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+ Technology transfer during the COVID-19 pandemic: report on the first face-to-face practical
+ training course in Brazil
+
+
Transferencia de tecnología durante la epidemia de COVID-19 en Brasil:
+ informe de la primera formación práctica presencial
+
+
+
+
+
+
+
Abstract
+
The objective of this report was to describe the first face-to-face course aimed at
+ training public health professionals in performing real-time genomic surveillance
+ during the pandemic period. Experience report on a theoretical-practical course
+ focusing on genomic research and surveillance, including mobile sequencing
+ technologies, bioinformatics, phylogenetics and epidemiological modeling. There were
+ 162 participants in the event and it was the first major face-to-face training
+ course conducted during the COVID-19 epidemic in Brazil. No cases of SARS-CoV-2
+ infection was detected among the participants at the end of the event, suggesting
+ the safety and effectiveness of all safety measures adopted. The results of this
+ experience suggest that it is possible to conduct professional training safely
+ during pandemics, as long as all safety protocols are followed.
+
Keywords: COVID-19; Pandemic; Professional Training; Health Human
+ Resources Development
+
+
+
Study contributions
+
Main results Technology transfer can take place at large events, as
+ long as safety protocols are strictly enforced. It is important to disseminate, at
+ these events, the concepts of the Responsible Research and Innovation (RRI).
+
Implications for services Face-to-face training course is
+ fundamental for training public health professionals. Technology transfer between
+ research institutions and health services results in updating and improving health
+ system performance.
+
Perspectives Based on the success of the reported technology
+ transfer, a new module will be incorporated into the next edition of VEME (Panama
+ 2022), entitled Virus Evolution to Public Health Policy Makers.
+
+
+
Resumo
+
O relato descrebeu o primeiro curso presencial visando capacitar profissionais de
+ saúde pública na realização de vigilância genômica em tempo real, durante períodos
+ pandêmicos. Relato de experiência sobre um curso teórico-prático com foco em
+ pesquisa e vigilância genômica, incluindo tecnologias de sequenciamento móvel,
+ bioinformática, filogenética e modelagem epidemiológica. O evento contou com 162
+ participantes e foi o primeiro grande treinamento presencial realizado durante a
+ epidemia de covid-19 no Brasil. Não foi detectada infecção pelo SARS-CoV-2 ao final
+ do evento em nenhum participante, sugerindo a segurança e efetividade de todas as
+ medidas de segurança adotadas. Os resultados do evento sugerem que é possível
+ executar capacitação profissional com segurança durante pandemias, desde que
+ seguidos todos os protocolos de segurança.
+
+
+
Contribuições do estudo
+
Principais resultados A transferência tecnológica pode acontecer em
+ grandes eventos, desde que protocolos de segurança sejam executados rigorosamente. É
+ importante disseminar, nesses eventos, os conceitos do movimento Responsible
+ Research and Innovation (RRI).
+
Implicações para os serviços Treinamentos presenciais são
+ fundamentais para a capacitação de profissionais de saúde pública. A transferência
+ tecnológica entre instituições de pesquisa e serviços de saúde resulta na
+ atualização e melhora do desempenho do sistema de saúde.
+
Perspectivas A partir do sucesso da transferência tecnológica
+ relatada, será incorporado um novo módulo na próxima edição do VEME (Panamá, 2022),
+ intitulado Virus Evolution to Public Health Policy Makers.
+
+
+
Resumen
+
Este estudio tuvo como objetivo describir el primer curso presencial para capacitar a
+ los profesionales de la salud pública para llevar a cabo la vigilancia genómica en
+ tiempo real durante los períodos de pandemia. Este es un informe de experiencia en
+ un curso teórico-práctico centrado en la investigación y vigilancia genómica, que
+ incluye secuenciación móvil, bioinformática, filogenética y tecnologías de modelado
+ epidemiológico. Este evento contó con la asistencia de 162 participantes y fue la
+ primera gran capacitación presencial realizada durante la epidemia de COVID-19 en
+ Brasil. No se detectó infección por SARS-CoV-2 al final del evento en ningún
+ participante, lo que sugiere la seguridad y efectividad de todas las medidas de
+ seguridad adoptadas. Por lo tanto, los resultados del evento sugieren que es posible
+ realizar entrenamientos profesionales de manera segura durante pandemias, siempre y
+ cuando se sigan todos los protocolos de seguridad.
+
Palabras-clave: COVID-19; Pandemia; Capacitación Profesional;
+ Capacitación de Recursos Humanos en Salud
+
+
+
INTRODUCTION
+
Pandemics are part of the group of natural disaster events triggered by
+ socio-environmental phenomena and imbalances that affect populations. In this
+ context, on January 30, 2020, the World Health Organization (WHO) characterized the
+ outbreak of Coronavirus Disease 2019 (COVID-19). Having started in Wuhan, China, as
+ a Public Health Emergency of International Concern,1
+ the disease quickly turned into a major global challenge and in March 2020, it was
+ declared as a pandemic, requiring a rapid health response.2
+
+
Understanding the spread of potentially pandemic viral infectious diseases is
+ fundamental in order to support public health decisions. An important method of
+ monitoring these diseases is genomic and epidemiological surveillance, which enables
+ the rapid identification of these infectious agents. Since the beginning of the3
+ pandemic, the spread of the causative agent - Severe Acute Respiratory Syndrome
+ Coronavirus 2 (SARS-CoV-2) - of COVID-19 has been monitored worldwide, with
+ different surveillance strategies, by which the virus evolution can be observed and
+ shared in real time.4
+
+
In Brazil, each Federative Unit (UF), including the Federal District, has a Central
+ Public Health Laboratory (Laboratório Central de Saúde Pública - LACEN),
+ under the General Coordination of Public Health Laboratories (Coordenação-Geral
+ de Laboratórios de Saúde Pública - CGLAB), within Health and Environment
+ Surveillance Secretariat of the Ministry of Health. The LACENs have, as their main
+ function, to assist the states in the areas of epidemiological, sanitary and
+ environmental surveillance (Organic Law No. 8080).5
+ Consequently, these laboratories are involved in the diagnosis and monitoring of
+ diseases of public health concern and are responsible for a significant portion of
+ the diagnosis of emerging and re-emerging diseases, such as arboviruses and
+ COVID-19.
+
During the COVID-19 pandemic, LACENs played a key role in identifying variants of
+ concern, given that they receive samples from all regions of the country. However,
+ in addition to the basic infrastructure, updating the bioinformatics tools necessary
+ for data analysis is extremely important. This analysis still represents a major
+ challenge for public health professionals, since it involves specific techniques
+ from the area of scientific research and that are not widely used in practical
+ experience at LACENs.
+
In an attempt to strengthen the action of national epidemiological surveillance
+ through technology transfer, in September 2021, the first face-to-face training was
+ held in Brazil, where the epidemiological and genomic data generated were analyzed
+ by health professionals from LACENs, during the event entitled Bioinformatics
+ Workshop on Virus Evolution and Molecular Epidemiology (VEME).
+
VEME is a traditional course aimed at training participants in the use of
+ bioinformatics tools applied to epidemiology and virus evolution. It features
+ internationally acclaimed professors who are expert on that field, and its founder
+ and organizer is Professor Anne-Mieke Vandamme from KU Leuven, University of Leuven,
+ Belgium. This is an annual event with more than 26 editions, each of them is held in
+ a different city in the world.6
+ The event’s basic premise is the dissemination of scientific knowledge, providing
+ quality training and capacity building, as well as technology transfer to students
+ and professionals from all continents.
+
With the support of the Pan American Health Organization/World Health Organization
+ (PAHO/WHO), the National Council for Scientific and Technological Development
+ (Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq) and
+ the Health Surveillance Secretariat/Ministry of Health (SVS/MS), VEME was held in
+ Brazil, in September 2021.6
+
+
This experience report aims to discuss a face-to-face theoretical and practical
+ course, conducted during the COVID-19 pandemic, for public health professionals,
+ focusing on genomic research and surveillance. The course included topics such as
+ mobile sequencing technologies, bioinformatics, phylogenetics and epidemiological
+ modeling.
+
METHODS
+
Traditionally, the previous 26 editions of VEME took place in a face-to-face format.
