Data

Tools

Indexes

Applications

Experiments

Open Source Science

chicago_sentinel_surveillance

Tracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA.

https://github.com/numalariamodeling/chicago_sentinel_surveillance

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov, nature.com, zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.8%) to scientific vocabulary

Keywords

covid-19 epidemiology sars-cov-2
Last synced: 6 months ago · JSON representation ·

Repository

Tracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA.

Basic Info
  • Host: GitHub
  • Owner: numalariamodeling
  • License: apache-2.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Homepage:
  • Size: 11.3 MB
Statistics
  • Stars: 4
  • Watchers: 3
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Topics
covid-19 epidemiology sars-cov-2
Created almost 4 years ago · Last pushed over 3 years ago
Metadata Files
Readme License Citation

README.md

Tracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA

DOI

This is the repository associated with the paper "Tracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA" Nature Communications (2022).

We investigated whether sentinel surveillance of recently symptomatic individuals receiving an outpatient diagnostic test for SARS-CoV-2 infection could accurately assess the instantaneous reproductive number R(t) and provide early warning of changes in transmission.

Timing of indicators relative to infection Figure 1. Timing of indicators relative to infection.

  • Reliable indicators of SARS-CoV-2 transmission and infection prevalence are necessary for timely intervention
  • Case-based indicators (e.g. incident cases in the general population) are subject to bias due to differences in access to and demand for testing1,3
  • Hospital-based indicators (e.g. emergency department visits, hospitalizations) lag infection by several weeks1,2,4,5
  • Symptom onset occurs relatively soon after infection and symptomatic individuals are far more likely to receive a diagnostic test1,2,3

References

  1. Evaluating Data Types: A Guide for Decision Makers using Data to Understand the Extent and Spread of COVID-19. 2020, The National Academies Press. 15.
  2. Lauer, S.A., et al., Annals of internal medicine, 2020. 172(9): p. 577-582.
  3. Brauner, J.M., et al., Science, 2021. 371(6531): p. eabd9338
  4. Faes, C., et al., International journal of environmental research and public health, 2020. 17(20): p. 7560
  5. Hawryluk, I., et al Journal of the Royal Society Interface 17.172 (2020): 20200596.

Owner

  • Name: NU Malaria Modeling Team
  • Login: numalariamodeling
  • Kind: organization
  • Location: Northwestern University, Chicago IL USA

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: >-
  Tracking changes in SARS-CoV-2 transmission with a
  novel outpatient sentinel surveillance system in
  Chicago, USA
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - orcid: 'https://orcid.org/0000-0002-6058-5886'
    given-names: Reese
    family-names: Richardson
  - given-names: Emile
    family-names: Jorgensen
  - given-names: Philip
    family-names: Arevalo
    orcid: 'https://orcid.org/0000-0003-1237-2314'
  - given-names: Tobias
    family-names: Holden
    orcid: 'https://orcid.org/0000-0002-0793-9585'
  - given-names: Katelyn
    orcid: 'https://orcid.org/0000-0002-9369-6371'
    family-names: Gostic
  - given-names: Massimo
    family-names: Pacilli
  - given-names: Isaac
    family-names: Ghinai
    orcid: 'https://orcid.org/0000-0003-1322-1331'
  - given-names: Shannon
    family-names: Lightner
    orcid: 'https://orcid.org/0000-0002-9414-1466'
  - given-names: Sarah
    family-names: Cobey
    orcid: 'https://orcid.org/0000-0001-5298-8979'
  - given-names: Jaline
    family-names: Gerardin
    orcid: 'https://orcid.org/0000-0001-8071-9928'

GitHub Events

Total
Last Year

Dependencies

requirements.txt pypi
  • epyestim ==0.1
  • matplotlib ==3.1.3
  • numpy ==1.21.5
  • pandas ==1.2.3
  • scipy ==1.4.1
  • seaborn ==0.10.0
  • statsmodels ==0.11.0