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Vítor Borges
Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA)

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Article
Published: 22 August 2021
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Background The SARS-CoV-2 Delta variant (B.1.617.2), initially identified in India, has become predominant in several countries, including Portugal. Few studies have compared the effectiveness of mRNA vaccines against Delta versus Alpha variant of concern (VOC) and estimated variant-specific viral loads in vaccine infection breakthroughs cases. In the context of Delta dominance, this information is critical to inform decision-makers regarding the planning of restrictions and vaccination roll-out. Methods We developed a case-case study to compare mRNA vaccines’ effectiveness against Delta (B.1.617.2) versus Alpha (B.1.1.7) variants. We used RT-PCR positive cases notified to the National Surveillance System between 17th of May and 4th of July 2021 (week 20 to 26) and information about demographics and vaccination status through the electronic vaccination register. Whole-genome sequencing (WGS) or spike (S) gene target failure (SGTF) data were used to classify SARS-CoV-2 variants. The odds of vaccinated individuals to become infected (odds of vaccine infection breakthrough) in Delta cases compared to Alpha SARS-CoV-2 cases was estimated by conditional logistic regression adjusted for age group, sex, and matched by the week of diagnosis. As a surrogate of viral load, mean RT-PCR Ct values were stratified and compared between vaccine status and VOC. Results Of the 2 097 SARS-CoV-2 RT-PCR positive cases included in the analysis, 966 (46.1%) were classified with WGS and 1131 (53.9%) with SGTF. Individuals infected with the Delta variant were more frequently vaccinated 162 (12%) than individuals infected with the Alpha variant 38 (5%). We report a statistically significant higher odds of vaccine infection breakthrough for partial (OR=1.70; CI95% 1.18 to 2.47) and complete vaccination (OR=1.96; CI95% 1.22 to 3.14) in the Delta cases when compared to the Alpha cases, suggesting lower mRNA vaccine effectiveness against Delta cases. On our secondary analysis, we observed lower mean Ct values for the Delta VOC cases versus Alpha, regardless the vaccination status. Additionally, the Delta variant cases revealed a Ct-value mean increase of 2.24 (CI95% 0.85 to 3.64) between unvaccinated and fully vaccinated breakthrough cases contrasting with 4.49 (CI95% 2.07 to 6.91) in the Alpha VOC, suggesting a lower impact of vaccine on viral load of Delta cases. Conclusions We found significantly higher odds of vaccine infection breakthrough in Delta cases when compared to Alpha cases, suggesting lower effectiveness of the mRNA vaccines in preventing infection with the Delta variant. Additionally, the vaccine breakthrough cases are estimated to be of higher mean Ct values, suggesting higher infectiousness with the Delta variant infection. These findings can help decision-makers weigh on the application or lifting of control measures and adjusting vaccine roll-out depending on the predominance of the Delta variant and the coverage of partial and complete mRNA vaccination.

ACS Style

Irina Kislaya; Eduardo Freire Rodrigues; Vítor Borges; João Paulo Gomes; Carlos Sousa; José Pedro Almeida; André Peralta-Santos; Baltazar Nunes. Delta variant and mRNA Covid-19 vaccines effectiveness: higher odds of vaccine infection breakthroughs. 2021, 1 .

AMA Style

Irina Kislaya, Eduardo Freire Rodrigues, Vítor Borges, João Paulo Gomes, Carlos Sousa, José Pedro Almeida, André Peralta-Santos, Baltazar Nunes. Delta variant and mRNA Covid-19 vaccines effectiveness: higher odds of vaccine infection breakthroughs. . 2021; ():1.

Chicago/Turabian Style

Irina Kislaya; Eduardo Freire Rodrigues; Vítor Borges; João Paulo Gomes; Carlos Sousa; José Pedro Almeida; André Peralta-Santos; Baltazar Nunes. 2021. "Delta variant and mRNA Covid-19 vaccines effectiveness: higher odds of vaccine infection breakthroughs." , no. : 1.

Article
Published: 28 July 2021 in mSphere
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Tracking the within-patient evolution of SARS-CoV-2 is key to understanding how this pandemic virus shapes its genome toward immune evasion and survival. In the present study, by monitoring a long-term COVID-19 immunocompromised patient, we observed the concurrent emergence of mutations potentially associated with immune evasion and/or enhanced transmission, mostly targeting the SARS-CoV-2 key host-interacting protein and antigen.

ACS Style

Vítor Borges; Joana Isidro; Mário Cunha; Daniela Cochicho; Luís Martins; Luís Banha; Margarida Figueiredo; Leonor Rebelo; Maria Céu Trindade; Sílvia Duarte; Luís Vieira; Maria João Alves; Inês Costa; Raquel Guiomar; Madalena Santos; Rita Cortê-Real; André Dias; Diana Póvoas; João Cabo; Carlos Figueiredo; Maria José Manata; Fernando Maltez; Maria Gomes da Silva; João Paulo Gomes. Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. mSphere 2021, e0024421 .

AMA Style

Vítor Borges, Joana Isidro, Mário Cunha, Daniela Cochicho, Luís Martins, Luís Banha, Margarida Figueiredo, Leonor Rebelo, Maria Céu Trindade, Sílvia Duarte, Luís Vieira, Maria João Alves, Inês Costa, Raquel Guiomar, Madalena Santos, Rita Cortê-Real, André Dias, Diana Póvoas, João Cabo, Carlos Figueiredo, Maria José Manata, Fernando Maltez, Maria Gomes da Silva, João Paulo Gomes. Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. mSphere. 2021; ():e0024421.

Chicago/Turabian Style

Vítor Borges; Joana Isidro; Mário Cunha; Daniela Cochicho; Luís Martins; Luís Banha; Margarida Figueiredo; Leonor Rebelo; Maria Céu Trindade; Sílvia Duarte; Luís Vieira; Maria João Alves; Inês Costa; Raquel Guiomar; Madalena Santos; Rita Cortê-Real; André Dias; Diana Póvoas; João Cabo; Carlos Figueiredo; Maria José Manata; Fernando Maltez; Maria Gomes da Silva; João Paulo Gomes. 2021. "Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma." mSphere , no. : e0024421.

