Combination of surveillance tools reveals that Yellow Fever virus can remain in the same Atlantic Forest area at least for three transmission seasons.

BACKGROUND: In Brazil, the Yellow Fever virus (YFV) is endemic in the Amazon, from where it eventually expands into epidemic waves. Coastal south-eastern (SE) Brazil, which has been a YFV-free region for eight decades, has reported a severe sylvatic outbreak since 2016. The virus spread from the north toward the south of the Rio de Janeiro (RJ) state, causing 307 human cases with 105 deaths during the 2016-2017 and 2017-2018 transmission seasons. It is unclear, however, whether the YFV would persist in the coastal Atlantic Forest of RJ during subsequent transmission seasons. OBJECTIVES: To conduct a real-time surveillance and assess the potential persistence of YFV in the coastal Atlantic Forest of RJ during the 2018-2019 transmission season. METHODS: We combined epizootic surveillance with fast diagnostic and molecular, phylogenetic, and evolutionary analyses. FINDINGS: Using this integrative strategy, we detected the first evidence of YFV re-emergence in the third transmission season (2018-2019) in a dying howler monkey from the central region of the RJ state. The YFV detected in 2019 has the molecular signature associated with the current SE YFV outbreak and exhibited a close phylogenetic relationship with the YFV lineage that circulated in the same Atlantic Forest fragment during the past seasons. This lineage circulated along the coastal side of the Serra do Mar mountain chain, and its evolution seems to be mainly driven by genetic drift. The potential bridge vector Aedes albopictus was found probing on the recently dead howler monkey in the forest edge, very close to urban areas. MAIN CONCLUSIONS: Collectively, our data revealed that YFV transmission persisted at the same Atlantic Forest area for at least three consecutive transmission seasons without the need of new introductions. Our real-time surveillance strategy permitted health authorities to take preventive actions within 48 h after the detection of the sick non-human primate. The local virus persistence and the proximity of the epizootic forest to urban areas reinforces the concern with regards to the risk of re-urbanisation and seasonal re-emergence of YFV, stressing the need for continuous effective surveillance and high vaccination coverage in the SE region, particularly in RJ, an important tourist location.

Genomic and structural features of the yellow fever virus from the 2016-2017 Brazilian outbreak.

Southeastern Brazil has been suffering a rapid expansion of a severe sylvatic yellow fever virus (YFV) outbreak since late 2016, which has reached one of the most populated zones in Brazil and South America, heretofore a yellow fever-free zone for more than 70 years. In the current study, we describe the complete genome of 12 YFV samples from mosquitoes, humans and non-human primates from the Brazilian 2017 epidemic. All of the YFV sequences belong to the modern lineage (sub-lineage 1E) of South American genotype I, having been circulating for several months prior to the December 2016 detection. Our data confirm that viral strains associated with the most severe YF epidemic in South America in the last 70 years display unique amino acid substitutions that are mainly located in highly conserved positions in non-structural proteins. Our data also corroborate that YFV has spread southward into Rio de Janeiro state following two main sylvatic dispersion routes that converged at the border of the great metropolitan area comprising nearly 12 million unvaccinated inhabitants. Our original results can help public health authorities to guide the surveillance, prophylaxis and control measures required to face such a severe epidemiological problem. Finally, it will also inspire other workers to further investigate the epidemiological and biological significance of the amino acid polymorphisms detected in the Brazilian 2017 YFV strains.

Spatio-Temporal Cluster Detection of Dengue, Chikungunya, and Zika Viruses' Infection in Rio de Janeiro State from 2010 to 2019.

Dengue (DENV), chikungunya (CHIKV), and Zika (ZIKV) virus infections are widespread throughout the Rio de Janeiro state. The co-circulation of these emergent arboviruses constitutes a serious public health problem, resulting in outbreaks that can spatially and temporally overlap. Environmental conditions favor the presence, maintenance, and expansion of Aedes aegypti, the primary vector of these urban arboviruses. This study assessed the detection of clusters of urban arboviruses in the Rio de Janeiro state from 2010 to 2019. Notified cases of dengue, chikungunya, and Zika were grouped by year according to the onset of symptoms and their municipality of residence. The study period recorded the highest number of dengue epidemics in the state along with the simultaneous circulation of chikungunya and Zika viruses. The analyzes showed that the central municipalities of the metropolitan regions were associated with higher risk areas. Central municipalities in metropolitan regions were the first most likely clusters for dengue and Zika, and the second most likely cluster for chikungunya. Furthermore, the northwest and north regions were comprised clusters with the highest relative risk for the three arboviruses, underscoring the impact of these arboviruses in less densely populated regions of Brazil. The identification of high-risk areas over time highlights the need for effective control measures, targeted prevention and control interventions for these urban arboviral diseases.

[Religious-spiritual coping and the consumption of alcoholic beverages in male patients with liver disease]. / Coping religioso-espiritual e consumo de alcoólicos em hepatopatas do sexo masculino.

