Browsing by Author "Fonseca, Vagner"
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- Correction to “Exploring the urban arbovirus landscape in Rio de Janeiro, Brazil: transmission dynamics and patterns of disease spread” The Lancet Regional Health – Americas 2024;35: 100786 (The Lancet Regional Health - Americas (2024) 35, (S2667193X24001133), (10.1016/j.lana.2024.100786))Publication . Schuab, Gabriel; Tosta, Stephane; Moreno, Keldenn; Fonseca, Vagner; Santos, Luciane Amorim; Slavov, Svetoslav Nanev; Kashima, Simone; Ciccozzi, Massimo; Lourenço, José; Cella, Eleonora; Oliveira, Carla de; Cavalcanti, Andréa Cony; Alcantara, Luiz Carlos Junior; Bruycker-Nogueira, Fernanda de; Filippis, Ana Maria Bispo de; Giovanetti, MartaThe authors wish to correct the data sharing statement, acknowledgments and include a citation for the published work and apologise for any inconvenience the error may have caused.
- Establishing a dengue genomic monitoring in Cuba: uncovering virus dynamics to enhance local responsePublication . Pérez, Melissa; Álvarez, Mayling; Perez, Lissette; Benitez, Ana Julia; Serrano, Silvia; Adelino, Talita Emile Ribeiro; Fonseca, Vagner; Resik, Sonia; Kouri, Vivian; Gresh, Lionel; Franco, Leticia; Rico, Jairo Mendez; Lourenço, José; Alcantara, Luiz Carlos Junior; Guzman, Maria G.; Giovanetti, MartaBackground: A major dengue outbreak was reported by the Cuban Ministry of Health in 2022, highlighting the need for strong surveillance, with high pediatric cases showing warning signs. Using phylogenetic and epidemiologic approaches, we provide evidence toward a better understanding of dengue's recent transmission history. Methods: This study details the implementation of the genomic surveillance system for Dengue virus. Pre-screened DENV-3 positive samples (reverse transcription–polymerase chain reaction [RT-PCR] cycle threshold [Ct] <30) with epidemiologic metadata—including symptom onset, sample collection date, sex, age, residence, symptoms, and disease classification—underwent whole genome sequencing using Nanopore technology. Results: Genome sequences from 2022 to 2023 confirmed DENV-3 genotype III circulation in western, central, and eastern Cuba, covering 15 provinces and one special municipality. All cases were autochthonous, with 93% classified as dengue without warning signs and 7% as severe dengue. Long-term analysis identified a seasonal window of heightened suitability from May to November. Phylogenetic analyses revealed that DENV-3 genotype III has been introduced into Cuba multiple times, primarily from Asia and the Americas. These independent introduction events, likely driven by international travel and trade, underscore the importance of continued viral importation monitoring. The newly sequenced Cuban DENV-3 genotype III genomes were assigned to two distinct sub-lineages within genotype III: 3III_C, corresponding to the older American lineage I (2001-2014), and 3III_B.3, representing a novel introduction into Cuba associated with the more recent American lineage II (2022-2023). Evidence suggests that 3III_C, previously circulating in the country, may have been replaced by 3III_B.3 around 2020. Conclusions: This study outlines the development of a dengue genomic monitoring system in the country. The system will contribute to Cuba's public health response, facilitating timely interventions and potentially reducing the disease's impact on the local population.