+ Due to the COVID-19 pandemic in 2021, VEME had two versions: (i) COVEME, a webinar
+ format event focused on the application of bioinformatics tools in corona virus
+ research; and (ii) VEME light, a face-to-face event focused on training and
+ technology transfer. The event was conducted in both formats based on the concept of
+ Responsible Research and Innovation (RRI), which aims to strengthen the interactions
+ between science and society.7 ),( 8
+
+
As a didactic strategy for training and updating health professionals enrolled in the
+ course, the most commonly used bioinformatics tools in high-impact research were
+ selected: Genome Detective for genome assembly; MAFFT for sequence alignment;
+ AliView for editing sequences manually; IQ-TREE, for estimating phylogenetic signal
+ and constructing maximum likelihood trees; TempEst for estimating the temporal
+ signal; BEAST for constructing dated trees; FigTree for visualizing generated
+ phylogenetic trees; and R Studio for epidemiological analyses and data
+ visualization.9 )-( 16
+
+
VEME light took place between September 5 and 10, 2021, at Ouro Minas Palace Hotel,
+ Belo Horizonte, state of Minas Gerais, Brazil, according to the activity program
+ described in Box 1 .
+ In order to ensure the safety of all participants, the event management team
+ established the sanitary protocols to be followed.
+
+
+
+
+
+ Box 1 Description of the activities
+ performed during VEME light
+
+
+
+
All participants, professors and organizers stayed in single rooms in the hotel where
+ the event took place. The hotel offered a buffet service, with alcohol-based hand
+ sanitizer available in order for all of them to use before putting on gloves (to
+ serve themselves) and settling down in a room specially organized for the
+ participants.
+
The course activities were carried out in a room named Salão Centenário, which was
+ capable of accommodating 900 people, with tables arranged to maintain the necessary
+ social distancing. Each student received a seat and a specific computer, for in
+ silico practices. It was not allowed to change the equipment during the event. The
+ seats and computers were arranged to ensure a minimum distance of 2 meters between
+ them. The hotel cleaning staff performed daily disinfection of the computers and
+ tables using 70% isopropyl alcohol. Water was served in an area outside the
+ classroom in order to ensure the necessary distancing.
+
Students and professors were provided with face shield and an adequate supply of
+ NK95/PFF2 masks that allowed their exchanged every five hours. The use of the
+ personal protective equipment (PPE) was mandatory throughout the course, with a
+ constant reminder to use 70% alcohol-based hand sanitizer.
+
Everyone was advised not to leave the hotel during the days of the event.
+
The training participants, organizing committee, professors and hotel staff were
+ tested for SARS-CoV-2 before the start and at the end of the event. Thus,
+ nasopharyngeal samples were collected and the polymerase chain reaction (PCR) test
+ was performed by employees of Fundação Ezequiel Dias (LACEN/MG), in an equipped
+ temporary room at the event venue. PCR test was performed using Allplex 2019-nCoV
+ Assay (Seegene), aiming to detect the envelope (E), the viral RNA-dependent
+ RNA-polymerase (RdRp) or RNA replicase and the nucleocapsid (N) gene.
+
RESULTS
+
VEME light had a total of 162 participants, including 146 students and 16 professors.
+ Among the students, 131 came from 21 different Brazilian institutions: 64 employees
+ of LACENs and CGLAB; and 67 came from other municipal, academic and research
+ institutions directly involved in emerging and re-emerging infections. The remaining
+ 15 students were from other countries: Mexico, Paraguay, Uruguay, Guatemala, the
+ Dominican Republic and Senegal.
+
For the selection of students, gender equity was taken into account, in addition to
+ the participation of two to three representatives of each of the 27 LACENs in the
+ country. These professionals work directly with the sequencing of SARS-CoV-2 and
+ data analysis. The training course enabled them to perform the necessary analyses
+ for genomic surveillance (genome assembly, phylogenetic analyses, identification of
+ viral variants) and as a result, several scientific publications authored by these
+ professionals are currently underway.17 )-( 20
+
+
All 162 participants, as well as Ouro Minas Palace Hotel staff, were tested for
+ SARS-CoV-2 before the start of the event. Only one hotel employee tested positive
+ and was removed from his activities; among the other participants and hotel staff,
+ no SARS-CoV-2 infection was detected, neither before nor at the end of the event,
+ indicating the safety and effectiveness of all the measures adopted ( Figure
+ 1 ).
+
+
+
+
+
+ Figure 1 VEME light flowchart with
+ description of safety protocols
+
+
+
+
DISCUSSION
+
In recent years, at the initiative of the Ministry of Health, the LACENs have been
+ implementing different Next-Generation Sequencing (NGS) strategies to perform
+ genomic surveillance. This process has enabled each LACEN to generate complete
+ genomes of emerging and re-emerging viral pathogens, circulating and co-circulating
+ in each state. In this scenario, the need arose to train healthcare workers in the
+ use of bioinformatics tools, enabling them to analyze genomic data generated in
+ their laboratories in real time. This would have facilitated the rapid dissemination
+ - among public health authorities - of the number of genotypes and subtypes of the
+ circulating viral strains detected by each of the 27 LACENs, so that control
+ measures could be promptly implemented. Given the demand, this training course has
+ initiated the technology transfer process and capacity building of public health
+ professionals in Brazil for the real-time monitoring and analysis of genomic data.
+
+
It is worth highlighting that during VEME light, concepts of Responsible Research and
+ Innovation RRI were addressed. It is a movement that aims to restructure the way
+ science is integrated into society.7 ),( 8
+ In Brazil, the RRI acronym is not widely adopted and promoted; however, many
+ everyday practices are in line with the spirit of RRI, which seeks a more
+ responsive, reflective, inclusive, and socially responsible science and technology.
+
+
The concept of RRI involves five key principles: Education; Open Access; Ethics;
+ Social Engagement; Gender Equality.7 ),( 8
+ These principles were put into practice during the training course, with education
+ remaining the core of VEME.
+
Education is the basis for technology transfer and capacity building, enabling the
+ dissemination and application of knowledge.21
+ During VEME, in addition to the participation of professors who are experts on that
+ field and internationally recognized for their work, the classes were based on a
+ practical learning approach.
+
The didactic strategy used ensured that the students could apply the tools in real
+ time and that the content covered was more suitable for the practice of each LACEN.
+ Furthermore, in order for each student and public health professional to master the
+ tools presented, they were granted autonomy to apply and disseminate the knowledge
+ acquired at the face-to-face VEME, in their state.
+
VEME provided public health professionals from all Brazilian states with access to
+ knowledge and tools used by leading research centers in the world. This training
+ course has enabled faster detection and monitoring of circulating viral variants in
+ the states, given that trained health professionals began performing real-time
+ genomic surveillance and publishing their results in high-impact journals.17 )-( 20
+
+
The fact that the event organizers only advised the participants to stay at the hotel
+ during the days of the event, without obligating them, and that there was no control
+ over their entry and exit, is a limitation of this study. However, the spirit of
+ collaboration of the professors and enrolled students was reflected in everyone
+ staying at the training location, respecting the proposed safety protocols.
+
The implementation of technology transfer in a face-to-face course, during the
+ COVID-19 epidemic in Brazil, was of great relevance for the training of public
+ health professionals involved. The topics covered during the event enabled not only
+ genomic data generation, but also their rapid analysis. This training process was
+ fundamental for monitoring the evolution of the epidemic at the local level.
+ Motivated by the success of this experience, a new module entitled Virus Evolution
+ to Public Health Policy Makers will be incorporated into the next edition of VEME in
+ Panama in 2022. This training course for health professionals in genomic data
+ analysis represents a milestone in epidemiological surveillance, allowing Brazil not
+ only to efficiently monitor endemic strains, but also to predict new outbreaks
+ through active monitoring and real-time data analysis.
+
+
+
REFERENCES
+
+
+
+
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+ 8 Declich A. RRI
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+ STARBIOS2 project [Internet]. Uppsala: Uppsala University; 2020 [cited
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+ 18 Oliveira EC,
+ Fonseca V, Xavier J, Adelino T, Claro IM, Fabri A, et al. Short report:
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+ 20 Giovanetti M,
+ Pereira LAP, Santiago GA, Fonseca V, Mendoza MPG, Oliveira C, et al.
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+ https://doi.org/10.3201/eid2808.220550
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+
+ 21 Giovanetti M,
+ Alcantara LCJ, Dorea AS, Ferreira QR, Marques WA, Barros JJF, et al.
