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Vítor Borges, PhD (Biology - Molecular Genetics). Researcher at Genomics and Bioinformatics Unit of the Department of Infectious Diseases of the National Institute of Health Dr. Ricardo Jorge (INSA), Portugal. During the last decade, VB has been actively involved in Portugal capacity building for nationwide genomics-informed surveillance of several human pathogens. For instance, he has been deeply engaged in the Portuguese SARS-CoV-2 genomics surveillance, from protocol implementation to sequence data analysis, being the scientific coordinator and co-developer of bioinformatics tools INSaFLU (https://insaflu.insa.pt/) and ReporTree (https://doi.org/10.1186/s13073-023-01196-1). He has participated in several collaborative research projects at national and international level, such as TELE-Vir and BeONE (as workpackage leader), TraSyph (as PI), INNUENDO and COVRIN (as task leader), or DURABLE (as INSA's coordinator). SInce 2024, he has been consultant as external expert for the European Centre for Disease Prevention and Control (ECDC) and/or the European Fodd Safety Authority (EFSA) on behalf of application of pathogen genome sequencing for outbreak investigation and public health surveillance, with emphasis on food- and waterborne diseses (FWD). He focuses on using genomics and transcriptomics to investigate pathogens with impact on public health in order to: i) perform epidemiological surveillance and investigate outbreaks; ii) predict relevant phenotypic properties, such as resistance and virulence; iii) establish or strengthen genotype-phenotype relationships; iv) identify and monitoring the emergence of new (or variant) organisms that may threat the human health; v) decipher the evolutionary history of human pathogens, with emphasis on exploring the pathogen adaptive traits during human infection (within-patient evolution of bacterial pathogens). VB published >75 scientific articles in international scientific journals with peer review [including >20 as first (co-)author)], one book chapter, 3 technical ECDC and/or EFSA expert reports, 1 EFSA funded Project Report, and 3 publications in national scientific journals (http://orcid.org/0000-0003-3767-2209). VB was recently awarded with the Heine-Medin Award 2022 by the European Society for Clinical Virology for his work in genomics surveillance of influenza virus, SARS-CoV-2 and Mpox.
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Identification

Personal identification

Full name
Vítor Manuel Monteiro Borges

Citation names

  • Borges, Vítor

Author identifiers

Ciência ID
111B-2D6F-A6FB
ORCID iD
0000-0003-3767-2209

Email addresses

  • vitor.borges@insa.min-saude.pt (Professional)

Telephones

Telephone
  • 217519227 (Professional)

Addresses

  • INSTITUTO NACIONAL DE SAÚDE DOUTOR RICARDO JORGE | NATIONAL INSTITUTE OF HEALTH DOUTOR RICARDO JORGE, Avenida Padre Cruz, 1649-016, Lisboa, Lisboa, Portugal (Professional)

Knowledge fields

  • Natural sciences - Biological Sciences - Microbiology
  • Medical and Health Sciences - Health Sciences - Infectious Diseases
  • Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Education
Degree Classification
2011 - 2015
Concluded
 Biologia (Doutoramento)
Major in Genética Molecular
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
"Evolutionary dynamics of Chlamydia trachomatis genome and identification of molecular patterns of hypothetical protein coding genes (https://run.unl.pt/handle/10362/15794)" (THESIS/DISSERTATION)
2002 - 2008
Concluded
 Ciências Farmacêuticas (Mestrado integrado)
Universidade de Coimbra Faculdade de Farmácia, Portugal
 16
Affiliation

Science

Category
Host institution 		Employer
2018 - Current Auxiliary Researcher (Research) Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
Instituto Nacional de Saúde Doutor Ricardo Jorge IP Departamento de Doenças Infeciosas, Portugal

Other Careers

Category
Host institution 		Employer
2014 - 2018 Técnico Superior (Técnico Superior) Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
Instituto Nacional de Saúde Doutor Ricardo Jorge IP Departamento de Doenças Infeciosas, Portugal

Others

Category
Host institution 		Employer
2011 - 2015 Bolseiro de Doutoramento Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
Instituto Nacional de Saúde Doutor Ricardo Jorge IP Departamento de Doenças Infeciosas, Portugal
2010 - 2011 Bolseiro de Investigação Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2008 - 2010 Bolseiro de Investigação Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
Instituto Nacional de Saúde Doutor Ricardo Jorge IP Departamento de Doenças Infeciosas, Portugal
Projects

Contract

Designation Funders
2020 - Current BeOne: Building Integrative Tools for One Health Surveillance
BeOne
Researcher
European Union
Ongoing
2020 - Current TELE-VIR: Point-of-incidence toolbox for emerging virus threats
TELE-Vir
Researcher
European Union
Ongoing
2020 - Current Genetic diversity of the novel coronavirus SARS-CoV-2 (COVID-19) in Portugal
234_596874175
Researcher
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2020 - Current FED-AMR - The role of free extracellular DNA in dissemination of antimicrobial resistance over ecosystem boundaries along the food/feed chain
FED-AMR
Researcher
European Union
Ongoing
2020 - Current I-MOVE-COVID-19 - Multidisciplinary European network for research, prevention and control of the COVID-19 pandemic
101003673
 Horizon 2020 Framework Programme
2018 - Current TraSyph - Tracing the Treponema pallidum genetic footprints associated with syphilis outcomes and stages
TraSyph
Principal investigator
European Society of Clinical Microbiology and Infectious Diseases (ESCMID)
Ongoing
2017 - Current GenomePT – National Laboratory for Genome Sequencing and Analysis
POCI-01-0145-FEDER-022184
Researcher
European Union
Ongoing
2015 - Current ANTARES - Anthrax analysis and screening in soils
ANTARES
Researcher
2023 - 2027 DURABLE - Delivering a Unified Research Alliance of Biomedical and public health Laboratories against Epidemics
101102733
Researcher
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
Ongoing
2022/01/01 - 2024/12/31 GenoPheno4trait - Genomic and phenotypic traits contributing to persistence of Listeria monocytogenes in food processing environment
PTDC/BAA-AGR/4194/2021
Researcher
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2021/03/01 - 2023/03/31 COVRIN - SARS-CoV-2 Research Integration and Preparedness - One Health research integration on SARS-CoV2 emergence, risk assessment and preparedness.
JIP06-COVID19-COVRIN-D.2.1. (Grant 773830)
Researcher
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
 Horizon 2020
2020 - 2021 Monitoring the integrity and genetic evolution of SARS-CoV-2 during infection, to support clinical and public health decision
657 (657 (Research4COVID19 - 2nd call)
Researcher
Fundação para a Ciência e a Tecnologia
Ongoing
2017 - 2018/05 Genome-scale scrutiny of chlamydial antigens
Chlantigens
Researcher
Genocea Biosciences Inc, United States
2016 - 2018 A novel cross-sectorial platform for the integration of genomics in surveillance of foodborne pathogens
GP/EFSA/AFSCO/2015/01/CT2 (New approaches in identifying and characterizing microbial and chemical hazards)
Researcher
European Food Safety Authority
Concluded
2016 - 2018 ELiTE - European Listeria Typing exercise
ELiTE
Researcher
European Centre for Disease Prevention and Control (ECDC), Sweden
2015 - 2017 EMERGE - Efficient response to highly dangerous and emerging pathogens at EU level
HP-JA-2014/JA-04-2014/677066
Researcher
European Union
2014/03 - 2015/03 Novel approach to "understand" syphilis
Provided by PTCRIS: 133331
133331
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2011/03 - 2014/08 Characterisation of host cell pathways altered by effectors of Brucella, Chlamydia, and Coxiella: identification of novel therapeutic targets
Provided by PTCRIS: 116473
116473
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
2010/01 - 2013/03 Tracking the synthesis of the Chlamydia cell wall - a biological paradox in intracellular and evasive bacteria
Provided by PTCRIS: 100747
100747
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2008/01 - 2011/04 Microarray-based surveying of Chlamydia trachomatis chromosomal mosaics
71117
Provided by PTCRIS: 71117
Research Fellow
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2009/01/01 - 2011 CHLTRT3SE – Analysis of the cellular function of type III secretion effectors of Chlamydia trachomatis
info:eu-repo/grantAgreement/EC/FP7/230954/EU
 European Commission
Concluded
Outputs

