H5N1 and Nextstrain updates
Trevor Bedford
Fred Hutchinson Cancer Center / Howard Hughes Medical Institute
12 Aug 2024
Monthly BAA call
CDC
Continued H5N1 epizootic
Cattle appear to be source population with frequent spillover into birds and non-human mammals
Continued H5N1 epizootic
Strong spatial structure apparent at the state-level
GenBank vs SRA release dates
Two month period from mid-May to mid-July with no GenBank submissions, but recent GenBank submissions from early Aug match to SRA submissions from early July
Timeline of ~1 month for collection to SRA and then a ~1 month delay to GenBank submission
Ongoing Nextstrain work
- Continuing to build out core pathogens, each with automated data ingest and analysis, including seasonal coronaviruses (live), rabies (in progress), West Nile virus (in progress), Lassa (in progress), yellow fever (in progress) and Oropouche (in progress)
- Weighted subsampling in augur
filter - Combining multiple metadata TSV files with augur
merge - Combining across multiple augur
filtercalls into a single augursubsamplecall with associated YAML (analogous toncovworkflow) - Splash page updates to highlight relevant datasets
Acknowledgements
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,
Amin Bemanian
