H5N1 and Nextstrain directions
Trevor Bedford
Fred Hutchinson Cancer Center / Howard Hughes Medical Institute
1 Oct 2024
Monthly BAA call
CDC
Continued H5N1 epizootic
Cattle appear to be source population with frequent spillover into birds and non-human mammals
Data system and GenBank vs SRA release dates
About a 2 month lag between sample collection and GenBank release
Data system and GenBank vs SRA release dates
About a 2 month lag between sample collection and GenBank release
Data system and GenBank vs SRA release dates
About a 2 month lag between sample collection and GenBank release
Ongoing Nextstrain work
Continuing to build out core pathogens, each with automated data ingest and analysis, including
- Lassa: GitHub repo / live view
- Oropouche: GitHub repo / live view
- rabies: GitHub repo / live view
- seasonal coronaviruses: GitHub repo / live view
- West Nile Virus: GitHub repo / (in progress)
- yellow fever: GitHub repo / (in progress)
Ongoing Nextstrain work
Updates to ncov analysis, including
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,
Nashwa Ahmed,
Cécile Tran Kiem,
Kim Andrews,
Cristian Ovaduic,
Philippa Steinberg,
Jacob Dodds,
John SJ Anderson
Amin Bemanian