Publications

Book chapter
  1. Borges, Vítor; Hyden, Patrick; Gomes, João Paulo; Rattei, Thomas. "Chlamydia Genomics". In Chlamydia Biology: From Genome to Disease. Caister Academic Press, 2020.
    10.21775/9781912530281.12
Journal article
  1. Áine O’Toole; Richard A. Neher; Nnaemeka Ndodo; Vitor Borges; Ben Gannon; João Paulo Gomes; Natalie Groves; et al. "APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016". Science (2023): https://doi.org/10.1126/science.adg8116.
    10.1126/science.adg8116
  2. Verónica Mixão; Miguel Pinto; Daniel Sobral; Adriano Di Pasquale; João Paulo Gomes; Vítor Borges. "ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data". Genome Medicine (2023): https://doi.org/10.1186/s13073-023-01196-1.
    10.1186/s13073-023-01196-1
  3. Rita Macedo; Joana Isidro; Rita Ferreira; Miguel Pinto; Vítor Borges; Sílvia Duarte; Luís Vieira; João Paulo Gomes. "Molecular Capture of Mycobacterium tuberculosis Genomes Directly from Clinical Samples: A Potential Backup Approach for Epidemiological and Drug Susceptibility Inferences". International Journal of Molecular Sciences (2023): https://doi.org/10.3390/ijms24032912.
    10.3390/ijms24032912
  4. Joana Praça; Rosália Furtado; Anabela Coelho; Cristina Belo Correia; Vítor Borges; João Paulo Gomes; Angela Pista; Rita Batista. "Listeria monocytogenes, Escherichia coli and Coagulase Positive Staphylococci in Cured Raw Milk Cheese from Alentejo Region, Portugal". Microorganisms (2023): https://doi.org/10.3390/microorganisms11020322.
    10.3390/microorganisms11020322
  5. Nunes, A.; Oleastro, M.; Alves, F.; Liassine, N.; Lowe, D.M.; Benejat, L.; Ducounau, A.; et al. "Erratum for Nunes et al., "Recurrent Campylobacter jejuni Infections with In Vivo Selection of Resistance to Macrolides and Carbapenems: Molecular Characterization of Resistance Determinants"". Microbiology spectrum 11 6 (2023): e0312123-e0312123. http://www.scopus.com/inward/record.url?eid=2-s2.0-85180005034&partnerID=MN8TOARS.
    10.1128/spectrum.03121-23
  6. Kislaya, I.; Casaca, P.; Borges, V.; Sousa, C.; Ferreira, B.I.; Fonte, A.; Fernandes, E.; et al. "Comparative Effectiveness of COVID-19 Vaccines in Preventing Infections and Disease Progression from SARS-CoV-2 Omicron BA.5 and BA.2, Portugal". Emerging Infectious Diseases 29 3 (2023): 569-575. http://www.scopus.com/inward/record.url?eid=2-s2.0-85148678879&partnerID=MN8TOARS.
    10.3201/eid2903.221367
  7. Nunes, A.; Oleastro, M.; Alves, F.; Liassine, N.; Lowe, D.M.; Benejat, L.; Ducounau, A.; et al. "Recurrent campylobacter jejuni infections with in vivo selection of resistance to macrolides and carbapenems: Molecular characterization of resistance determinants". Microbiology Spectrum 11 4 (2023): http://www.scopus.com/inward/record.url?eid=2-s2.0-85168243847&partnerID=MN8TOARS.
    10.1128/spectrum.01070-23
  8. Chen, N.F.G.; Chaguza, C.; Gagne, L.; Doucette, M.; Smole, S.; Buzby, E.; Hall, J.; et al. "Development of an amplicon-based sequencing approach in response to the global emergence of mpox". PLoS Biology 21 6 (2023): http://www.scopus.com/inward/record.url?eid=2-s2.0-85161937127&partnerID=MN8TOARS.
    10.1371/journal.pbio.3002151
  9. Kislaya, I.; Peralta-Santos, A.; Borges, V.; Vieira, L.; Sousa, C.; Ferreira, B.; Pelerito, A.; et al. "Comparative complete scheme and booster effectiveness of COVID-19 vaccines in preventing SARS-CoV-2 infections with SARS-CoV-2 Omicron (BA.1) and Delta (B.1.617.2) variants: A case–case study based on electronic health records". Influenza and other Respiratory Viruses 17 3 (2023): http://www.scopus.com/inward/record.url?eid=2-s2.0-85150531666&partnerID=MN8TOARS.
    10.1111/irv.13121
  10. Borges, V.; Duque, M.P.; Martins, J.V.; Vasconcelos, P.; Ferreira, R.; Sobral, D.; Pelerito, A.; et al. "Viral genetic clustering and transmission dynamics of the 2022 mpox outbreak in Portugal". Nature Medicine 29 10 (2023): 2509-2517. http://www.scopus.com/inward/record.url?eid=2-s2.0-85170528891&partnerID=MN8TOARS.
    10.1038/s41591-023-02542-x
  11. Vítor Borges; Joana Isidro; Nídia Sequeira Trovão; Sílvia Duarte; Helena Cortes-Martins; Hugo Martiniano; Isabel Gordo; et al. "SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal". Communications Medicine 2 1 (2022): https://doi.org/10.1038/s43856-022-00072-0.
    10.1038/s43856-022-00072-0
  12. Frederico Bonito; João Alves; Zohra Lodhia; Dora Cordeiro; Vítor Borges; Jacinta Azevedo; Maria José Borrego. "Clinical and Epidemiological Characterization of Lymphogranuloma Venereum in a Sexually Transmitted Diseases Clinic in Lisbon, 2001 to 2020". Sexually Transmitted Diseases (2022): https://doi.org/10.1097/OLQ.0000000000001634.
    10.1097/OLQ.0000000000001634
  13. Angela Pista; Pista Angela; A Pista; Pista A; Â Pista; Pista Â; Ângela Pista; Leonor Silveira; Sofia Ribeiro; Mariana Fontes; Rita Castro; Anabela Coelho; Rosália Furtado; et al. "Pathogenic Escherichia coli, Salmonella spp. and Campylobacter spp. in Two Natural Conservation Centers of Wildlife in Portugal: Genotypic and Phenotypic Characterization". Microorganisms (2022): https://www.mdpi.com/2076-2607/10/11/2132.
    10.3390/microorganisms10112132
  14. Matúš Štefánek; Sigurd Wenner; Vítor Borges; Miguel Pinto; João Paulo Gomes; João Rodrigues; Isabel Faria; et al. "Antimicrobial Resistance and Biofilms Underlying Catheter-Related Bloodstream Coinfection by Enterobacter cloacae Complex and Candida parapsilosis". Antibiotics (2022): https://doi.org/10.3390/antibiotics11091245.
    10.3390/antibiotics11091245
