John Huddleston

Sep 25, 2024 | elifesciences.org | Amanda Perofsky |John Huddleston |Chelsea Hansen |John Barnes

Influenza-like illness and virological surveillance data We obtained weekly epidemiological and virological data for influenza seasons 1997–1998 to 2018–2019, at the U.S. HHS region level. We defined influenza seasons as calendar week 40 in a given year to calendar week 20 in the following year, with the exception of the 2008–2009 season, which ended in 2009 week 16 due to the emergence of the A(H1N1)pdm09 virus (Goldstein et al., 2011).

Sep 13, 2024 | medrxiv.org | John Huddleston |Trevor Bedford

The authors have declared no competing interest. This work was funded by NIAID R01 AI165821-01. TB is a Howard Hughes Medical Institute Investigator. I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Aug 29, 2024 | biorxiv.org | Sravani Nanduri |Allison Black |Trevor Bedford |John Huddleston

AbstractPublic health researchers and practitioners commonly infer phylogenies from viral genome sequences to understand transmission dynamics and identify clusters of genetically-related samples. However, viruses that reassort or recombine violate phylogenetic assumptions and require more sophisticated methods. Even when phylogenies are appropriate, they can be unnecessary or difficult to interpret without specialty knowledge.

Mar 9, 2024 | biorxiv.org | Andrea N Loes |John Huddleston |Samuel MS Cheng |Lisa Touyon

AbstractThe high genetic diversity of influenza viruses means that traditional serological assays have too low throughput to measure serum antibody neutralization titers against all relevant strains. To overcome this challenge, we have developed a sequencing-based neutralization assay that simultaneously measures titers against many viral strains using small serum volumes via a workflow similar to traditional neutralization assays.

Feb 8, 2024 | biorxiv.org | Allison Black |Trevor Bedford |John Huddleston |Sravani Nanduri

AbstractPublic health researchers and practitioners commonly infer phylogenies from viral genome sequences to understand transmission dynamics and identify clusters of genetically-related samples. However, viruses that reassort or recombine violate phylogenetic assumptions and require more sophisticated methods. Even when phylogenies are appropriate, they can be unnecessary or difficult to interpret without specialty knowledge.