Conference paper
Published: 28 May 2021 in ARPHA Conference Abstracts
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A new era of virus surveillance is emerging based on the real-time monitoring of virus evolution at whole-genome scale (World Health Organization 2021). Although national and international health authorities have strongly recommended this technological transition, especially for influenza and SARS-CoV-2 (World Health Organization 2021, Revez et al. 2017), the implementation of genomic surveillance can be particularly challenging due to the lack of bioinformatics infrastructures and/or expertise to process and interpret next-generation sequencing (NGS) data (Oakeson et al. 2017). We developed and implemented INSaFLU-TELE-Vir platform (https://insaflu.insa.pt/) (Borges et al. 2018), which is an influenza- and SARS-CoV-2-oriented bioinformatics free web-based suite that handles primary NGS data (reads) towards the automatic generation of the main “genetic requests'' for effective and timely laboratory surveillance. By handling NGS data collected from any amplicon-based schema (making it applicable for other pathogens), INSaFLU-TELE-Vir enables any laboratory to perform multi-step and intensive bioinformatics analyses in a user-oriented manner without requiring advanced training. INSaFLU-TELE-Vir handles NGS data collected from distinct sequencing technologies (Illumina, Ion Torrent and Oxford Nanopore Technologies), with the possibility of constructing comparative analyses using different technologies. It gives access to user-restricted sample databases and project management, being a transparent and flexible tool specifically designed to automatically update project outputs as more samples are uploaded. Data integration is thus cumulative and scalable, fitting the need for both routine surveillance and outbreak investigation activities. The bioinformatics pipeline consists of six core steps: read quality analysis and improvement, human betacoronaviruses (including SARS-CoV-2 Pango lineages) and influenza type/subtype classification, mutation detection and consensus generation, coverage analysis, alignment/phylogeny, intra-host minor variant detection (and automatic detection of putative mixed infections). read quality analysis and improvement, human betacoronaviruses (including SARS-CoV-2 Pango lineages) and influenza type/subtype classification, mutation detection and consensus generation, coverage analysis, alignment/phylogeny, intra-host minor variant detection (and automatic detection of putative mixed infections). The multiple outputs are provided in nomenclature-stable and standardized formats that can be visualized and explored in situ or through multiple compatible downstream applications for fine-tuned data analysis. Novel features are being implemented into the INSaFLU-TELE-Vir bioinformatics toolkit as part of the OHEJP TELE-Vir (https://onehealthejp.eu/jrp-tele-vir/) project, including rapid detection of selected genotype-phenotype associations, and enhanced geotemporal data visualization. All the code is available in github (https://github.com/INSaFLU) with the possibility of a local docker installation (https://github.com/INSaFLU/docker). A detailed documentation and tutorial is also available (https://insaflu.readthedocs.io/en/latest/). In summary, INSaFLU supplies public health laboratories and researchers with an open and user-friendly framework, potentiating a strengthened and timely multi-country genome-based virus surveillance.

ACS Style

Miguel Pinheiro; Ricardo Pais; Joana Isidro; Miguel Pinto; Carlijn Bogaardt; Joaquin Prada; Daniel Horton; João Gomes; Vítor Borges. INSaFLU-TELE-Vir: an open web-based bioinformatics suite for influenza and SARS-CoV-2 genome-based surveillance. ARPHA Conference Abstracts 2021, 4, e68845 .

AMA Style

Miguel Pinheiro, Ricardo Pais, Joana Isidro, Miguel Pinto, Carlijn Bogaardt, Joaquin Prada, Daniel Horton, João Gomes, Vítor Borges. INSaFLU-TELE-Vir: an open web-based bioinformatics suite for influenza and SARS-CoV-2 genome-based surveillance. ARPHA Conference Abstracts. 2021; 4 ():e68845.

Chicago/Turabian Style

Miguel Pinheiro; Ricardo Pais; Joana Isidro; Miguel Pinto; Carlijn Bogaardt; Joaquin Prada; Daniel Horton; João Gomes; Vítor Borges. 2021. "INSaFLU-TELE-Vir: an open web-based bioinformatics suite for influenza and SARS-CoV-2 genome-based surveillance." ARPHA Conference Abstracts 4, no. : e68845.

Preprint content
Published: 19 May 2021
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“How predictable is evolution?” is a key question in evolutionary biology. Experimental evolution has shown that the evolutionary path of microbes can be extraordinarily reproducible. Here, using experimental evolution in two circulating SARS-CoV-2, we estimate its mutation rate and demonstrate the repeatability of its evolution when facing a new cell type but no immune or drug pressures. We estimate a genomic mutation rate of 3.7×10-6 nt-1 cycle-1 for a lineage of SARS-CoV-2 with the originally described spike protein (CoV-2-D) and of 2.9×10-6 nt-1 cycle-1 for a lineage carrying the D614G mutation that has spread worldwide (CoV-2-G). We further show that mutation accumulation is heterogeneous along the genome, with the spike gene accumulating mutations at a mean rate 16×10-6 nt-1 per infection cycle across backgrounds, five-fold higher than the genomic average. We observe the emergence of mutators in the CoV-2-G background, likely linked to mutations in the RNA-dependent RNA polymerase and/or in the error-correcting exonuclease protein. Despite strong bottlenecks, several de novo mutations spread to high frequencies by selection and considerable convergent evolution in spike occurs. These results demonstrate the high adaptive potential of SARS-CoV-2 during the first stages of cell infection in the absence of immune surveillance.

ACS Style

Vítor Borges; Maria João Alves; Massimo Amicone; Joana Isidro; Líbia Zé-Zé; Sílvia Duarte; Luís Vieira; Raquel Guiomar; João Paulo Gomes; Isabel Gordo. Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. 2021, 1 .

AMA Style

Vítor Borges, Maria João Alves, Massimo Amicone, Joana Isidro, Líbia Zé-Zé, Sílvia Duarte, Luís Vieira, Raquel Guiomar, João Paulo Gomes, Isabel Gordo. Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. . 2021; ():1.

Chicago/Turabian Style

Vítor Borges; Maria João Alves; Massimo Amicone; Joana Isidro; Líbia Zé-Zé; Sílvia Duarte; Luís Vieira; Raquel Guiomar; João Paulo Gomes; Isabel Gordo. 2021. "Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution." , no. : 1.

Article
Published: 01 April 2021 in Viruses
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Dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare institutions affects both patients and health-care workers (HCW), as well as the institutional capacity to provide essential health services. Here, we investigated an outbreak of SARS-CoV-2 in a “non-COVID-19” hospital ward unveiled by massive testing, which challenged the reconstruction of transmission chains. The contacts network during the 15-day period before the screening was investigated, and positive SARS-CoV-2 RNA samples were subjected to virus genome sequencing. Of the 245 tested individuals, 48 (21 patients and 27 HCWs) tested positive for SARS-CoV-2. HCWs were mostly asymptomatic, but the mortality among patients reached 57.1% (12/21). Phylogenetic reconstruction revealed that all cases were part of the same transmission chain. By combining contact tracing and genomic data, including analysis of emerging minor variants, we unveiled a scenario of silent SARS-CoV-2 dissemination, mostly driven by the close contact within the HCWs group and between HCWs and patients. This investigation triggered enhanced prevention and control measures, leading to more timely detection and containment of novel outbreaks. This study shows the benefit of combining genomic and epidemiological data for disclosing complex nosocomial outbreaks, and provides valuable data to prevent transmission of COVID-19 in healthcare facilities.

ACS Style

Vítor Borges; Joana Isidro; Filipe Macedo; José Neves; Luís Silva; Mário Paiva; José Barata; Judite Catarino; Liliana Ciobanu; Sílvia Duarte; Luís Vieira; Raquel Guiomar; João Paulo Gomes. Nosocomial Outbreak of SARS-CoV-2 in a “Non-COVID-19” Hospital Ward: Virus Genome Sequencing as a Key Tool to Understand Cryptic Transmission. Viruses 2021, 13, 604 .

