H5N1 sequence data update

Trevor Bedford

Fred Hutchinson Cancer Center / Howard Hughes Medical Institute
12 Jun 2024
Monthly SPHERES call
CDC
 
Slides at: bedford.io/talks

Genomic data available as of today

H5N1 genomes from samples collected in 2024 from the USA

GISAID

424 consensus genomes with metadata (274 cattle sequences)

GenBank

383 consensus genomes with metadata available via this NCBI Virus query (239 cattle sequences)

SRA

Additional 399 samples lacking collection date and collection state available from BioProject PRJNA1102327 (additional 230 cattle samples)

Curated sequence data

• We fetch data from Genbank via combination of NCBI Datasets and NCBI Virus, including matching across segments and annotating admin division from strain name
• Data from SRA BioProject PRJNA1102327 is assembled into consensus genomes and shared to GitHub by the Andersen Lab at Scripps. We fetch this data from GitHub and merge with GenBank based on SRA accession.
• This ingest routine is run daily and resulting sequence data available at:
  • data.nextstrain.org/files/workflows/avian-flu/h5n1/ha/sequences.fasta.zst
  • data.nextstrain.org/files/workflows/avian-flu/h5n1/na/sequences.fasta.zst
  • etc...
  and metadata available at:
  • data.nextstrain.org/files/workflows/avian-flu/h5n1/metadata.tsv.zst

GenBank vs SRA release dates

GenBank has seen 66 submissions since May 4 (with the 27 from USDA representing backfill of April SRA releases), while SRA has seen 295 submissions

Full genome phylogenetic analysis shows SRA samples are more derived than GenBank samples

Molecular clock estimates SRA samples as primarily collected in April

Continuing evolution of H5N1 with new lineages revealed in the SRA data

Timely analyses of H5N1 require SRA data

Acknowledgements

H5N1 data curation and analysis: Jover Lee, Kartik Gangavarapu, Praneeth Gangavarapu, Louise Moncla, James Hadfield, John Huddleston, Kristian Andersen

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 and NCBI for providing data systems

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,   Cécile Tran Kiem,   Kim Andrews,   Cristian Ovaduic,   Philippa Steinberg,   Jacob Dodds,   John SJ Anderson