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Article: Resurgence of Dengue Virus Serotype 3 in Minas Gerais, Brazil: A Case Report.

Adelino, Talita / Lima, Maurício / Guimarães, Natália R / Xavier, Joilson / Fonseca, Vagner / Tomé, Luiz Marcelo R / Pereira, Maira Alves / Machado, Vanessa Ferreira / Alcantara, Luiz Carlos Junior / Iani, Felipe C de Melo / Giovanetti, Marta

Pathogens (Basel, Switzerland)

2024 Volume 13, Issue 3

Abstract: This report provides a detailed overview of the resurgence of DENV-3 in the state of Minas Gerais, Brazil, which is a concerning scenario in the context of dengue, a mosquito-borne viral disease. Historically, Brazil has grappled with dengue epidemics ... ...

Abstract	This report provides a detailed overview of the resurgence of DENV-3 in the state of Minas Gerais, Brazil, which is a concerning scenario in the context of dengue, a mosquito-borne viral disease. Historically, Brazil has grappled with dengue epidemics caused primarily by the DENV-1 and DENV-2 serotypes. However, in 2023, a significant shift in this pattern was observed as DENV-3 made a notable resurgence. This resurgence was characterized by the increase in DENV-3 cases within the country and the region of the Americas. Given the absence of sustained DENV-3 circulation in Brazil in previous years, this situation poses a significant risk, making the population highly susceptible to a potential novel epidemic. In November 2023, a 31-year-old male patient in Belo Horizonte exhibited symptoms of acute febrile syndrome. Multiplex RT-qPCR using the Kit Molecular ZC D-Tipagem confirmed DENV-3 infection, suggesting a likely autochthonous case, as the patient reported no travel history. To promptly assess this resurgence, we applied the nanopore sequencing technology. This allowed for the rapid characterization of the initial DENV-3 case isolated in Minas Gerais in 2023, representing a 13-year interval since the serotype's previous documented circulation in that state. This case report underscores the critical importance of proactive monitoring and the swift implementation of targeted control strategies to address the evolving dynamics of dengue, with a specific emphasis on the resurgence of DENV-3 in the state.
Language	English
Publishing date	2024-02-24
Publishing country	Switzerland
Document type	Case Reports
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens13030202
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Growth Functions as a tool to model SARS-CoV-2 pandemic trajectory and related-deaths worldwide

Fonseca, Vagner / Mascarenhas, Edson / Ramos, Paulo / Coelho, Leandro / Frias, Diego

medRxiv

Abstract: The international scientific community from different areas of knowledge has made efforts to provide information and methods that contribute to the adoption of the most appropriate measures to curb the spread of the COVID-19 disease. In particular, the ... ...

Abstract	The international scientific community from different areas of knowledge has made efforts to provide information and methods that contribute to the adoption of the most appropriate measures to curb the spread of the COVID-19 disease. In particular, the data analysis community has been very active in publishing a large number of papers. A good part of them is related to the prediction of epidemic variables (number of cases and deaths) in different time horizons. To solve the problem of the prediction of COVID-19, an important place is occupied by the sigmoidal growth functions, as they have often been used successfully in previous epidemic outbreaks. The objective of this work was to investigate, on a statistical basis, the ability of classical growth functions to model the data from the COVID-19 pandemic. But for that, it was necessary to establish a clear classification of the 5 types of problems that can be faced with data analysis techniques in this specific context and to define a methodology based on quantitative metrics to measure the performance in solving these different types of problems. The basic concept used was that of an epidemic wave consisting of an initial-increasing and a final-decreasing phase. A classification of the COVID-19 waves in 4 types was done based on mining data from all available countries. Thus, it was possible to determine the resolvability of each type of problem depending on the stage of the epidemic wave. The biggest conclusion was the impossibility of solving the long-term forecasting problems (problem 5 - to estimate the total value of an epidemic wave) with data from the first phase only. Using this theoretical-methodological framework, we evaluated, using metrics specifically designed for these types of problems, the performance of 3 classic growth functions: Logistics, Gompertz and Richards (a generalization of the previous two) in 2 types of problems: (1) Description of the trajectory of the epidemic and (2) Prediction of the total numbers of cases and deaths. We used data from 10 countries, 7 of them with more than 100 daily deaths on the peak day. The results show a generalized underperformance of the logistic function in all aspects and place the Gompertz function as the best cost-benefit alternative, as it has performance comparable to the Richards function, but it has one less parameter to be adjusted, in the process of regression of the model to the observed data.
Keywords	covid19
Language	English
Publishing date	2021-04-05
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.04.01.21254495
Database	COVID19

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Article ; Online: Genomic and eco-epidemiological investigations in Uruguay reveal local Chikungunya virus transmission dynamics during its expansion across the Americas in 2023.