AMA Style

Vítor Borges, Joana Isidro, Filipe Macedo, José Neves, Luís Silva, Mário Paiva, José Barata, Judite Catarino, Liliana Ciobanu, Sílvia Duarte, Luís Vieira, Raquel Guiomar, João Paulo Gomes. Nosocomial Outbreak of SARS-CoV-2 in a “Non-COVID-19” Hospital Ward: Virus Genome Sequencing as a Key Tool to Understand Cryptic Transmission. Viruses. 2021; 13 (4):604.

Chicago/Turabian Style

Vítor Borges; Joana Isidro; Filipe Macedo; José Neves; Luís Silva; Mário Paiva; José Barata; Judite Catarino; Liliana Ciobanu; Sílvia Duarte; Luís Vieira; Raquel Guiomar; João Paulo Gomes. 2021. "Nosocomial Outbreak of SARS-CoV-2 in a “Non-COVID-19” Hospital Ward: Virus Genome Sequencing as a Key Tool to Understand Cryptic Transmission." Viruses 13, no. 4: 604.

Journal article
Published: 11 March 2021 in Eurosurveillance
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We show that the SARS-CoV-2 B.1.1.7 lineage is highly disseminated in Portugal, with the odds of B.1.1.7 proportion increasing at an estimated 89% (95% confidence interval: 83–95%) per week until week 3 2021. RT-PCR spike gene target late detection (SGTL) can constitute a useful surrogate to track B.1.1.7 spread, besides the spike gene target failure (SGTF) proxy. SGTL/SGTF samples were associated with statistically significant higher viral loads, but not with substantial shift in age distribution compared to non-SGTF/SGTL cases.

ACS Style

Vítor Borges; Carlos Sousa; Luís Menezes; António Maia Gonçalves; Miguel Picão; José Pedro Almeida; Margarida Vieita; Rafael Santos; Ana Rita Silva; Mariana Costa; Luís Carneiro; Pedro Casaca; Pedro Pinto-Leite; André Peralta-Santos; Joana Isidro; Sílvia Duarte; Luís Vieira; Raquel Guiomar; Susana Silva; Baltazar Nunes; João P Gomes. Tracking SARS-CoV-2 lineage B.1.1.7 dissemination: insights from nationwide spike gene target failure (SGTF) and spike gene late detection (SGTL) data, Portugal, week 49 2020 to week 3 2021. Eurosurveillance 2021, 26, 2100131 .

AMA Style

Vítor Borges, Carlos Sousa, Luís Menezes, António Maia Gonçalves, Miguel Picão, José Pedro Almeida, Margarida Vieita, Rafael Santos, Ana Rita Silva, Mariana Costa, Luís Carneiro, Pedro Casaca, Pedro Pinto-Leite, André Peralta-Santos, Joana Isidro, Sílvia Duarte, Luís Vieira, Raquel Guiomar, Susana Silva, Baltazar Nunes, João P Gomes. Tracking SARS-CoV-2 lineage B.1.1.7 dissemination: insights from nationwide spike gene target failure (SGTF) and spike gene late detection (SGTL) data, Portugal, week 49 2020 to week 3 2021. Eurosurveillance. 2021; 26 (10):2100131.

Chicago/Turabian Style

Vítor Borges; Carlos Sousa; Luís Menezes; António Maia Gonçalves; Miguel Picão; José Pedro Almeida; Margarida Vieita; Rafael Santos; Ana Rita Silva; Mariana Costa; Luís Carneiro; Pedro Casaca; Pedro Pinto-Leite; André Peralta-Santos; Joana Isidro; Sílvia Duarte; Luís Vieira; Raquel Guiomar; Susana Silva; Baltazar Nunes; João P Gomes. 2021. "Tracking SARS-CoV-2 lineage B.1.1.7 dissemination: insights from nationwide spike gene target failure (SGTF) and spike gene late detection (SGTL) data, Portugal, week 49 2020 to week 3 2021." Eurosurveillance 26, no. 10: 2100131.

Preprint content
Published: 23 February 2021
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Background Dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare institutions affects both patients and health-care workers (HCW), as well as the institutional capacity to provide essential health services. Methods We conducted an investigation of a cluster of SARS-CoV-2 positive cases detected in a “non-COVID-19” hospital ward during Summer 2020. The magnitude of the nosocomial outbreak was disclosed by massive testing, challenging the retrospective reconstruction of the introduction and transmission events. An in-depth contact tracing investigation was carried out to identify the contacts network during the 15-day period before the screening. In parallel, positive SARS-CoV-2 RNA samples were subjected to virus genome sequencing. Results Of the 245 tested individuals, 48 (21 patients and 27 HCWs) tested positive for SARS-CoV-2. HCWs were mostly asymptomatic, but the mortality among the vulnerable patient group reached 57.1% (12/21). Phylogenetic reconstruction revealed that all cases were part of the same transmission chain, thus confirming a single origin behind this nosocomial outbreak. By combining vast epidemiological and genomic data, including analysis of emerging minor variants, we unveiled a scenario of silent SARS-CoV-2 dissemination within the hospital ward, mostly driven by the close contact within the HCWs group and between HCWs and patients. This investigation triggered enhanced prevention and control measures, leading to a more timely detection and containment of novel nosocomial outbreaks. Conclusions The present study shows the benefit of combining genomic and epidemiological data for the investigation of complex nosocomial outbreaks, and provides valuable data to minimize the risk of transmission of COVID-19 in healthcare facilities. Short summary SARS-CoV-2 nosocomial outbreaks are of utmost public health concern. Here, we performed an in-depth investigation of a high-fatality rate nosocomial outbreak by combining vast genomic and epidemiological data, providing valuable information to understand cryptic transmission of SARS-CoV-2 within healthcare institutions.

ACS Style

Vítor Borges; Joana Isidro; Filipe Macedo; José Neves; Luís Silva; Mário Paiva; José Barata; Judite Catarino; Liliana Ciobanu; Sílvia Duarte; Luís Vieira; Raquel Guiomar; João Paulo Gomes. Nosocomial outbreak of SARS-CoV-2 in a “non-COVID-19” hospital ward: virus genome sequencing as a key tool to understand cryptic transmission. 2021, 1 .

AMA Style

Vítor Borges, Joana Isidro, Filipe Macedo, José Neves, Luís Silva, Mário Paiva, José Barata, Judite Catarino, Liliana Ciobanu, Sílvia Duarte, Luís Vieira, Raquel Guiomar, João Paulo Gomes. Nosocomial outbreak of SARS-CoV-2 in a “non-COVID-19” hospital ward: virus genome sequencing as a key tool to understand cryptic transmission. . 2021; ():1.

Chicago/Turabian Style

Vítor Borges; Joana Isidro; Filipe Macedo; José Neves; Luís Silva; Mário Paiva; José Barata; Judite Catarino; Liliana Ciobanu; Sílvia Duarte; Luís Vieira; Raquel Guiomar; João Paulo Gomes. 2021. "Nosocomial outbreak of SARS-CoV-2 in a “non-COVID-19” hospital ward: virus genome sequencing as a key tool to understand cryptic transmission." , no. : 1.

