Dr José Lourenço


Other functions

Member of the Equality and Diversity committee at the Department of Zoology

Editorial board member of Nature Scientific Reports (Infectious Diseases)


Open-source projects

MANTIS is the Multi-locus ANTIgenic Simulator, an R-package offering tools to simulate the transmission dynamics of multi-strain pathogens according to strain theory.

 Download MANTIS R Package


MVSE is the Mosquito-borne Viral Suitability index Estimator, an R-package offering tools to estimate the climate-driven transmission potential of a mosquito-borne pathogen.

Download MVSE


HBV control R-tool implements a dynamic model of HBV transmission recently developed to explore the likelihood of reaching elimination goals by 2030. This code allows to fit the model to prevalence data.

Download HBV interventions model



Contact Details

Selected Publications

For complete list: see Google Scholar page 

(2020) High residual carriage of vaccine-serotype Streptococcus pneumoniae after introduction of pneumococcal conjugate vaccine in Malawi. Nature Communications.

(2020) Hepatitis B virus seroepidemiology data for Africa: Modelling intervention strategies based on a systematic review and meta-analysis. PLoS Medicine.

(2019) Determinants of high residual post-PCV13 pneumococcal vaccine-type carriage in Blantyre, Malawi: a modelling study. BMC Medicine.

(2019) MVSE: An R‐package that estimates a climate‐driven mosquito‐borne viral suitability index. Methods in Ecology and Evolution.

(2019) HBV vaccination and PMTCT as elimination tools in the presence of HIV: insights from a clinical cohort and dynamic model. BMC Medicine.

(2019) Reverse immunodynamics: a new method for identifying targets of protective immunity. Nature Scientific Reports.

(2018) A naturally protective epitope of limited variability as an influenza vaccine target. Nature Communications.

(2018) Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science

(2018) The generation of a simian adenoviral vectored HCV vaccine. Vaccine 

(2018) Vaccination Can Drive An Increase In Frequencies Of Antibiotic Resistance Among Non-Vaccine Serotypes Of Streptococcus pneumoniae. PNAS 

(2017) Lineage structure of Streptococcus pneumoniae may be driven by immune selection on the groEL heat-shock protein. Nature Scientific reports 

(2017) Epidemiological and ecological determinants of Zika virus transmission in an urban setting. eLife

(2016) The Long-Term Safety, Public Health Impact, and Cost-Effectiveness of Routine Vaccination with a Recombinant, Live-Attenuated Dengue Vaccine (Dengvaxia)... PLoS medicine 

(2016) Zika virus in the Americas: Early epidemiological and genetic findings. Science 

(2015) MANTIS: an R package that simulates multilocus models of pathogen evolution. BMC bioinformatics

(2014) The 2012 Madeira dengue outbreak: epidemiological determinants and future epidemic potential. PLoS NTDs 

(2014) Natural, Persistent Oscillations in a Spatial Multi-Strain Disease System with Application to Dengue. PLoS Comp Bio 

(2010) Viral and epidemiological determinants of the invasion dynamics of novel dengue genotypes. PLoS NTDs