This is a small pull request to make cattle a separate host category during fauna upload. This was motivated by the recent cattle outbreaks of H5N1 in the US. Currently, host species are grouped into avian, human, nonhuman mammal, environment, and other. cattle will now be its own category.
The changes include adding a list of cattle-related species, and adding a small test to query entries with nonhuman mammal annotations to find those with strain names that indicate that they are derived from cattle.
Checklist
I tested this with the original dairy cattle sequences from Texas, which were annotated with strain names including dairy cattle, but with the host field annotated as Other Mammals. The changes worked as expected.
Description of proposed changes
This is a small pull request to make
cattlea separate host category during fauna upload. This was motivated by the recent cattle outbreaks of H5N1 in the US. Currently, host species are grouped intoavian,human,nonhuman mammal,environment, andother.cattlewill now be its own category.The changes include adding a list of cattle-related species, and adding a small test to query entries with
nonhuman mammalannotations to find those with strain names that indicate that they are derived from cattle.Checklist
I tested this with the original dairy cattle sequences from Texas, which were annotated with strain names including
dairy cattle, but with the host field annotated asOther Mammals. The changes worked as expected.