Preprint content
Published: 23 February 2021
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Background Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. This unprecedented collaborative effort culminated in the generation of 1275 SARS-CoV-2 genome sequences, which represent 15.5% of all confirmed cases in March 2020, making Portugal one of the countries generating the highest volumes of SARS-CoV-2 genomic data during early COVID-19 pandemic. Methods We reconstructed and characterized the spatio-temporal dynamics of SARS-CoV-2 introductions and early dissemination in Portugal using recent phylodynamic models that allow integration of individual-based travel history, in order to obtain a more realistic reconstruction of the viral dynamics. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy and Switzerland), which was broadly consistent with the available travel history data, as well as with the countries with most frequent connectivity and/or with the highest number of Portuguese immigrants. Although most introductions were estimated to have occurred during the last week of February and the first week of March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal several weeks before the first confirmed local cases on March 2, 2020. Discussion and Conclusion While the implemented preventive and early control measures seem to have been successful in mitigating community transmission from most independent introductions, our results suggest that their earlier implementation could have largely minimized the number of introductions and subsequent virus expansion. Here we lay the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlight the need for systematic, continuous and geographically-representative genomic surveillance to guide national and international public health authorities toward the characterization and control of SARS-CoV-2 circulating diversity.

ACS Style

V Borges; J Isidro; Ns Trovão; S Duarte; H Cortes-Martins; H Martiniano; I Gordo; R Leite; L Vieira; Portuguese network for SARS-CoV-2 genomics (Consortium); R Guiomar; Jp Gomes. The early dynamics of the SARS-CoV-2 epidemic in Portugal. 2021, 1 .

AMA Style

V Borges, J Isidro, Ns Trovão, S Duarte, H Cortes-Martins, H Martiniano, I Gordo, R Leite, L Vieira, Portuguese network for SARS-CoV-2 genomics (Consortium), R Guiomar, Jp Gomes. The early dynamics of the SARS-CoV-2 epidemic in Portugal. . 2021; ():1.

Chicago/Turabian Style

V Borges; J Isidro; Ns Trovão; S Duarte; H Cortes-Martins; H Martiniano; I Gordo; R Leite; L Vieira; Portuguese network for SARS-CoV-2 genomics (Consortium); R Guiomar; Jp Gomes. 2021. "The early dynamics of the SARS-CoV-2 epidemic in Portugal." , no. : 1.

Journal article
Published: 01 February 2021 in Microbial Genomics
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Neisseria gonorrhoeae , the bacterium responsible for the sexually transmitted disease gonorrhoea, has shown an extraordinary ability to develop antimicrobial resistance (AMR) to multiple classes of antimicrobials. With no available vaccine, managing N. gonorrhoeae infections demands effective preventive measures, antibiotic treatment and epidemiological surveillance. The latter two are progressively being supported by the generation of whole-genome sequencing (WGS) data on behalf of national and international surveillance programmes. In this context, this study aims to perform N. gonorrhoeae clustering into genogroups based on WGS data, for enhanced prospective laboratory surveillance. Particularly, it aims to identify the major circulating WGS-genogroups in Europe and to establish a relationship between these and AMR. Ultimately, it enriches public databases by contributing with WGS data from Portuguese isolates spanning 15 years of surveillance. A total of 3791 carefully inspected N. gonorrhoeae genomes from isolates collected across Europe were analysed using a gene-by-gene approach (i.e. using cgMLST). Analysis of cluster composition and stability allowed the classification of isolates into a two-step hierarchical genogroup level determined by two allelic distance thresholds revealing cluster stability. Genogroup clustering in general agreed with available N. gonorrhoeae typing methods [i.e. MLST (multilocus sequence typing), NG-MAST ( N. gonorrhoeae multi-antigen sequence typing) and PubMLST core-genome groups], highlighting the predominant genogroups circulating in Europe, and revealed that the vast majority of the genogroups present a dominant AMR profile. Additionally, a non-static gene-by-gene approach combined with a more discriminatory threshold for potential epidemiological linkage enabled us to match data with previous reports on outbreaks or transmission chains. In conclusion, this genogroup assignment allows a comprehensive analysis of N. gonorrhoeae genetic diversity and the identification of the WGS-based genogroups circulating in Europe, while facilitating the assessment (and continuous monitoring) of their frequency, geographical dispersion and potential association with specific AMR signatures. This strategy may benefit public-health actions through the prioritization of genogroups to be controlled, the identification of emerging resistance carriage, and the potential facilitation of data sharing and communication.

ACS Style

Miguel Pinto; Vítor Borges; Joana Isidro; João Carlos Rodrigues; Luís Vieira; Maria José Borrego; João Paulo Gomes. Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance. Microbial Genomics 2021, 7, 000481 .

AMA Style

Miguel Pinto, Vítor Borges, Joana Isidro, João Carlos Rodrigues, Luís Vieira, Maria José Borrego, João Paulo Gomes. Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance. Microbial Genomics. 2021; 7 (2):000481.

Chicago/Turabian Style

Miguel Pinto; Vítor Borges; Joana Isidro; João Carlos Rodrigues; Luís Vieira; Maria José Borrego; João Paulo Gomes. 2021. "Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance." Microbial Genomics 7, no. 2: 000481.

Preprint content
Published: 20 December 2020
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Retracing microbial emergence and spread is essential to understanding the evolution and dynamics of pathogens. The bacterial foodborne pathogenListeria monocytogenesclonal complex 1 (Lm-CC1) is the most prevalent clonal group associated with listeriosis, and is strongly associated with cattle and dairy products. Here we analysed 2,021Lm-CC1 isolates collected from 40 countries, since the firstLmisolation to the present day, to define its evolutionary history and population dynamics. Our results suggest thatLm-CC1 spread worldwide from North America following the Industrial Revolution through two waves of expansion, coinciding with the transatlantic livestock trade in the second half of the 19thcentury and the rapid growth of cattle farming in the 20thcentury.Lm-CC1 then firmly established at a local level, with limited inter-country spread. This study provides an unprecedented insight intoLm-CC1 phylogeography and dynamics and can contribute to effective disease surveillance to reduce the burden of listeriosis.

ACS Style

Alexandra Moura; Noemie Lefrancq; Alexandre Leclercq; Thierry Wirth; Vitor Borges; Brent Gilpin; Timothy J. Dallman; Joachim Frey; Eelco Franz; Eva M. Nielsen; Juno Thomas; Arthur Pightling; Benjamin P. Howden; Cheryl L. Tarr; Peter Gerner-Smidt; Simon Cauchemez; Henrik Salje; Sylvain Brisse; Marc Lecuit; for the Listeria CC1 Study Group. Emergence and global spread ofListeria monocytogenesmain clinical clonal complex. 2020, 1 .

AMA Style

Alexandra Moura, Noemie Lefrancq, Alexandre Leclercq, Thierry Wirth, Vitor Borges, Brent Gilpin, Timothy J. Dallman, Joachim Frey, Eelco Franz, Eva M. Nielsen, Juno Thomas, Arthur Pightling, Benjamin P. Howden, Cheryl L. Tarr, Peter Gerner-Smidt, Simon Cauchemez, Henrik Salje, Sylvain Brisse, Marc Lecuit, for the Listeria CC1 Study Group. Emergence and global spread ofListeria monocytogenesmain clinical clonal complex. . 2020; ():1.

