In the last decades, the amount of genomic information available in public or private databases has become enormous. In our lab, we use this information to investigate transmission and drug resistance of infectious diseases and, particularly, of fast-evolving viruses.
Our work can tentatively be divided in three main topics:
1. Investigation and characterization of HIV and HCV transmission clusters, either for forensics or for public health purposes
An HIV-1 transmission cluster has been defined as a set of HIV-1 sequences that are aggregated nonrandomly, linked to their epidemiology. For fast-evolving viruses, transmission clusters can be reconstructed using evolutionary and phylogenetic analyses, based on the amount of relatedness between viral strains infecting different individuals. The characterization of such reconstructed transmission clusters can be used to investigate determinants of transmission and propagation of particular viral epidemics in specific settings or can be used in court settings as a forensic tool in transmission investigations. We have recently published a review paper in AIDS discussing aspects of HIV transmission investigations for forensic purposes. These analyses are increasingly important to inform public health bodies about determinants of transmission of infectious diseases and to develop better prevention measures to target such epidemics.
2. Large scale phylodynamics
This type of analyses can be used to reconstruct the dispersal of fast evolving viruses. It uses advanced phylogenetic and phylogeographical approaches to reconstruct the spread of viral organisms in a large scale. We have used this approach example to understand the role of Angola for the early dispersal of HIV. We also use this approach for other fast evolving viruses, such as arboviruses.
3. Drug resistance investigations
We have and are developing several projects in the field of HIV drug resistance. This has started with my own doctorate thesis, where I investigated the differences in drug resistance pathways between HIV subtypes. In 2014, we started a European project, where we set up a network of Portuguese-wide hospitals, that collect genomic, clinical and socio-behavioral information from newly diagnosed HIV individuals. This project is still ongoing. Other projects started afterwards, which focus on transmission of drug resistance in migrants and on the impact of late presenters for HIV transmission in Portugal. Another project is about to start, where we investigate drug resistance to integrase inhibitors, a class of drugs that has been recently recommended as 1st line therapy. We expect that many outputs will begin to come out in the next few months.
- Grant JC, González-Beiras C, Amick KM, Fortney KR, Gangaiah D, Humphreys TL,Mitjà O, Abecasis A, Spinola SM. Multiple class I and class II Haemophilus ducreyi strains cause cutaneous ulcers in children on an endemic island. Clin Infect Dis. 2018 Apr 20. doi: 10.1093/cid/ciy343. [Epub ahead of print] PubMed PMID: 29897409.
- Abecasis AB, Pingarilho M, Vandamme AM. Phylogenetic analysis as a forensictool in HIV transmission investigations. AIDS. 2018 Mar 13;32(5):543-554. doi:10.1097/QAD.0000000000001728. PubMed PMID: 29280759.
- Theys K, Libin P, Pineda-Peña AC, Nowé A, Vandamme AM, Abecasis AB. The impact of HIV-1 within-host evolution on transmission dynamics. Curr Opin Virol. 2018 Feb;28:92-101. doi: 10.1016/j.coviro.2017.12.001. Epub 2017 Dec 21. Review. PubMed PMID: 29275182.
- Paraschiv S, Banica L, Nicolae I, Niculescu I, Abagiu A, Jipa R, Pineda-Peña AC, Pingarilho M, Neaga E, Theys K, Libin P, Otelea D, Abecasis A. Epidemic dispersion of HIV and HCV in a population of co-infected Romanian injecting drug users. PLoS One. 2017 Oct 9;12(10):e0185866. doi: 10.1371/journal.pone.0185866. eCollection 2017. PubMed PMID: 29016621; PubMed Central PMCID: PMC5633171.
- Pineda-Peña AC, Varanda J, Sousa JD, Theys K, Bártolo I, Leitner T, TaveiraN, Vandamme AM, Abecasis AB. On the contribution of Angola to the initial spread of HIV-1. Infect Genet Evol. 2016 Dec;46:219-222. doi: 10.1016/j.meegid.2016.08.009. Epub 2016 Aug 10. PubMed PMID: 27521160; PubMed Central PMCID: PMC5774217.