- Exploring the urban arbovirus landscape in Rio de Janeiro, Brazil: transmission dynamics and patterns of disease spreadPublication . Schuab, Gabriel; Tosta, Stephane; Moreno, Keldenn; Fonseca, Vagner; Santos, Luciane Amorim; Slavov, Svetoslav Nanev; Kashima, Simone; Ciccozzi, Massimo; Lourenço, José; Cella, Eleonora; Oliveira, Carla de; Cavalcanti, Andréa Cony; Alcantara, Luiz Carlos Junior; Bruycker-Nogueira, Fernanda de; Filippis, Ana Maria Bispo de; Giovanetti, MartaBackground: This study focuses on urban arboviruses, specifically dengue (DENV), chikungunya (CHIKV), and Zika (ZIKV), which pose a significant public health challenge in Rio de Janeiro state, Southeast Brazil. In our research, we highlight critical findings on the transmission dynamics of these arboviruses in Rio de Janeiro, identifying distinct patterns of disease spread. Methods: By combining genomic data with case reports from the Brazilian Ministry of Health, we have analysed the phylogenetics, prevalence and spatial distribution of these endemic viruses within the state. Findings: Our results revealed sustained DENV transmission primarily in the northern part of the state, a significant ZIKV epidemic in 2016 affecting all mesoregions, and two major CHIKV outbreaks in 2018 and 2019, predominantly impacting the northern and southern areas. Our analysis suggests an inverse relationship between arboviral case incidence and urban density, with less populous regions experiencing higher transmission rates, potentially attributed to a complex interplay of factors such as the efficacy of vector control measures, environmental conditions, local immunity levels, and human mobility. Furthermore, our investigation unveiled distinct age and gender trends among affected individuals. Notably, dengue cases were predominantly observed in young adults aged 32, while chikungunya cases were more prevalent among individuals over 41. In contrast, cases of ZIKV were concentrated around the 33-year age group. Intriguingly, females accounted for nearly 60% of the cases, suggesting a potential gender-based difference in infection rates. Interpretation: Our findings underscore the complexity of arbovirus transmission and the need for interventions tailored to different geographical mesoregions. Enhanced surveillance and genomic sequencing will be essential for a deeper, more nuanced understanding of regional arbovirus dynamics. Identifying potential blind spots within the state will be pivotal for developing and implementing more effective public health strategies, specifically designed to address the unique challenges posed by these viruses throughout the state. Funding: This study was supported by the National Institutes of Health USA grant U01 AI151698 for the United World Arbovirus Research Network (UWARN) and the CRP-ICGEB RESEARCH GRANT 2020 Project CRP/BRA20-03.
- Genomic and eco-epidemiological investigations in Uruguay reveal local Chikungunya virus transmission dynamics during its expansion across the Americas in 2023Publication . 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; Alcantara, Luiz Carlos Junior; Chiparelli, HectorUruguay 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.
- Genomics-based timely detection of dengue virus type I genotypes I and V in UruguayPublication . Morel, Noelia; Giovanetti, Marta; Fonseca, Vagner; Burgueño, Analía; Lima, Mauricio; Castro, Emerson; Guimarães, Natália R.; Iani, Felipe C. M.; Bormida, Victoria; Cortinas, Maria Noel; Ramas, Viviana; Coppola, Leticia; Bento, Ana I.; Rosewell, Alexander; Franco, Leticia; Rico, Jairo Mendez; Lourenço, José; Alcantara, Luiz Carlos Junior; Chiparelli, HectorThis study details a genomics-based approach for the early detection of mosquito-borne pathogens, marked by Uruguay's first ever complete genomic sequencing of Dengue Virus type I genotypes I and V. This pioneering effort has facilitated the prompt identification of these genotypes within the country, enabling Uruguayan public health authorities to develop timely and effective response strategies. Further integrated into this approach is a climate-driven suitability measure, closely associated with Dengue case reports and indicative of the local climate's role in the virus's transmission in the country within the changing climate context. The detection of multiple DENV-1 genotypes co-circulating in Uruguay underscores the necessity for proactive surveillance, particularly at borders, to prevent the introduction and dissemination of novel viral strains within the country and the region. This approach aids in facilitating prompt public health responses and intervention strategies, which are crucial in mitigating the impact of dengue outbreaks.
- Insights into SARS-CoV-2 surveillance among prison populations in Mato Grosso do Sul, Brazil, in 2022Publication . Silva, Liliane Ferreira da; Alcantara, Luiz Carlos Junior; Fonseca, Vagner; Frias, Diego; Zardin, Marina Castilhos Souza Umaki; Lichs, Gislene Garcia de Castro; Esposito, Ana Olivia Pascoto; Xavier, Joilson; Fritsch, Hegger; Lima, Mauricio; Oliveira, Carla de; Arruda, Larissa Domingues Castilho de; Maziero, Livia de Mello Almeida; Barretos, Ellen Caroline Rodrigues; Oshiro, Paulo Eduardo Tsuha; Menezes, Evellyn Fernanda Gimenes Mendes; Cardoso, Lucélia de Freitas; Lemos, Everton Ferreira; Lourenço, José; Albuquerque, Carlos F. C. de; Said, Rodrigo Fabiano do Carmo; Rosewell, Alexander; Demarchi, Luiz Henrique Ferraz; Croda, Julio; Giovanetti, Marta; Gonçalves, Crhistinne Cavalheiro MaymoneThis study examines the epidemiological and genomic characteristics, along with the transmission dynamics, of SARS-CoV-2 within prison units I and II in Campo Grande, Mato Grosso do Sul, Brazil. Conducted between May and October 2022, it reveals how the virus spreads in the confined settings of prisons, emphasizing the roles of overcrowded cells, frequent transfers, and limited healthcare access. The research involved 1927 participants (83.93% of the total prison population) and utilized nasopharyngeal swabs and RT-qPCR testing for detection. Contact tracing monitored exposure within cells. Out of 2108 samples, 66 positive cases were identified (3.13%), mostly asymptomatic (77.27%), with the majority aged 21–29 and varying vaccination statuses. Next-generation sequencing generated 28 whole genome sequences, identifying the Omicron variant (subtypes BA.2 and BA.5) with 99% average coverage. Additionally, the study seeks to determine the relationship between immunization levels and the incidence of SARS-CoV-2 cases within this enclosed population. The findings underscore the necessity of comprehensive control strategies in prisons, including rigorous screening, isolation protocols, vaccination, epidemiological monitoring, and genomic surveillance to mitigate disease transmission and protect both the incarcerated population and the broader community.