Chicago/Turabian Style

Alexandra Moura; Noemie Lefrancq; Alexandre Leclercq; Thierry Wirth; Vitor Borges; Brent Gilpin; Timothy J. Dallman; Joachim Frey; Eelco Franz; Eva M. Nielsen; Juno Thomas; Arthur Pightling; Benjamin P. Howden; Cheryl L. Tarr; Peter Gerner-Smidt; Simon Cauchemez; Henrik Salje; Sylvain Brisse; Marc Lecuit; for the Listeria CC1 Study Group. 2020. "Emergence and global spread ofListeria monocytogenesmain clinical clonal complex." , no. : 1.

Other
Published: 12 August 2020
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Mutations in the Spike motif predicted to correspond to the fusion peptide are considered of interest as this domain is a potential target for anti-viral drug development that plays a pivotal role in inserting SARS-CoV-2 into human cell membranes. We tracked the temporal and geographical spread of a SARS-CoV-2 variant with the Spike D839Y mutation in the fusion peptide, which was detected early during the COVID-19 epidemic in Portugal. We show that this variant was most likely imported from Italy in mid-late February 2020, becoming prevalent in the Northern and Central regions of Portugal, where represented 22% and 59% of the sampled genomes, respectively, until the end of April 2020. 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 March 14th and April 9th (covering the exponential phase of the epidemic), the relative frequency of Spike Y839 variant increased at a rate of 12.1% (6.1%-18.2%, CI 95%) at every three days, being potentially associated with one in each four (20.8-29.7%, CI 95%) COVID-19 cases in Portugal during the same period. This observation places the Spike Y839 variant in the origin of the largest SARS-CoV-2 transmission chain during the first month of the COVID-19 epidemic in Portugal. We hypothesize that population/epidemiological effects (founder effects) and enhanced selective advantage might have concomitantly contributed to the increasing frequency trajectory of the Spike Y839 variant. Screening of the D839Y mutation globally confirmed its detection in 12 additional countries, even though the huge differences in genome sampling between countries hampers any accurate estimate of D839Y global frequency. In summary, our data points out that SARS-CoV-2 Spike Y839 variants, namely the descendent variant of the globally spread G614 variant detected in Portugal, need continuous and close surveillance.

ACS Style

Vítor Borges; Joana Isidro; Helena Cortes-Martins; Sílvia Duarte; Luís Vieira; Ricardo Leite; Isabel Gordo; Constantino P. Caetano; Baltazar Nunes; Regina Sá; Ana Oliveira; Raquel Guiomar; João Paulo Gomes. On the track of the D839Y mutation in the SARS-CoV-2 Spike fusion peptide: emergence and geotemporal spread of a highly prevalent variant in Portugal. 2020, 1 .

AMA Style

Vítor Borges, Joana Isidro, Helena Cortes-Martins, Sílvia Duarte, Luís Vieira, Ricardo Leite, Isabel Gordo, Constantino P. Caetano, Baltazar Nunes, Regina Sá, Ana Oliveira, Raquel Guiomar, João Paulo Gomes. On the track of the D839Y mutation in the SARS-CoV-2 Spike fusion peptide: emergence and geotemporal spread of a highly prevalent variant in Portugal. . 2020; ():1.

Chicago/Turabian Style

Vítor Borges; Joana Isidro; Helena Cortes-Martins; Sílvia Duarte; Luís Vieira; Ricardo Leite; Isabel Gordo; Constantino P. Caetano; Baltazar Nunes; Regina Sá; Ana Oliveira; Raquel Guiomar; João Paulo Gomes. 2020. "On the track of the D839Y mutation in the SARS-CoV-2 Spike fusion peptide: emergence and geotemporal spread of a highly prevalent variant in Portugal." , no. : 1.

Short communication
Published: 10 March 2020 in Science of The Total Environment
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A methicillin-resistant Staphylococcus aureus CC398 was recovered from a wild female boar (Sus scrofa) in the north of Portugal, in 2013 (Sousa et al. 2017). Whole genome sequencing (WGS) revealed this strain carries a new variant of a mecA-containing staphylococcal chromosomal gene cassette (SCCmec) type IV with an uncommon J3 region. WGS studies can facilitate surveillance and provide more detailed characterization of bacterial clones circulating in the wild, reinforcing the need for a one health perspective to better understand and control antimicrobial resistance.

ACS Style

Margarida Sousa; Nuno Silva; Vítor Borges; João P. Gomes; Luís Vieira; Manuela Caniça; Carmen Torres; Gilberto Igrejas; Patrícia Poeta. MRSA CC398 recovered from wild boar harboring new SCCmec type IV J3 variant. Science of The Total Environment 2020, 722, 137845 .

AMA Style

Margarida Sousa, Nuno Silva, Vítor Borges, João P. Gomes, Luís Vieira, Manuela Caniça, Carmen Torres, Gilberto Igrejas, Patrícia Poeta. MRSA CC398 recovered from wild boar harboring new SCCmec type IV J3 variant. Science of The Total Environment. 2020; 722 ():137845.

Chicago/Turabian Style

Margarida Sousa; Nuno Silva; Vítor Borges; João P. Gomes; Luís Vieira; Manuela Caniça; Carmen Torres; Gilberto Igrejas; Patrícia Poeta. 2020. "MRSA CC398 recovered from wild boar harboring new SCCmec type IV J3 variant." Science of The Total Environment 722, no. : 137845.

Preprint content
Published: 13 February 2020
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Aedes albopictus, along with Ae. aegypti, are key arbovirus vectors that have been expanding their geographic range over the last decades. In 2017, Ae. albopictus was detected for the first time at two distinct locations in Portugal. In order to understand how the Ae. albopictus populations recently introduced in Portugal are genetically related and which is their likely route of invasion, we performed an integrative cytochrome C oxidase I gene (COI)- and mitogenome-based phylogeographic analysis of mosquitoes samples collected in Portugal in 2017 and 2018 in the context of the global Ae. albopictus diversity. COI-based analysis (31 partial sequences obtained from 83 mosquitoes) revealed five haplotypes (1 to 5), with haplotype 1 (which is widely distributed in temperate areas worldwide) being detected in both locations. Haplotypes 2 and 3 were exclusively found in Southern region (Algarve), while haplotype 4 and 5 were only detected in the North of Portugal (Penafiel, Oporto region). Subsequent high discriminatory analyses based on Ae. albopictus mitogenome (17 novel sequences) not only confirmed a high degree of genetic variability within and between populations at both geographic locations (compatible with the Ae. albopictus mosquito populations circulating in Europe), but also revealed two mitogenome mutational signatures not previously reported at worldwide level. While our results generally sustain the occurrence of multiple introduction events, fine mitogenome sequence inspection further indicates a possible Ae. albopictus migration within the country, from the Northern introduction locality to the Southern region. In summary, the observed scenario of high Ae. albopictus genetic diversity in Portugal, together with the detection of mosquitoes in successive years since 2017 in Algarve and Penafiel, points that both Ae. albopictus populations seem to be already locally establish, as its presence has been reported for three consecutive years, raising the public health awareness for future mosquito-borne diseases outbreaks.Author SummaryIn 2017, Aedes albopictus was reported for the first time in Portugal at two distinct locations, in the premises of a tyre company in Penafiel, in the North, and nearby a golf course in Algarve, a tourism destination in the southernmost country region. The geographical spread of this species is boosted by larvae and desiccation-resistant eggs transport in aquatic trade goods, as tires and aquatic plants, and adult anthropophilic behavior that favors passive land transportation. In Portugal, especially in the Southern region, temperate climate conditions are adequate for adult mosquitoes survival most of the year. In a way to understand the genetic variability of Ae. albopictus populations introduced in Portugal, we analyzed 31 cytochrome C oxidase I gene (COI) partial sequences and 17 mitogenome sequences, integrating them in the context of the global Ae. albopictus phylogeographic diversity (i.e., 183 COI and 26 mitogenome sequences previously reported at worldwide level). Although COI haplotype 1 predominated, four additional haplotypes (2 to 5) were detected in Portugal. Subsequent in-depth mitogenome analysis revealed considerable genetic diversity, including not only sequences relating to mitogenomes reported mainly from Italy, Japan and China, but also two novel mitogenome mutational signatures.Our study indicate that Ae. albopictus is locally established in Portugal and intra-country dispersal may have already happened, highlighting the challenges for vector surveillance and control programs aiming at restraining arbovirus disease burden in the future.

