Pathogen Evolutionary Genomics and Experimental Genetics

Microbial adaptability to the human host environment is crucial for disease causation. Pathogens like Plasmodium falciparum, Mycobacterium tuberculosis, and HIV-1, despite their differences in complexity, share the ability to replicate, persist, and transmit within hosts. The evolutionary and adaptive mechanisms enabling these capabilities also drive antimicrobial resistance, regulated at genomic and epigenomic levels.

The Pathogen Evolutionary Genomics and Experimental Genetics (PEvoGen) team employs cutting-edge functional and experimental genetics, including genome editing and multiple levels of gene-expression modulation, to explore how pathogen genetic variations impact biological functions. By integrating evolutionary genomics with “Omics” technologies and bioinformatics, PEvoGen provides novel insights into microbial pathogenicity, paving the way for innovative diagnostic and therapeutic solutions.

Understanding pathogen evolution through computational and experimental biology helps us anticipate and counter emerging infectious threats, particularly antimicrobial resistance. This research aligns with the principles of the One Health concept and supports the Sustainable Development Goals (SDGs).

Team Members

Maria Isabel Veiga

Principal Investigator Team Coordinator

Nuno S. Osório

Principal Investigator

Ana Santos-Pereira

Postdoctoral Researcher

Claudia Fançony

Postdoctoral Researcher

Vitória da Cunha Baptista

Postdoctoral Researcher

Vera Cristina Aguieiras Triunfante

Affiliated Researcher

Beatriz Velosa da Fonseca

PhD Student

Bruno José Ferreira Freitas

PhD Student

Carlos Magalhães

PhD Student

Domingos Oliveira

PhD Student

Filipa Tavares

PhD Student

Flávia Figueira

PhD Student

Maria Pereira

PhD Student

Matheus Tavares

PhD Student

Nuno Alves

PhD Student

Pedro Araújo

PhD Student

Plácida Maholela

PhD Student

Ruth Victoria Esho

PhD Student

Talita Nicolau

PhD Student

Claudia Alejandra Cabrera Federo

MSc Student

Margarida Gonçalves

MSc Student

Sonia Carvalho

MSc Student

Team Members

Projects

Ana Santos-Pereira

Advancing current understanding on the clinical impact of HIV-1 subtype C diversity

There is still no cure for HIV infection and the extensive viral genetic diversity represents the one of the biggest obstacles to develop an effective therapy…

Maria Isabel Veiga

Deep into haemozoin formation complex: a target for antimalarial drugs and novel diagnostic tools

The clinical manifestation of malaria starts when parasites invade human red blood cells (RBCs) and feed on haemoglobin, releasing a toxic by-product, polymerized by the parasite into the inert crystal hemozoin..

Maria Isabel Veiga

Defining drug resistance pathways in the malaria parasite

Hampering malaria control and elimination efforts is the resilient capacity of the parasite Plasmodium falciparum to develop resistance, including resistance to the presently…

Maria Isabel Veiga

MAL-PREDICT: Malaria Therapeutic Failure Prediction using Machine Learning

This project aims to develop a machine learning model to predict malaria treatment failure at the patient level, enabling more personalized and effective care…

Nuno S. Osório

Molecular Evolution of the Mycobacterium tuberculosis Complex

Tuberculosis (TB) is one of the oldest and deadliest human infectious disease. Only innovative tools will allow realistic approximations to TB eradication…

Nuno S. Osório

Phylodynamic studies on SARS-CoV-2 and its application to improve viral detection and prevent transmission.

The extremely high human-to-human transmissibility of SARS-CoV-2 allows the generation of thousands of mutations within its genome fueling the evolution and selection of several viral lineages with different characteristics…

Claudia Fançony

Probing the future of triple Artemisinin-based combination therapy um Angola

There is still no cure for HIV infection and the extensive viral genetic diversity represents the one of the biggest obstacles to develop an effective therapy…

Success Story

Selected Research Outputs

PEvoGen team main achievements:
– Contributed to the knowledge of the mechanisms of resistance to antimalarial treatments in the malaria parasite Plasmodium falciparum
– Improved antimalarial drug discovery by identifying new, essential, druggable targets and test compounds that may be advanced into drug candidates suitable for preclinical development and subsequent clinical testing in humans.
– Explored better malaria diagnosis, using differential physical properties of the malaria parasite regarding the hemozoin biological pathway.
– Highlighted relevant factors contributing to the colonization of human populations by viruses of different HIV-1 subtypes.
– Endeavored the challenge of investigating Mycobacterium tuberculosis mutations accumulated during the transmission between individuals infected in the same transmission chain.
– Advanced the study of phylogeny, transmission and dissemination of HIV-1, M. tuberculosis and more recently SARS-CoV-2 through Bioinformatics.

Former lab members
• Carla Sofia Calçada, PhD (Scientific Researcher, Toronto, Canada)
• Deisy Rocha, PhD (Postdoctoral Researcher, IPBS-Toulouse, France)
• Diana Granja, MSc (Bioengineer, Anocca biotech company, Sweden)
• Francisco Araujo, MD, MSc (Project leader, Autonomous University of Santo Domingo, Dominican Republic)
• Geniss Nhapulo, MD
• Isaac Sanchéz, MSc (Technical Coordinator at the National Reference Public Health Laboratory, Dominican Republic)
• Leyre Lau (PhD student, Karolinska Institute, Sweden)
• Miguel João Ferreira da Silva, PhD (Postdoctoral Researcher, Masaryk University, Czechia)