+ Promoting Responsible Research and Innovation (RRI) during Brazilian
+ activities of genomic and epidemiological surveillance of arboviruses.
+ Front Public Health. 2021;9:693743. doi: 10.3389/fpubh.2021.693743»
+ https://doi.org/10.3389/fpubh.2021.693743
+
+
+
+
+
+
+
+
+
+
+ FUNDING
+ The author Luiz Carlos Júnior Alcântara received financial support
+ from the National Council for Scientific and Technological
+ Development/Ministry of Science, Technology and Innovations
+ (Conselho Nacional de Desenvolvimento Científico e Tecnológico -
+ CNPq/MCTI) (SCON2021-00180).
+
+
+ ACKNOWLEDGEMENTS
+ The authors would like to thank the heads of the Central Public
+ Health Laboratories for their effort in the fight against COVID-19
+ in Brazil; all the professors and students involved in the
+ Bioinformatics Workshop on Virus Evolution and Molecular
+ Epidemiology (VEME) course, for their participation, as well as the
+ staff of Ouro Minas Palace Hotel; special thanks are extended to Dr.
+ Anne-Mieke Vandamme from the Catholic University of Leuven, Belgium.
+
+
+
+ Associate editor:
+
+
+
+
+
+
+
+
Publication Dates
+
+
+
+
+ Publication in this collection 18 Aug 2023
+
+
+ Date of issue 2023
+
+
+
+
+
+
+
History
+
+
+
+
+ Received 18 Aug 2022
+
+
+ Accepted 06 June 2023
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Universidade Federal da Bahia, Instituto Multidisciplinar
+ em Saúde, Vitória da Conquista, BA, Brazil Universidade Federal da Bahia Brazil Vitória da Conquista,
+ BA, Brazil Universidade Federal da Bahia,
+ Instituto Multidisciplinar em Saúde, Vitória da Conquista, BA, Brazil
+
+
+
Escola Bahiana de Medicina e Saúde Pública, Salvador, BA,
+ Brazil Escola Bahiana de Medicina e
+ Saúde Pública Brazil Salvador, BA, Brazil Escola Bahiana de Medicina e Saúde Pública, Salvador,
+ BA, Brazil
+
+
+
Fundação Instituto Oswaldo Cruz, Laboratório de Mosquitos
+ Vetores - Endossimbiontes e Interação Patógeno-Vetor, Belo Horizonte, MG,
+ Brazil Fundação Instituto Oswaldo
+ Cruz Brazil Belo Horizonte, MG, Brazil Fundação Instituto Oswaldo Cruz, Laboratório de
+ Mosquitos Vetores - Endossimbiontes e Interação Patógeno-Vetor, Belo Horizonte, MG,
+ Brazil
+
+
+
Organização Pan-Americana da Saúde, Organização
+ Mundial da Saúde, Brasília, DF, Brazil Organização Mundial da Saúde Brazil Brasília, DF,
+ Brazil Organização Pan-Americana da
+ Saúde, Organização Mundial da Saúde, Brasília, DF, Brazil
+
+
+
Universidade Federal de Minas Gerais, Belo Horizonte, MG,
+ Brazil Universidade Federal de Minas
+ Gerais Brazil Belo Horizonte, MG, Brazil Universidade Federal de Minas Gerais, Belo Horizonte,
+ MG, Brazil
+
+
+
Ministério da Saúde, Secretaria de Vigilância em Saúde e
+ Ambiente, Coordenação-Geral das Arboviroses, Brasília, DF, Brazil Ministério da Saúde Brazil Brasília, DF,
+ Brazil Ministério da Saúde, Secretaria de
+ Vigilância em Saúde e Ambiente, Coordenação-Geral das Arboviroses, Brasília, DF,
+ Brazil
+
+
+
Ministério da Saúde, Secretaria de Vigilância em Saúde e
+ Ambiente, Coordenação-Geral de Laboratórios de Saúde Pública, Brasília, DF,
+ Brazil Ministério da Saúde Brazil Brasília, DF,
+ Brazil Ministério da Saúde, Secretaria de
+ Vigilância em Saúde e Ambiente, Coordenação-Geral de Laboratórios de Saúde Pública,
+ Brasília, DF, Brazil
+
+
+
Pan American Health Organization, Health Emergencies
+ Department, Washington, DC, United States Pan American Health Organization United States Washington, DC, United
+ States Pan American Health Organization,
+ Health Emergencies Department, Washington, DC, United States
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Sunday, September 5
+
+
+
+
+ Registration and Accreditation + sample collection for
+ SARS-CoV-2 diagnosis
+
+
+ Linux command line
+
+
+ Panorama and Surveillance of COVID-19 in Brazil and Latin
+ America Panorama and Surveillance of Arboviruses in Brazil
+
+
+ Yellow Fever, Mayaro, Oropouche and Mayaro viruses in the
+ Brazilian North and Northeast regions Zika, Dengue and Chikungunya viruses
+ in the Brazilian Southeast and Northeast regions SARS-CoV-2 in Brazil
+
+
+ Zoonoses and the Emergence of COVID-19
+
+
+ Monday, September 6
+
+
+ Linux command line
+
+
+ Reference-based genome assembly and error correction algorithms
+
+
+
+ Real time genomic surveillance of SARS-CoV-2 in South Africa
+
+
+
+ De novo genome assembly using Genome Detective software
+
+
+ Tuesday, September 7
+
+
+ Constructing a proper dataset using NCBI web-based tools
+
+
+ Alignment algorithms and Aliview
+
+
+ COVID-19: how sharing, communication and Nextstrain have played
+ a part in the outbreak
+
+
+ IQ-TREE
+
+
+ Alignment and Phylogenetic signal
+
+
+ Wednesday, September 8
+
+
+ Methods for phylogenetic tree reconstruction (NJ e ML)
+
+
+ TempEST
+
+
+ Predicting mosquito-borne transmission using climate data
+
+
+ IQ-TREE e TempEST
+
+
+ Thursday, September 9
+
+
+ Molecular clocks (applications + TreeTime)
+
+
+ TreeTime and BEAST
+
+
+ Friday, September 10
+
+
+ Rstudio
+
+
+ Sample collection for SARS-CoV-2 diagnosis
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Technology transfer during the COVID-19 pandemic: report on the first face-to-face practical
+ training course in Brazil
+
+
Transferencia de tecnología durante la epidemia de COVID-19 en Brasil:
+ informe de la primera formación práctica presencial
+
+
+
+
+
+
+
Abstract
+
The objective of this report was to describe the first face-to-face course aimed at
+ training public health professionals in performing real-time genomic surveillance
+ during the pandemic period. Experience report on a theoretical-practical course
+ focusing on genomic research and surveillance, including mobile sequencing
+ technologies, bioinformatics, phylogenetics and epidemiological modeling. There were
+ 162 participants in the event and it was the first major face-to-face training
+ course conducted during the COVID-19 epidemic in Brazil. No cases of SARS-CoV-2
+ infection was detected among the participants at the end of the event, suggesting
+ the safety and effectiveness of all safety measures adopted. The results of this
+ experience suggest that it is possible to conduct professional training safely
+ during pandemics, as long as all safety protocols are followed.
+
Keywords: COVID-19; Pandemic; Professional Training; Health Human
+ Resources Development
+
+
+
Study contributions
+
Main results Technology transfer can take place at large events, as
+ long as safety protocols are strictly enforced. It is important to disseminate, at
+ these events, the concepts of the Responsible Research and Innovation (RRI).
+
Implications for services Face-to-face training course is
+ fundamental for training public health professionals. Technology transfer between
+ research institutions and health services results in updating and improving health
+ system performance.
+
Perspectives Based on the success of the reported technology
+ transfer, a new module will be incorporated into the next edition of VEME (Panama
+ 2022), entitled Virus Evolution to Public Health Policy Makers.
+
+
+
Resumo
+
O relato descrebeu o primeiro curso presencial visando capacitar profissionais de
+ saúde pública na realização de vigilância genômica em tempo real, durante períodos
+ pandêmicos. Relato de experiência sobre um curso teórico-prático com foco em
+ pesquisa e vigilância genômica, incluindo tecnologias de sequenciamento móvel,
+ bioinformática, filogenética e modelagem epidemiológica. O evento contou com 162
+ participantes e foi o primeiro grande treinamento presencial realizado durante a
+ epidemia de covid-19 no Brasil. Não foi detectada infecção pelo SARS-CoV-2 ao final
+ do evento em nenhum participante, sugerindo a segurança e efetividade de todas as
+ medidas de segurança adotadas. Os resultados do evento sugerem que é possível
+ executar capacitação profissional com segurança durante pandemias, desde que
+ seguidos todos os protocolos de segurança.