  15. Maria João Gargaté; Anabela Vilares; Idalina Ferreira; Tânia Reis; Susana Martins; Joana Mendonça; Vítor Borges; João Paulo Gomes. "Parallel Propagation of Toxoplasma gondii In Vivo, In Vitro and in Alternate Model: Towards Less Dependence on the Mice Model". Pathogens (2022): https://doi.org/10.3390/pathogens11091038.
    10.3390/pathogens11091038
  16. Regina Sá; Joana Isidro; Vítor Borges; Sílvia Duarte; Luís Vieira; João P Gomes; Sofia Tedim; Judite Matias; Andreia Leite. "Unraveling the hurdles of a large COVID-19 epidemiological investigation by viral genomics". Journal of Infection (2022): https://doi.org/10.1016/j.jinf.2022.05.013.
    10.1016/j.jinf.2022.05.013
  17. Monteiro, Inês P.; Sousa, Sofia; Borges, Vítor; Gonçalves, Paulo; Gomes, João Paulo; Mota, Luís Jaime; Franco, Irina S.. "A Search for Novel Legionella pneumophila Effector Proteins Reveals a Strain Specific Nucleotropic Effector". Frontiers in Cellular and Infection Microbiology 12 (2022): http://dx.doi.org/10.3389/fcimb.2022.864626.
    10.3389/fcimb.2022.864626
  18. Pinto, Miguel; Borges, Vítor; Nascimento, Maria; Martins, Filomena; Pessanha, Maria Ana; Faria, Isabel; Rodrigues, João; et al. "Insights on catheter-related bloodstream infections: a prospective observational study on the catheter colonization and multi-drug resistance". Journal of Hospital Infection (2022): http://dx.doi.org/10.1016/j.jhin.2022.01.025.
    10.1016/j.jhin.2022.01.025
  19. Kislaya, Irina; Rodrigues, Eduardo Freire; Borges, Vítor; Gomes, João P.; Sousa, Carlos; Almeida, José P.; Peralta-Santos, André; Nunes, Baltazar. "Comparative Effectiveness of Coronavirus Vaccine in Preventing Breakthrough Infections among Vaccinated Persons Infected with Delta and Alpha Variants". Emerging Infectious Diseases 28 2 (2022): 331-337. http://dx.doi.org/10.3201/eid2802.211789.
    10.3201/eid2802.211789
  20. Massimo Amicone; Vítor Borges; Maria João Alves; Joana Isidro; Líbia Zé-Zé; Sílvia Duarte; Luís Vieira; et al. "Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution". Evolution, Medicine, and Public Health 10 1 (2022): 142-155. https://doi.org/10.1093/emph/eoac010.
    Accepted • 10.1093/emph/eoac010
  21. Isidro, J.; Borges, V.; Pinto, M.; Sobral, D.; Santos, J.D.; Nunes, A.; Mixão, V.; et al. "Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus". Nature Medicine 28 8 (2022): 1569-1572. http://www.scopus.com/inward/record.url?eid=2-s2.0-85133727701&partnerID=MN8TOARS.
    10.1038/s41591-022-01907-y
  22. Isidro, J.; Borges, V.; Pinto, M.; Sobral, D.; Santos, J.D.; Nunes, A.; Mixão, V.; et al. "Addendum: Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus". Nature medicine 28 10 (2022): 2220-2221. http://www.scopus.com/inward/record.url?eid=2-s2.0-85139804253&partnerID=MN8TOARS.
    10.1038/s41591-022-02036-2
  23. Pereira, I.S.; Pais, S.V.; Borges, V.; Borrego, M.J.; Gomes, J.P.; Mota, L.J.. "The Type III Secretion Effector CteG Mediates Host Cell Lytic Exit of Chlamydia trachomatis". Frontiers in Cellular and Infection Microbiology 12 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85134904576&partnerID=MN8TOARS.
    10.3389/fcimb.2022.902210
  24. Silvestre, I.; Borges, V.; Duarte, S.; Nunes, A.; Sobral, R.; Vieira, L.; Gomes, J.P.; Borrego, M.J.. "Global gene expression analysis of Streptococcus agalactiae at the exponential growth phase". Cellular and Molecular Biology 68 7 (2022): 1-8. http://www.scopus.com/inward/record.url?eid=2-s2.0-85143917237&partnerID=MN8TOARS.
    10.14715/cmb/2022.68.7.1
  25. Ribeiro, M.; Sousa, M.; Borges, V.; Gomes, J.P.; Duarte, S.; Isidro, J.; Vieira, L.; et al. "Bioinformatics study of expression from genomes of epidemiologically related MRSA CC398 isolates from human and wild animal samples". Journal of Proteomics 268 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85138085633&partnerID=MN8TOARS.
    10.1016/j.jprot.2022.104714
  26. Happi, C.; Adetifa, I.; Mbala, P.; Njouom, R.; Nakoune, E.; Happi, A.; Ndodo, N.; et al. "Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus". PLoS Biology 20 8 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85138125659&partnerID=MN8TOARS.
    10.1371/journal.pbio.3001769
  27. Áine O'Toole; Verity Hill; Oliver G. Pybus; Alexander Watts; Issac I. Bogoch; Kamran Khan; Jane P. Messina; et al. "Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch [version 2; peer review: 3 approved]". (2021): https://wellcomeopenresearch.org/articles/6-121/v2.
    10.12688/wellcomeopenres.16661.2
  28. Ana M Correia; Vítor Borges; Joana Isidro; Ana R Lima; Alberto Fernandes; Maria Leonor Godinho; Sílvia Duarte; et al. "Potential recurrence of COVID-19 in a healthcare professional: SARS-CoV-2 genome sequencing confirms contagiousness after re-positivity". International Journal of Infectious Diseases (2021): https://doi.org/10.1016/j.ijid.2021.09.035.
    10.1016/j.ijid.2021.09.035
  29. Vítor Borges; Joana Isidro; Mário Cunha; Daniela Cochicho; Luís Martins; Luís Banha; Margarida Figueiredo; et al. "Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma". mSphere 6 4 (2021): https://doi.org/10.1128/mSphere.00244-21.
    10.1128/mSphere.00244-21
  30. Vítor Borges; Joana Isidro; Filipe Macedo; José Neves; Luís Silva; Mário Paiva; José Barata; et al. "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 4 (2021): 604-604. https://doi.org/10.3390/v13040604.
    10.3390/v13040604
  31. Vítor Borges; Carlos Sousa; Luís Menezes; António Maia Gonçalves; Miguel Picão; José Pedro Almeida; Margarida Vieita; et al. "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 10 (2021): https://doi.org/10.2807/1560-7917.ES.2021.26.10.2100130.
    10.2807/1560-7917.ES.2021.26.10.2100130
  32. 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 7 2 (2021): https://doi.org/10.1099/mgen.0.000481.
    10.1099/mgen.0.000481