ACS Style

Libia Ze-Ze; Vitor Borges; Hugo Costa Osório; Jorge Machado; Joao Paulo Gomes; Maria Joao Alves. Mitogenome diversity of Aedes (Stegomyia) albopictus: Detection of multiple introduction events in Portugal and potential within-country dispersal. 2020, 1 .

AMA Style

Libia Ze-Ze, Vitor Borges, Hugo Costa Osório, Jorge Machado, Joao Paulo Gomes, Maria Joao Alves. Mitogenome diversity of Aedes (Stegomyia) albopictus: Detection of multiple introduction events in Portugal and potential within-country dispersal. . 2020; ():1.

Chicago/Turabian Style

Libia Ze-Ze; Vitor Borges; Hugo Costa Osório; Jorge Machado; Joao Paulo Gomes; Maria Joao Alves. 2020. "Mitogenome diversity of Aedes (Stegomyia) albopictus: Detection of multiple introduction events in Portugal and potential within-country dispersal." , no. : 1.

Journal article
Published: 01 February 2020 in OMICS: A Journal of Integrative Biology
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Antibiotic resistance and hospital acquired infections are on the rise worldwide. Vancomycin-resistant enterococci have been reported in clinical settings in recent decades. In this multiomics study, we provide comprehensive proteomic and transcriptomic analyses of a vancomycin-resistant Enterococcus faecalis clinical isolate from a patient with a urinary tract infection. The previous genotypic profile of the strain C2620 indicated the presence of antibiotic resistance genes characteristic of the vanB cluster. To further investigate the transcriptome of this pathogenic strain, we used whole genome sequencing and RNA-sequencing to detect and quantify the genes expressed. In parallel, we used two-dimensional gel electrophoresis followed by MALDI-TOF/MS (Matrix-assisted laser desorption/ionization-Time-of-flight/Mass spectrometry) to identify the proteins in the proteome. We studied the membrane and cytoplasm subproteomes separately. From a total of 207 analysis spots, we identified 118 proteins. The protein list was compared to the results obtained from the full transcriptome assay. Several genes and proteins related to stress and cellular response were identified, as well as some linked to antibiotic and drug responses, which is consistent with the known state of multiresistance. Even though the correlation between transcriptome and proteome data is not yet fully understood, the use of multiomics approaches has proven to be increasingly relevant to achieve deeper insights into the survival ability of pathogenic bacteria found in health care facilities.

ACS Style

Luís Pinto; Carmen Torres; Concha Gil; Hugo Santos; José Luís Capelo; Vítor Borges; João Paulo Gomes; Catarina Silva; Luís Vieira; Patrícia Poeta; Gilberto Igrejas. Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-ResistantEnterococcus faecalisClinical Strain. OMICS: A Journal of Integrative Biology 2020, 24, 81 -95.

AMA Style

Luís Pinto, Carmen Torres, Concha Gil, Hugo Santos, José Luís Capelo, Vítor Borges, João Paulo Gomes, Catarina Silva, Luís Vieira, Patrícia Poeta, Gilberto Igrejas. Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-ResistantEnterococcus faecalisClinical Strain. OMICS: A Journal of Integrative Biology. 2020; 24 (2):81-95.

Chicago/Turabian Style

Luís Pinto; Carmen Torres; Concha Gil; Hugo Santos; José Luís Capelo; Vítor Borges; João Paulo Gomes; Catarina Silva; Luís Vieira; Patrícia Poeta; Gilberto Igrejas. 2020. "Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-ResistantEnterococcus faecalisClinical Strain." OMICS: A Journal of Integrative Biology 24, no. 2: 81-95.

Journal article
Published: 30 January 2020 in Infection, Genetics and Evolution
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Arcobacter butzleri is a foodborne emerging human pathogen, frequently displaying a multidrug resistant character. Still, the lack of comprehensive genome-scale comparative analysis has limited our knowledge on A. butzleri diversification and pathogenicity. Here, we performed a deep genome analysis of A. butzleri focused on decoding its core- and pan-genome diversity and specific genetic traits underlying its pathogenic potential and diverse ecology. A. butzleri (genome size 2.07–2.58 Mbp) revealed a large open pan-genome with 7474 genes (about 50% being singletons) and a small but diverse core-genome with 1165 genes. It presents a plastic virulome (including newly identified determinants), marked by the differential presence of multiple adaptation-related virulence factors, such as the urease cluster ureD(AB)CEFG (phenotypically confirmed), the hypervariable hemagglutinin-encoding hecA, a type I secretion system (T1SS) harboring another agglutinin and a novel VirB/D4 T4SS likely linked to interbacterial competition and cytotoxicity. In addition, A. butzleri harbors a large repertoire of efflux pumps (EPs) and other antibiotic resistant determinants. We unprecedentedly describe a genetic mechanism of A. butzleri macrolides resistance, (inactivation of a TetR repressor likely regulating an EP). Fluoroquinolones resistance correlated with Thr-85-Ile in GyrA and ampicillin resistance was linked to an OXA-15-like β-lactamase. Remarkably, by decoding the polymorphism pattern of the main antigen PorA, we show that A. butzleri is able to exchange porA as a whole and/or hypervariable epitope-encoding regions separately, leading to a multitude of chimeric PorA presentations that can impact pathogen-host interaction during infection. Ultimately, our unprecedented screening of short sequence repeats indicates that phase variation likely modulates A. butzleri key adaptive functions. In summary, this study constitutes a turning point on A. butzleri comparative genomics revealing that this human gastrointestinal pathogen is equipped with vast and diverse virulence and antibiotic resistance arsenals that open a multitude of phenotypic fingerprints for environmental/host adaptation and pathogenicity.

ACS Style

Joana Isidro; Susana Ferreira; Miguel Pinto; Fernanda Domingues; Mónica Oleastro; João Paulo Gomes; Vítor Borges. Virulence and antibiotic resistance plasticity of Arcobacter butzleri: Insights on the genomic diversity of an emerging human pathogen. Infection, Genetics and Evolution 2020, 80, 104213 .

