WellsRC/Optimizing-COVID19-Quarantine-and-Testing-Strategies: Optimal COVID-19 quarantine and testing strategies

This repository contains codes and data used to simulate and analyze COVID-19 quarantine and testing strategies in the scenarios of

1. Entry into quarantine uniformly during the incubation period or the course of disease
2. Entry into quarantine through contact tracing

Note: The code is set up for homogeneous transmission for symptomatic and asymptomatic individuals (i.e. R0_S=R0_A) for the purpose of the manuscript, and only partially set-up for heterogeneous transmission. See https://github.com/WellsRC/Optimizing-COVID19-Quarantine-and-Testing-Strategies for any relevant updates.

The model code is written in MATLAB and results are saved as MATLAB data files (extension .mat), with plots also being constructed in MATLAB. As MATLAB is not an open-source software/programming language, a compatible code that can be run using GNU Octave can be found in the directory named Octave in the repository.

 

OS System requirements

The codes developed here are tested on Windows operating system (Windows 10 Home: 64-bit). However as Matlab and Octave are available for most operating systems, codes should run on Mac OSX and Linux as well.

Installation guide

MATLAB

Installation instruction for MATLAB can be found at https://www.mathworks.com/help/install/install-products.html. Typical install time for MATLAB on a "normal" desktop is around 30-40 minutes. The current codes were developed and tested on MATLAB R2018b.

GNU Octave

When MATLAB is not accessible due to lack of license or any other reason, the open-source GNU Octave can be used to test the code. We tested our code with GNU Octave version 4.2.2. Necessary adjustment to code was done to make it compatible with GNU Octave and it can be found in the directory named Octave in the repository. Installation instruction for GNU octave can be found at https://www.gnu.org/software/octave/. Typical install time for GNU Octave on a "normal" desktop is 15 minutes or less. As most data is saved in MATLAB data file format as well, they can be read directly in GNU Octave for speed. If testing the code that reads the raw data and formats them (format_data.m), it may be essential to install 'io' package in GNU Octave and can be installed using pkg install -forge io, which can then be loaded in work environment using pkg load io

Demo

Figure1 generates Figure 1 in the main text; Figure S2 and Figure S3 (Run Time: 22 seconds). All mat files to run this script are avaialble. This figure script requires the scripts IPQ,ITE,ITXD, and ITEXD to be run if parsmeters changed in the analysis in order to update 'ImpactQuarantine.mat'; 'TestingonEntry.mat'; 'TestingonExit_OneDayDelay.mat'; 'TestingonEntryExit_OneDayDelay.mat'. Estimated run times for the analysis scripts on 6 processor in parallel (IPQ ~ 8 hrs; ITE ~ 16 hrs; ITXD ~ 16 hrs; ITEXD ~ 24 hrs) (Note: These scripts run two scenarios. Run time can be cut in half by commenting out one of the scenarios)

Instructions for use

To generate the Figures and output of the calculations, select a script from Figures section to run in MATLAB and enter the name in the command line. All mat file are availble to generate figures and conduct the calculations. To run analysis on a different set of parameters, adjust the parameters in the script and enter the name of the script in the command line to run.

Analysis scripts

IS

Generates the infectivity profile for R0=2.5 and R0=2.0, as well as pA=30.8% and pA=22.6%.

IPQ

Runs the analysis for uniform entry into quarantine with 30.8% infections being asymptomatic, and 22.6% being asymptomatic, for quarantine durations from 0 to 21 days with no testing and R0=2.5

ITE

Runs the analysis for uniform entry into quarantine with 30.8% infections being asymptomatic, and 22.6% being asymptomatic, for quarantine durations from 0 to 21 days with testing on entry and R0=2.5

ITX

Runs the analysis for uniform entry into quarantine with 30.8% infections being asymptomatic, and 22.6% being asymptomatic, for quarantine durations from 0 to 21 days with testing on exit (with negligible delay in test result) and R0=2.5

ITEX

Runs the analysis for uniform entry into quarantine with 30.8% infections being asymptomatic, and 22.6% being asymptomatic, for quarantine durations from 0 to 21 days with testing on both entry and exit (with negligible delay in test result) and R0=2.5

ITXD

Runs the analysis for uniform entry into quarantine with 30.8% infections being asymptomatic, and 22.6% being asymptomatic, for quarantine durations from 0 to 21 days with testing on exit (with one day delay to obtain test result) and R0=2.5

