Browsing by Author "Caetano, Constantino P."
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- Massive dissemination of a SARS-CoV-2 Spike Y839 variant in PortugalPublication . Borges, Vítor; Isidro, Joana; Cortes-Martins, Helena; Duarte, Sílvia; Vieira, Luís; Leite, Ricardo; Gordo, Isabel; Caetano, Constantino P.; Nunes, Baltazar; Sá, Regina; Oliveira, Ana; Guiomar, Raquel; Portuguese network for SARS-CoV-2 genomics; Gomes, João PauloGenomic surveillance of SARS-CoV-2 was rapidly implemented in Portugal by the National Institute of Health in collaboration with a nationwide consortium of >50 hospitals/laboratories. Here, we track the geotemporal spread of a SARS-CoV-2 variant with a mutation (D839Y) in a potential host-interacting region involving the Spike fusion peptide, which is a target motif of anti-viral drugs that plays a key role in SARS-CoV-2 infectivity. The Spike Y839 variant was most likely imported from Italy in mid-late February and massively disseminated in Portugal during the early epidemic, becoming prevalent in the Northern and Central regions of Portugal where it represented 22% and 59% of the sampled genomes, respectively, by 30 April. Based on our high sequencing sampling during the early epidemics [15.5% (1275/8251) and 6.0% (1500/24987) of all confirmed cases until the end of March and April, respectively], we estimate that, between 14 March and 9 April (covering the epidemic exponential phase) the relative frequency of the Spike Y839 variant increased at a rate of 12.1% (6.1%-18.2%, CI 95%) every three days, being potentially associated with 24.8% (20.8-29.7%, CI 95%; 3177-4542 cases, CI 95%) of all COVID-19 cases in Portugal during this period. Our data supports population/epidemiological (founder) effects contributing to the Y839 variant superspread. The potential existence of selective advantage is also discussed, although experimental validation is required. Despite huge differences in genome sampling worldwide, SARS-CoV-2 Spike D839Y has been detected in 13 countries in four continents, supporting the need for close surveillance and functional assays of Spike variants.
- Viral genetics and transmission dynamics in the second wave of mpox outbreak in Portugal and forecasting public health scenariosPublication . Cordeiro, Rita; Caetano, Constantino P.; Sobral, Daniel; Ferreira, Rita; Coelho, Luís; Pelerito, Ana; de Carvalho, Isabel Lopes; Namorado, Sónia; Loyens, Dinis B.; Mexia, Ricardo; Fernandes, Cândida; Neves, José Miguel; João, Ana Luísa; Rocha, Miguel; Duque, Luís Miguel; Correia, Inês; Baptista, Teresa; Brazão, Cláudia; Sousa, Diogo; Filipe, Paulo; Alpalhão, Miguel; Maltez, Fernando; Póvoas, Diana; Pinto, Raquel; Caria, João; Patrocínio de Jesus, Rita; Pacheco, Patrícia; Peruzzu, Francesca; Méndez, Josefina; Ferreira, Luís; Mansinho, Kamal; Alves, João Vaz; Vasconcelos, Joana; Domingos, João; Casanova, Sara; Duarte, Frederico; Gonçalves, Maria João; Salvador, Mafalda Brito; Guimarães, Mafalda Andresen; Martins, Sueila; Oliveira, Marvin Silva; Santos, Daniela; Vieira, Luís; Núncio, Maria Sofia; Borges, Vítor; Gomes, João PauloIn 2023, a second wave of the global mpox epidemic, which is mainly affecting men who have sex with men (MSM), was observed in some countries. Herein, we benefited from a large viral sequence sampling (76/121; 63%) and vast epidemiological data to characterise the re-emergence and circulation of the (MPXV) in Portugal during 2023. We also modelled transmission and forecasted public health scenarios through a compartmental susceptible-exposed-infectious-recovered (SEIR) model. Our results suggest that the 2023 mpox wave in Portugal resulted from limited introduction(s) of MPXV belonging to C.1.1 sublineage, hypothetically from Asia, followed by sustained viral transmission and potential exportation to other countries. We estimated that the contribution of the MSM high sexual activity group to mpox transmission was 120 (95% CrI: 30-3553) times higher than that of the low sexual activity group. However, among the high sexual activity group, vaccinated individuals likely contributed approximately eight times less [0.123 (95% CrI: 0.068-0.208)] than the unvaccinated ones. Vaccination was also linked to potential reduced disease severity, with a Mpox Severity Score of 6.0 in the vaccinated group compared to 7.0 in unvaccinated individuals. Scenario analysis indicated that transmission is highly sensitive to sexual behaviour, projecting that a slight increase in the MSM sub-population with high sexual activity can trigger new mpox waves. This study strongly supports that continued vaccination, targeted awareness among risk groups and routine genomic epidemiology is needed to anticipate and respond to novel MPXV threats (e.g. global dissemination of clade I viruses).