gene: NP

previous_residue: Q

new_residue: R

type: aa

gene: PA

previous_residue: L

new_residue: L

previous_residue: M

new_residue: I

gene: HA

previous_residue: F

new_residue: F

previous_residue: I

previous_residue: S

new_residue: C

new_residue: N

previous_residue: T

new_residue: T

previous_residue: V

previous_residue: E

new_residue: G

previous_residue: D

new_residue: D

new_residue: M

previous_residue: K

new_residue: E

previous_residue: Y

new_residue: H

new_residue: V

previous_residue: P

new_residue: P

new_residue: Y

new_residue: Q

previous_residue: C

previous_residue: A

previous_residue: R

meta_mouse_escape: HA Mouse sera escape relative to AmWigeon/SC/2021

meta_ferret_escape: HA Ferret sera escape relative to AmWigeon/SC/2021

meta_mutdiffsel: PB2 Differential selection in human vs. avian cells

title: 2024 H5N1 B3.13 outbreak in USA, concatenated segments from INSDC and SRA (2026-02-24)

overlay:
About Taxonium

  Taxonium is a web application for exploring phylogenetic trees. Find out more at the
  Github repository (https://github.com/theosanderson/taxonium)
  or
  read the documentation (https://docs.taxonium.org).

About the tree

  This tree was constructed by the
  Pathogen Genomics Group
  at the University of California Santa Cruz (UCSC) Genomics Institute.
  Our automated pipeline downloads Influenza A sequences from
  GenBank
  (i.e. the INSDC databases) and SRA assemblies from
  https://github.com/andersen-lab/avian-influenza/,
  identifies isolates that belong to the H5N1 clade 2.3.4.4b genotype B3.13 branches of per-segment trees,
  concatenates the segments of each isolate in largest to smallest order (PB2, PB1, PA, HA, NP, NA, MP, NS),
  aligns the concantenated sequences to a concatenated reference
  (PP755620.1, PP755619.1, PP755618.1, PP753693.1, PP755616.1, PP753695.1, PP755614.1, PP753097.1)
  using nextclade,
  and runs UShER
  to infer the tree structure and
  matOptimize
  to improve it under maximum parsimony.

About the metadata

  In addition to metadata from GenBank and https://github.com/andersen-lab/avian-influenza
  (date, country, host, etc.), five HA phenotype scores were calculated from
  Deep Mutational Scanning (DMS) experiments performed by the Bloom lab at the
  Fred Hutchinson Cancer Center
  (https://dms-vep.org/Flu_H5_American-Wigeon_South-Carolina_2021-H5N1_DMS/):

Mouse sera escape relative to AmWigeon/SC/2021

Ferret sera escape relative to AmWigeon/SC/2021

Cell entry

Stability

Increase in a2,6 sialic acid usage

  as well as one PB2 phenotype: Differential selection in human vs. avian cells.
  The scores displayed for each sequence were calculated by summing the per-mutation scores
  for all mutations found in that sequence.

Downloads

  The tree and metadata files can be downloaded from
  https://hgdownload.gi.ucsc.edu/hubs/__ASMDIR__/UShER___SEGREF__ .

Citations

  If you use Taxonium in your research, please cite:

  Theo Sanderson (2022)
  Taxonium, a web-based tool for exploring large phylogenetic trees
  eLife 11:e82392.

  https://doi.org/10.7554/eLife.82392

  If you use the tree in your research, please cite:

  Jakob McBroome et al. (2021)
  A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees
  Mol Biol Evol 38(12):5819-5824.

  https://doi.org/10.1093/molbev/msab264

  If you use the Deep Mutational Scanning HA phenotype scores in your research, please cite:

  Bernadeta Dadonaite et al. (2024)
  Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance

  https://doi.org/10.1371/journal.pbio.3002916

  If you use the Deep Mutational Scanning PB2 phenotype scores in your research, please cite:

  Shirleen YQ Soh et al. (2019)
  Comprehensive mapping of adaptation of the avian influenza polymerase protein PB2 to humans
  eLife 8:e45079.

