Bernadeta Dadonaite, Jack Brown et al.

SARS-CoV-2 variants acquire mutations in the spike protein that promote immune evasion1 and affect other properties that contribute to viral fitness, such as ACE2 receptor binding and cell entry2,3. Knowledge of how mutations affect these spike phenotypes…

Kangchon Kim, Marcos C Vieira et al.

For antigenically variable pathogens such as influenza, strain fitness is partly determined by the relative availability of hosts susceptible to infection with that strain compared with others…

Amanda C Perofsky, John Huddleston et al.

Influenza viruses continually evolve new antigenic variants, through mutations in epitopes of their major surface proteins, hemagglutinin (HA) and neuraminidase (NA). Antigenic drift potentiates the reinfection of previously infected individuals, but the contribution of this process to variability in annual epidemics is not well understood ...

Frances C. Welsh, Rachel T. Eguia et al.

Human influenza virus evolves to escape neutralization by polyclonal antibodies. However, we have a limited understanding of how the antigenic effects of viral mutations vary across the human population…

A. E. Roder, K. E. E. Johnson et al.

High error rates of viral RNA-dependent RNA polymerases lead to diverse intra-host viral populations during infection. Errors made during replication that are not strongly deleterious to the virus can lead to the generation of minority variants. However, accurate detection of minority variants…

Annika Rössler, Antonia Netzl, Ludwig Knabl, David Bante, Samuel H. Wilks, Wegene Borena, Dorothee von Laer, Derek J. Smith, and Janine Kimpel

Since emergence of the initial SARS-CoV-2 BA.1, BA.2 and BA.5 variants, Omicron has diversified substantially. Antigenic characterization of these new variants …

Dennis Maletich Junqueira, Caroline Tochetto, Tavis K. Anderson, Danielle Gava, Vanessa Haach, Maurício E. Cantão, Amy L. Vincent Baker, and Rejane Schaefer

Once established in the human population, the 2009 H1N1 pandemic virus (H1N1pdm09) was repeatedly introduced into swine populations globally with subsequent onward transmission among pigs. To identify and characterize human-to-swine H1N1pdm09 introductions in Brazil …

Jonathan Cheung, Anh Ngoc Bui, Sonia Younas, Kimberly M. Edwards, Huy Quang Nguyen, Ngoc Thi Pham, Vuong Nghia Bui, Malik Peiris, and Vijaykrishna Dhanasekaran

Influenza A viruses are a One Health threat because they can spill over between host populations, including among humans, swine, and birds. Surveillance of swine influenza virus in Hanoi, Vietnam …

Jonathon D. Gass, Jr., Nichola J. Hill, Lambodhar Damodaran, Elena N. Naumova, Felicia B. Nutter, and Jonathan A. Runstadler

H5Nx highly pathogenic avian influenza (HPAI) viruses of clade 2.3.4.4 have caused outbreaks in Europe among wild and domestic birds since 2016 and were introduced to North America via wild migratory birds in December 2021. We examined the spatiotemporal extent of HPAI viruses …

Alexey Markin, Sanket Wagle, Siddhant Grover, Amy L Vincent Baker , Oliver Eulenstein, Tavis K Anderson

The use of next-generation sequencing technology has enabled phylogenetic studies with hundreds of thousands of taxa. Such large-scale phylogenies have become a critical component in genomic epidemiology…

Qifang Bi, Barbra A. Dickerman, Huong Q. McLean, Emily T. Martin, Manjusha Gaglani, Karen J. Wernli, Balasubramani Goundappa, Brendan Flannery, Marc Lipsitch, Sarah Cobey, the US Flu Vaccine Effectiveness Network Investigators

Studies have reported that prior-season influenza vaccination is associated with higher
risk of clinical influenza infection among vaccinees in a given season…