- Integrated analyses of the transmission history of SARS-CoV-2 and its association with molecular evolution of the virus underlining the pandemic outbreaks in Italy, 2019-2023Publication . Cella, Eleonora; Fonseca, Vagner; Branda, Francesco; Tosta, Stephane; Moreno, Keldenn; Schuab, Gabriel; Ali, Sobur; Slavov, Svetoslav Nanev; Scarpa, Fabio; Santos, Luciane Amorim; Kashima, Simone; Wilkinson, Eduan; Tegally, Houriiyah; Mavian, Carla; Borsetti, Alessandra; Caccuri, Francesca; Salemi, Marco; Oliveira, Tulio de; Azarian, Taj; Filippis, Ana Maria Bispo de; Alcantara, Luiz Carlos Junior; Ceccarelli, Giancarlo; Caruso, Arnaldo; Colizzi, Vittorio; Marcello, Alessandro; Lourenço, José; Ciccozzi, Massimo; Giovanetti, MartaBackground: Italy was significantly affected by the COVID-19 pandemic, experiencing multiple waves of infection following the sequential emergence of new variants. Understanding the transmission patterns and evolution of SARS-CoV-2 is vital for future preparedness. Methods: We conducted an analysis of viral genome sequences, integrating epidemiological and phylodynamic approaches, to characterize how SARS-CoV-2 variants have spread within the country. Results: Our findings indicate bidirectional international transmission, with Italy transitioning between importing and exporting the virus. Italy experienced four distinct epidemic waves, each associated with a significant reduction in fatalities from 2021 to 2023. These waves were primarily driven by the emergence of VOCs such as Alpha, Delta, and Omicron, which were reflected in observed transmission dynamics and effectiveness of public health measures. Conclusions: The changing patterns of viral spread and variant prevalence throughout Italy's pandemic response underscore the continued importance of flexible public health strategies and genomic surveillance, both of which are crucial for tracking the evolution of variants and adapting control measures effectively to ensure preparedness for future outbreaks.
- North–south pathways, emerging variants, and high climate suitability characterize the recent spread of dengue virus serotypes 2 and 3 in the Dominican RepublicPublication . Miguel, Isaac; Feliz, Edwin P.; Agramonte, Robinson; Martinez, Pedro V.; Vergara, Carlos; Imbert, Yvonne; Cruz, Lucia De la; Castro, Nurys de; Cedano, Odalis; Paz, Yamilka De la; Fonseca, Vagner; Santiago, Gilberto A.; Muñoz-Jordán, Jorge L.; Peguero, Armando; Paulino-Ramírez, Robert; Grubaugh, Nathan D.; Filippis, Ana Maria Bispo de; Alcantara, Luiz Carlos Junior; Rico, Jairo Mendez; Lourenço, José; Franco, Leticia; Giovanetti, MartaBackground: Dengue fever remains a significant public health challenge in tropical and subtropical regions, with its transmission dynamics being influenced by both environmental factors and human mobility. The Dominican Republic, a biodiversity hotspot in the Caribbean, has experienced recurrent dengue outbreaks, yet detailed understanding of the virus's transmission pathways and the impact of climatic factors remains limited. This study aims to elucidate the recent transmission dynamics of the dengue virus (DENV) in the Dominican Republic, utilizing a combination of genomic sequencing and epidemiological data analysis, alongside an examination of historical climate patterns. Methods: We conducted a comprehensive study involving the genomic sequencing of DENV samples collected from patients across different regions of the Dominican Republic over a two-year period. Phylogenetic analyses were performed to identify the circulation of DENV lineages and to trace transmission pathways. Epidemiological data were integrated to analyze trends in dengue incidence and distribution. Additionally, we integrated historical climate data spanning several decades to assess trends in temperature and their potential impact on DENV transmission potential. Results: Our results highlight a previously unknown north–south transmission pathway within the country, with the co-circulation of multiple virus lineages. Additionally, we examine the historical climate data, revealing long-term trends towards higher theoretical potential for dengue transmission due to rising temperatures. Conclusion: This multidisciplinary study reveals intricate patterns of dengue virus transmission in the Dominican Republic, characterized by the co-circulation of multiple DENV lineages and a novel transmission pathway. The observed correlation between rising temperatures and increased dengue transmission potential emphasizes the need for integrated climate-informed strategies in dengue control efforts. Our findings offer critical insights for public health authorities in the Dominican Republic and similar settings, guiding resource allocation and the development of preparedness strategies to mitigate the impacts of climate change on dengue transmission.