+
+
+
Contribuições do estudo
+
Principais resultados A transferência tecnológica pode acontecer em
+ grandes eventos, desde que protocolos de segurança sejam executados rigorosamente. É
+ importante disseminar, nesses eventos, os conceitos do movimento Responsible
+ Research and Innovation (RRI).
+
Implicações para os serviços Treinamentos presenciais são
+ fundamentais para a capacitação de profissionais de saúde pública. A transferência
+ tecnológica entre instituições de pesquisa e serviços de saúde resulta na
+ atualização e melhora do desempenho do sistema de saúde.
+
Perspectivas A partir do sucesso da transferência tecnológica
+ relatada, será incorporado um novo módulo na próxima edição do VEME (Panamá, 2022),
+ intitulado Virus Evolution to Public Health Policy Makers.
+
+
+
Resumen
+
Este estudio tuvo como objetivo describir el primer curso presencial para capacitar a
+ los profesionales de la salud pública para llevar a cabo la vigilancia genómica en
+ tiempo real durante los períodos de pandemia. Este es un informe de experiencia en
+ un curso teórico-práctico centrado en la investigación y vigilancia genómica, que
+ incluye secuenciación móvil, bioinformática, filogenética y tecnologías de modelado
+ epidemiológico. Este evento contó con la asistencia de 162 participantes y fue la
+ primera gran capacitación presencial realizada durante la epidemia de COVID-19 en
+ Brasil. No se detectó infección por SARS-CoV-2 al final del evento en ningún
+ participante, lo que sugiere la seguridad y efectividad de todas las medidas de
+ seguridad adoptadas. Por lo tanto, los resultados del evento sugieren que es posible
+ realizar entrenamientos profesionales de manera segura durante pandemias, siempre y
+ cuando se sigan todos los protocolos de seguridad.
+
Palabras-clave: COVID-19; Pandemia; Capacitación Profesional;
+ Capacitación de Recursos Humanos en Salud
+
+
+
INTRODUCTION
+
Pandemics are part of the group of natural disaster events triggered by
+ socio-environmental phenomena and imbalances that affect populations. In this
+ context, on January 30, 2020, the World Health Organization (WHO) characterized the
+ outbreak of Coronavirus Disease 2019 (COVID-19). Having started in Wuhan, China, as
+ a Public Health Emergency of International Concern,1
+ the disease quickly turned into a major global challenge and in March 2020, it was
+ declared as a pandemic, requiring a rapid health response.2
+
+
Understanding the spread of potentially pandemic viral infectious diseases is
+ fundamental in order to support public health decisions. An important method of
+ monitoring these diseases is genomic and epidemiological surveillance, which enables
+ the rapid identification of these infectious agents. Since the beginning of the3
+ pandemic, the spread of the causative agent - Severe Acute Respiratory Syndrome
+ Coronavirus 2 (SARS-CoV-2) - of COVID-19 has been monitored worldwide, with
+ different surveillance strategies, by which the virus evolution can be observed and
+ shared in real time.4
+
+
In Brazil, each Federative Unit (UF), including the Federal District, has a Central
+ Public Health Laboratory (Laboratório Central de Saúde Pública - LACEN),
+ under the General Coordination of Public Health Laboratories (Coordenação-Geral
+ de Laboratórios de Saúde Pública - CGLAB), within Health and Environment
+ Surveillance Secretariat of the Ministry of Health. The LACENs have, as their main
+ function, to assist the states in the areas of epidemiological, sanitary and
+ environmental surveillance (Organic Law No. 8080).5
+ Consequently, these laboratories are involved in the diagnosis and monitoring of
+ diseases of public health concern and are responsible for a significant portion of
+ the diagnosis of emerging and re-emerging diseases, such as arboviruses and
+ COVID-19.
+
During the COVID-19 pandemic, LACENs played a key role in identifying variants of
+ concern, given that they receive samples from all regions of the country. However,
+ in addition to the basic infrastructure, updating the bioinformatics tools necessary
+ for data analysis is extremely important. This analysis still represents a major
+ challenge for public health professionals, since it involves specific techniques
+ from the area of scientific research and that are not widely used in practical
+ experience at LACENs.
+
In an attempt to strengthen the action of national epidemiological surveillance
+ through technology transfer, in September 2021, the first face-to-face training was
+ held in Brazil, where the epidemiological and genomic data generated were analyzed
+ by health professionals from LACENs, during the event entitled Bioinformatics
+ Workshop on Virus Evolution and Molecular Epidemiology (VEME).
+
VEME is a traditional course aimed at training participants in the use of
+ bioinformatics tools applied to epidemiology and virus evolution. It features
+ internationally acclaimed professors who are expert on that field, and its founder
+ and organizer is Professor Anne-Mieke Vandamme from KU Leuven, University of Leuven,
+ Belgium. This is an annual event with more than 26 editions, each of them is held in
+ a different city in the world.6
+ The event’s basic premise is the dissemination of scientific knowledge, providing
+ quality training and capacity building, as well as technology transfer to students
+ and professionals from all continents.
+
With the support of the Pan American Health Organization/World Health Organization
+ (PAHO/WHO), the National Council for Scientific and Technological Development
+ (Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq) and
+ the Health Surveillance Secretariat/Ministry of Health (SVS/MS), VEME was held in
+ Brazil, in September 2021.6
+
+
This experience report aims to discuss a face-to-face theoretical and practical
+ course, conducted during the COVID-19 pandemic, for public health professionals,
+ focusing on genomic research and surveillance. The course included topics such as
+ mobile sequencing technologies, bioinformatics, phylogenetics and epidemiological
+ modeling.
+
METHODS
+
Traditionally, the previous 26 editions of VEME took place in a face-to-face format.
+ Due to the COVID-19 pandemic in 2021, VEME had two versions: (i) COVEME, a webinar
+ format event focused on the application of bioinformatics tools in corona virus
+ research; and (ii) VEME light, a face-to-face event focused on training and
+ technology transfer. The event was conducted in both formats based on the concept of
+ Responsible Research and Innovation (RRI), which aims to strengthen the interactions
+ between science and society.7 ),( 8
+
+
As a didactic strategy for training and updating health professionals enrolled in the
+ course, the most commonly used bioinformatics tools in high-impact research were
+ selected: Genome Detective for genome assembly; MAFFT for sequence alignment;
+ AliView for editing sequences manually; IQ-TREE, for estimating phylogenetic signal
+ and constructing maximum likelihood trees; TempEst for estimating the temporal
+ signal; BEAST for constructing dated trees; FigTree for visualizing generated
+ phylogenetic trees; and R Studio for epidemiological analyses and data
+ visualization.9 )-( 16
+
+
VEME light took place between September 5 and 10, 2021, at Ouro Minas Palace Hotel,
+ Belo Horizonte, state of Minas Gerais, Brazil, according to the activity program
+ described in Box 1 .
+ In order to ensure the safety of all participants, the event management team
+ established the sanitary protocols to be followed.
+
+
+
+
+
+ Box 1 Description of the activities
+ performed during VEME light
+
+
+
+
All participants, professors and organizers stayed in single rooms in the hotel where
+ the event took place. The hotel offered a buffet service, with alcohol-based hand
+ sanitizer available in order for all of them to use before putting on gloves (to
+ serve themselves) and settling down in a room specially organized for the
+ participants.
+
The course activities were carried out in a room named Salão Centenário, which was
+ capable of accommodating 900 people, with tables arranged to maintain the necessary
+ social distancing. Each student received a seat and a specific computer, for in
+ silico practices. It was not allowed to change the equipment during the event. The
+ seats and computers were arranged to ensure a minimum distance of 2 meters between
+ them. The hotel cleaning staff performed daily disinfection of the computers and
+ tables using 70% isopropyl alcohol. Water was served in an area outside the
+ classroom in order to ensure the necessary distancing.
+
Students and professors were provided with face shield and an adequate supply of
+ NK95/PFF2 masks that allowed their exchanged every five hours. The use of the
+ personal protective equipment (PPE) was mandatory throughout the course, with a
+ constant reminder to use 70% alcohol-based hand sanitizer.