Burgueño, Analía / Giovanetti, Marta / Fonseca, Vagner / Morel, Noelia / Lima, Mauricio / Castro, Emerson / Guimarães, Natália R / Iani, Felipe C M / Bormida, Victoria / Cortinas, Maria Noel / Ramas, Viviana / Coppola, Leticia / Bento, Ana I / Franco, Leticia / Rico, Jairo Mendez / Lourenço, José / Junior Alcantara, Luiz Carlos / Chiparelli, Hector

Emerging microbes & infections

2024 Volume 13, Issue 1, Page(s) 2332672

Abstract: Uruguay experienced its first Chikungunya virus outbreak in 2023, resulting in a significant burden to its healthcare system. We conducted analysis based on real-time genomic surveillance (30 novel whole genomes) to offer timely insights into recent ... ...

Abstract	Uruguay experienced its first Chikungunya virus outbreak in 2023, resulting in a significant burden to its healthcare system. We conducted analysis based on real-time genomic surveillance (30 novel whole genomes) to offer timely insights into recent local transmission dynamics and eco-epidemiological factors behind its emergence and spread in the country.
MeSH term(s)	Chikungunya virus/genetics ; Uruguay/epidemiology ; Americas/epidemiology ; Disease Outbreaks ; Genomics
Language	English
Publishing date	2024-04-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2681359-2
ISSN	2222-1751 ; 2222-1751
ISSN (online)	2222-1751
ISSN	2222-1751
DOI	10.1080/22221751.2024.2332672
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Article ; Online: Global SARS-CoV-2 genomic surveillance: What we have learned (so far)

Tosta, Stephane / Moreno, Keldenn / Schuab, Gabriel / Fonseca, Vagner / Segovia, Fátima María Cardozo / Kashima, Simone / Elias, Maria Carolina / Sampaio, Sandra Coccuzzo / Ciccozzi, Massimo / Alcantara, Luiz Carlos Junior / Slavov, Svetoslav Nanev / Lourenço, José / Cella, Eleonora / Giovanetti, Marta

Infection, Genetics and Evolution. 2023 Mar., v. 108 p.105405-

2023

Abstract: The COVID-19 pandemic has brought significant challenges for genomic surveillance strategies in public health systems worldwide. During the past thirty-four months, many countries faced several epidemic waves of SARS-CoV-2 infections, driven mainly by ... ...

Abstract	The COVID-19 pandemic has brought significant challenges for genomic surveillance strategies in public health systems worldwide. During the past thirty-four months, many countries faced several epidemic waves of SARS-CoV-2 infections, driven mainly by the emergence and spread of novel variants. In that line, genomic surveillance has been a crucial toolkit to study the real-time SARS-CoV-2 evolution, for the assessment and optimization of novel diagnostic assays, and to improve the efficacy of existing vaccines. During the pandemic, the identification of emerging lineages carrying lineage-specific mutations (particularly those in the Receptor Binding domain) showed how these mutations might significantly impact viral transmissibility, protection from reinfection and vaccination. So far, an unprecedented number of SARS-CoV-2 viral genomes has been released in public databases (i.e., GISAID, and NCBI), achieving 14 million genome sequences available as of early-November 2022. In the present review, we summarise the global landscape of SARS-CoV-2 during the first thirty-four months of viral circulation and evolution. It demonstrates the urgency and importance of sustained investment in genomic surveillance strategies to timely identify the emergence of any potential viral pathogen or associated variants, which in turn is key to epidemic and pandemic preparedness.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; evolution ; genomics ; infection ; landscapes ; monitoring ; pandemic ; pathogens ; public health ; vaccination ; viral genome ; SARS-CoV-2 ; Viral evolution ; Genomic surveillance ; Epidemic-pandemic preparedness
Language	English
Dates of publication	2023-03
Publishing place	Elsevier B.V.
Document type	Article ; Online
Note	Use and reproduction
ZDB-ID	2037068-4
ISSN	1567-1348
ISSN	1567-1348
DOI	10.1016/j.meegid.2023.105405
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Technology transfer during the COVID-19 pandemic: report on the first face-to-face practical training course in Brazil.