  https://doi.org/10.7554/eLife.45079


meta_country: USA

meta_host: Bos taurus

meta_authors: Nguyen,T., Hutter,C., Markin,A., Thomas,M., Lantz,K., Killian,M.L., Janzen,G.M., Vijendran,S., Wagle,S., Inderski,B., Magstadt,D.R., Li,G., Diel,D.G., Frye,E.A., Dimitrov,K.M., Swinford,A.K., Thompson,A.C., Snevik,K.R., Suarez,D.L., Spackman,E., Lakin,S.M., C,S., Johnson,K.R., Baker,A.L., Robbe-Austerman,S., Torchetti,M.K., Anderson,T.K., Anderson,T.


meta_location: NM

meta_host: Accipitridae

meta_authors: Aufderhar,M., Franzen,K., Killian,M., Lantz,K., Stuber,T., Hicks,J., Norris,C., Lakin,S.


meta_host: Gallus gallus


meta_authors: Aufderhar,M., Franzen,K., Killian,M.L., Lantz,K., Stuber,T., Hicks,J., Norris,C., Lakin,S.


meta_authors: Hicks,J.A., Stuber,T., Norris,C., Lakin,S., Killian,M.L., Franzen,K., Aufderhar,M.


meta_location: OK


meta_host: Mus musculus


meta_host: Passer domesticus


meta_location: TX


meta_authors: Norris,C., Tod,S., Jessica,H., Matthew,A., Kerrie,F., Mary,K., Steven,L., Kris,L.


meta_host: Felis catus


meta_location: New Mexico

meta_authors: Guan,L., Eisfeld,A.J., Pattinson,D., Gu,C., Biswas,A., Maemura,T., Trifkovic,S., Babujee,L., Presler,R. Jr., Dahn,R., Halfmann,P.J., Barnhardt,T., Neumann,G., Thompson,A., Swinford,A.K., Dimitrov,K.M., Poulsen,K., Kawaoka,Y., Presler,R.


meta_location: CO


meta_location: Kansas

meta_host: Sus scrofa

meta_authors: Kwon,T., Trujillo,J.D., Carossino,M., Machkovech,H.M., Cool,K., Lyoo,E.L., Singh,G., Kafle,S., Elango,S., Vediyappan,G., Wei,W., Minor,N., Matias-Ferreyra,F.S., Morozov,I., Gaudreault,N.N., Balasuriya,U.B.R., Hensley,L.E., Diel,D.G., Ma,W., Friedrich,T.C., Richt,J.A., Lim Lyoo,E., Govindsamy,G., Gaudreault,N., Hensley,L.


meta_location: Texas

meta_authors: Messer,K., Gnirke,A., McMahon,K., Gomez,M., Stetson,L., Stachler,E., Hill,T., Hill,S., Knoll,H., Curtis,E., Samani,P., Wewior,N., Vuyk,W., O'Connor,D., Brown,C., Madoff,L., Wohl,S., Ozonoff,A., Park,D., MacInnis,B., Sabeti,P.


meta_host: Procyon lotor


meta_authors: Halwe,N.J., Cool,K., Breithaupt,A., Schon,J., Trujillo,J.D., Nooruzzaman,M., Kwon,T., Ahrens,A.K., Britzke,T., McDowell,C.D., Piesche,R., Singh,G., Pinho dos Reis,V., Kafle,S., Pohlmann,A., Gaudreault,N., Corleis,B., Matias Ferreyra,F., Carossino,M., Balasuriya,U.B.R., Hensley,L., Morozov,I., Covaleda,L.M., Diel,D., Ulrich,L., Hoffmann,D., Beer,M., Richt,J.A.


meta_authors: Moreira,E.A., Constant,S., Constant,C., Butticaz,L., Wyler,M., David,T., Grin,P.M., Benarafa,C., Thiel,V., Alves,M., Zimmer,G.


meta_authors: Halwe,N.J., Ulrich,L., Schoen,J., Piesche,R., Britzke,T., Ahrens,A.K., Pinho dos Reis,V., Grund,C., Pohlmann,A., Breithaupt,A., Hoffmann,D., Beer,M., Harder,T.