  33. Borges, Vítor. "Transcontinental dissemination of the L2b/D-Da recombinant Chlamydia trachomatis Lymphogranuloma venereum (LGV) strain: need of broad multi-country molecular surveillance". Clinical Infectious Diseases (2021):
    https://doi.org/10.1093/cid/ciab067
  34. Funk, T.; Pharris, A.; Spiteri, G.; Bundle, N.; Melidou, A.; Carr, M.; Gonzalez, G.; et al. "Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021". Eurosurveillance 26 16 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85105089603&partnerID=MN8TOARS.
    10.2807/1560-7917.ES.2021.26.16.2100348
  35. Silvestre, I.; Nunes, A.; Borges, V.; Isidro, J.; Silva, C.; Vieira, L.; Gomes, J.P.; Borrego, M.J.. "Genomic insights on DNase production in Streptococcus agalactiae ST17 and ST19 strains". Infection, Genetics and Evolution 93 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85108876433&partnerID=MN8TOARS.
    10.1016/j.meegid.2021.104969
  36. Líbia Zé-Zé; Borges, Vítor; Hugo Costa Osório; Jorge Machado; João Paulo Gomes; Maria João Alves. "Mitogenome diversity of Aedes (Stegomyia) albopictus: Detection of multiple introduction events in Portugal.". PLoS neglected tropical diseases (2020): https://europepmc.org/articles/PMC7549828.
    10.1371/journal.pntd.0008657
  37. 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 80 (2020): 104213-104213. https://doi.org/10.1016/j.meegid.2020.104213.
    10.1016/j.meegid.2020.104213
  38. Sousa, Margarida; Silva, Nuno; Borges, Vítor; P. Gomes, João; Vieira, Luís; Caniça, Manuela; Torres, Carmen; Igrejas, Gilberto; Poeta, Patrícia. "MRSA CC398 recovered from wild boar harboring new SCCmec type IV J3 variant". Science of The Total Environment 722 (2020): 137845. http://dx.doi.org/10.1016/j.scitotenv.2020.137845.
    10.1016/j.scitotenv.2020.137845
  39. Pinto, Luís; Torres, Carmen; Gil, Concha; Santos, Hugo M.; Capelo, José Luís; Borges, Vítor; Gomes, João Paulo; et al. "Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-Resistant Enterococcus faecalis Clinical Strain". OMICS: A Journal of Integrative Biology 24 2 (2020): 81-95. http://dx.doi.org/10.1089/omi.2019.0164.
    10.1089/omi.2019.0164
  40. Vilares, Anabela; Borges, Vítor; Sampaio, Daniel; Ferreira, Idalina; Martins, Susana; Vieira, Luis; Gargaté, Maria João; Gomes, João Paulo. "Towards a rapid sequencing-based molecular surveillance and mosaicism investigation of Toxoplasma gondii". Parasitology Research 119 2 (2020): 587-599. http://dx.doi.org/10.1007/s00436-019-06523-3.
    10.1007/s00436-019-06523-3
  41. Vítor Borges; Joana Isidro; Helena Cortes-Martins; Sílvia Duarte; Luís Vieira; Ricardo Leite; Isabel Gordo; et al. "Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal". Emerging Microbes & Infections 9 1 (2020): 2488-2496. https://doi.org/10.1080/22221751.2020.1844552.
    10.1080/22221751.2020.1844552
  42. Schäfer, W.; Schmidt, T.; Cordsmeier, A.; Borges, V.; Beare, P.A.; Pechstein, J.; Schulze-Luehrmann, J.; et al. "The anti-apoptotic Coxiella burnetii effector protein AnkG is a strain specific virulence factor". Scientific Reports 10 1 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85091279422&partnerID=MN8TOARS.
    10.1038/s41598-020-72340-9
  43. Correia, C.R.; Marçal, M.; Vieira, F.; Santos, E.; Novais, C.; Maria, A.T.; Malveiro, D.; et al. "Congenital SARS-CoV-2 Infection in a Neonate With Severe Acute Respiratory Syndrome". Pediatric Infectious Disease Journal 39 12 (2020): E439-E443. http://www.scopus.com/inward/record.url?eid=2-s2.0-85096509200&partnerID=MN8TOARS.
    10.1097/INF.0000000000002941
  44. Alm, E.; Broberg, E.K.; Connor, T.; Hodcroft, E.B.; Komissarov, A.B.; Maurer-Stroh, S.; Melidou, A.; et al. "Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020". Eurosurveillance 25 32 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85089543989&partnerID=MN8TOARS.
    10.2807/1560-7917.ES.2020.25.32.2001410
  45. Sara V. Pais; Charlotte E. Key; Vítor Borges; Inês S. Pereira; João Paulo Gomes; Derek J. Fisher; Luís Jaime Mota. "CteG is a Chlamydia trachomatis effector protein that associates with the Golgi complex of infected host cells". Scientific Reports 9 1 (2019): https://doi.org/10.1038/s41598-019-42647-3.
    10.1038/s41598-019-42647-3
  46. Borges, Vítor. "Low 2018/19 vaccine effectiveness against influenza A(H3N2) among 15–64-year-olds in Europe: exploration by birth cohort". Eurosurveillance (2019): http://dx.doi.org/10.2807/1560-7917.es.2019.24.48.1900604.
    10.2807/1560-7917.es.2019.24.48.1900604
  47. Borges, Vítor; Cordeiro, Dora; Salas, Ana Isabel; Lodhia, Zohra; Correia, Cristina; Isidro, Joana; Fernandes, Cândida; et al. "Chlamydia trachomatis: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature". Microbial Genomics 5 11 (2019): http://dx.doi.org/10.1099/mgen.0.000313.
    10.1099/mgen.0.000313
  48. Brinkmann, Annika; Andrusch, Andreas; Belka, Ariane; Wylezich, Claudia; Höper, Dirk; Pohlmann, Anne; Nordahl Petersen, Thomas; et al. "Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets". Journal of Clinical Microbiology 57 8 (2019): http://dx.doi.org/10.1128/jcm.00466-19.
    10.1128/jcm.00466-19
  49. Borges, Vítor. "Multiomics Assessment of Gene Expression in a Clinical Strain of CTX-M-15-Producing ST131 Escherichia coli". (2019): http://dx.doi.org/10.3389/fmicb.2019.00831.
    10.3389/fmicb.2019.00831
  50. Borges, Vítor. "Nontuberculous Mycobacteria Persistence in a Cell Model Mimicking Alveolar Macrophages.". Microorganisms (2019): https://doi.org/10.3390/microorganisms7050113.
    10.3390/microorganisms7050113
  51. Macedo, Rita; Pinto, Miguel; Borges, Vítor; Nunes, Alexandra; Oliveira, Olena; Portugal, Isabel; Duarte, Raquel; Gomes, João Paulo. "Evaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosis". Tuberculosis 115 (2019): 81-88. http://dx.doi.org/10.1016/j.tube.2019.02.006.