This cross-sectional study was performed with the objective to evaluate the use of Religious Spiritual Coping (RSC) and verify its relationship with the pattern of alcoholic beverage consumption in patients attending a liver disease outpatient clinic between April and December of 2009, using the CAGE, AUDIT and RSC Scale. Associations were observed between negative religious-spiritual coping (NRSC) and the consumption of alcoholic beverages over the last year and with the resulting combination. Subjects identified as negative CAGE with low-risk consumption over the last year had a frequency above the expected in the category below the median. Those identified as positive CAGE with moderate-risk consumption were relatively more frequent in the category above the median (p=0.017). Results reinforce the relevance of the NRSC in the evaluation of health-related events.

Dengue, Chikungunya, and Zika: Spatial and Temporal Distribution in Rio de Janeiro State, 2015-2019.

Simultaneous spatial circulation of urban arboviral diseases, such as dengue, chikungunya, and Zika, is a major challenge. In this ecological study of urban arboviruses performed from 2015 to 2019, we analyzed the spatial and temporal dynamics of these arboviruses in all 92 municipalities and nine health regions of Rio de Janeiro state. Annual cumulative incidences are presented for all three arboviruses throughout the study period. Spatial analyses of the three studied arboviruses showed distinct behaviors among municipalities and health regions. Co-circulation of the three arboviruses in the state and a heterogeneous spatiotemporal pattern was observed for each disease and region, with dengue having a higher annual incidence during the five years of the study, as well as two consecutive epidemic years in the state. The increase in transmission in different regions of the state in one year culminated in an epidemic in the state in the following year. A high annual cumulative incidence of chikungunya occurred in municipalities from 2017 to 2019 and of Zika only in 2016. Some municipalities with higher population densities showed higher incidences for some arboviruses and appeared to contribute to the dissemination to cities of lower demographic density and maintenance of these urban arboviruses. Thus, regions recording increased incidences of the three diseases in their territories for long periods should be considered municipal poles, as they initiated and sustained high transmission within their region.

Ecological and environmental factors affecting transmission of sylvatic yellow fever in the 2017-2019 outbreak in the Atlantic Forest, Brazil.

BACKGROUND: Yellow fever virus (YFV) is an arbovirus that, despite the existence of a safe and effective vaccine, continues to cause outbreaks of varying dimensions in the Americas and Africa. Between 2017 and 2019, Brazil registered un unprecedented sylvatic YFV outbreak whose severity was the result of its spread into zones of the Atlantic Forest with no signals of viral circulation for nearly 80 years. METHODS: To investigate the influence of climatic, environmental, and ecological factors governing the dispersion and force of infection of YFV in a naïve area such as the landscape mosaic of Rio de Janeiro (RJ), we combined the analyses of a large set of data including entomological sampling performed before and during the 2017-2019 outbreak, with the geolocation of human and nonhuman primates (NHP) and mosquito infections. RESULTS: A greater abundance of Haemagogus mosquitoes combined with lower richness and diversity of mosquito fauna increased the probability of finding a YFV-infected mosquito. Furthermore, the analysis of functional traits showed that certain functional groups, composed mainly of Aedini mosquitoes which includes Aedes and Haemagogus mosquitoes, are also more representative in areas where infected mosquitoes were found. Human and NHP infections were more common in two types of landscapes: large and continuous forest, capable of harboring many YFV hosts, and patches of small forest fragments, where environmental imbalance can lead to a greater density of the primary vectors and high human exposure. In both, we show that most human infections (~ 62%) occurred within an 11-km radius of the finding of an infected NHP, which is in line with the flight range of the primary vectors. CONCLUSIONS: Together, our data suggest that entomological data and landscape composition analyses may help to predict areas permissive to yellow fever outbreaks, allowing protective measures to be taken to avoid human cases.

Emergence of Within-Host SARS-CoV-2 Recombinant Genome After Coinfection by Gamma and Delta Variants: A Case Report.

In this study, we report the first case of intra-host SARS-CoV-2 recombination during a coinfection by the variants of concern (VOC) AY.33 (Delta) and P.1 (Gamma) supported by sequencing reads harboring a mosaic of lineage-defining mutations. By using next-generation sequencing reads intersecting regions that simultaneously overlap lineage-defining mutations from Gamma and Delta, we were able to identify a total of six recombinant regions across the SARS-CoV-2 genome within a sample. Four of them mapped in the spike gene and two in the nucleocapsid gene. We detected mosaic reads harboring a combination of lineage-defining mutations from each VOC. To our knowledge, this is the first report of intra-host RNA-RNA recombination between two lineages of SARS-CoV-2, which can represent a threat to public health management during the COVID-19 pandemic due to the possibility of the emergence of viruses with recombinant phenotypes.

Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants.