meta_location: Ohio

meta_authors: Perkins,J., Shiplett,K., Johnson,A., Prarat,M.


meta_location: OH


meta_location: MI


meta_authors: Fabrizio,T.P., Daniels,C.S., Jeevan,T., Webby,R.J.


meta_host: Icteridae


meta_host: Columbidae


meta_location: ID


meta_authors: Kandel,S., Babujee,L., Guan,L., Dahn,R., Pattinson,D., Halfmann,P.J., Eisfeld,A.J., Neumann,G., Thompson,A.C., Morris,E.R.A., Swinford,A.K., Poulsen,K., Dimitrov,K.M., Kawaoka,Y.


meta_host: Vulpes vulpes


meta_authors: Fabrizio,T.P., Kieffer,J.D., Franks,J., Jeevan,T., Kandeil,A., Walker,D., DeBeauchamp,J., Lowe,J.F., Bowman,A.S., Webby,R.J.


meta_authors: Fabrizio,T.P., Kieffer,J.D., Franks,J., Jeevan,T., DeBeauchamp,J., Lowe,J.F., Bowman,A.S., Webby,R.J.


meta_host: Meleagris gallopavo


meta_authors: Fabrizio,T.P., Kieffer,J.D., Jeevan,T., Franks,J., DeBeauchamp,J., Lowe,J.F., Bowman,A.S., Webby,R.J.


meta_authors: Nguyen,T., Hutter,C., Markin,A., Thomas,M., Lantz,K., Killian,M.L., Janzen,G.M., Vijendran,S., Wagle,S., Inderski,B., Magstadt,D.R., Li,G., Diel,D.G., Frye,E.A., Dimitrov,K.M., Swinford,A.K., Thompson,A.C., Snevik,K.R., Suarez,D.L., Spackman,E., Lakin,S.M., C,S., Johnson,K.R., Baker,A.L., Robbe-Austerman,S., Torchetti,M.K., Anderson,T.K., Anderson,T.


meta_authors: Aufderhar,M., Franzen,K., Killian,M., Lantz,K., Stuber,T., Hicks,J., Norris,C., Lakin,S.


meta_location: Michigan

meta_host: Homo sapiens

meta_authors: Barnes,J., Steel,J., Garten,R., Davis,T., Dugan,V., Riner,D.A., Soehnlen,M., Dover,M., Kirby,M.K., Sheffield,S., Liddell,J., Frederick,J.C., Di,H., Pusch,E., De La Cruz,J., Lacek,K.A.


meta_authors: Aufderhar,M., Franzen,K., Killian,M.L., Lantz,K., Stuber,T., Hicks,J., Norris,C., Lakin,S.


meta_authors: Hicks,J.A., Stuber,T., Norris,C., Lakin,S., Killian,M.L., Franzen,K., Aufderhar,M.


meta_authors: Aufderhar,M., Franzen,K., Killian,M.L., Lantz,K., Stuber,T., Hicks,J., Lakin,S.


meta_host: Turdus merula


meta_location: Colorado

meta_authors: Roychoudhury,P., Han,P., Kong,K., Xie,H., Gamboa,L., Rodriguez-Salas,L., Ellis,S.E., Greninger,A., Bedford,T., Starita,L., Chu,H.


meta_location: texas

meta_authors: Burrough,E.R., Magstadt,D.R., Petersen,B., Timmermans,S.J., Gauger,P.C., Zhang,J., Siepker,C., Mainenti,M., Li,G., Thompson,A.C., Gorden,P.J., Plummer,P.J., Main,R., Hu,X.


meta_location: Missouri

meta_authors: Messer,K., Gnirke,A., McMahon,K., Gomez,M., Stetson,L., Stachler,E., Hill,T., Hill,S., Knoll,H., Curtis,E., Samani,P., Wewior,N., Vuyk,W., O'Connor,D., Brown,C., Madoff,L., Wohl,S., Ozonoff,A., Park,D., MacInnis,B., Sabeti,P.


meta_host: Feliformia


meta_authors: Suarez,D.L., Goraichuk,I.V., Killmaster,L., Spackman,E., Clausen,N.J., Colonius,T.J., Leonard,C.L., Metz,M.L.