AMA Style

Joana Isidro, Susana Ferreira, Miguel Pinto, Fernanda Domingues, Mónica Oleastro, João Paulo Gomes, Vítor Borges. Virulence and antibiotic resistance plasticity of Arcobacter butzleri: Insights on the genomic diversity of an emerging human pathogen. Infection, Genetics and Evolution. 2020; 80 ():104213.

Chicago/Turabian Style

Joana Isidro; Susana Ferreira; Miguel Pinto; Fernanda Domingues; Mónica Oleastro; João Paulo Gomes; Vítor Borges. 2020. "Virulence and antibiotic resistance plasticity of Arcobacter butzleri: Insights on the genomic diversity of an emerging human pathogen." Infection, Genetics and Evolution 80, no. : 104213.

Protozoology original paper
Published: 02 January 2020 in Parasitology Research
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Advances in molecular epidemiology of Toxoplasma gondii are hampered by technical and cost-associated hurdles underlying the acquisition of genomic data from parasites. In order to implement an enhanced genotyping approach for molecular surveillance of T. gondii, we applied a multi-locus amplicon-based sequencing strategy to samples associated with human infection. This approach, targeting genome-dispersed polymorphic loci potentially involved in adaptation and virulence, genetically discriminated almost all 68 studied strains and revealed a scenario of marked genomic mosaicism. Two-thirds (n = 43) of all strains were classified as recombinant, although recombination seemed to be linked to the classical archetypal lineage. While 92% of the Sag2 archetype I strains revealed genetic mosaicism, only 45% of Sag2 archetype II strains were identified as recombinant. Contrarily to the virulence-associated archetype I, most type II strains (regardless of their recombination background) were non-virulent in mouse. Besides Sag2, some of the newly studied loci (namely the type I/I-like alleles of Sag1, B17, PK1, and Sag3 and type III/III-like alleles of TgM-A) constitute promising candidates to rapidly infer T. gondii mouse virulence. Our successful attempt to capture microsatellite length variation launches good perspectives for the straightforward transition from the laborious intensive historical method to more informative next-generation sequencing (NGS)/bioinformatics-based methodologies. Overall, while T. gondii whole-genome sequencing will be hardly feasible in most laboratories, this study shows that a discrete loci panel has the potential to improve the molecular epidemiology of T. gondii towards a better monitoring of circulating genotypes with clinical importance.

ACS Style

Anabela Vilares; Vítor Borges; Daniel Sampaio; Idalina Ferreira; Susana Martins; Luís Vieira; Maria João Gargaté; João Paulo Gomes. Towards a rapid sequencing-based molecular surveillance and mosaicism investigation of Toxoplasma gondii. Parasitology Research 2020, 119, 587 -599.

AMA Style

Anabela Vilares, Vítor Borges, Daniel Sampaio, Idalina Ferreira, Susana Martins, Luís Vieira, Maria João Gargaté, João Paulo Gomes. Towards a rapid sequencing-based molecular surveillance and mosaicism investigation of Toxoplasma gondii. Parasitology Research. 2020; 119 (2):587-599.

Chicago/Turabian Style

Anabela Vilares; Vítor Borges; Daniel Sampaio; Idalina Ferreira; Susana Martins; Luís Vieira; Maria João Gargaté; João Paulo Gomes. 2020. "Towards a rapid sequencing-based molecular surveillance and mosaicism investigation of Toxoplasma gondii." Parasitology Research 119, no. 2: 587-599.

Book chapter
Published: 01 January 2020 in Chlamydia Biology: From Genome to Disease
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Vítor Borges; Patrick Hyden; João Paulo Gomes; Thomas Rattei. Chlamydia Genomics. Chlamydia Biology: From Genome to Disease 2020, 1 .

AMA Style

Vítor Borges, Patrick Hyden, João Paulo Gomes, Thomas Rattei. Chlamydia Genomics. Chlamydia Biology: From Genome to Disease. 2020; ():1.

Chicago/Turabian Style

Vítor Borges; Patrick Hyden; João Paulo Gomes; Thomas Rattei. 2020. "Chlamydia Genomics." Chlamydia Biology: From Genome to Disease , no. : 1.

Journal article
Published: 01 January 2020 in Emerging Microbes & Infections
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Genomic 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.

ACS Style

Vítor Borges; Joana Isidro; Helena Cortes-Martins; Sílvia Duarte; Luís Vieira; Ricardo Leite; Isabel Gordo; Constantino P. Caetano; Baltazar Nunes; Regina Sá; Ana Oliveira; Raquel Guiomar; João Paulo Gomes. Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Emerging Microbes & Infections 2020, 9, 2488 -2496.

AMA Style

Vítor Borges, Joana Isidro, Helena Cortes-Martins, Sílvia Duarte, Luís Vieira, Ricardo Leite, Isabel Gordo, Constantino P. Caetano, Baltazar Nunes, Regina Sá, Ana Oliveira, Raquel Guiomar, João Paulo Gomes. Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Emerging Microbes & Infections. 2020; 9 (1):2488-2496.

Chicago/Turabian Style

Vítor Borges; Joana Isidro; Helena Cortes-Martins; Sílvia Duarte; Luís Vieira; Ricardo Leite; Isabel Gordo; Constantino P. Caetano; Baltazar Nunes; Regina Sá; Ana Oliveira; Raquel Guiomar; João Paulo Gomes. 2020. "Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal." Emerging Microbes & Infections 9, no. 1: 2488-2496.

Journal article
Published: 01 November 2019 in Microbial Genomics
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Chlamydia trachomatis is the most prevalent sexually transmitted bacterium worldwide and the causative agent of trachoma. Its strains are classified according to their ompA genotypes, which are strongly linked to differential tissue tropism and disease outcomes [ocular disease, urogenital disease and lymphogranuloma venereum (LGV)]. While the genome-based species phylogenetic tree presents four main clades correlating with tropism/prevalence, namely ocular, LGV, urogenital T1 (more prevalent genotypes) and urogenital T2 (less prevalent genotypes), inter-clade exchange of ompA is considered a rare phenomenon probably mediating marked tropism alterations. An LGV epidemic, associated with the clonal expansion of the L2b genotype, has emerged in the last few decades, raising concerns particularly due to its atypical clinical presentation (ulcerative proctitis) and circulation among men who have sex with men (MSM). Here, we report an LGV outbreak, mostly affecting human immunodeficiency virus-positive MSM engaging in high-risk sexual practices, caused by an L2b strain with a rather unique non-LGV ompA signature that precluded the laboratory notification of this outbreak as LGV. C. trachomatis whole-genome capture and sequencing directly from clinical samples was applied to deeply characterize the genomic backbone of this novel LGV outbreak-causing clone. It revealed a chimeric genome structure due to the genetic transfer of ompA and four neighbouring genes from a serovar D/Da strain, likely possessing the genomic backbone associated with the more prevalent urogenital genotypes (T1 clade), to an LGV (L2b) strain. The hybrid L2b/D-Da strain presents the adhesin and immunodominant antigen MOMP (major outer membrane protein) (encoded by ompA) with an epitope repertoire typical of non-invasive genital strains, while keeping the genome-dispersed virulence fingerprint of a classical LGV strain. As previously reported for inter-clade ompA exchange among non-LGV clades, this novel C. trachomatis genomic mosaic involving a contemporary epidemiologically and clinically relevant LGV strain may have implications on its transmission, tissue tropism and pathogenic capabilities. The emergence of variants with epidemic and pathogenic potential highlights the need for more focused surveillance strategies to capture C. trachomatis evolution in action.

