Thompson, Jeffrey S. Duchin, Lea M. Starita, Helen Y. Chu, Jay Shendure, Keith R. Jerome, Scott Lindquist, Alexander L. Greninger‡, Deborah A. Nickerson‡, Trevor Bedford‡. Science Translational Medicine, May 3, 2021, DOI: 10.1126/scitranslmed.abf0202

2020

Cryptic Transmission of SARS-CoV2 in Washington State
Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang ML, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, Giroux D, Han PD, Fay K, Frazar CD, Ilcisin M, Lacombe K, Lee J, Kiavand A, Richardson M, Sibley TR, Truong M, Wolf CR, Nickerson DA, Rieder MJ, Englund JA, Hadfield J, Hodcroft EB, Huddleston J, Moncla LH, Müller NF, Neher RA, Deng X, Gu W, Federman S, Chiu C, Duchin J, Gautom R, Melly G, Hiatt B, Dykema P, Lindquist S, Queen K, Tao Y, Uehara A, Tong S, MacCannell D, Armstrong GL, Baird GS, Chu HY, Shendure J, Jerome KR. Science, October 30, 2020, DOI: 10.1126/science.abc0523

Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia
Louise H. Moncla‡, Trevor Bedford, Philippe Dussart, Srey Viseth Horm, Sareth Rith, Philippe Buchy, Erik A. Karlsson, Lifeng Li, Yongmei Liu, Huachen Zhu, Yi Guan, Thomas C. Friedrich, Paul F. Horwood‡. PLOS Pathogens, January 17, 2020, DOI: 10.1371/journal.ppat.1008191

2019

Genomic Epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia
Allison Black, Louise H. Moncla, Katherine Laiton-Donato, Barney Potter, Lissethe Pardo, Angelica Rico, Catalina Tovar, Diana P. Rojas, Ira M. Longini, M. Elizabeth Halloran, Dioselina Peláez-Varvajal, Juan D. Ramírez, Marcela Mercado-Reyes, Trevor Bedford‡. BMC Infectious Diseases, November 12, 2019. DOI: DOI: 10.1186/s12879-019-4566-2

Comprehensive mapping of the avian influenza polymerase protein PB2 to humans
YQ Shirleen Soh, Louise H. Moncla, Rachel Eguia, Trevor Bedford, Jesse D. Bloom. eLife, April 30, 2019. DOI: 10.7554/eLife.45079

Tracking dengue virus type 1 genetic diversity during lineage replacement in an hyperendemic are in Colombia
Mauricio A. Salvo, Mathew T. Aliota, Louise H. Moncla, ID Velez, AL Trujillo, Thomas C. Friedrich, Jorge E. Osorio‡. PLOS One, March 7, 2019. DOI: 10.1371/journal.pone.0212947

2018

Diversity of influenza A(H5N1) viruses in infected humans, northern Vietnam, 2004-2010
Hirotaka Imai, Jorge M. Dinis, Gongxun Zhong, Louise H. Moncla, Tiago J.S. Lopexs, Ryan McBride, Andrew J. Thompson, Wenjie Peng, Mai thi Q. Le, Anthony Hanson, Michael Lauck, Yuko Sakai-Tagawa, Shinya Yamada, Julie Eggenberger, David H. O’Connor, Yasuo Suzuki, Masato Hatta, James C. Paulson, Gabriele Neumann, Yoshihiro Kawaoka‡. Emerging Infectious Diseases 24, 7, July 2018. DOI: 10.3201/eid2407.171441

Within-host evolution of human influenza virus
Katherine S. Xue, Louise H. Moncla, Trevor Bedford, Jesse D. Bloom‡. Trends in Microbiology, March 10, 2018. DOI: 10.1016/j.tim.2018.02.007

2017

Emergence of oseltamivir-resistant H7N9 influenza viruses in immunosuppressed cynomolgus macaques
Maki Kiso, Kiyoko Iwatsuki-Horimoto, Seiya Yamayoshi, Ryuta Uraki, Mutsumi Ito, Eiryo Kawakami, Yuriko Tomita, Satoshi Fukuyama, Tiago J.S. Lopes, Tokiko Watanabe, Louise H. Moncla, Thomas C. Friedrich, Gabriele Neumann, Yoshihiro Kawaoka‡. Journal of Infectious Diseases, Volume 216, issue 5, September 1, 2017. DOI: 10.1093/infdis/jix296