meta_authors: Nguyen,T., C,C., Markin,A., Thomas,M., Lantz,K., Killian,M.L., Janzen,G.M., Vijendran,S., Wagle,S., Inderski,B., Magstadt,D.R., Li,G., Diel,D.G., Frye,E.A., Dimitrov,K.M., Swinford,A.K., Thompson,A.C., Snevik,K.R., Suarez,D.L., Spackman,E., Lakin,S.M., C,S., Johnson,K.R., Baker,A.L., Robbe-Austerman,S., Torchetti,M.K., Anderson,T.K., Anderson,T.


meta_location: KS


meta_authors: Liu,Y., Deng,S., Ren,S., Tam,R.C., Liu,S., Zhang,A.J., To,K.K., Yuen,K., Chen,H., Wang,P., Pui,W., Oong,O.


meta_authors: Waltzek,T.B., Torrevillas,B.K., Falghoush,A.M., Wolking,R.M., Snekvik,K.R.


meta_authors: Norris,C., Tod,S., Jessica,H., Matthew,A., Kerrie,F., Mary,K., Steven,L., Kris,L.


meta_location: NC


meta_location: IA


meta_host: Turdus migratorius


meta_location: SD


meta_location: MN


meta_host: Canidae


meta_host: Panthera tigris


meta_location: WA

meta_host: Lynx rufus


meta_host: Puma concolor


meta_location: CO


meta_location: OR


meta_host: Gallus gallus


meta_host: Leptailurus serval


meta_host: Lynx


meta_host: Leopardus geoffroyi


meta_host: Panthera leo


meta_host: Bos taurus


meta_location: Texas

meta_authors: Oguzie,J.U., Marushchak,L.V., Shittu,I., Lednicky,J.A., Miller,A.L., Hao,H., Nelson,M.I., Gray,G.C., Rodriguez,A.


meta_authors: Shittu,I., Silva,D., Oguzie,J.U., Marushchak,L.V., Olinger,G., Lednicky,J.A., Trujillo-Vargas,C.M., Schneider,N.E., Hao,H., Gray,G.C.


meta_host: Icteridae


meta_location: Kansas

meta_authors: Guan,L., Eisfeld,A.J., Pattinson,D., Gu,C., Biswas,A., Maemura,T., Trifkovic,S., Babujee,L., Presler,R. Jr., Dahn,R., Halfmann,P.J., Barnhardt,T., Neumann,G., Thompson,A., Swinford,A.K., Dimitrov,K.M., Poulsen,K., Kawaoka,Y., Presler,R.


meta_authors: Singh,G., Trujillo,J.D., Mcdowell,C., Fitz,I., Noll,L., Gaudreault,N., Retallick,J., Richt,J.


meta_authors: Nguyen,T., Hutter,C., Markin,A., Thomas,M., Lantz,K., Killian,M.L., Janzen,G.M., Vijendran,S., Wagle,S., Inderski,B., Magstadt,D.R., Li,G., Diel,D.G., Frye,E.A., Dimitrov,K.M., Swinford,A.K., Thompson,A.C., Snevik,K.R., Suarez,D.L., Spackman,E., Lakin,S.M., C,S., Johnson,K.R., Baker,A.L., Robbe-Austerman,S., Torchetti,M.K., Anderson,T.K., Anderson,T.


meta_authors: Aufderhar,M., Franzen,K., Killian,M., Lantz,K., Stuber,T., Hicks,J., Norris,C., Lakin,S.


meta_host: Procyon lotor

meta_authors: Aufderhar,M., Franzen,K., Killian,M.L., Lantz,K., Stuber,T., Hicks,J., Norris,C., Lakin,S.


meta_host: Meleagris gallopavo


meta_location: WY


meta_authors: Hicks,J.A., Stuber,T., Norris,C., Lakin,S., Killian,M.L., Franzen,K., Aufderhar,M.


meta_host: Homo sapiens

meta_authors: Barnes,J., Steel,J., Garten,R., Davis,T., Dugan,V., Matzinger,S.R., Kirby,M.K., Sheffield,S., Liddell,J., Frederick,J.C., Di,H., Pusch,E., De La Cruz,J., Keong,L., Lacek,K.A.


