Browsing by Author "Nunes, Alexandra"
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- Impact of Loci Nature on Estimating Recombination and Mutation Rates in Chlamydia trachomatisPublication . Ferreira, Rita; Borges, Vítor; Nunes, Alexandra; Nogueira, Paulo; Borrego, Maria José; Gomes, João PauloThe knowledge of the frequency and relative weight of mutation and recombination events in evolution is essential for understanding how microorganisms reach fitted phenotypes. Traditionally, these evolutionary parameters have been inferred by using data from multilocus sequence typing (MLST), which is known to have yielded conflicting results. In the near future, these estimations will certainly be performed by computational analyses of full-genome sequences. However, it is not known whether this approach will yield accurate results as bacterial genomes exhibit heterogeneous representation of loci categories, and it is not clear how loci nature impacts such estimations. Therefore, we assessed how mutation and recombination inferences are shaped by loci with different genetic features, using the bacterium Chlamydia trachomatis as the study model. We found that loci assigning a high number of alleles and positively selected genes yielded nonconvergent estimates and incongruent phylogenies and thus are more prone to confound algorithms. Unexpectedly, for the model under evaluation, housekeeping genes and noncoding regions shaped estimations in a similar manner, which points to a nonrandom role of the latter in C. trachomatis evolution. Although the present results relate to a specific bacterium, we speculate that microbe-specific genomic architectures (such as coding capacity, polymorphism dispersion, and fraction of positively selected loci) may differentially buffer the effect of the confounding factors when estimating recombination and mutation rates and, thus, influence the accuracy of using full-genome sequences for such purpose. This putative bias associated with in silico inferences should be taken into account when discussing the results obtained by the analyses of full-genome sequences, in which the “one size fits all” approach may not be applicable.
- Viral genetic clustering and transmission dynamics of the 2022 mpox outbreak in PortugalPublication . Borges, Vítor; Duque, Mariana Perez; Martins, João Vieira; Vasconcelos, Paula; Ferreira, Rita; Sobral, Daniel; Pelerito, Ana; de Carvalho, Isabel Lopes; Núncio, Maria Sofia; Borrego, Maria José; Roemer, Cornelius; Neher, Richard A.; O’Driscoll, Megan; Rocha, Raquel; Lopo, Sílvia; Neves, Raquel; Palminha, Paula; Coelho, Luís; Nunes, Alexandra; Isidro, Joana; Pinto, Miguel; Santos, João Dourado; Mixão, Verónica; Santos, Daniela; Duarte, Silvia; Vieira, Luís; Martins, Fátima; Machado, Jorge; Veríssimo, Vítor Cabral; Grau, Berta; Peralta-Santos, André; Neves, José; Caldeira, Margarida; Pestana, Mafalda; Fernandes, Cândida; Caria, João; Pinto, Raquel; Póvoas, Diana; Maltez, Fernando; Sá, Ana Isabel; Salvador, Mafalda Brito; Teófilo, Eugénio; Rocha, Miguel; Moneti, Virginia; Duque, Luis Miguel; e Silva, Francisco Ferreira; Baptista, Teresa; Vasconcelos, Joana; Casanova, Sara; Mansinho, Kamal; Alves, João Vaz; Alves, João; Silva, António; Alpalhão, Miguel; Brazão, Cláudia; Sousa, Diogo; Filipe, Paulo; Pacheco, Patrícia; Peruzzu, Francesca; de Jesus, Rita Patrocínio; Ferreira, Luís; Mendez, Josefina; Jordão, Sofia; Duarte, Frederico; Gonçalves, Maria João; Pena, Eduarda; Silva, Claúdio Nunes; Guimarães, André Rodrigues; Tavares, Margarida; Freitas, Graça; Cordeiro, Rita; Gomes, João PauloPathogen genome sequencing during epidemics enhances our ability to identify and understand suspected clusters and investigate their relationships. Here, we combine genomic and epidemiological data of the 2022 mpox outbreak to better understand early viral spread, diversification and transmission dynamics. By sequencing 52% of the confirmed cases in Portugal, we identified the mpox virus sublineages with the highest impact on case numbers and fitted them into a global context, finding evidence that several international sublineages probably emerged or spread early in Portugal. We estimated a 62% infection reporting rate and that 1.3% of the population of men who have sex with men in Portugal were infected. We infer the critical role played by sexual networks and superspreader gatherings, such as sauna attendance, in the dissemination of mpox virus. Overall, our findings highlight genomic epidemiology as a tool for the real-time monitoring and control of mpox epidemics, and can guide future vaccine policy in a highly susceptible population.