add MHC-II / HA preprint

papers/2023_bloom_c.md

@@ -9,7 +9,7 @@ journal: "Virus Evolution"
 doi: "10.1093/ve/veae026"
 link: "https://academic.oup.com/ve/article/9/2/vead055/7265011"
 image: "/assets/papers/2023_bloom_c.jpg"
-selected: true
+selected: false
 keywords:
     - "SARS-CoV-2"
     - "Phylogenetics"

papers/2026_ahn.md

@@ -1,16 +1,16 @@
 ---
 layout: paper
 title: "Influenza hemagglutinin subtypes have different sequence constraints despite sharing extremely similar structures"
-date: "2026-01-05"
+date: "2026-03-21"
 authors: 
     - "Jenny J Ahn"
     - "Timothy C Yu"
     - "Bernadeta Dadonaite"
     - "Caelan E Radford"
     - "Jesse D Bloom"
-journal: "bioRxiv"
-doi: "10.64898/2026.01.05.697808"
-link: "https://doi.org/10.64898/2026.01.05.697808"
+journal: "Virus Evolution"
+doi: "10.1093/ve/veag018"
+link: "https://doi.org/10.1093/ve/veag018"
 image: "/assets/papers/2026_ahn.jpg"
 keywords:
     - "Influenza"

papers/2026_dadonaite.md

@@ -0,0 +1,30 @@
+---
+layout: paper
+title: "Defining the molecular interaction between influenza hemagglutinin and MHC-II"
+date: "2026-07-23"
+authors: 
+    - "Bernadeta Dadonaite"
+    - "Annie Dosey"
+    - "Jenny J Ahn"
+    - "Timothy C Yu"
+    - "Sara A Sunshine"
+    - "Ariana G Farrell"
+    - "Neil P King"
+    - "Jesse D Bloom"
+journal: "bioRxiv"
+doi: "10.64898/2026.07.17.738765"
+link: "https://doi.org/10.64898/2026.07.17.738765"
+image: "/assets/papers/2026_dadonaite.png"
+keywords:
+    - "Influenza"
+    - "Deep mutational scanning"
+    - "Pseudovirus"
+selected: true
+---
+
+## Abstract
+
+The hemagglutinin (HA) of some influenza viruses can interact with major histocompatibility complex class II (MHC-II), but how these proteins interact is unclear. Here we demonstrate that diverse H5 HAs can use MHC-II to enter cells, with avian MHC-II enabling more efficient entry than human MHC-II for most H5 HAs. To define the molecular interface, we use pseudovirus deep mutational scanning to measure how mutations to H5 HA affect its interaction with tufted duck MHC-II, and identify mutations that restrict HA to exclusively MHC-II or sialic acid receptors. We leverage identification of H5 HA mutations that increase binding to tufted duck MHC-II to determine a 4.8 Å cryo-EM model of the complex. To support the structural model, we measure how all mutations to tufted duck MHC-II affect its interaction with H5 HA, and find the alpha chain is the dominant determinant but beta chain sites near the peptide-binding groove also contribute. To generalize these findings, we use deep mutational scanning to show that a H7 HA interacts with MHC-II similarly to H5 HA. Finally, we show that H1, H2, H3, and H9 HAs interact with avian or human MHC-II, although interactions vary among strains that evolved in different hosts.
+
+## Interactive visualizations
+The results described in this paper can be interactively visualized at [https://dms-vep.org/Flu-H5N1-American-Wigeon-2021-HA-tufted-duck-MHCII-DMS/](https://dms-vep.org/Flu-H5N1-American-Wigeon-2021-HA-tufted-duck-MHCII-DMS/).

posts/2026-07-23_ha_mhcii.md

@@ -0,0 +1,29 @@
+---
+layout: post
+title: Defining the molecular interaction between influenza hemagglutinin and MHC-II
+date: 2026-07-23
+author: Jesse Bloom
+---
+
+We just [posted to bioRxiv](https://doi.org/10.64898/2026.07.17.738765) a new study led by Bernadeta Dadonaite that uses a novel combination of deep mutational scanning and cryo-EM to show how influenza HA interacts with MHC-II.
+Many important questions remain about how this interaction evolves and its biological role, and determining its structural basis is a first step towards answering those questions.
+
+---
+
+Influenza hemagglutinin (HA) has long been known to use sialic acid as a receptor, but about 7 years ago it was [shown](https://www.nature.com/articles/s41586-019-0955-3) that some highly diverged bat influenza HAs use MHC-II as their entry receptor.
+Subsequently it was shown some H2 and H3 HAs could also use MHC-II.
+However, the structural basis of this interaction has remained unclear.
+
+We first showed that many H5 HAs can bind to avian MHC-II, and then used pseudovirus deep mutational scanning to measure how all mutations to a H5 HA affect entry and binding to tufted duck MHC-II.
+This work enabled us to functionally define a surface on the HA head that binds MHC-II.
+We then used identification of mutations that increase HA binding to tufted duck MHC-II to solve a cryo-EM structure of the complex.
+We also measured how MHC-II mutations affect the interaction.
+
+Our [preprint](https://doi.org/10.64898/2026.07.17.738765) also has lots of other interesting findings related to HA's ability to interact with MHC-II and how this varies across HAs of many subtypes and MHC-II alleles.
+
+In addition to reading the preprint, for more details see:
+
+  - [This Bluesky thread](https://bsky.app/profile/jbloomlab.bsky.social/post/3mrdg5udgvk2j), which can be read more easily in [threaded form here](https://skywriter.blue/pages/jbloomlab.bsky.social/post/3mrdg5udgvk2j).
+  - [This X thread](https://x.com/jbloom_lab/status/2080358310562365796)
+
+To access and view the data, see the following links: [https://dms-vep.org/Flu-H5N1-American-Wigeon-2021-HA-tufted-duck-MHCII-DMS/](https://dms-vep.org/Flu-H5N1-American-Wigeon-2021-HA-tufted-duck-MHCII-DMS/).