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. While several of these lineages become rare, others largely increase in prevalence, potentially jeopardizing the efficacy of vaccines and epidemic control strategies. SARS-CoV-2 is widely spread globally and is still responsible for large mobility/mortality and economical burden. This project focus on investigating molecular factors that mediate genomic evolution of SARS-CoV-2 aiming to provide knowledge to advance current viral detection and transmission preventing strategies.

Funding Agency


Project Reference

Project Members

Main Project Outcomes

S. Queirós, “Right ventricular segmentation in multi-view cardiac MRI using a unified U-net model”, in E. Puyol Antón et al. (eds) Statistical Atlases and Computational Models of the Heart. Multi-Disease, Multi-View, and Multi-Center Right Ventricular Segmentation in Cardiac MRI Challenge. STACOM 2021. Lecture Notes in Computer Science, vol 13131, pp. 287-295, Springer, Cham, 2022.

“Best Paper Award in the M&Ms-2 Challenge”, by M&Ms2 Challenge organizers and the Medical Image Computing and Computer Assisted Intervention (MICCAI) Society.

Main Project Outcomes


Development of an Ultraviolet-C Irradiation Room in a Public Portuguese Hospital for Safe Re-Utilization of Personal Protective Respirators.

Padrão J, Nicolau T, Felgueiras HP, Calçada C, Veiga MI, Osório NS, Martins MS, Dourado N, Taveira-Gomes A, Ferreira F, Zille A.Int J Environ Res Public Health. 2022 Apr 16;19(8):4854. doi: 10.3390/ijerph19084854.PMID: 35457722

OmniSARS2: A Highly Sensitive and Specific RT-qPCR-Based COVID-19 Diagnostic Method Designed to Withstand SARS-CoV-2 Lineage Evolution.

Carvalho-Correia E, Calçada C, Branca F, Estévez-Gómez N, De Chiara L, Varela N, Gallego-García P, Posada D, Sousa H, Sousa J, Veiga MI, Osório NS.Biomedicines. 2021 Sep 26;9(10):1314. doi: 10.3390/biomedicines9101314.PMID: 34680431

SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

Authors:  Vítor Borges; Joana Isidro; Nídia Sequeira Trovão; …  Portuguese network for SARS-CoV-2 genomics (Consortium); see more

Published:Jan 2022 in Communications Medicine

DOI: 10.1038/S43856-022-00072-0

Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal

Authors:  Borges, Vitor; Isidro, Joana; Cortes-Martins, Helena; …  Gomes, Joao Paulo; see more

Published:Jan 2020 in Emerging Microbes & Infections

DOI: 10.1080/22221751.2020.1844552

Implication of SARS-CoV-2 evolution in the sensitivity of RT-qPCR diagnostic assays.

Osório NS, Correia-Neves M.Lancet Infect Dis. 2021 Feb;21(2):166-167. doi: 10.1016/S1473-3099(20)30435-7. Epub 2020 May 28.PMID: 32473662