- Travel-associated international spread of Oropouche virus beyond the AmazonPublication . Iani, Felipe Campos de Melo; Pereira, Felicidade Mota; Oliveira, Elaine Cristina de; Rodrigues, Janete Taynã Nascimento; Machado, Mariza Hoffmann; Fonseca, Vagner; Adelino, Talita Emile Ribeiro; Guimarães, Natalia Rocha; Tomé, Luiz Marcelo Ribeiro; Gómez, Marcela Kelly Astete; Nardy, Vanessa Brandão; Ribeiro, Adriana Aparecida; Rosewell, Alexander; Ferreira, Álvaro Gil A.; Mello, Arabela Leal e Silva de; Fernandes, Brenda Machado Moura; Albuquerque, Carlos Frederico Campelo de; Pereira, Dejanira dos Santos; Pimentel, Eline Carvalho; Lima, Fábio Guilherme Mesquita; Silva, Fernanda Viana Moreira; Pereira, Glauco de Carvalho; Tegally, Houriiyah; Almeida, Júlia Deffune Profeta Cidin; Moreno, Keldenn Melo Farias; Vasconcelos, Klaucia Rodrigues; Santos, Leandro Cavalcante; Silva, Lívia Cristina Machado; Frutuoso, Livia C. V.; Lamounier, Ludmila Oliveira; Costa, Mariana Araújo; Oliveira, Marília Santini de; Anjos, Marlei Pickler Dediasi dos; Ciccozzi, Massimo; Lima, Maurício Teixeira; Pereira, Maira Alves; Rocha, Marília Lima Cruz; Silva, Paulo Eduardo de Souza da; Rabinowitz, Peter M.; Almeida, Priscila Souza de; Lessells, Richard; Gazzinelli, Ricardo T.; Cunha, Rivaldo Venancio da; Gonçalves, Sabrina; Santos, Sara Cândida Ferreira dos; Belettini, Senele Ana de Alcântara; Pedroso, Silvia Helena Sousa Pietra; Araújo, Sofia Isabel Rótulo; Silva, Stephanni Figueiredo da; Croda, Julio; Maciel, Ethel; Voorhis, Wes Van; Martin, Darren P.; Holmes, Edward C.; Oliveira, Tulio de; Lourenço, José; Alcantara, Luiz Carlos Junior; Giovanetti, MartaOropouche virus (OROV), first detected in Trinidad and Tobago in 1955, was historically confined to the Brazilian Amazon Basin. However, since late 2022, an increasing number of OROV cases have been reported across various regions of Brazil as well as in urban centers in Bolivia, Ecuador, Guyana, Colombia, Cuba, Panama, and Peru. In collaboration with Central Public Health Laboratories across Brazil, we integrated epidemiological metadata with genomic analyses from recent cases, generating 133 whole-genome sequences covering the virus’s three genomic segments (L, M, and S). These include the first genomes from regions outside the Amazon and from the first recorded fatal cases. Phylogenetic analyses show that the 2024 OROV genomes form a monophyletic group with sequences from the Amazon Basin sampled since 2022, revealing a rapid north-to-south viral movement into historically non-endemic areas. We identified 21 reassortment events, though it remains unclear whether these genomic changes have facilitated viral adaptation to local ecological conditions or contributed to phenotypic traits of public health significance. Our findings demonstrate how OROV has evolved through reassortment and spread rapidly across multiple states in Brazil, leading to the largest outbreak ever recorded outside the Amazon and the first confirmed fatalities. Additionally, by analysing travel-related cases, we provide the first insights into the international spread of OROV beyond Brazil, further highlighting the role of human mobility in its dissemination. The virus’s recent rapid geographic expansion and the emergence of severe cases emphasize the urgent need for enhanced surveillance across the Americas. In the absence of significant human population changes over the past two years, factors such as viral adaptation, deforestation, and climate shifts—either individually or in combination— may have facilitated the spread of OROV beyond the Amazon Basin through both local and travel-associated transmission.