Genomics update on the H5N1 outbreak in US cattle


Trevor Bedford

Fred Hutchinson Cancer Center / Howard Hughes Medical Institute
21 May 2024
Viruses and Vaccines Seminar Series
Brotman Baty Institute
Slides at:

Confirmed infections in cattle in nine states with first detection on March 25

Genomic analysis

with Louise Moncla, James Hadfield and John Huddleston

Broader context of H5N1 evolution and spread

Spread in the Americas characterized by spillover to multiple mammalian hosts

Cattle infections form distinct clade across segments indicative of single spillover and cow-to-cow spread

HA, PB2, PA,

Growing epizootic in cattle after introduction in ~Dec with subsequent spillback into birds

Epizootic origin appears to be Texas congruent with initial cases

But note sampling bias, where 119 of 189 cattle-derived sequences were sampled from Texas

Specific amino acid changes associated with cattle adaptation

Scientific questions addressable by genomic epi

  • Is the epizootic rate of growth slowing?
  • Are movement restrictions working to keep geographic spread contained?
  • Is adaptive evolution to novel cattle host continuing?

Potential for milk surveillance

  • Locally sourced commerical milk screened by Peter Han, Lea Starita and colleagues
  • Full genome sequence from CO-derived positive sample by Pavitra Roychoudhury
  • Released to GenBank under accessions PP796043 through PP796050


H5N1 genomic analysis: Louise Moncla, James Hadfield, John Huddleston

H5N1 genomic data: APHIS National Veterinary Services lab at the USDA for sharing cattle sequences, other data producers from all over the world for sharing contextual sequences, GISAID for collating data and Karthik Gangavarapu and colleagues for sharing assembled consensus genomes

Milk surveillance: Peter Han, Lea Starita, Pavitra Roychoudhury, Helen Chu, Sean Ellis, Luis Gamboa, Alex Greninger, Kevin Kong, Leslie Rodriguez-Salas, Hong Xie

Nextstrain: Richard Neher, Ivan Aksamentov, John Anderson, Kim Andrews, Jennifer Chang, James Hadfield, Emma Hodcroft, John Huddleston, Jover Lee, Victor Lin, Cornelius Roemer, Thomas Sibley

Bedford Lab: John Huddleston, James Hadfield, Katie Kistler, Thomas Sibley, Jover Lee, Miguel Paredes, Marlin Figgins, Victor Lin, Jennifer Chang, Eslam Abousamra, Nashwa Ahmed, C├ęcile Tran Kiem, Kim Andrews, Cristian Ovaduic, Philippa Steinberg, Jacob Dodds, John SJ Anderson