    10.1016/j.tube.2019.02.006
  52. Borges, Vítor. "Infeções bacterianas sexualmente transmissíveis na era da sequenciação total do genoma". Infecção e Sepsis Ano 6 1 (2019):
    Published
  53. Borges, Vítor. "Genomic Study of a Clostridium difficile Multidrug Resistant Outbreak-Related Clone Reveals Novel Determinants of Resistance". Front Microbiol (2018):
    10.3389/fmicb.2018.02994
  54. Borges, Vítor. "Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015". Eurosurveillance (2018):
    10.2807/1560-7917.ES.2018.23.33.1700798
  55. Borges, Vítor. "Phenotypic signatures and genetic determinants of oxacillin tolerance in a laboratory mutant of Staphylococcus aureus". PlosOne (2018):
    https://doi.org/10.1371/journal.pone.0199707
  56. Borges, Vítor; Pinheiro, Miguel; Pechirra, Pedro; Guiomar, Raquel; Gomes, João Paulo; Vítor Borges; Miguel Pinheiro; et al. "INSaFLU: an automated open web-based bioinformatics suite “from-reads” for influenza whole-genome-sequencing-based surveillance". Genome Medicine 10 1 (2018): http://dx.doi.org/10.1186/s13073-018-0555-0.
    10.1186/s13073-018-0555-0
  57. Isidro, Joana; Santos, Andrea; Nunes, Alexandra; Borges, Vítor; Silva, Catarina; Vieira, Luís; Mendes, Aristides L.; et al. "Imipenem Resistance in Clostridium difficile Ribotype 017, Portugal". Emerging Infectious Diseases 24 4 (2018): 741-745. http://dx.doi.org/10.3201/eid2404.170095.
    10.3201/eid2404.170095
  58. Pardos de la Gandara, Maria; Borges, Vitor; Chung, Marilyn; Milheiriço, Catarina; Gomes, João Paulo; de Lencastre, Herminia; Tomasz, Alexander. "Genetic Determinants of High-Level Oxacillin Resistance in Methicillin-Resistant Staphylococcus aureus". Antimicrobial Agents and Chemotherapy 62 6 (2018): http://dx.doi.org/10.1128/aac.00206-18.
    10.1128/aac.00206-18
  59. Borges, Vítor. "Genetic determinants of high-level oxacillin resistance in MRSA". Antimicrob Agents Chemother (2018):
    10.1128/AAC.00206-18
  60. De La Gandara, M.P.; Borges, V.; Chung, M.; Milheiriço, C.; Gomes, J.P.; De Lencastre, H.; Tomasz, A.. "Correction: Genetic determinants of high-level oxacillin resistance in methicillin-resistant staphylococcus aureus (Antimicrob Agents Chemother (2018) 62: 7 (e01096-18) DOI: 10.1128/AAC.00206-18)". Antimicrobial Agents and Chemotherapy 62 7 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85049103304&partnerID=MN8TOARS.
    10.1128/AAC.01096-18
  61. Repizo, Guillermo D.; Viale, Alejandro M.; Borges, Vítor; Cameranesi, María M.; Taib, Najwa; Espariz, Martín; Brochier-Armanet, Céline; Gomes, João Paulo; Salcedo, Suzana P.. "The Environmental Acinetobacter baumannii Isolate DSM30011 Reveals Clues into the Preantibiotic Era Genome Diversity, Virulence Potential, and Niche Range of a Predominant Nosocomial Pathogen". Genome Biology and Evolution 9 9 (2017): 2292-2307. http://dx.doi.org/10.1093/gbe/evx162.
    10.1093/gbe/evx162
  62. Ferreira, Rita; Borges, Vítor; Borrego, Maria José; Gomes, João Paulo. "Global survey of mRNA levels and decay rates of Chlamydia trachomatis trachoma and lymphogranuloma venereum biovars". Heliyon 3 7 (2017): e00364. http://dx.doi.org/10.1016/j.heliyon.2017.e00364.
    10.1016/j.heliyon.2017.e00364
  63. Borges, Vítor. "PulseNet International: Vision for the Implementation of Whole Genome Sequencing (WGS) for Global Food-borne Disease Surveillance". Eurosurveillance (2017): http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=22807.
    10.2807/1560-7917.ES.2017.22.23.30544
  64. Borges, Vítor. "Insights on Klebsiella pneumoniae Biofilms Assembled on Different Surfaces Using Phenotypic and Genotypic Approaches". Microorganisms (2017): http://www.mdpi.com/2076-2607/5/2/16.
    10.3390/microorganisms5020016
  65. Pinto, Miguel; Borges, Vítor; Antelo, Minia; Pinheiro, Miguel; Nunes, Alexandra; Azevedo, Jacinta; Borrego, Maria José; et al. "Genome-scale analysis of the non-cultivable Treponema pallidum reveals extensive within-patient genetic variation". Nature Microbiology 2 1 (2016): http://dx.doi.org/10.1038/nmicrobiol.2016.190.
    10.1038/nmicrobiol.2016.190
  66. George, Francisco; Shivaji, Tara; Pinto, Catia Sousa; Serra, Luis Antonio Oliveira; Valente, João; Albuquerque, Maria João; Vicêncio, Paula Cristina Olivença; et al. "A large outbreak of Legionnaires’ Disease in an industrial town in Portugal". Revista Portuguesa de Saúde Pública 34 3 (2016): 199-208. http://dx.doi.org/10.1016/j.rpsp.2016.10.001.
    10.1016/j.rpsp.2016.10.001
  67. Borges, Vítor; Nunes, Alexandra; Sampaio, Daniel A.; Vieira, Luís; Machado, Jorge; Simões, Maria J.; Gonçalves, Paulo; Gomes, João P.. "Legionella pneumophila strain associated with the first evidence of person-to-person transmission of Legionnaires’ disease: a unique mosaic genetic backbone". Scientific Reports 6 1 (2016): http://dx.doi.org/10.1038/srep26261.
    10.1038/srep26261
  68. Correia, Ana M.; Ferreira, Joana S.; Borges, Vítor; Nunes, Alexandra; Gomes, Bernardo; Capucho, Rui; Gonçalves, Jorge; et al. "Probable Person-to-Person Transmission of Legionnaires’ Disease". New England Journal of Medicine 374 5 (2016): 497-498. http://dx.doi.org/10.1056/nejmc1505356.
    10.1056/nejmc1505356
  69. Bisle, Stephanie; Klingenbeck, Leonie; Borges, Vítor; Sobotta, Katharina; Schulze-Luehrmann, Jan; Menge, Christian; Heydel, Carsten; Gomes, João Paulo; Lührmann, Anja. "The inhibition of the apoptosis pathway by theCoxiella burnetiieffector protein CaeA requires the EK repetition motif, but is independent of survivin". Virulence 7 4 (2016): 400-412. http://dx.doi.org/10.1080/21505594.2016.1139280.