ITEXD

Runs the analysis for uniform entry into quarantine with 30.8% infections being asymptomatic, and 22.6% being asymptomatic, for quarantine durations from 0 to 21 days with testing on both entry and exit (with one day delay to obtain test result) and R0=2.5

ITE4Q7

Runs the analysis for uniform entry into quarantine with 30.8% infections being asymptomatic for quarantine duration of 7 days with testing on both entry and 96 hrs after the first test and R0=2.5

CT

Runs the analysis for contact tracing with 30.8% infections being asymptomatic, and 22.6% being asymptomatic, for quarantine durations from 0 to 21 days with no testing and R0=2.5

CTTE

Runs the analysis for contact tracing with 30.8% infections being asymptomatic, and 22.6% being asymptomatic, for quarantine durations from 0 to 21 days with testing on entry and R0=2.5

CTTX

Runs the analysis for contact tracing with 30.8% infections being asymptomatic, and 22.6% being asymptomatic, for quarantine durations from 0 to 21 days with testing on exit (with negligible delay in test result) and R0=2.5

CTTEX

Runs the analysis for contact tracing with 30.8% infections being asymptomatic, and 22.6% being asymptomatic, for quarantine durations from 0 to 21 days with testing on both entry and exit (with negligible delay in test result) and R0=2.5

CTTXD

Runs the analysis for contact tracing with 30.8% infections being asymptomatic, and 22.6% being asymptomatic, for quarantine durations from 0 to 21 days with testing on exit (with one day delay to obtain test result) and R0=2.5

CTTEXD

Runs the analysis for contact tracing with 30.8% infections being asymptomatic, and 22.6% being asymptomatic, for quarantine durations from 0 to 21 days with testing on both entry and exit (with one day delay to obtain test result) and R0=2.5

VPAD

Runs the analysis for uniform entry into quarantine for quarantine durations of five and seven days days with testing on both entry and 96 hrs after the first test and R0=2.5 for 0% to 100% (at 5% increase in incrementes) infections being asymptomatic.

VPANT

Runs the analysis for uniform entry into quarantine for quarantine durations of five and seven days days with no testing and R0=2.5 for 0% to 100% (at 5% increase in incrementes) infections being asymptomatic.

Prob_Estimate_Data

Returns the estimates for the benefit of extending the quarantine from three-day and test on entry to a five/seven day quarantine with testing on entry and testing 96 hrs follwoing first test. Also, calcualtes the probability of post-quarantine transmission for the cases detected on exit.

DayTest

Computes the number of secodnary infections for quarantine durations for 0 to 21 days, as well as evaluting the number of secondary infections if tested on day X of quanratine.

AIC_St

Runs the fitting and AIC comparison for the sensitivity function

Figures

FigureGen

Generates all figures in the main text and the supplementary material

Figure1A

Constructs the line graph of the probability of post-quarantine transmission for quarantine for the scenarios of i) no testing, ii) texting on entry, iii) testing on exit, and iv) testing on both entry and exit for an incubation period of 8.29 days .

This script also generates Figure S2 (Secondary number of cases post-quarantine) and Figure S3 (Probability of post-quarantine transmission).

Figure2

Constructs the bar graph of the positivity for the testing data from the two site for the different strategies (testing only on entry versus testing on entry and exit).

Figure =3A

Constructs the line graph of the probability of post-quarantine transmission for contact tracing for the scenarios of i) no testing, ii) texting on entry, iii) testing on exit, and iv) testing on both entry and exit for an incubation period of 8.29 days
This script also generates Figure S7 and Figure S8.

Figure1B_3B

Constructs the line graph of the optimal day to test for uniform entry (Figure 1B) and contact tracing (Figure 3B) under the assumption of one day delay to test result and a negligible delay to test result.

Figure 4

Plots the optimal day to test for a known time of exposure under the assumption of one day delay to test result and a negligible delay to test result for quarantine periods of 14,7,5, and 3 days.

FigureS1

Plots the infectivity profile for R_0=2.5 and 30.8% infections being asymptomatic, R_0=2.5 and 22.6% infections being asymptomatic, R_0=2.0 and 30.8% infections being asymptomatic, and R_0=2.0 and 22.6% infections being asymptomatic.

