cfa-viral-lineage-model

⚠️ The work in this repository is experimental, though currently not under active development. ⚠️

Overview

This repo hosts work on modeling how the composition of viral lineages, such as SARS-CoV-2 Pango lineages, changes over time.

The repo has the following structure:

• linmod/, with a poetry package for downloading lineage count data, and fitting and evaluating models with this data; and
• retrospective-forecasting/, with code that uses this package to automate the retrospective evaluation of models.

Documentation

• Documentation for linmnod is best viewed with mkdocs. After cloning this repo and poetry installing, run poetry run mkdocs serve.
• For use of the restrospective-forecasting pipeline, see the README.

Architecture

The model is provided with lightly-preprocessed data of variant sequences from humans in the USA, from Nextstrain (data dictionary). An Apache Parquet is provided, with columns date, fd_offset, division, lineage, count. Rows are uniquely identified by (date, division, lineage). date and fd_offset can be computed from each other, given the forecast date.

Note that date is the sample collection date. fd refers to the forecast date. fd_offset is date - fd measured in days. Sequences are filtered to have a collection date no later than the forecast date.

| date | fd_offset | division | lineage | count | | ---------- | ---------- | ------------ | ------- | ----- | | 2024-05-07 | -12 | Arizona | 24A | 1 | | 2024-05-04 | -15 | Pennsylvania | 24A | 2 | | ... | ... | ... | ... | ... |

The model must output samples of population-level lineage proportions. An Apache Parquet should be provided, with columns fd_offset, division, lineage, sample_index, and phi (the population proportion), for fd_offset = -30, ..., 14. Rows are uniquely identified by (fd_offset, division, lineage, sample_index).

| fdoffset | division | lineage | sampleindex | phi | | ---------- | -------- | ------- | ------------ | -------------- | | -30 | Alabama | 22B | 1 | 0.000014979599 | | -30 | Alabama | 22B | 2 | 9.945703e-7 | | ... | ... | ... | ... | ... |

General Disclaimer

This repository was created for use by CDC programs to collaborate on public health related projects in support of the CDC mission. GitHub is not hosted by the CDC, but is a third party website used by CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise.

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This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.

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