Disclaimer: This repository is under active development and may be incomplete.
This repository was developed by Mike Jackson at the Kaiser Permanente Washington Health Research Institute. For more infomation, please e-mail michael.l.jackson@kp.org.
Epidemics of bacterial meningitis caused by Neisseria meningitidis occur worldwide. The so-called "African Meningitis Belt" is a region of sub-Saharan Africa that covers parts of 26 nations, within which meningococcal epidemics occur with a frequency and intensity that is not seen elsewhere in the world. These epidemics are predominantly caused by serogroup A N. meningitidis (NmA), although epidemics can be caused by other serogroups as well. To combat these epidemics, the low-cost protein conjugate vaccine MenAfriVac (PsA-TT) has been developed for countries within the Belt.
As the vaccine was first licensed, some key questions remained regarding vaccination strategy and target age groups. Our research team developed a mathematical model of NmA transmission and PsA-TT vaccination to address these questions.
Tartof S, Cohn A, Tarbangdo F, Djingarey MH, Messonnier N, Clark TA, et al.
"Identifying Optimal Vaccination Strategies for Serogroup A Neisseria meningitidis Conjugate Vaccine in the African Meningitis Belt"
PLoS One 2013; 8(5):e63605
Substantial funding for MenAfriVac, including mass campaigns and routine childhodd immunization, has come from Gavi, the Vaccine Alliance. As part of its mission, Gavi has worked to quantify the expected impact of the vaccination programs it funds. This effort has evolved into the Vaccine Impact Modelling Consortium. Our research team has participated in the VIMC since its inception, using our model to predict the expected number of NmA cases and deaths under various assumptions about vaccination coverage.
Li X, Mukandavire C, Cucunuba ZM, Londono SE, Abbas K, Clapham HE, et al.
"Estimating the health impact of vaccination against ten pathogens in 98 low-income and middle-income countries from 2000 to 2030: a modelling study"
The Lancet 2021; 387:398-408
As part of our work with VIMC we have refined our initial simulation model. The current version based on our most recent publication:
Jackson ML, Diallo AO, Medah I, Bicaba BW, Yameogo I, Koussoube D, et al.
"Initial validation of a simulation model for estimating the impact of serogroup A Neisseria meningitidis vaccination in the African meningitis belt"
PLoS One 2018; 13(10):e0206117
This repository contains the R code and several ancillary files needed to run the epidemic simulation model. A description of the individual programs is provided in the file "Program_descriptions.md". Note that this repository does not contain all the data needed to run the simulations. Input files (including demographics and vaccine coverage) are stored in a separate directory that is not included in this repository. Those files include proprietary data on Gavi's demand forecasts, which cannot be publically posted here.
The master branch is currently version 2019.02 of the project, which is the version used for the 2019 round of impact estimates for Gavi. The COVID branch is not under active development, but was used for estimating the impact of COVID-related disruptions on MenA vaccination programs.