PRR Project

Summary

Job DescriptionThe researcher hired for this position will be integrated in the GHTM’s PRIME research group, within the scope of the Genomic Surveillance and Population Mobility (GS&PM) cross-cutting issue.S/he is expected to assist the supervising responsibilities within the GHTM genomic surveillance team and to actively seek funding within the scope of the PRIME group and of the GS&PM cross-cutting issue.The researcher should have solid experience on genomic surveillance of infectious diseases. A background on microbiology and evolution and previous experience on phylodynamics and phylogeography will be valued.  S/he main tasks will be data collection; laboratory work using Next-Generation sequencing (Nanopore); analyses of next-generation sequencing data; programming in R and Python; analysis of genome-wide genetic diversity of pathogenic microorganisms, both viruses or bacteria; database management using SQL; phylogenetic and phylodynamic analyses and statistical analyses of large datasets with genomic data. Will also promote the metavirome/metagenome analysis of environmental sources related with GHTM’s cohorts as tools for surveillance of transmissible diseases, further promoting genome-wide diversity and phylodynamics of relevant viruses and preparedness for viral and other microbiological threats. Scientific ProfilePhD in Microbiology, Biomedical Sciences, Biology, Computational Biology or Global HealthSolid background on evolutionary biology, virology and microbiology.Experience in writing technical reports and scientific articles.Experience in supervision and training students of all levels;Proactivity in developing contacts and research collaborations.Excellent publication recordExperience in writing Grant proposalsExcellent communication skillsTeam player RationaleIHMT and GHTM have a recognized track record on molecular epidemiology for several years. This research area ranges from detection and classification of specific viral or bacterial variants to the analyses of its worldwide dissemination, with a specific focus on drug resistance. Such microorganisms include those causing major pandemics, such as tuberculosis, HIV, hepatitis B, SARS-CoV-2 and dengue; or other pandemic threats, such as Zika. In the latest years, GHTM moved towards the establishment of genomic surveillance studies in different settings with a One Global Health vision. Important research projects have been funded, aimed at e.g. genomic surveillance of respiratory viruses in school settings, metavirome analyses in wastewaters, microbial drug resistance studies at the animal-human interface or HIV genomic surveillance in low-income Portuguese-speaking African countries. All these projects have contributed to an embedded vision of One Global Health within GHTM, with a particular focus on Pandemic Preparedness.Within the scope of PRIME research group of GHTM and GS&PM cross-cutting issue, researchers were previously hired to boost the scientific impact and outputs of the RD&I unit in the field of genomic surveillance. This resulted in the many publications and projects funded and the establishment of a transmissible diseases surveillance platform. To keep track of this research path, it is important to maintain the human resources that were previously hired through grants. Furthermore, GHTM hosts a unique cohort of 1000 immigrant and native children living in the Lisbon metropolitan area, who are followed over time together with their families. This infrastructure has been particularly useful for analyzing the impact of transmissible diseases, migration, conflicts and climate change on migrant children and their family’s health. To extend this initiative further and to study additional aspects of health determinants as well as the on genomic surveillance and phylogenetics of infectious diseases, GHTM developed two further cohorts of children of the same age in Cape Verde and Brazil (the main countries of origin for the children´s cohort in Portugal), with the implementation of a cohort study following the health of 1000 Cape Verdean children from the island of Santiago. These cohorts will be studied in connection with the Biostatistics and Clinical Epidemiology profiles, promoting a One Global Health approach while connecting the microbiological determinants of health with metavirome/metagenome analysis of environmental sources associated with GHTM’s cohorts (eg. wastewaters among other sources), as tools for surveillance of infectious diseases, promoting genome-wide diversity and phylodynamics studies of relevant viruses and preparedness for microbiological threats.All these databases need to be integrated and analyzed at multiple levels to extract rich and useful information to guide regional and national health policies, that has not yet been explored in all its dimensions and that will benefit greatly from the presence of a researcher with the proposed profile.