    10.1080/21505594.2016.1139280
  70. Borges, Vítor; Borges, Vítor; Santos, Andrea; Correia, Cristina Belo; Saraiva, Margarida; Ménard, Armelle; Vieira, Luís; et al. "Helicobacter pullorum isolated from fresh chicken meat - antibiotic resistance and genomic traits of an emerging foodborne pathogen". Applied and Environmental Microbiology 81 23 (2015): 8155-8163. http://dx.doi.org/10.1128/aem.02394-15.
    10.1128/aem.02394-15
  71. Borges, Vítor. "Differential Role of the T6SS in Acinetobacter baumannii Virulence". PLoS ONE (2015): http://www.ncbi.nlm.nih.gov/pubmed/26401654.
    10.1371/journal.pone.0138265
  72. Borges, Vítor. "Chlamydia trachomatis In Vivo to In Vitro Transition Reveals Mechanisms of Phase Variation and Down-Regulation of Virulence Factors". Plos One (2015):
    10.1371/journal.pone.0133420
  73. Borges, Vítor; Gomes, João Paulo. "Deep comparative genomics among Chlamydia trachomatis lymphogranuloma venereum isolates highlights genes potentially involved in pathoadaptation". Infection, Genetics and Evolution 32 (2015): 74-88. http://dx.doi.org/10.1016/j.meegid.2015.02.026.
    10.1016/j.meegid.2015.02.026
  74. Ferreira, Rita; Antelo, Minia; Nunes, Alexandra; Borges, Vítor; Damião, Vera; Borrego, Maria José; Gomes, João Paulo; Borges, Vítor. "In Silico Scrutiny of Genes Revealing Phylogenetic Congruence with Clinical Prevalence or Tropism Properties of Chlamydia trachomatis Strains". G3: Genes|Genomes|Genetics 5 1 (2014): 9-19. http://dx.doi.org/10.1534/g3.114.015354.
    10.1534/g3.114.015354
  75. Borges V; Pinheiro M; Vieira L; Sampaio DA; Nunes A; Borrego MJ; Gomes JP; et al. "Complete Genome Sequence of Chlamydia trachomatis Ocular Serovar C Strain TW-3.". Genome Announcements 2 1 (2014): http://europepmc.org/abstract/med/24459269.
    10.1128/genomeA.01204-13
  76. da Cunha, Maria; Milho, Catarina; Almeida, Filipe; Pais, Sara V; Borges, Vítor; Maurício, Rui; Borrego, Maria; Gomes, João; Mota, Luís. "Identification of type III secretion substrates of Chlamydia trachomatis using Yersinia enterocolitica as a heterologous system". BMC Microbiology 14 1 (2014): 40. http://dx.doi.org/10.1186/1471-2180-14-40.
    10.1186/1471-2180-14-40
  77. Ferreira R; Borges V; Nunes A; Borrego MJ; Gomes JP. "Assessment of the load and transcriptional dynamics of Chlamydia trachomatis plasmid according to strains' tissue tropism.". (2013): http://europepmc.org/abstract/med/23590987.
    10.1016/j.micres.2013.02.001
  78. Borges V; Ferreira R; Nunes A; Sousa-Uva M; Abreu M; Borrego MJ; Gomes JP. "Effect of long-term laboratory propagation on Chlamydia trachomatis genome dynamics.". (2013): http://europepmc.org/abstract/med/23542454.
    10.1016/j.meegid.2013.03.035
  79. Almeida F; Borges V; Ferreira R; Borrego MJ; Gomes JP; Mota LJ. "Polymorphisms in inc proteins and differential expression of inc genes among Chlamydia trachomatis strains correlate with invasiveness and tropism of lymphogranuloma venereum isolates.". (2012): http://europepmc.org/abstract/med/23042990.
    10.1128/JB.01428-12
  80. Borges V; Nunes A; Ferreira R; Borrego MJ; Gomes JP. "Directional evolution of Chlamydia trachomatis towards niche-specific adaptation.". (2012): http://europepmc.org/abstract/med/22961851.
    10.1128/JB.01291-12
  81. Florindo C; Ferreira R; Borges V; Spellerberg B; Gomes JP; Borrego MJ. "Selection of reference genes for real-time expression studies in Streptococcus agalactiae.". (2012): http://europepmc.org/abstract/med/22634000.
    10.1016/j.mimet.2012.05.011
  82. Ferreira R; Borges V; Nunes A; Nogueira PJ; Borrego MJ; Gomes JP. "Impact of loci nature on estimating recombination and mutation rates in Chlamydia trachomatis.". (2012): http://europepmc.org/abstract/med/22870399.
    10.1534/g3.112.002923
  83. Borges V; Ferreira R; Nunes A; Nogueira P; Borrego MJ; Gomes JP. "Normalization strategies for real-time expression data in Chlamydia trachomatis.". (2010): http://europepmc.org/abstract/med/20619305.
    10.1016/j.mimet.2010.06.013
Magazine article
  1. Alexandra Nunes; Borges, Vítor; Miguel Cascais Pinto; 6212-831B-E115. "A Sequenciação Total do Genoma na monitorização de surtos: exemplo do grande surto da Doença dos Legionários em Vila Franca de Xira", Magazine da Sociedade Portuguesa de Microbiologia, 2017, http://www.spmicrobiologia.pt/.
Report
  1. European Centre for Disease Prevention and Control; European Food Safety Authority. 2019. EFSA and ECDC technical report on the collection and analysis of whole genome sequencing data from food-borne pathogens and other relevant microorganisms isolated from human, animal, food, feed and food/feed environmental samples in the joint ECDC–EFSA molecular typing database. https://www.efsa.europa.eu/en/supporting/pub/en-1337.
    10.2903/sp.efsa.2019.EN-1337
  2. Llarena et al. 2018. INNUENDO: A cross-sectoral platform for the integration of genomics in the surveillance of food-borne pathogens.
    10.2903/sp.efsa.2018.EN-1498
  3. European Centre for Disease Prevention and Control. 2016. European Centre for Disease Prevention and Control. Expert opinion on whole genome sequencing for public health surveillance. https://op.europa.eu/en/publication-detail/-/publication/06c035f9-7bd1-11e6-b076-01aa75ed71a1/language-en.
    10.2900/12442
  4. European Centre for Disease Prevention and Control. 2015. European Centre for Disease Prevention and Control. Expert Opinion on the introduction of next-generation typing methods for food- and waterborne diseases in the EU and EEA.. https://www.ecdc.europa.eu/en/publications/Publications/food-and-waterborne-diseases-next-generation-typing-methods.pdf.
    10.2900/453641

