README.md

COVID_prison_model

This repository contains the code for the manuscript "Controlling COVID-19 outbreaks in the correctional setting: a mathematical modelling study"

#Running the code

This code assumes you have C++ and gsl libraries installed in your machine

To run the code, enter the following script via the console

gcc -c ./individual.c -lgsl -lgslcblas -lm

gcc -c -Werror -Wall main.o individual.o -lgsl -lgslcblas -o <instance_name>

./<instance_name>.exe ./input_file.xls ./output_file.xls b

#Input File

The input file contains the initial data that is used to populate the model. It also includes the number of days needed for the simulation.

Opening the input file, the format is as follows:

number of simulation days

number of people in the general community

number of inmates in minimum security prisons

number of prison staff in minimum security prisons

number of healthcare staff in minimum security prisons

number of essential visitors in minimum security prisons

number of family visitors in minimum security prisons

number of inmates in medium security prisons

number of prison staff in medium security prisons

number of healthcare staff in medium security prisons

number of essential visitors in medium security prisons

number of family visitors in medium security prisons

number of inmates in maximum security prisons

number of prison staff in maximum security prisons

number of healthcare staff in maximum security prisons

number of essential visitors in maximum security prisons

number of family visitors in maximum security prisons

This data can be modified

#Baseline model

The BaselineInmate folder contains the Baseline model. Use the individual.o, main.o, and individual.c files here to run the baseline model as defined below:

COVID-19 entry via an infected inmate on day 1; inmates can intermingle with other inmates in the same prison area; SARS-CoV-2 delta strain disease-related parameters applied.

#Variations of this model can be found on the BaselineHS model to set the first COVID-19 infected entrant as a healthcare worker, or BaselinePS to set the first infected entrant as a prison staff.

#Standard PPE model

The StandardPPE folder contains the Standard PPE model. Use the individual.o, main.o, and individual.c files here to run the baseline model as defined below:

Standard face masks in use for all inmates, correctional staff, and healthcare staff; This applies a 5% reduction in probability of onward transmission from the source; and a 67% protection of infection for the recipient. This scenario assumes 100% PPE compliance.

#PPE + Quarantine + Isolation model

The PIQincMask folder contains the PPE + Quarantine + Isolation model. Use the individual.o, main.o, and individual.c files here to run the baseline model as defined below:

Standard face masks are used by inmates everywhere including outside quarantine; new inmates are quarantined for 14 days with PCR tests at day 1 and day 12. If the PCR test returns a positive result (assuming 100% accuracy), the inmate is put into isolation for 14 days; N95 masks are used by staff in the isolation area with an 18% reduction in probability of onward transmission for the source; and an 85% protection from infection for the recipient is applied. This scenario assumes 100% PPE compliance.

#Daily RAT model

The RATdaily folder contains the Daily RAT model. Use the individual.o, main.o, and individual.c files here to run the baseline model as defined below:

COVID-19 entry assumed to be from 1 infected inmate on day 1; correctional staff and healthcare staff are subjected to RAT testing every day before entering the prison. A pooled RAT sensitivity of 71% and a specificity of 99% was applied. Prison and healthcare staff returning a positive RAT result are assumed to be sent home and subjected to PCR testing within 24 hours.

#Standard mask during transit model

The PPEtransit folder contains the Standard mask during transit model. Use the individual.o, main.o, and individual.c files here to run the baseline model as defined below:

Standard PPE masks are used by all inmates in-transit with 100% compliance.

#Standard mask during transit model

The PPEtransit folder contains the Standard mask during transit model. Use the individual.o, main.o, and individual.c files here to run the baseline model as defined below:

Standard PPE masks are used by all inmates in-transit with 100% compliance.

A variation of this model uses N95 mask during transit and is within the N95 folder of the PPEtransit folder.

#Restrict prison transfer model

The StopMove folder contains the Restrict prison transfer model. Use the individual.o, main.o, and individual.c files here to run the baseline model as defined below:

Symptomatic inmates are tested using PCR with results returned the next day. If a COVID-19 positive inmate is confirmed, all prison transfers and all court visits are stopped for all inmates across the whole prison system.

#Cell isolation model

The PPELockCell folder contains the Cell isolation model. Use the individual.o, main.o, and individual.c files here to run the baseline model as defined below:

Symptomatic inmates are isolated in their cell for 14 days with PCR tests at day 1 and day 12; N95 masks are used by staff interacting with isolated inmates; standard PPE masks are used by isolated inmates; isolation occurs on a rolling basis while prison interactions outside isolated cells continue as normal.

#Unit isolation model

The PPELockUnit folder contains the Unit isolation model. Use the individual.o, main.o, and individual.c files here to run the baseline model as defined below:

Symptomatic inmates are tested using PCR with results by the next day. Units with symptomatic inmates are locked down until no one is actively infected with COVID-19; N95 masks are used by staff interacting with isolated inmates; standard PPE masks are used by isolated inmates; inmates within the unit are free to move within the same unit, but there is no travel to or from another unit within the area of the centre; isolation occurs on a rolling basis while prison interactions outside isolated units continue as normal.

#Area isolation model

The PPELockArea folder contains the Area isolation model. Use the individual.o, main.o, and individual.c files here to run the baseline model as defined below:

Symptomatic inmates are tested using PCR with results by the next day. Areas with symptomatic inmates are locked down until no one is actively infected with COVID-19; N95 masks are used by staff interacting with isolated inmates; standard PPE masks are used by isolated inmates; inmates within the area are free to move within the area but there is no travel to or from another area within the centre; isolation occurs on a rolling basis while prison interactions outside isolated areas continue as normal.

#Pison lockdown model

The PPELockPrison folder contains the Prison isolation model. Use the individual.o, main.o, and individual.c files here to run the baseline model as defined below:

Symptomatic inmates are tested using PCR with results by the next day. Prisons with symptomatic inmates with confirmed COVID-19 infection are locked down until no one is actively infected with COVID-19; N95 masks are used by staff interacting with isolated inmates; standard PPE masks are used by isolated inmates; prisons are locked on a rolling basis; inmates within the centre are free to move within the prison but there are no movements to or from other prisons (which operate as normal).

Variations of this model implementing a 1-week, 3-week, 6-week, and 9-week delay in initiating prison lockdown after first detection of COVD-19 case can be found inside the PPELockPrison folder.

#Immunisation model

The Immunisation folder contains the Immunisation model. Use the individual.o, main.o, and individual.c files here to run the baseline model as defined below:

Assumes standard PPE is in place; 80% of the inmate population are assumed to have had a single dose and 50% to have had double dose immunisation; the same vaccination rate is applied for correctional and healthcare staff. We assumed the use of Pfizer mRNA vaccine. After the first dose, we applied a 46% reduction in onward COVID-19 transmission a 30% reduction in COVID-19 infection. After two doses, we applied a 65% reduction in onward COVID-19 transmission a 79% reduction in COVID-19 infection.

Variations of this model implementing a high coverage or low coverage for inmates and staff are found inside the Immunisation folder.