Influenza Strain Name Generator

Overview

The purpose of this tool is to establish a standard for influenza strain names which is readable, concise, and data-rich.

The names this tool generates encode isolate metadata and are completely reversible so that a samples context will be preserved. Each strain name contains: host name, host taxonomic record, location (country and subdivision), collection month, collection year, and a unique code for the original lab.

[Type]/[Vernacular Host]/[ISO 3166 Location]/[Catalogue of Life Taxonomy ID]-[Lab Identifier]-[Month]/[Year]

Usage

Setup

To use this tool first install it as a package and install the requirements. We strongly recommend you use a virtual environment.

pip install .

Generating Names

To generate names from a file:

strain-gen file --input .\test_data\example.csv --output ./out.csv

To generate a single name:

strain-gen single --virus-type "A" --host "Gallus gallus domesticus" --location "Virginia" --country "United States" --sequence "01" --lab-id "MN.26A" --date "2026-02-28"

Decoding Names

strain-read "A/Chicken/US-VA/3F72J.1-01-MN.26A-02/2026"

Inputs

1. --virus-type

2. --host Latin Name of host species. Domestic and wild sub-species are differentiated. e.g. "Gallus gallus" != "Gallus gallus domesticus"

3. --location Name of the ISO 3166 subdivision where the sample was taken. e.g. "Virginia"

4. --country Name of the country where the sample was taken. e.g. "Mexico"

5. --sequence This is an internal lab ID. If a lab has ten samples from the same host type/location they might label them 1-10.

6. --lab-id Unique identifier for a lab. This is comprised of a two letter initial of the labs PI and a 3 character alphanumeric code.

7. --date Date in YYYY-MM-DD format.