+
Everyone was advised not to leave the hotel during the days of the event.
+
The training participants, organizing committee, professors and hotel staff were
+ tested for SARS-CoV-2 before the start and at the end of the event. Thus,
+ nasopharyngeal samples were collected and the polymerase chain reaction (PCR) test
+ was performed by employees of Fundação Ezequiel Dias (LACEN/MG), in an equipped
+ temporary room at the event venue. PCR test was performed using Allplex 2019-nCoV
+ Assay (Seegene), aiming to detect the envelope (E), the viral RNA-dependent
+ RNA-polymerase (RdRp) or RNA replicase and the nucleocapsid (N) gene.
+
RESULTS
+
VEME light had a total of 162 participants, including 146 students and 16 professors.
+ Among the students, 131 came from 21 different Brazilian institutions: 64 employees
+ of LACENs and CGLAB; and 67 came from other municipal, academic and research
+ institutions directly involved in emerging and re-emerging infections. The remaining
+ 15 students were from other countries: Mexico, Paraguay, Uruguay, Guatemala, the
+ Dominican Republic and Senegal.
+
For the selection of students, gender equity was taken into account, in addition to
+ the participation of two to three representatives of each of the 27 LACENs in the
+ country. These professionals work directly with the sequencing of SARS-CoV-2 and
+ data analysis. The training course enabled them to perform the necessary analyses
+ for genomic surveillance (genome assembly, phylogenetic analyses, identification of
+ viral variants) and as a result, several scientific publications authored by these
+ professionals are currently underway.17 )-( 20
+
+
All 162 participants, as well as Ouro Minas Palace Hotel staff, were tested for
+ SARS-CoV-2 before the start of the event. Only one hotel employee tested positive
+ and was removed from his activities; among the other participants and hotel staff,
+ no SARS-CoV-2 infection was detected, neither before nor at the end of the event,
+ indicating the safety and effectiveness of all the measures adopted ( Figure
+ 1 ).
+
+
+
+
+
+ Figure 1 VEME light flowchart with
+ description of safety protocols
+
+
+
+
DISCUSSION
+
In recent years, at the initiative of the Ministry of Health, the LACENs have been
+ implementing different Next-Generation Sequencing (NGS) strategies to perform
+ genomic surveillance. This process has enabled each LACEN to generate complete
+ genomes of emerging and re-emerging viral pathogens, circulating and co-circulating
+ in each state. In this scenario, the need arose to train healthcare workers in the
+ use of bioinformatics tools, enabling them to analyze genomic data generated in
+ their laboratories in real time. This would have facilitated the rapid dissemination
+ - among public health authorities - of the number of genotypes and subtypes of the
+ circulating viral strains detected by each of the 27 LACENs, so that control
+ measures could be promptly implemented. Given the demand, this training course has
+ initiated the technology transfer process and capacity building of public health
+ professionals in Brazil for the real-time monitoring and analysis of genomic data.
+
+
It is worth highlighting that during VEME light, concepts of Responsible Research and
+ Innovation RRI were addressed. It is a movement that aims to restructure the way
+ science is integrated into society.7 ),( 8
+ In Brazil, the RRI acronym is not widely adopted and promoted; however, many
+ everyday practices are in line with the spirit of RRI, which seeks a more
+ responsive, reflective, inclusive, and socially responsible science and technology.
+
+
The concept of RRI involves five key principles: Education; Open Access; Ethics;
+ Social Engagement; Gender Equality.7 ),( 8
+ These principles were put into practice during the training course, with education
+ remaining the core of VEME.
+
Education is the basis for technology transfer and capacity building, enabling the
+ dissemination and application of knowledge.21
+ During VEME, in addition to the participation of professors who are experts on that
+ field and internationally recognized for their work, the classes were based on a
+ practical learning approach.
+
The didactic strategy used ensured that the students could apply the tools in real
+ time and that the content covered was more suitable for the practice of each LACEN.
+ Furthermore, in order for each student and public health professional to master the
+ tools presented, they were granted autonomy to apply and disseminate the knowledge
+ acquired at the face-to-face VEME, in their state.
+
VEME provided public health professionals from all Brazilian states with access to
+ knowledge and tools used by leading research centers in the world. This training
+ course has enabled faster detection and monitoring of circulating viral variants in
+ the states, given that trained health professionals began performing real-time
+ genomic surveillance and publishing their results in high-impact journals.17 )-( 20
+
+
The fact that the event organizers only advised the participants to stay at the hotel
+ during the days of the event, without obligating them, and that there was no control
+ over their entry and exit, is a limitation of this study. However, the spirit of
+ collaboration of the professors and enrolled students was reflected in everyone
+ staying at the training location, respecting the proposed safety protocols.
+
The implementation of technology transfer in a face-to-face course, during the
+ COVID-19 epidemic in Brazil, was of great relevance for the training of public
+ health professionals involved. The topics covered during the event enabled not only
+ genomic data generation, but also their rapid analysis. This training process was
+ fundamental for monitoring the evolution of the epidemic at the local level.
+ Motivated by the success of this experience, a new module entitled Virus Evolution
+ to Public Health Policy Makers will be incorporated into the next edition of VEME in
+ Panama in 2022. This training course for health professionals in genomic data
+ analysis represents a milestone in epidemiological surveillance, allowing Brazil not
+ only to efficiently monitor endemic strains, but also to predict new outbreaks
+ through active monitoring and real-time data analysis.
+
+
+
REFERENCES
+
+
+
+
+ 1 Marques RC,
+ Silveira AJT, Pimenta DN. A pandemia de covid-19: interseções e desafios
+ para a história da saúde e do tempo presente. In: Reis TS, Souza CM,
+ Oliveira MP, Lyra Júnior AA, organizadores. Coleção história do tempo
+ presente: volume 3. Boa Vista: Editora da UFRR; 2020. p. 225-49.
+
+
+ 2 Organização
+ Pan-Americana da Saúde. OMS afirma que COVID-19 é agora caracterizada
+ como pandemia [Internet]. [Washington]: Organização Pan-Americana da
+ Saúde; 2020 [atualizado 2020 Mar 11; citado 2022 Mar 15]. Disponível em:
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+ »
+ https://www.paho.org/pt/news/11-3-2020-who-characterizes-covid-19-pandemic
+
+
+ 3 Giovanetti M,
+ Faria NR, Lourenço J, Jesus JG, Xavier J, Claro IM, et al. Genomic and
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+
+ 4 Adelino TÉR,
+ Giovanetti M, Fonseca V, Xavier J, Abreu ÁS, Nascimento VA, et al. Field
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+
+ 5 Brasil.
+ Ministério da Saúde. Lei nº 8.080, de 19 de setembro de 1990. Dispõe
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+ organização e o funcionamento dos serviços correspondentes e dá outras
+ providências [Internet]. Diário Oficial da União, Brasília (DF), 1990
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+ http://www.planalto.gov.br/ccivil_03/leis/l8080.htm
+
+
+ 6 Bioinformatics
+ Workshop on Virus Evolution and Molecular Epidemiology - Face-to-face
+ Workshop (VEME Light) [Internet];2021 Sep 5-10. Belo Horizonte: KU
+ Leuven [cited 2022 Mar 15]. Available from: Available from:
+ https://rega.kuleuven.be/cev/veme-workshop/2021/bioinformatics-workshop-2021
+ »
+ https://rega.kuleuven.be/cev/veme-workshop/2021/bioinformatics-workshop-2021
+
+
+ 7 Colizzi V,
+ Mezzana D, Ovseiko PV, Caiati G, Colonnello C, Declich A, et al.
+ Structural Transformation to Attain Responsible BIOSciences (STARBIOS2):
+ protocol for a Horizon 2020 Funded European Multicenter Project to
+ Promote Responsible Research and Innovation. JMIR Res Protoc.