meta_host: Streptopelia decaocto


meta_host: Felis catus


meta_host: Vicugna pacos


meta_host: Anatidae


meta_location: Idaho


meta_location: ID


meta_location: UT


meta_host: Columba livia


meta_host: Zenaida asiatica


meta_authors: Hicks,J.A., Stuber,T., Lakin,S., Killian,M.L., Franzen,K., Aufderhar,M.


meta_authors: Aufderhar,M., Franzen,K., Killian,M.L., Lantz,K., Stuber,T., Hicks,J., Lakin,S.


meta_authors: Hicks,J.A., Stuber,T., Killian,M.L., Franzen,K., Aufderhar,M.


meta_location: CA


meta_location: California

meta_authors: Rejmanek,D., Crossley,B.


meta_authors: Kirby,M.K., Steel,J., Garten,R., Davis,T., Dugan,V., DaSilva,J., Liddell,J., Frederick,J.C., Di,H., Sheffield,S., Radford,K., De La Cruz,J., Keong,L., Lacek,K.A., Shu,B., Lopez,D., Seliskar,L., Le,H., Cadiz,V., Hua,C., Hok,S., Millena,S.


meta_authors: Kirby,M.K., Steel,J., Garten,R., Davis,T., Dugan,V., Sheffield,S., Liddell,J., Frederick,J.C., Di,H., Radford,K., De La Cruz,J., Keong,L., Lacek,K.A., Shu,B., Lopez,D., Seliskar,L., Le,H., Cadiz,V., Hua,C., Hok,S., Millena,S.


meta_authors: Kirby,M.K., Steel,J., Garten,R., Davis,T., Dugan,V., Sheffield,S., Liddell,J., Frederick,J.C., Di,H., Radford,K., De La Cruz,J., Keong,L., Lacek,K.A., Shu,B., Molinar,B., Wright,C., Guevara,H., Pan,C.-Y., Morales,C., Wadford,D.


meta_host: Panthera tigris


meta_location: California, San Bernardino County

meta_host: Feliformia

meta_authors: Frye,E.A., Nooruzzaman,M., Cronk,B.D., Laverack,M., Sebastian Britto de Oliveira,P., Caserta,L.C., Lejeune,M., Diel,D.G.


meta_location: NV

meta_host: Puma concolor


meta_host: Leptailurus serval


meta_host: Gallus gallus


meta_host: Larus occidentalis


meta_host: Bos taurus


meta_authors: Kirby,M.K., Steel,J., Garten,R., Davis,T., Dugan,V., Wilson,M., Liddell,J., Frederick,J.C., Di,H., Radford,K., De La Cruz,J., Keong,L., Lacek,K.A., Shu,B., Lopez,D., Seliskar,L., Le,H., Cadiz,V., Hua,C., Hok,S., Millena,S.


meta_location: NE


meta_host: Plegadis chihi


meta_host: Dromaius novaehollandiae


meta_host: Meleagris gallopavo


meta_location: NY


meta_location: New York

meta_authors: Chen,C., Naru,A., Mareddy,V.R., Lanka,S., Sherman,M., Yee,H., Loose,N., Vieson,M.D., Fang,Y.


meta_host: Homo sapiens

meta_authors: Tobolowsky,F., Morris,E., Castro,L., Schaff,T., Jacinto,M., Clement,J., Levine,M., Frederick,J., Li,F., Holiday,C., Kirby,M., Davis,C., Kniss,K., Olsen,S., Ryder,R., Wadford,D., Masinde,G., Han,G., Iuliano,A., Jain,S.


meta_authors: Kirby,M.K., Steel,J., Garten,R., Davis,T., Dugan,V., Sheffield,S., Liddell,J., Frederick,J.C., Di,H., Radford,K., De La Cruz,J., Keong,L., Lacek,K.A., Shu,B., Schatzman,S., Nguyen,H., Molinar,B., Wright,C., Guevara,H., Pan,C.-Y., Morales,C., Wadford,D.


meta_host: Galliformes