Other

Other output
  1. INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance. 2023. Santos, J.D.; Sobral, D.; Pinheiro, M.; Isidro, J.; Bogaardt, C.; Pinto, M.; Eusébio, R.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85179037871&partnerID=MN8TOARS.
    10.21203/rs.3.rs-3556988/v1
  2. Comparative complete scheme and booster effectiveness of COVID-19 vaccines in preventing SARS-CoV-2 infections with SARS-CoV-2 Omicron (BA.1) and Delta (B.1.617.2) variants. 2022.
    https://doi.org/10.1101/2022.01.31.22270200
  3. Omicron (BA.1) SARS-CoV-2 variant is associated with reduced risk of hospitalization and length of stay compared with Delta (B.1.617.2). 2022. https://www.medrxiv.org/content/10.1101/2022.01.20.22269406v2.
    https://doi.org/10.1101/2022.01.20.22269406
  4. Multi-country outbreak of monkeypox virus: phylogenomic characterization and signs of microevolution. 2022. Gomes, J.P.; Isidro, J.; Borges, V.; Pinto, M.; Sobral, D.; Santos, J.; Mixão, V.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85167254651&partnerID=MN8TOARS.
    10.21203/rs.3.rs-1700947/v1
  5. B.1.617.2 SARS-CoV-2 (Delta) variant is associated with increased risk of hospitalization and death compared with B.1.1.7 SARS-CoV-2 (Alpha) variant. 2022. Rodrigues, E.F.; Moreno, J.; Leite, P.P.; Casaca, P.; Nunes, B.; Gomes, J.P.; Ferreira, R.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85125200512&partnerID=MN8TOARS.
    10.1101/2022.01.21.22268602
  6. Delta variant and mRNA Covid-19 vaccines effectiveness: higher odds of vaccine infection breakthroughs. 2021. Irina Kislaya; Eduardo Freire Rodrigues; Vítor Borges; João Paulo Gomes; Carlos Sousa; José Pedro Almeida; André Peralta-Santos; Baltazar Nunes. https://doi.org/10.1101/2021.08.14.21262020.
    10.1101/2021.08.14.21262020
  7. The early dynamics of the SARS-CoV-2 epidemic in Portugal. 2021. V Borges; J Isidro; NS Trovão; S Duarte; H Cortes-Martins; H Martiniano; I Gordo; et al. https://doi.org/10.1101/2021.02.22.21252216.
    10.1101/2021.02.22.21252216
  8. Emergence and global spread of Listeria monocytogenes main clinical clonal complex. Science Advances. 2020. Alexandra Moura; Noémie Lefrancq; Alexandre Leclercq; Thierry Wirth; Vítor Borges; Brent Gilpin; Timothy J. Dallman; et al. https://doi.org/10.1101/2020.12.18.423387.
    10.1101/2020.12.18.423387
  9. Mitogenome diversity of Aedes (Stegomyia) albopictus: Detection of multiple introduction events in Portugal and potential within-country dispersal. 2020. Zé-Zé, L.; Borges, V.; Osório, H.C.; Machado, J.; Gomes, J.P.; Alves, M.J.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85098822506&partnerID=MN8TOARS.
    10.1101/2020.02.12.945741
  10. 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. Borges, V.; Isidro, J.; Cortes-Martins, H.; Duarte, S.; Vieira, L.; Leite, R.; Gordo, I.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85098615611&partnerID=MN8TOARS.
    10.1101/2020.08.10.20171884
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2021/10/19 INSaFLU-TELE-Vir: an open web-based bioinformatics suite for genome-based surveillance of influenza, SARS-CoV-2 and other pathogens ISIRV-WHO Virtual Conference, COVID-19, Influenza and RSV: Surveillance-Informed Prevention and Treatment, 19-21 October 2021
ISIRV-WHO
2021/04/27 Genomic epidemiology of SARS-CoV-2 in Portugal: supporting evidence-informed public health decision-making International Open Conference | Emerging Infectious Diseases
University of Coimbra, Portugal (Coimbra, Portugal)
2021/01/27 Transcontinental dissemination of the L2b/D-Da recombinant Chlamydia trachomatis Lymphogranuloma venereum (LGV) strain: need of broad multi-country molecular surveillance ChlamTalks 2021
CBRS - Chlamydia Basic Research Society
2020/10/02 Genetic diversity of the novel coronavirus SARS-CoV-2 (COVID-19) in Portugal XV CICS-UBI Symposium
CICS-UBI
2020/06/01 INSaFLU: open web-based bioinformatics suite for genome-based surveillance of influenza virus and other pathogens, such as SARS-CoV-2 WHO Europe Laboratory Workshop
World Health Organization (WHO)
2020/05/20 INSaFLU: open web-based bioinformatics suite for genome-based surveillance of influenza virus and other pathogens, such as SARS-CoV-2 ECDC COVID-19 Laboratory Networks Influenza
European Centre for Disease Prevention and Control (ECDC)
2020/05/05 Estudo da diversidade genética do novo coronavírus SARS-CoV-2 (COVID-19) em Portugal Webinar “Testes de Diagnóstico da Infeção por SARS-CoV-2”
Ordem dos farmacêuticos
2020/04/09 Diversidade genética do novo coronavírus SARS-CoV-2 (COVID-19) em Portugal Ciclo de Conferências AE FFUL
Associação de Estudantes da Faculdade de Farmácia da Universidade de Lisboa (Lisboa, Portugal)
2019/09/19 Chlamydia trachomatis outbreak: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature 12th International Meeting on Microbial Epidemiological Markers (IMMEM XII)
European Society of Clinical Microbiology and Infectious Diseases (ESCMID) (Dubrovnik, Croatia)
2019/06/24 INSaFLU: an influenza-oriented open web-based bioinformatics suite for next-generation sequencing-based surveillance 2nd Workshop on Next Generation Sequencing in Clinical Virology
European Society for Clinical Virology (Valência, Spain)
2019/06/04 INSaFLU - a bioinformatics framework that potentiates the integration of influenza genome sequencing data for an enhanced and harmonized global flu surveillance Seminário Ricardo Jorge
Instituto Nacional de Saúde Doutor Ricardo Jorge (Lisboa, Portugal)
2019/03/21 INSaFLU: Vigilância da Gripe à Escala Global Portugal eHealth Summit
Serviços Partilhados do Ministério da Saúde (SPMS) (Lisboa, Portugal)
2019/03 Insights on the intra-patient genetic heterogeneity of Chlamydia trachomatis Chlamydia Basic Research Society (CBRS) - Ninth Biennial Meeting
Chlamydia Basic Research Society (CBRS)
2018/11/23 Infecções Sexualmente Transmissíveis na era da sequenciação total do genoma . 39.º Ciclos de Conferências sobre Doenças Infecciosas do Serviço de Doenças Infecciosas do CHLN
Hospital de Santa Maria, Lisboa (Lisboa, Portugal)
2018/11 Whole genome analysis of influenza A(H3) viruses detected between 2016-2018 in the scope of EuroEVA/I-MOVE vaccine effectiveness study European Scientific Conference on Applied Infectious Disease Epidemiology (ESCAIDE)
European Centre for Disease Prevention and Control (ECDC) (St Julian, Malta)
2018/09/27 Nova era na vigilância laboratorial de perigos microbiológicos: aplicação da sequenciação total do genoma (WGS) 5º Simpósio Nacional Promoção de uma Alimentação Saudável e Segura. Perigos Microbiológicos – Estratégias e Perspectivas
Instituto Nacional de Saúde (INSA) Doutor Ricardo Jorge (Lisboa, Portugal)
2018/06 INSaFLU: an automated open web-based bioinformatics suite “from-reads” for influenza whole-genome-sequencing-based surveillance The Joint WHO/Europe-ECDC Annual Influenza Meeting
World Health Organization (WHO) - Regional Office for Europe (Copenhaga, Denmark)
2018/05/02 Aplicação da sequenciação total do genoma para o estudo de agentes patogénicos XXIV Jornadas de Ciências Farmacêuticas do Instituto Universitário Egas Moniz
Instituto Universitário Egas Moniz (Caparica, Portugal)
2017/10/10 A nova era da vigilância da gripe com o conhecimento do genoma total do vírus ornadas de Doenças Infeciosas - 6ª Reunião Vigilância Epidemiológica da Gripe em Portugal
Instituto Nacional de Saúde (INSA) Doutor Ricardo Jorge (Lisboa, Portugal)
2017/09/28 Porquê transitar para a aplicação da sequenciação total do genoma (WGS)? Fórum de Discussão 'Virar de página na vigilância laboratorial de doenças infeciosas: aplicação da sequenciação total do genoma (WGS)
Instituto Nacional de Saúde (INSA) Doutor Ricardo Jorge (Lisboa, Portugal)
2017/05/08 Within-patient evolution of blood-invading Campylobacter jejuni reveals bacterial genetic drivers of the pathogen-host “arms-race” 2º Dia do Jovem Investigador do Instituto Nacional de Saúde (INSA) Doutor Ricardo Jorge
Instituto Nacional de Saúde (INSA) Doutor Ricardo Jorge (Lisboa, Portugal)
2016/06/21 Application of Next-Generation Sequencing (NGS) to the study of infectious diseases: overview of the three years experience at the National Institute of Health, Portugal European Food- and Waterborne Diseases and Zoonoses network workshop on application of whole genome sequencing (WGS) for surveillance of food- and waterborne diseases in EU/EEA with special focus on Listeria monocytogenes
European Centre for Disease Prevention and Control (ECDC) (Estocolmo, Sweden)
2016/05/11 Targeted WGS of the non-cultivable syphilis-causing agent Treponema pallidum directly from clinical samples - Using SureSelect as a tool for clinical approach Workshop - Next Generation Sequencing
SOQUIMICA (Lisboa, Portugal)
2016/03 Phylogenomic characterization of the causative strain of one of the largest worldwide outbreaks of Legionnaires’ disease that occurred in Portugal in 2014 11th International Meeting on Microbial Epidemiological Markers (IMMEM XI) – Navigating Microbial Genomes: Insights from Next Generation
ESCMID-ESGEM (Estoril, Portugal)
2015/04 Genomic and transcriptomic evaluation of the tropism-specific adaptation of Chlamydia trachomatis to epithelial cells unveils the impact of CT135 loss on the expression of multiple virulence-associated genes Chlamydia Basic Research Society (CBRS) - Seventh Biennial Meeting
Chlamydia Basic Research Society (CBRS) (New Orleans, United States)
2014/12/01 Typing of Food- and Waterborne pathogens and introduction of next generation sequencing in the Portuguese NIH First meeting of the FWD-NEXT Expert Group on Introduction of next generation typing methods for Food- and Waterborne Diseases
European Centre for Disease Prevention and Control (ECDC) (Estocolmo, Sweden)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2020 - Current Genomic and transcriptomic traits driving intra- and inter-patient evolution of clinically relevant Chlamydia trachomatis strains
Co-supervisor of Zohra Gulzar Lodhia
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2019 - Current Development of tools for detection and characterization of two sexually transmitted bacteria: Chlamydia trachomatis and Treponema pallidum.
Co-supervisor of Geraldine Muylder
 EUPHEM (Specialization course)
European Centre for Disease Prevention and Control, Sweden

Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2015 - 2026 Transition from the traditional typing methods to the application of whole genome sequencing (WGS) for surveillance of food- and waterborne diseases
Co-supervisor of Marta Patrícia Ribeiro Ferreira
 Pharmaceutical Engineering Master (Master)
Universidade de Lisboa Faculdade de Farmácia, Portugal
2020 - 2022 Large-scale investigation of a COVID-19 high-incidence region of Portugal: an outbreak analysis using Genomic Epidemiology
Co-supervisor
 Master of Public Health Ana Regina Serra Sá November (Master)
Universidade Nova de Lisboa Escola Nacional de Saúde Pública, Portugal

Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal

Public Health Unit of Baixo Vouga, Portugal
2019 - 2019 Community Finding with Applications on Phylogenetic Networks (Co-supervisor of the internship)
Co-supervisor of Luís Artur Domingues Rita
 EIT Health Master in Technological Innovation in Health (Master)
Instituto Superior Técnico Departamento de Física, Portugal

Conference scientific committee

Conference name Conference host
2019 - 2019 European Scientific Conference on Applied Infectious Disease Epidemiology, ESCAIDE, 2019 Stockholm, Sweden
2018 - 2018 European Scientific Conference on Applied Infectious Disease Epidemiology, ESCAIDE, 2018 Saint Julian's, Malta

Consulting

Activity description Institution / Organization
2019 - Current Consultant as advisor for European Centre for Disease Prevention and Control (ECDC) on behalf of the Advisory Group to update the Applied Epidemiology Competencies. European Centre for Disease Prevention and Control (ECDC), Sweden
2017 - 2019 Consultant as external expert for the European Centre for Disease Prevention and Control (ECDC) on behalf of the joint ECDC-EFSA ad hoc Working Group focused on providing technical support to collect and analyze whole genome sequencing (WGS) data in the joint ECDC-EFSA molecular typing database (as requested by the European Commission). (https://www.efsa.europa.eu/en/supporting/pub/en-1337) European Centre for Disease Prevention and Control (ECDC), Sweden
2014 - 2017 Consultant as external expert for the European Centre for Disease Prevention and Control (ECDC) on behalf of the FWD-NEXT Member State Expert Group of the ECDC regarding the "Introduction of next generation typing methods for Food- and Waterborne Diseases in EU and EEA" (http://ecdc.europa.eu/en/publications/Publications/food-and-waterborne-diseases-next-generation-typing-methods.pdf; http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=22807) European Centre for Disease Prevention and Control (ECDC), Sweden
2016 - 2016 Consultant as external expert for the European Centre for Disease Prevention and Control (ECDC) on behalf of the ECDC strategy to harness whole genome sequencing to strengthen EU outbreak investigations and public health surveillance (http://ecdc.europa.eu/en/publications/Publications/whole-genome-sequencing-for-public-health-surveillance.pdf; https://ecdc.europa.eu/sites/portal/files/media/en/publications/Publications/molecular-typing-EU-surveillance-epidemic-preparedness-2016-19-roadmap.pdf). European Centre for Disease Prevention and Control (ECDC), Sweden

Journal scientific committee

Journal title (ISSN) Publisher
2019 - 2019 Influenza and Other Respiratory Viruses (1750-2659) Wiley (Blackwell Publishing)
2018 - 2018 PLoS ONE (1932-6203) Public Library of Science
2017 - 2017 American Journal of Tropical Medicine and Hygiene (1476-1645) American Society of Tropical Medicine and Hygiene
2017 - 2017 Scientific Reports (2045-2322) Springer Science and Business Media LLC
2017 - 2017 BMC Microbiology (1471-2180) Springer (Biomed Central Ltd.)
2017 - 2017 Journal of Clinical Case Reports and Case Studies Northern California Open Access Publications
2017 - 2017 Frontiers in Microbiology (1664-302X) Frontiers Media SA
2016 - 2016 Infection Genetics and Evolution (1567-1348) Elsevier
2016 - 2016 Mini-Reviews in Medicinal Chemistry (1389-5575) Bentham Science
2015 - 2016 BioMed Research International (2314-6141) Hindawi Limited
Distinctions

Award

2023 Prémio Arnaldo Sampaio 2023
Associação Portuguesa para a Promoção da Saúde Pública (APPSP), Portugal
2022 Heine-Medin Award 2022 by the European Society for Clinical Virology (ESV)
European Society for Clinical Virology, United Kingdom
2022 Medalha de Serviços Distintos - Grau Ouro, do Ministério da Saúde pelo contributo para a Saúde Pública no âmbito do controlo da pandemia de COVID-19 (2020-2022).
Governo da República Portuguesa Ministério da Saúde, Portugal
2018 European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Research Grant 2018 - award for outstanding research projects proposed by young ESCMID members
European Society of Clinical Microbiology and Infectious Diseases (ESCMID) , Switzerland