+ 2019;8(3):e11745. doi: 10.2196/11745»
+ https://doi.org/10.2196/11745
+
+
+ 8 Declich A. RRI
+ implementation in bioscience organisations: guidelines from the
+ STARBIOS2 project [Internet]. Uppsala: Uppsala University; 2020 [cited
+ 2020 Aug 12]. Available from: Available from:
+ http://uu.diva-portal.org/smash/get/diva2:1396179/FULLTEXT01.pdf »
+ http://uu.diva-portal.org/smash/get/diva2:1396179/FULLTEXT01.pdf
+
+
+ 9 Vilsker M, Moosa
+ Y, Nooij S, Fonseca V, Ghysens Y, Dumon K, et al. Genome detective: an
+ automated system for virus identification from high-throughput
+ sequencing data. Bioinformatics. 2019;35(5):871-3. doi:
+ 10.1093/bioinformatics/bty695»
+ https://doi.org/10.1093/bioinformatics/bty695
+
+
+ 10 Katoh K,
+ Rozewicki J, Yamada KD. MAFFT online service: multiple sequence
+ alignment, interactive sequence choice and visualization. Brief
+ Bioinform. 2019;20(4):1160-6. doi: 10.1093/bib/bbx108»
+ https://doi.org/10.1093/bib/bbx108
+
+
+ 11 Larsson A.
+ AliView: a fast and lightweight alignment viewer and editor for large
+ datasets. Bioinformatics. 2014;30(22):3276-8. doi:
+ 10.1093/bioinformatics/btu531»
+ https://doi.org/10.1093/bioinformatics/btu531
+
+
+ 12 Nguyen LT,
+ Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective
+ stochastic algorithm for estimating maximum-likelihood phylogenies. Mol
+ Biol Evol. 2015;32(1):268-74. doi: 10.1093/molbev/msu300»
+ https://doi.org/10.1093/molbev/msu300
+
+
+ 13 Rambaut A, Lam
+ TT, Carvalho LM, Pybus OG. Exploring the temporal structure of
+ heterochronous sequences using TempEst (formerly Path-O-Gen). Virus
+ Evol. 2016;2(1): vew007. doi: 10.1093/ve/vew007»
+ https://doi.org/10.1093/ve/vew007
+
+
+ 14 Suchard MA,
+ Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A. Bayesian
+ phylogenetic and phylodynamic data integration using BEAST 1.10. Virus
+ Evol. 2018;4(1):vey016. doi: 10.1093/ve/vey016»
+ https://doi.org/10.1093/ve/vey016
+
+
+ 15 Rambaut A.
+ Molecular Evolution, Phylogenetics and Epidemiology [Internet].
+ [Edinburgh]: [Rambaut A]; c2007 [cited 2022 Aug 18]. Available from:
+ Available from: http://tree.bio.ed.ac.uk/ »
+ http://tree.bio.ed.ac.uk/
+
+
+ 16 Chernomor O,
+ von Haeseler A, Minh BQ. Terrace Aware Data Structure for Phylogenomic
+ Inference from Supermatrices. Syst Biol. 2016;65(6):997-1008. doi:
+ 10.1093/sysbio/syw037»
+ https://doi.org/10.1093/sysbio/syw037
+
+
+ 17 Posit.
+ RStudio: Open source & professional software for data science teams
+ [Internet]. Boston: Posit; c2022 [cited 2022 Aug 18]. Available from:
+ Available from: https://www.rstudio.com/ »
+ https://www.rstudio.com/
+
+
+ 18 Oliveira EC,
+ Fonseca V, Xavier J, Adelino T, Claro IM, Fabri A, et al. Short report:
+ introduction of chikungunya virus ECSA genotype into the Brazilian
+ midwest and its dispersion through the Americas. PLoS Negl Trop Dis.
+ 2021;15(4):e0009290. doi: 10.1371/journal.pntd.0009290»
+ https://doi.org/10.1371/journal.pntd.0009290
+
+
+ 19 Pereira F,
+ Tosta S, Lima MM, Silva LRO, Nardy VB, Gómez MKA, et al. Genomic
+ surveillance activities unveil the introduction of the SARS‐CoV‐2
+ B.1.525 variant of interest in Brazil: case report. J Med Virol.
+ 2021;93(9):5523-6. doi: 10.1002/jmv.27086»
+ https://doi.org/10.1002/jmv.27086
+
+
+ 20 Giovanetti M,
+ Pereira LAP, Santiago GA, Fonseca V, Mendoza MPG, Oliveira C, et al.
+ Emergence of dengue virus serotype 2 cosmopolitan genotype, Brazil.
+ Emerg Infect Dis. 2022;28(8):1725-7. doi: 10.3201/eid2808.220550»
+ https://doi.org/10.3201/eid2808.220550
+
+
+ 21 Giovanetti M,
+ Alcantara LCJ, Dorea AS, Ferreira QR, Marques WA, Barros JJF, et al.
+ Promoting Responsible Research and Innovation (RRI) during Brazilian
+ activities of genomic and epidemiological surveillance of arboviruses.
+ Front Public Health. 2021;9:693743. doi: 10.3389/fpubh.2021.693743»
+ https://doi.org/10.3389/fpubh.2021.693743
+
+
+
+
+
+
+
+
+
+
+ FUNDING
+ The author Luiz Carlos Júnior Alcântara received financial support
+ from the National Council for Scientific and Technological
+ Development/Ministry of Science, Technology and Innovations
+ (Conselho Nacional de Desenvolvimento Científico e Tecnológico -
+ CNPq/MCTI) (SCON2021-00180).
+
+
+ ACKNOWLEDGEMENTS
+ The authors would like to thank the heads of the Central Public
+ Health Laboratories for their effort in the fight against COVID-19
+ in Brazil; all the professors and students involved in the
+ Bioinformatics Workshop on Virus Evolution and Molecular
+ Epidemiology (VEME) course, for their participation, as well as the
+ staff of Ouro Minas Palace Hotel; special thanks are extended to Dr.
+ Anne-Mieke Vandamme from the Catholic University of Leuven, Belgium.
+
+
+
+ Associate editor:
+
+
+
+
+
+
+
+
Publication Dates
+
+
+
+
+ Publication in this collection 18 Aug 2023
+
+
+ Date of issue 2023
+
+
+
+
+
+
+
History
+
+
+
+
+ Received 18 Aug 2022
+
+
+ Accepted 06 June 2023
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Universidade Federal da Bahia, Instituto Multidisciplinar
+ em Saúde, Vitória da Conquista, BA, Brazil Universidade Federal da Bahia Brazil Vitória da Conquista,
+ BA, Brazil Universidade Federal da Bahia,
+ Instituto Multidisciplinar em Saúde, Vitória da Conquista, BA, Brazil
+
+
+
Escola Bahiana de Medicina e Saúde Pública, Salvador, BA,
+ Brazil Escola Bahiana de Medicina e
+ Saúde Pública Brazil Salvador, BA, Brazil Escola Bahiana de Medicina e Saúde Pública, Salvador,
+ BA, Brazil
+
+
+
Fundação Instituto Oswaldo Cruz, Laboratório de Mosquitos
+ Vetores - Endossimbiontes e Interação Patógeno-Vetor, Belo Horizonte, MG,
+ Brazil Fundação Instituto Oswaldo
+ Cruz Brazil Belo Horizonte, MG, Brazil Fundação Instituto Oswaldo Cruz, Laboratório de
+ Mosquitos Vetores - Endossimbiontes e Interação Patógeno-Vetor, Belo Horizonte, MG,
+ Brazil
+
+
+
Organização Pan-Americana da Saúde, Organização
+ Mundial da Saúde, Brasília, DF, Brazil Organização Mundial da Saúde Brazil Brasília, DF,
+ Brazil Organização Pan-Americana da
+ Saúde, Organização Mundial da Saúde, Brasília, DF, Brazil
+
+
+
Universidade Federal de Minas Gerais, Belo Horizonte, MG,
+ Brazil Universidade Federal de Minas
+ Gerais Brazil Belo Horizonte, MG, Brazil Universidade Federal de Minas Gerais, Belo Horizonte,
+ MG, Brazil
+
+
+
Ministério da Saúde, Secretaria de Vigilância em Saúde e
+ Ambiente, Coordenação-Geral das Arboviroses, Brasília, DF, Brazil Ministério da Saúde Brazil Brasília, DF,
+ Brazil Ministério da Saúde, Secretaria de
+ Vigilância em Saúde e Ambiente, Coordenação-Geral das Arboviroses, Brasília, DF,
