This study identifies evolutionary constraints linking Zika virus NS5 replication and interferon antagonism by analyzing fitness landscapes and attenuation in mice.

Nature Communications · Oct 28, 2026Peer-reviewedMicrobiology

Near real-time data on the human neutralizing antibody landscape to influenza virus in summer of 2026 shows antigenic advance of H3N2 subclade K region D mutants and H1N1 D.3.1.1 Sa mutants

Caroline Kikawa, Andrew Butler, John Huddleston, Samuel A. Turner, Heidi Peck, Janet A. Englund, Kirsten Lacombe, Michael Paul Busch, Marion C. Lanteri, Mars Stone, Bryan Spencer, Alexander L. Greninger, Derek J. Smith, Stephanie Wallace, Helen Siobhan Marshall, , Jesse D. Bloom

This study reports neutralization titers from 355 human sera against 148 influenza strains, showing reduced neutralization of new H3N2 and H1N1 variants.

bioRxiv · Sep 21, 2026 · PreprintMicrobiology

mRNA-based influenza vaccine expands breadth of B cell response in humans

Hanover C. Matz, Tae-Geun Yu, Kritika Dixit, Caroline Kikawa, Julian Q. Zhou, Garazi Peña Alzua, Lowrey Peyton, Anders Madsen, Fangjie Han, Ariana Ghez Farrell, Robert Hoelzl, Aaron J. Schmitz, Stephen C. Horvath, Hunter K. Keplinger, Benjamin S. Strnad, , Ali H. Ellebedy

An mRNA-based influenza vaccine induces broader and more durable B cell responses compared to inactivated influenza virus vaccine in humans.

Nature Immunology · Jun 15, 2026Peer-reviewedImmunology

Strain-specific differences in the response to egg-derived versus recombinant protein influenza vaccines

Andrea N. Loes, Rosario Araceli L Tarabi, Shuk Hang Li, Reilly K. Atkinson, John Huddleston, Caroline Kikawa, Tachianna Griffiths, Elizabeth M. Drapeau, Sook‐San Wong, SW Cheng, Nancy Leung, Sarah E. Cobey, Benjamin John Cowling, Trevor Bedford, Scott E. Hensley, Jesse D. Bloom

This study compares neutralizing antibody titers from egg-derived and recombinant protein influenza vaccines against diverse H1N1 strains, finding that egg-derived vaccines induce less boost against a new clade with specific antigenic mutations.

Journal of Virology · May 27, 2026Peer-reviewedImmunology

High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains

Caroline Kikawa, Andrea N. Loes, John Huddleston, Marlin D Figgins, Philippa L. Steinberg, Tachianna Griffiths, Elizabeth M. Drapeau, Heidi Peck, Ian Barr, Janet A. Englund, Scott E. Hensley, Trevor Bedford, Jesse D. Bloom

A sequencing-based neutralization assay across 78 H3N2 HA strains and 150 sera shows strain growth in 2023 tracks the fraction of sera with low titers, but not pooled-serum titers.

eLife · Feb 23, 2026Peer-reviewedEvolutionary Biology✦ In-depth digest

Near real-time data on the human neutralizing antibody landscape to influenza virus as of early 2026 to inform vaccine-strain selection

Caroline Kikawa, John Huddleston, Samuel A. Turner, Andrea N. Loes, Jiaojiao Liu, Sydney Gang, Tachianna Griffiths, Elizabeth M. Drapeau, Benjamin John Cowling, Faith C. S. Ho, Nancy Leung, Janet A. Englund, Kirsten Lacombe, Shinji Watanabe, Hideki Hasegawa, , Jesse D. Bloom

Sequencing-based neutralization of 91 H3N2 and H1N1 hemagglutinins against 302 human sera (27,409 titers) shows reduced titers to H3N2 subclade K and H1N1 D.3.1.1.

Virus Evolution · Jan 1, 2026Peer-reviewedMicrobiology✦ In-depth digest

Crystallographic fragment screening and deep mutational scanning of Zika virus NS2B-NS3 protease enable development of resistance-resilient inhibitors

Xiaomin Ni, R. Blake Richardson, Andre Schutzer Godoy, Matteo Paolo Ferla, Caroline Kikawa, Jenke Scheen, William W. Hannon, Eda Çapkın, Noa Lahav, Blake H. Balcomb, Peter George Marples, M. Fairhead, Si-Yi Wang, Eleanor Williams, Charles W.E. Tomlinson, , F. von Delft

The paper identifies fragment binders and mutationally intolerant sites in Zika virus NS2B-NS3 protease to develop resistance-resilient antiviral inhibitors.

Nature Communications · Oct 8, 2025Peer-reviewedBiochemistry

Pleiotropic mutational effects on function and stability constrain the antigenic evolution of influenza hemagglutinin

Timothy C. Yu, Caroline Kikawa, Bernadeta Dadonaite, Andrea N. Loes, Janet A. Englund, Jesse D. Bloom

The paper measures how mutations in influenza HA affect function, stability, and antibody neutralization, showing epistasis enables antigenic change but cannot overcome pleiotropic costs that restrict evolutionary trajectories.

bioRxiv · May 24, 2025 · PreprintEvolutionary Biology

Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025

Caroline Kikawa, John Huddleston, Andrea N. Loes, Sam A Turner, Jover Lee, Ian Barr, Benjamin John Cowling, Janet A. Englund, Alexander L. Greninger, Ruth Harvey, Hideki Hasegawa, Faith C. S. Ho, Kirsten Lacombe, Nancy Leung, Nicola S. Lewis, , Jesse D. Bloom

The paper quantifies neutralizing antibody responses to influenza strains using sera collected in 2024-2025 to inform vaccine-strain selection for 2025.

Virus Evolution · Jan 1, 2025Peer-reviewedMicrobiology