Barreto, Fernanda Khouri / Santos, Luciane Amorim / Giovanetti, Marta / Fonseca, Vagner / Aburjaile, Flavia / Silva, Joscelio Aguiar / Freitas, Carla / Peterka, Cassio Roberto Leonel / Rico, Jairo Mendez / Almiron, Maria / Melo, Carlos Frederico Campelo de Albuquerque E / Alcântara, Luiz Carlos Júnior

Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil

2023 Volume 32, Issue 2, Page(s) e2022614

Abstract: 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 ... ...

Abstract	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. 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.
MeSH term(s)	Humans ; Brazil/epidemiology ; COVID-19/epidemiology ; Pandemics ; SARS-CoV-2 ; Technology Transfer ; Education, Public Health Professional/methods
Language	Portuguese
Publishing date	2023-08-18
Publishing country	Brazil
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2880588-4
ISSN	2237-9622 ; 1679-4974
ISSN (online)	2237-9622
ISSN	1679-4974
DOI	10.1590/S2237-96222023000200017
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Global SARS-CoV-2 genomic surveillance: What we have learned (so far).

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2023 Volume 108, Page(s) 105405

Abstract	The COVID-19 pandemic has brought significant challenges for genomic surveillance strategies in public health systems worldwide. During the past thirty-four months, many countries faced several epidemic waves of SARS-CoV-2 infections, driven mainly by the emergence and spread of novel variants. In that line, genomic surveillance has been a crucial toolkit to study the real-time SARS-CoV-2 evolution, for the assessment and optimization of novel diagnostic assays, and to improve the efficacy of existing vaccines. During the pandemic, the identification of emerging lineages carrying lineage-specific mutations (particularly those in the Receptor Binding domain) showed how these mutations might significantly impact viral transmissibility, protection from reinfection and vaccination. So far, an unprecedented number of SARS-CoV-2 viral genomes has been released in public databases (i.e., GISAID, and NCBI), achieving 14 million genome sequences available as of early-November 2022. In the present review, we summarise the global landscape of SARS-CoV-2 during the first thirty-four months of viral circulation and evolution. It demonstrates the urgency and importance of sustained investment in genomic surveillance strategies to timely identify the emergence of any potential viral pathogen or associated variants, which in turn is key to epidemic and pandemic preparedness.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; Pandemics/prevention & control ; COVID-19/epidemiology ; COVID-19/prevention & control ; Genomics ; Databases, Factual ; Mutation ; Genome, Viral
Language	English
Publishing date	2023-01-18
Publishing country	Netherlands
Document type	Review ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2023.105405
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Article ; Online: Exploring the Genomic Dynamics of the Monkeypox Epidemic in Paraguay.

Viruses

2024 Volume 16, Issue 1

Abstract: In recent months, Paraguay has been grappled with a notable monkeypox outbreak, straining its healthcare infrastructure. The sudden spike in cases underlines the imperative need for a comprehensive understanding of the virus's dynamics, enabling the ... ...

Abstract	In recent months, Paraguay has been grappled with a notable monkeypox outbreak, straining its healthcare infrastructure. The sudden spike in cases underlines the imperative need for a comprehensive understanding of the virus's dynamics, enabling the formulation of robust containment measures. To address this challenge, our team joined forces with the Central Public Health Laboratory of Asunción and the Pan-American Health Organization. Through this collaboration, we employed portable whole-genome sequencing combined with phylodynamic analysis to examine the MPXV strains circulating in Paraguay. Our genomic monitoring approach has produced the first 30 whole-genome sequences from Paraguay, all of which were identified under lineage IIb. Interestingly, our data suggest that the origin of the monkeypox virus in Paraguay at the beginning of 2022 can be traced back to Brazil. This introduction subsequently catalyzed further community spread that was further exacerbated by several independent introduction events as time progressed. These findings not only shed light on the transmission patterns of the virus but also highlight the pivotal role such insights play in sculpting effective response strategies and driving impactful public health measures. Furthermore, our findings strongly advocate intensified surveillance at international borders, ensuring swift detection and proactive countermeasures against potential outbreaks in the future.
MeSH term(s)	Humans ; Mpox (monkeypox)/epidemiology ; Paraguay/epidemiology ; Genomics ; Epidemics ; Disease Outbreaks
Language	English
Publishing date	2024-01-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v16010083
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Simultaneous Dengue and Chikungunya Coinfection in Endemic Area in Brazil: Clinical Presentation and Implications for Public Health.