+ Brazil
+
+
+
Ministério da Saúde, Secretaria de Vigilância em Saúde e
+ Ambiente, Coordenação-Geral de Laboratórios de Saúde Pública, Brasília, DF,
+ Brazil Ministério da Saúde Brazil Brasília, DF,
+ Brazil Ministério da Saúde, Secretaria de
+ Vigilância em Saúde e Ambiente, Coordenação-Geral de Laboratórios de Saúde Pública,
+ Brasília, DF, Brazil
+
+
+
Pan American Health Organization, Health Emergencies
+ Department, Washington, DC, United States Pan American Health Organization United States Washington, DC, United
+ States Pan American Health Organization,
+ Health Emergencies Department, Washington, DC, United States
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Sunday, September 5
+
+
+
+
+ Registration and Accreditation + sample collection for
+ SARS-CoV-2 diagnosis
+
+
+ Linux command line
+
+
+ Panorama and Surveillance of COVID-19 in Brazil and Latin
+ America Panorama and Surveillance of Arboviruses in Brazil
+
+
+ Yellow Fever, Mayaro, Oropouche and Mayaro viruses in the
+ Brazilian North and Northeast regions Zika, Dengue and Chikungunya viruses
+ in the Brazilian Southeast and Northeast regions SARS-CoV-2 in Brazil
+
+
+ Zoonoses and the Emergence of COVID-19
+
+
+ Monday, September 6
+
+
+ Linux command line
+
+
+ Reference-based genome assembly and error correction algorithms
+
+
+
+ Real time genomic surveillance of SARS-CoV-2 in South Africa
+
+
+
+ De novo genome assembly using Genome Detective software
+
+
+ Tuesday, September 7
+
+
+ Constructing a proper dataset using NCBI web-based tools
+
+
+ Alignment algorithms and Aliview
+
+
+ COVID-19: how sharing, communication and Nextstrain have played
+ a part in the outbreak
+
+
+ IQ-TREE
+
+
+ Alignment and Phylogenetic signal
+
+
+ Wednesday, September 8
+
+
+ Methods for phylogenetic tree reconstruction (NJ e ML)
+
+
+ TempEST
+
+
+ Predicting mosquito-borne transmission using climate data
+
+
+ IQ-TREE e TempEST
+
+
+ Thursday, September 9
+
+
+ Molecular clocks (applications + TreeTime)
+
+
+ TreeTime and BEAST
+
+
+ Friday, September 10
+
+
+ Rstudio
+
+
+ Sample collection for SARS-CoV-2 diagnosis
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
From 24cffb827cc31d784471717e5dc677a00c1b259a Mon Sep 17 00:00:00 2001
From: Ramon Cordini
Date: Tue, 29 Apr 2025 11:18:05 -0300
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MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
.../abstracts/modal-autoria.en.3_0-v2.html | 133 +++++++++---------
.../abstracts/static/css/article.css | 4 +
.../abstracts/static/css/bootstrap.css | 10 ++
3 files changed, 81 insertions(+), 66 deletions(-)
create mode 100644 tests/fixtures/htmlgenerator/abstracts/static/css/article.css
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diff --git a/tests/fixtures/htmlgenerator/abstracts/modal-autoria.en.3_0-v2.html b/tests/fixtures/htmlgenerator/abstracts/modal-autoria.en.3_0-v2.html
index 768d36ade..a00b09bcc 100644
--- a/tests/fixtures/htmlgenerator/abstracts/modal-autoria.en.3_0-v2.html
+++ b/tests/fixtures/htmlgenerator/abstracts/modal-autoria.en.3_0-v2.html
@@ -6,8 +6,8 @@
-
-
+
+
@@ -49,7 +49,7 @@ Transferencia de tecnología durante la epidemia de CO
-
Abstract
+
Abstract
The objective of this report was to describe the first face-to-face course aimed at
training public health professionals in performing real-time genomic surveillance
during the pandemic period. Experience report on a theoretical-practical course
@@ -66,7 +66,7 @@
Abstract
-
Study contributions
+
Study contributions
Main results Technology transfer can take place at large events, as
long as safety protocols are strictly enforced. It is important to disseminate, at
these events, the concepts of the Responsible Research and Innovation (RRI).
@@ -79,7 +79,7 @@
Study contributions
2022), entitled Virus Evolution to Public Health Policy Makers.
-
Resumo
+
Resumo
O relato descrebeu o primeiro curso presencial visando capacitar profissionais de
saúde pública na realização de vigilância genômica em tempo real, durante períodos
pandêmicos. Relato de experiência sobre um curso teórico-prático com foco em
@@ -94,7 +94,7 @@
Resumo
-
Contribuições do estudo
+
Contribuições do estudo
Principais resultados A transferência tecnológica pode acontecer em
grandes eventos, desde que protocolos de segurança sejam executados rigorosamente. É
importante disseminar, nesses eventos, os conceitos do movimento Responsible
@@ -108,7 +108,7 @@
Contribuições do estudo
intitulado Virus Evolution to Public Health Policy Makers.
-
Resumen
+
Resumen
Este estudio tuvo como objetivo describir el primer curso presencial para capacitar a
los profesionales de la salud pública para llevar a cabo la vigilancia genómica en
tiempo real durante los períodos de pandemia. Este es un informe de experiencia en
@@ -125,7 +125,7 @@
Resumen
Capacitación de Recursos Humanos en Salud
-
INTRODUCTION
+
INTRODUCTION
Pandemics are part of the group of natural disaster events triggered by
socio-environmental phenomena and imbalances that affect populations. In this
context, on January 30, 2020, the World Health Organization (WHO) characterized the
@@ -206,7 +206,7 @@
INTRODUCTION
focusing on genomic research and surveillance. The course included topics such as
mobile sequencing technologies, bioinformatics, phylogenetics and epidemiological
modeling.
-
METHODS
+
METHODS
Traditionally, the previous 26 editions of VEME took place in a face-to-face format.
Due to the COVID-19 pandemic in 2021, VEME had two versions: (i) COVEME, a webinar
format event focused on the application of bioinformatics tools in corona virus
@@ -282,7 +282,7 @@
METHODS
temporary room at the event venue. PCR test was performed using Allplex 2019-nCoV
Assay (Seegene), aiming to detect the envelope (E), the viral RNA-dependent
RNA-polymerase (RdRp) or RNA replicase and the nucleocapsid (N) gene.
-
RESULTS
+
RESULTS
VEME light had a total of 162 participants, including 146 students and 16 professors.
Among the students, 131 came from 21 different Brazilian institutions: 64 employees
of LACENs and CGLAB; and 67 came from other municipal, academic and research
@@ -328,7 +328,7 @@
RESULTS
- DISCUSSION
+ DISCUSSION
In recent years, at the initiative of the Ministry of Health, the LACENs have been
implementing different Next-Generation Sequencing (NGS) strategies to perform
genomic surveillance. This process has enabled each LACEN to generate complete
@@ -408,7 +408,7 @@
DISCUSSION
through active monitoring and real-time data analysis.