ACS Style

Vítor Borges; Dora Cordeiro; Ana Isabel Salas; Zohra Lodhia; Cristina Correia; Joana Isidro; Cândida Fernandes; Ana Maria Rodrigues; Jacinta Azevedo; João Alves; João Roxo; Miguel Rocha; Rita Côrte-Real; Luís Vieira; Maria José Borrego; João Paulo Gomes. Chlamydia trachomatis: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature. Microbial Genomics 2019, 5, e000313 .

AMA Style

Vítor Borges, Dora Cordeiro, Ana Isabel Salas, Zohra Lodhia, Cristina Correia, Joana Isidro, Cândida Fernandes, Ana Maria Rodrigues, Jacinta Azevedo, João Alves, João Roxo, Miguel Rocha, Rita Côrte-Real, Luís Vieira, Maria José Borrego, João Paulo Gomes. Chlamydia trachomatis: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature. Microbial Genomics. 2019; 5 (11):e000313.

Chicago/Turabian Style

Vítor Borges; Dora Cordeiro; Ana Isabel Salas; Zohra Lodhia; Cristina Correia; Joana Isidro; Cândida Fernandes; Ana Maria Rodrigues; Jacinta Azevedo; João Alves; João Roxo; Miguel Rocha; Rita Côrte-Real; Luís Vieira; Maria José Borrego; João Paulo Gomes. 2019. "Chlamydia trachomatis: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature." Microbial Genomics 5, no. 11: e000313.

Preprint content
Published: 19 September 2019
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Arcobacter butzleriis a food and waterborne bacteria and an emerging human pathogen, frequently displaying a multidrug resistant character. Still, no comprehensive genome-scale comparative analysis has been performed so far, which has limited our knowledge onA. butzleridiversification and pathogenicity. Here, we performed a deep genome analysis ofA. butzlerifocused on decoding its core- and pan-genome diversity and specific genetic traits underlying its pathogenic potential and diverse ecology. In total, 49A. butzleristrains (collected from human, animal, food and environmental sources) were screened.A. butzleri(genome size 2.07-2.58 Mbp) revealed a large open pan-genome with 7474 genes (about 50% being singletons) and a small core-genome with 1165 genes. The core-genome is highly diverse (≥55% of the core genes presenting at least 40/49 alleles), being enriched with genes associated with housekeeping functions. In contrast, the accessory genome presented a high proportion of loci with an unknown function, also being particularly overrepresented by genes associated with defence mechanisms.A. butzlerirevealed a plastic virulome (including newly identified determinants), marked by the differential presence of multiple adaptation-related virulence factors, such as the urease clusterureD(AB)CEFG(phenotypically confirmed), the hypervariable hemagglutinin-encodinghecA, a putative type I secretion system (T1SS) harboring another agglutinin potentially related to adherence and a novel VirB/D4 T4SS likely linked to interbacterial competition and cytotoxicity. In addition,A. butzleriharbors a large repertoire of efflux pumps (EPs) (ten “core” and nine differentially present) and other antibiotic resistant determinants. We provide the first description of a genetic determinant of macrolides resistance inA. butzleri, by associating the inactivation of a TetR repressor (likely regulating an EP) with erythromycin resistance. Fluoroquinolones resistance correlated with the Thr-85-Ile substitution in GyrA and ampicillin resistance was linked to an OXA-15-like β-lactamase. Remarkably, by decoding the polymorphism pattern of the porin- and adhesin-encoding main antigen PorA, this study strongly supports that this pathogen is able to exchangeporAas a whole and/or hypervariable epitope-encoding regions separately, leading to a multitude of chimeric PorA presentations that can impact pathogen-host interaction during infection. Ultimately, our unprecedented screening of short sequence repeats detected potential phase-variable genes related to adaptation and host/environment interaction, such as lipopolysaccharide modification and motility/chemotaxis, suggesting that phase variation likely modulateA. butzlerikey adaptive functions.In summary, this study constitutes a turning point onA. butzlericomparative genomics revealing that this human gastrointestinal pathogen is equipped with vast virulence and antibiotic resistance arsenals, which, coupled with its remarkable core- and pan-genome diversity, opens a multitude of phenotypic fingerprints for environmental/host adaptation and pathogenicity.IMPACT STATEMENTDiarrhoeal diseases are the most common cause of human illness caused by foodborne hazards, but the surveillance of diarrhoeal diseases is biased towards the most commonly searched infectious agents (namelyCampylobacter jejuniandC. coli). In fact, other less studied pathogens are frequently found as the etiological agent when refined non-selective culture conditions are applied. A hallmark example is the diarrhoeal-causingArcobacter butzleriwhich, despite being also associated with extra-intestinal diseases, such as bacteremia in humans and mastitis in animals, and displaying high rates of antibiotic resistance, has not yet been profoundly investigated regarding its epidemiology, diversity and pathogenicity. To overcome the general lack of knowledge onA. butzlericomparative genomics, we provide the first comprehensive genome-scale analysis ofA. butzlerifocused on exploring the intraspecies virulome content and diversity, resistance determinants, as well as how this pathogen shapes its genome towards ecological adaptation and host invasion. The unveiled scenario ofA. butzlerirampant diversity and plasticity reinforces the pathogenic potential of this food and waterborne hazard, while opening multiple research lines that will certainly contribute to the future development of more robust species-oriented diagnostics and molecular surveillance ofA. butzleri.DATA SUMMARYA. butzleriraw sequence reads generated in the present study were deposited in the European Nucleotide Archive (ENA) (BioProject PRJEB34441). The assembled contigs (.fasta and .gbk files), the nucleotide sequences of the predicted transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) (.ffn files) and the respective amino acid sequences of the translated CDS sequences (.faa files) are available athttp://doi.org/10.5281/zenodo.3434222. Detailed ENA accession numbers, as well as the draft genome statistics are described in Table S1.

ACS Style

Joana Isidro; Susana Ferreira; Miguel Pinto; Fernanda Domingues; Mónica Oleastro; João Paulo Gomes; Vítor Borges. Virulence and antibiotic resistance plasticity ofArcobacter butzleri: insights on the genomic diversity of an emerging human pathogen. 2019, 775932 .

AMA Style

Joana Isidro, Susana Ferreira, Miguel Pinto, Fernanda Domingues, Mónica Oleastro, João Paulo Gomes, Vítor Borges. Virulence and antibiotic resistance plasticity ofArcobacter butzleri: insights on the genomic diversity of an emerging human pathogen. . 2019; ():775932.

Chicago/Turabian Style

Joana Isidro; Susana Ferreira; Miguel Pinto; Fernanda Domingues; Mónica Oleastro; João Paulo Gomes; Vítor Borges. 2019. "Virulence and antibiotic resistance plasticity ofArcobacter butzleri: insights on the genomic diversity of an emerging human pathogen." , no. : 775932.