Torres, Paula Marilia Afonso / Roque, Debora Glenda Lima de La / Policastro, Lucca Rocha / Chagas, Lilian Beatriz Moreira Oliveira / Giomo, Denise Bergamaschi / Gentil, Danielle Cristina Dacanal / Fonseca, Vagner / Elias, Maria Carolina / Sampaio, Sandra Coccuzzo / Giovanetti, Marta / Fonseca, Benedito Antônio Lopes / Calado, Rodrigo Tocantins / Alcantara, Luiz Carlos / Covas, Dimas Tadeu / Santos, Flávia Leite Souza / Kashima, Simone / Passos, Luzia Márcia Romanholi

Research square

2024

Abstract: Background Dengue virus (DENV) and Chikungunya virus (CHIKV) pose significant public health threats in Brazil, where favorable conditions facilitated the proliferation ... ...

Abstract	Background Dengue virus (DENV) and Chikungunya virus (CHIKV) pose significant public health threats in Brazil, where favorable conditions facilitated the proliferation of
Language	English
Publishing date	2024-04-22
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-4277561/v1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Genomic Epidemiology and Lineage Dynamics of SARS-CoV-2 in Bulgaria: Insights from a Three-Year Pandemic Analysis.

Giovanetti, Marta / Cella, Eleonora / Ivanov, Ivan / Grigorova, Lyubomira / Stoikov, Ivan / Donchev, Deyan / Dimitrova, Reneta / Slavov, Svetoslav Nanev / Mavian, Carla / Fonseca, Vagner / Scarpa, Fabio / Borsetti, Alessandra / Korsun, Neli / Trifonova, Ivelina / Dobrinov, Veselin / Kantardjiev, Todor / Christova, Iva / Ciccozzi, Massimo / Alexiev, Ivailo

Viruses

2023 Volume 15, Issue 9

Abstract: The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has brought about significant challenges worldwide. In this study, we present a comprehensive analysis of the genomic epidemiology and lineage dynamics of SARS- ... ...

Abstract	The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has brought about significant challenges worldwide. In this study, we present a comprehensive analysis of the genomic epidemiology and lineage dynamics of SARS-CoV-2 in Bulgaria over a three-year period. Through extensive genomic sequencing and data analysis, we investigated the evolution of the virus, the emergence of variants of concern (VOCs), and their impact on the country's pandemic trajectory. We also assessed the relationship between viral diversity and COVID-19 morbidity and mortality in Bulgaria. Our findings shed light on the temporal and spatial distribution of SARS-CoV-2 lineages and provide crucial insights into the dynamics of the pandemic in the country. The interplay between international travel and viral transmission plays a significant role in the emergence and dissemination of different SARS-CoV-2 variants. The observed proportions of exportation to various continents provide insights into the potential pathways through which these lineages spread globally. Understanding the genomic epidemiology of SARS-CoV-2 in Bulgaria is essential for formulating targeted public health strategies, enhancing vaccination efforts, and effectively managing future outbreaks.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; Pandemics ; Bulgaria/epidemiology ; COVID-19/epidemiology ; Genomics
Language	English
Publishing date	2023-09-15
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15091924
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Genomic and eco-epidemiological investigations in Uruguay reveal local Chikungunya virus transmission dynamics during its expansion across the Americas in 2023.

medRxiv : the preprint server for health sciences

2023

Abstract	Uruguay experienced its first Chikungunya virus outbreak in 2023, resulting in a significant burden to its healthcare system. We conducted analysis based on real-time genomic surveillance (30 novel whole genomes) to offer timely insights into recent local transmission dynamics and eco-epidemiological factors behind its emergence and spread in the country.
Language	English
Publishing date	2023-08-20
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.08.17.23294156
Database	MEDical Literature Analysis and Retrieval System OnLINE

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