Marcos C. Vieira, Anna-Karin E. Palm, Christopher T. Stamper, Micah E. Tepora, Khoa D. Nguyen, Tho D. Pham, Scott D. Boyd, Patrick C. Wilson, Sarah Cobey

Antibodies result from the competition of B cell lineages evolving under selection for improved antigen recognition, a process known as affinity maturation…

Tim K Tsang, Katelyn M Gostic, Sijie Chen, Yifan Wang, Philip Arevalo, Eric H Y Lau, Sarah Cobey, Benjamin J Cowling

Influenza imprinting reduces risks of influenza A virus clinical infection by 40%–90%, estimated from surveillance data in western countries. We analyzed surveillance data from 2010 to 2019 in Hong Kong…

Timothy C. Yu, Zorian T. Thornton, William W. Hannon, William S. DeWitt, Caelan E. Radford, Frederick A. Matsen IV, Jesse D. Bloom

A challenge in studying viral immune escape is determining how mutations combine to escape polyclonal antibodies, which can potentially target multiple distinct viral epitopes…

Allison J Greaney, Tyler N Starr, Rachel T Eguia, Andrea N Loes, Khadija Khan, Farina Karim, Sandile Cele, John E Bowen, Jennifer K Logue, Davide Corti, David Veesler, Helen Y Chu, Alex Sigal, Jesse D Bloom

Many SARS-CoV-2 variants have mutations at key sites targeted by antibodies. However, it is unknown if antibodies elicited by infection with these variants target…

Alexey Markin, Sanket Wagle, Tavis K Anderson, Oliver Eulenstein

A phylogenetic network is a powerful model to represent entangled evolutionary histories with both divergent (speciation) and convergent (e.g. hybridization, reassortment, recombination) evolution…

Dillon Adam, Katelyn Gostic, Tim Tsang, Peng Wu, Wey Wen Lim, Amy Yeung, Jessica Wong, Eric Lau, Zhanwei Du, Dongxuan Chen, Lai-Ming Ho, Mario Martín-Sánchez, Simon Cauchemez, Sarah Cobey, Gabriel Leung, Benjamin Cowling

Transmission heterogeneity is a notable feature of the severe acute respiratory syndrome (SARS) and coronavirus disease 2019 (COVID-19) epidemics, though previous efforts to estimate how…

Weijia Xiong, Tim K Tsang, Ranawaka A P M Perera, Nancy H L Leung, Vicky J Fang, Ian G Barr, J S Malik Peiris, Benjamin J Cowling

We explored the potential for a biphasic pattern in waning of antibody titers after influenza vaccination. We collected blood samples in a randomized controlled trial…

Tyler N Starr, Allison J Greaney, William W Hannon, Andrea N Loes, Kevin Hauser, Josh R Dillen, Elena Ferri, Ariana Ghez Farrell, Bernadeta Dadonaite, Matthew McCallum, Kenneth A Matreyek, Davide Corti, David Veesler, Gyorgy Snell, Jesse D Bloom

SARS-CoV-2 has evolved variants with substitutions in the spike receptor-binding domain (RBD) that impact its affinity for ACE2 receptor and recognition by antibodies…

Katia Koelle, Jack Lin, Huisheng Zhu, Rustom Antia, Anice C. Lowen, Daniel Weissman

Masking serves an important role in reducing the transmission of respiratory viruses, including SARS-CoV-2. During the COVID-19 pandemic, several perspective and review articles have also…

Tavis K Anderson, Jennifer Chang, Zebulun W Arendsee, Divya Venkatesh, Carine K Souza, J Brian Kimble, Nicola S Lewis, C Todd Davis, Amy L Vincent

Influenza A viruses (IAVs) are the causative agents of one of the most important viral respiratory diseases in pigs and humans…

Allison J Greaney, Tyler N Starr, Jesse D Bloom

A key goal of SARS-CoV-2 surveillance is to rapidly identify viral variants with mutations that reduce neutralization by polyclonal antibodies elicited by vaccination or infection…