-
REFERENCES
+
REFERENCES
@@ -639,7 +639,7 @@ REFERENCES
-
Publication Dates
+
Publication Dates
@@ -654,7 +654,7 @@ Publication Dates
-
History
+
History
@@ -736,122 +736,122 @@ Authorship
-
-
-
person Fernanda Khouri Barreto
-
conception and design · analysis and interpretation · drafting and reviewing · integrity · planning
-
school Universidade Federal da Bahia, Instituto Multidisciplinar em Saúde, Vitória da Conquista, BA, Brazil
-
+
conception and design · analysis and interpretation · drafting and reviewing · integrity · planning
+
school Universidade Federal da Bahia, Instituto Multidisciplinar em Saúde, Vitória da Conquista, BA, Brazil
+
person Luciane Amorim Santos
-
conception and design · analysis and interpretation · drafting and reviewing · integrity · planning
-
school Escola Bahiana de Medicina e Saúde Pública, Salvador, BA, Brazil
-
+
conception and design · analysis and interpretation · drafting and reviewing · integrity · planning
+
school Escola Bahiana de Medicina e Saúde Pública, Salvador, BA, Brazil
+
person Marta Giovanetti
-
conception and design · analysis and interpretation · drafting and reviewing · integrity · planning
-
school Fundação Instituto Oswaldo Cruz, Laboratório de Mosquitos Vetores - Endossimbiontes e Interação Patógeno-Vetor, Belo Horizonte, MG, Brazil
-
+
conception and design · analysis and interpretation · drafting and reviewing · integrity · planning
+
school Fundação Instituto Oswaldo Cruz, Laboratório de Mosquitos Vetores - Endossimbiontes e Interação Patógeno-Vetor, Belo Horizonte, MG, Brazil
+
person Vagner Fonseca
-
planning · integrity · analysis and interpretation
-
school Organização Pan-Americana da Saúde, Organização Mundial da Saúde, Brasília, DF, Brazil
-
+
planning · integrity · analysis and interpretation
+
school Organização Pan-Americana da Saúde, Organização Mundial da Saúde, Brasília, DF, Brazil
+
person Flavia Aburjaile
-
planning · integrity · analysis and interpretation
-
school Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
-
+
planning · integrity · analysis and interpretation
+
school Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
+
person Joscelio Aguiar Silva
-
integrity · funding and feasibility · analysis and interpretation
-
school Ministério da Saúde, Secretaria de Vigilância em Saúde e Ambiente, Coordenação-Geral das Arboviroses, Brasília, DF, Brazil
-
+
integrity · funding and feasibility · analysis and interpretation
+
school Ministério da Saúde, Secretaria de Vigilância em Saúde e Ambiente, Coordenação-Geral das Arboviroses, Brasília, DF, Brazil
+
person Carla Freitas
-
planning · integrity · analysis and interpretation
-
school Ministério da Saúde, Secretaria de Vigilância em Saúde e Ambiente, Coordenação-Geral de Laboratórios de Saúde Pública, Brasília, DF, Brazil
-
+
planning · integrity · analysis and interpretation
+
school Ministério da Saúde, Secretaria de Vigilância em Saúde e Ambiente, Coordenação-Geral de Laboratórios de Saúde Pública, Brasília, DF, Brazil
+
person Cassio Roberto Leonel Peterka
-
integrity · funding and feasibility · analysis and interpretation
-
school Ministério da Saúde, Secretaria de Vigilância em Saúde e Ambiente, Coordenação-Geral das Arboviroses, Brasília, DF, Brazil
-
+
integrity · funding and feasibility · analysis and interpretation
+
school Ministério da Saúde, Secretaria de Vigilância em Saúde e Ambiente, Coordenação-Geral das Arboviroses, Brasília, DF, Brazil
+
person Jairo Mendez Rico
-
integrity · funding and feasibility · analysis and interpretation
-
school Pan American Health Organization, Health Emergencies Department, Washington, DC, United States
-
+
integrity · funding and feasibility · analysis and interpretation
+
school Pan American Health Organization, Health Emergencies Department, Washington, DC, United States
+
person Maria Almiron
-
integrity · funding and feasibility · analysis and interpretation
-
school Pan American Health Organization, Health Emergencies Department, Washington, DC, United States
-
+
integrity · funding and feasibility · analysis and interpretation
+
school Pan American Health Organization, Health Emergencies Department, Washington, DC, United States
+
person Carlos Frederico Campelo de Albuquerque e Melo
-
integrity · funding and feasibility · analysis and interpretation
-
school Organização Pan-Americana da Saúde, Organização Mundial da Saúde, Brasília, DF, Brazil
-
+
integrity · funding and feasibility · analysis and interpretation
+
school Organização Pan-Americana da Saúde, Organização Mundial da Saúde, Brasília, DF, Brazil
+
person Luiz Carlos Júnior Alcântara
-
conception and design · analysis and interpretation · drafting and reviewing · integrity · funding and feasibility
-
school Fundação Instituto Oswaldo Cruz, Laboratório de Mosquitos Vetores - Endossimbiontes e Interação Patógeno-Vetor, Belo Horizonte, MG, Brazil
-
+
conception and design · analysis and interpretation · drafting and reviewing · integrity · funding and feasibility
+
school Fundação Instituto Oswaldo Cruz, Laboratório de Mosquitos Vetores - Endossimbiontes e Interação Patógeno-Vetor, Belo Horizonte, MG, Brazil
+
-
-
-
-
AUTHOR CONTRIBUTIONS
-
Barreto FK, Santos LA, Giovanetti M and Alcântara LCJ collaborated with the study conception and design, analysis and interpretation of the results, drafting and critical reviewing of the manuscript content.
-
Fonseca V, Aburjaile F, Freitas C, Santos LA and Giovanetti M collaborated with the planning and implementation of the course, analysis and interpretation of the results.
-
Silva JA, Peterka CRL, Rico JM, Almiron M, Medeiros AC, Melo CFCA and Alcântara LCJ collaborated with funding and feasibility, analysis and interpretation of the results. All authors have approved the final version of the manuscript and declared themselves to be responsible for all aspects of the work, including ensuring its accuracy and integrity.
+
+
+
AUTHOR CONTRIBUTIONS
+
Barreto FK, Santos LA, Giovanetti M and Alcântara LCJ collaborated with the study conception and design, analysis and interpretation of the results, drafting and critical reviewing of the manuscript content.
+
Fonseca V, Aburjaile F, Freitas C, Santos LA and Giovanetti M collaborated with the planning and implementation of the course, analysis and interpretation of the results.
+
Silva JA, Peterka CRL, Rico JM, Almiron M, Medeiros AC, Melo CFCA and Alcântara LCJ collaborated with funding and feasibility, analysis and interpretation of the results. All authors have approved the final version of the manuscript and declared themselves to be responsible for all aspects of the work, including ensuring its accuracy and integrity.
+
+
+
+
CONFLICTS OF INTEREST
+
The authors declare they have no conflicts of interest.
+
-
-
CONFLICTS OF INTEREST
-
The authors declare they have no conflicts of interest.
-
-
+
+
@@ -1040,6 +1040,7 @@
+ Box 1 Description of the activities performed during VEME light
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new file mode 100644
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+/*# sourceMappingURL=bootstrap.css.map */
From eae170c19bc29755d06f6beb33565897a5997f8c Mon Sep 17 00:00:00 2001
From: Ramon Cordini
Date: Thu, 8 May 2025 12:08:28 -0300
Subject: [PATCH 3/3] =?UTF-8?q?Fix:=20Inser=C3=A7=C3=A3o=20de=20=C3=ADcone?=
=?UTF-8?q?s=20no=20modal=20autoria.?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
.../abstracts/modal-autoria.en.3_0-v2.html | 23 +++++++++++--------
1 file changed, 13 insertions(+), 10 deletions(-)
diff --git a/tests/fixtures/htmlgenerator/abstracts/modal-autoria.en.3_0-v2.html b/tests/fixtures/htmlgenerator/abstracts/modal-autoria.en.3_0-v2.html
index a00b09bcc..ebc57d705 100644
--- a/tests/fixtures/htmlgenerator/abstracts/modal-autoria.en.3_0-v2.html
+++ b/tests/fixtures/htmlgenerator/abstracts/modal-autoria.en.3_0-v2.html
@@ -833,20 +833,23 @@ Authorship
-
-
AUTHOR CONTRIBUTIONS
-
Barreto FK, Santos LA, Giovanetti M and Alcântara LCJ collaborated with the study conception and design, analysis and interpretation of the results, drafting and critical reviewing of the manuscript content.
-
Fonseca V, Aburjaile F, Freitas C, Santos LA and Giovanetti M collaborated with the planning and implementation of the course, analysis and interpretation of the results.
-
Silva JA, Peterka CRL, Rico JM, Almiron M, Medeiros AC, Melo CFCA and Alcântara LCJ collaborated with funding and feasibility, analysis and interpretation of the results. All authors have approved the final version of the manuscript and declared themselves to be responsible for all aspects of the work, including ensuring its accuracy and integrity.
+
+
groups Author contributions
+
Barreto FK, Santos LA, Giovanetti M and Alcântara LCJ collaborated with the study conception and design, analysis and interpretation of the results, drafting and critical reviewing of the manuscript content.
+
Fonseca V, Aburjaile F, Freitas C, Santos LA and Giovanetti M collaborated with the planning and implementation of the course, analysis and interpretation of the results.
+
Silva JA, Peterka CRL, Rico JM, Almiron M, Medeiros AC, Melo CFCA and Alcântara LCJ collaborated with funding and feasibility, analysis and interpretation of the results. All authors have approved the final version of the manuscript and declared themselves to be responsible for all aspects of the work, including ensuring its accuracy and integrity.
+
+
+
how_to_reg Associate editor:
+
Augusto Schrank
-
-
CONFLICTS OF INTEREST
-
The authors declare they have no conflicts of interest.
+
feedback Conflicts of interest
+
The authors declare they have no conflicts of interest.