FigureS4

Plots the optimal time to conduct the test for different quarantine durations

FigureS5

Plots the probability of post-quarantine transmission for quarantine for a five-day quarantine and a seven day quarantine with no testing and testing on entry and 96 hrs after the initial test for various proportions of infections being asymptomatic

FigureS6

Plots the probability of post-quarantine transmission for quarantine for a three-day, five-day, seven-day, and 14-day quarnatine, with testing on entry, testing on exit, and testing on entry and exit when accounting for underlying prevalence in the community and a crew size of 40.

FigureS9_S10

This script generates the figures for the secondary number of cases post-quarantine and probability of post-quarantine transmission when entering quarantine through contact tracing.

FigureS11

This script generates the infectivity profile for the 8.29 day incubation period and a 2.9, 1.9 and 3.9 latent period

FigureS12_S13_S16_S17

This script generates the figures for the secondary number of cases post-quarantine and probability of post-quarantine transmission when entering quarantine uniformly and through contact tracing for a latent period of 1.9 days.

FigureS14_S15_S18_S19

This script generates the figures for the secondary number of cases post-quarantine and probability of post-quarantine transmission when entering quarantine uniformly and through contact tracing for a latent period of 3.9 days.

FigureS20_S21

This script generates the figures for the secondary number of cases post-quarantine and probability of post-quarantine transmission when entering quarantine not through contact tracing, with no delay between the test sample and test result (i.e. delay is negligible in receiveing test result)

FigureS22_S23

This script generates the figures for the secondary number of cases post-quarantine and probability of post-quarantine transmission when entering quarantine through contact tracing, with no delay between the test sample and test result (i.e. delay is negligible in receiveing test result

FigureS24_S25

This script generates the figures for the secondary number of cases post-quarantine and probability of post-quarantine transmission when entering quarantine not through contact tracing, with 22.6% infections being asymptomatic

FigureS26_S27

This script generates the figures for the secondary number of cases post-quarantine and probability of post-quarantine transmission when entering quarantine through contact tracing, with 22.6% infections being asymptomatic

FigureS28

Generates the plot for the temporal diagnostic sensitivity

FigureS24_S25

This script generates the figures for the probability of post-quarantine transmission when entering quarantine not through contact tracing, as well as through contact tracing, assuming transmisison post-quarantine is Poisson distributed

FigureS30

Generates the plot for pdf in which individuals enter quarantine uniformly versus contact tracing

Functions

BaselineParameters

Returns the baseline parameters for the analysis

DurationInfected

The duration in which a contact of a symptomatic index case has been infected for

FigureChart

Generates the Figure chart for the Secondary infections post quarantine with and without testing, assuming delay from sample to result is irrelevant

FigureChartDelay

Generates the Figure chart for the Secondary infections post quarantine with and without testing, assuming one day delay from sample to result

InfectiousnessfromInfection

The temporal number of secondary infections post-quarantine given no testing

InfectiousnessfromInfectionTestingEntry

The temporal number of secondary infections post-quarantine given single test time (does both entry/exit). Entry and exit can both be done using this function as it only requires the time in quarantine in which the test is done

InfectiousnessfromInfectionTestingEntryExit

The temporal number of secondary infections post-quarantine given timing of two tests

Probability_Onward

The probability of psot-quarantine transmission given how secondafy cases are distributed

RiskChart

Generates the Figure chart for the probabaility of post quarantine trasnmisison, assuming delay from sample to result is negligible. It also generates the the equivialent duration of quaratnine with testing to a duration of quarantine with no testing

RiskChartDelay

Generates the Figure chart for the probabaility of post quarantine trasnmisison, assuming one day delay from sample to result. . It also generates the the equivialent duration of quaratnine with testing to a duration of quarantine with no testing

SensitivityTimeSamp

Temporal sensitiviity of the RT-PCR assay with respect to time (dependent on the incubation period)

SensitivityvsViralLoad

The sensitiviity of the RT-PCR assay given the viral load

TimeInfection

The time in which a contact was infected from a symptomatic index case

ViralShedding_Asymptomatic

The infectity profile of an asymptomatic individual (independent of R0)

ViralShedding_Symptomatic

The infectity profile of an symptomatic individual (independent of R0)

MAT files

TableData_A

The data for region A

TableData_B

The data for region B