Influenza evolution: new insights into an old foe
Louise H. Moncla, Nicholas W. Florek, Thomas C. Friedrich‡. Trends in Microbiology, June 25, 2017. PMID: 28478941. DOI: 10.1016/j.tim.2017.04.003

2016

Within-host evolution of simian arteriviruses in crab-eating macaques
*Louise H. Moncla**, Andrea M. Weiler, Gabrielle Barry, Jason Weinfurter, Jorge M. Dinis, Olivia Charlier, Michael Lauck, Adam Bailey, Jens Kuhn, Victoria Wahl-Jensen, Joshua C. Johnson, Peter B. Jahrling, Tony L. Goldberg, David H. O’Connor, Thomas C. Friedrich‡. Journal of Virology, August 12, 2016.DOI: 10.1128/JVI.02231-16

A Single Mutation in the VP1 of Enterovirus 71 is Responsible for Increased Virulence and Neurotropism in Adult Interferon Deficient Mice
Elizabeth A. Caine, Louise H. Moncla, Monica Ronderos, Thomas C. Friedrich, Jorge E. Osorio‡. Journal of Virology. July 20, 2016. DOI: 10.1128/JVI.01370-16

A rhesus macaque model of Asian-lineage Zika virus infection
*Dudley DM**, Aliota MT, Mohr EL, Weiler AM, Lehrer-Brey G, Weisgrau KL, Mohns MS, Breitbach ME, Rasheed MN, Newman CM, Gellerup DD, Moncla LH, Post J, Schultz-Darken N, Schotzko ML, Hayes JM, Eudailey JA, Moody MA, Permar SR, O’Connor SL, Rakasz EG, Simmons HA, Capuano S, Golos TG, Osorio JE, Friedrich TC, O’Connor DH‡. Nature Communications; 7:12204. Jun 28, 2016. DOI: 10.1038/ncomms12204

Selective bottlenecks shape evolutionary pathways taken during mammalian adaptation of a 1918-like avian influenza virus
*Louise H. Moncla**, Gongxun Zhong, Chase W. Nelson, Austin L. Hughes, James Mutschler, Tokiko Watanabe, Yoshihiro Kawaoka, Thomas C. Friedrich‡. Cell Host and Microbe 19, 169-190, February 10, 2016. (Featured Article)DOI: 10.1016/j.chom.2016.01.011

Divergent simian arteriviruses cause simian hemorrhagic fever of different severity in macaques
Victoria Wahl-Jensen, Joshua Johnson, Michael Lauck, Jason Weinfurter, Louise Moncla, Andrea Weiler, Olivia Charlier, Oscar Rojas, Russell Byrum, Dan Ragland, Louis Huzella, Erika Zommer, Melanie Cohen, John Bernbaum, Yíngyún Caì, Hannah Sanford, Steven Mazur, Reed Johnson, Gustavo Palacios, Adam Bailey, Peter Jahrling, Tony Goldberg, David O’Connor, Thomas Friedrich, and Jens Kuhn‡. MBio. 2016 Febraury 23; 7(1). DOI: 10.1128/mBio.02009-15

Deep sequencing reveals potential antigenic drift variants at low frequency in influenza A-infected humans
Jorge M. Dinis, Nicholas W. Florek, Omolayo O. Fatola, Louise H. Moncla, James P. Mutschler, Jennifer K. Meece, Edward A. Belongia, Thomas C. Friedrich‡. Journal of Virology. 2016 January 6. DOI: 10.1128/JVI.03248-15

Pre-2016

SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data
*Nelson CW**, Moncla LH, Hughes AL‡. Bioinformatics. 2015 July 29. DOI: 10.1093/bioinformatics/btv449

A novel nonhuman primate model for influenza transmission
Louise H. Moncla**, Ted M. Ross, Jorge M. Dinis, Jason T. Weinfurter, Tatum D. Mortimer, Nancy Schultz-Darken, Kevin Brunner, Saverio V. Capuano III, Carissa Boettcher, Jennifer Post, Michael Johnson, Chalise E. Bloom, Andrea M. Weiler, Thomas C. Friedrich‡. PLOS One 8, e78750. November 14, 2013. DOI: 10.1371/journal.pone.0078750