During the first semester of 2021, all of Brazil has suffered an intense wave of COVID-19 associated with the Gamma variant. In July, the first cases of Delta variant were detected in the state of Rio de Janeiro. In this work, we have employed phylodynamic methods to analyse more than 1 600 genomic sequences of Delta variant collected until September in Rio de Janeiro to reconstruct how this variant has surpassed Gamma and dispersed throughout the state. After the introduction of Delta, it has initially spread mostly in the homonymous city of Rio de Janeiro, the most populous of the state. In a second stage, dispersal occurred to mid- and long-range cities, which acted as new close-range hubs for spread. We observed that the substitution of Gamma by Delta was possibly caused by its higher viral load, a proxy for transmissibility. This variant turnover prompted a new surge in cases, but with lower lethality than was observed during the peak caused by Gamma. We reason that high vaccination rates in the state of Rio de Janeiro were possibly what prevented a higher number of deaths.

[Aedes aegypti larval indices and dengue incidence: an ecological study in the state of Rio de Janeiro, Brazil]. / Índices larvais de Aedes aegypti e incidência de dengue: um estudo ecológico no Estado do Rio de Janeiro, Brasil.

The simultaneous circulation of dengue, Zika, and chikungunya poses major challenges for Brazil. Due to climate changes and other associated factors, more than two billion people in the world may be exposed to these arbovirus infections, according to the World Health Organization. The principal strategy for Aedes aegypti control programs is based on the Infestation Index Rapid Survey for Ae. aegypti (LIRAa), a sample survey in which the Building Infestation Index (BII) is used to prioritize areas for intervention. This study analyzed the performance of LIRAa in terms of its sensitivity for predicting dengue epidemics in municipalities in the state of Rio de Janeiro in epidemic years. Incidence rates per municipality for the years 2011, 2012, 2013, 2015, and 2016, plus the BII in October of the previous years. Scatterplots were created, aimed at an exploratory analysis and graphic visualizations of the relationship between the above-mentioned variables, as well as analyses of the Spearman correlation between the BII and the Breteau Index for each year, aimed at estimating the quality of the LIRAa. Comparative analysis of the values for the BII and the respective incidence rates in the period only indicated significant correlation between these variables in 2011/2012 (rs = 0.479; p < 0.01). There was also a correlation between BII and Breteau Index. It is urgent to rethink the parameters established by the LIRAa methodology and invest in alternative methodologies in entomological and epidemiological surveillance that reliably measure transmission risk in the territory and thus design more effective strategies to control these arbovirus infections.

A circulação simultânea da dengue, Zika e chikungunya impõe desafios importantes para o Brasil, que em decorrência das mudanças climáticas e outros fatores associados, estas arboviroses podem expor mais de 2 bilhões de pessoas no mundo, segundo a Organização Mundial da Saúde. A principal estratégia dos programas de controle do Aedes aegypti baseia-se no Levantamento de Índice Rápido para o Ae. aegypti (LIRAa), um inquérito amostral no qual o Índice de Infestação Predial (IIP) obtido é utilizado para priorizar áreas de intervenção. Neste estudo, analisou-se o desempenho do LIRAa quanto à sua sensibilidade na previsão de epidemias de dengue em municípios do Estado do Rio de Janeiro, em anos considerados epidêmicos. Foram obtidas as taxas de incidência (TI) por município nos anos de 2011, 2012, 2013, 2015 e 2016, e os IIP de outubro dos anos anteriores. Foram elaborados diagramas de dispersão, visando à análise exploratória e à visualização gráfica da relação entre as referidas variáveis, assim como análises de correlação de Spearman entre o IIP e o Índice de Breteau (IB) de cada ano, a fim de estimar a qualidade do LIRAa. A análise comparativa dos valores dos IIP e as respectivas TI no período indicou correlação significativa entre estas variáveis apenas em 2011/2012 (rs = 0,479; p < 0,01). Adicionalmente, foi observada correlação entre os IIP e IB. É urgente repensar os parâmetros estabelecidos pela metodologia LIRAa e investir em metodologias alternativas de vigilância entomoepidemiológica, que mensurem de forma confiável o risco de transmissão no território e assim delinear estratégias mais efetivas para o controle dessas arboviroses.

La circulación simultánea del dengue, Zika y chikungunya impone desafíos importantes para Brasil, que, a consecuencia del cambio climático y otros factores asociados, pueden estar expuestas a estas arbovirosis más de 2 billones de personas en el mundo, según la Organización Mundial de la Salud. La principal estrategia de los programas de control del Aedes aegypti se basa en el Levantamento de Índice Rápido para el Ae. aegypti (LIRAa), una encuesta de muestreo en la que el Índice de Infestación de Edificios (IIP) obtenido es utilizado para priorizar áreas de intervención. En este estudio se analizó el desempeño del LIRAa, en cuanto a su sensibilidad en la previsión de epidemias de dengue en municipios del estado de Río de Janeiro, durante años considerados epidémicos. Se obtuvieron tasas de incidencia (TI) por municipio de los años de 2011, 2012, 2013, 2015 y 2016, y los IIP de octubre de años anteriores. Se elaboraron diagramas de dispersión, visando el análisis exploratorio y visualización gráfica de la relación entre las referidas variables, así como análisis de correlación de Spearman entre el IIP y el Índice de Breteau (IB) de cada año, con el objetivo estimar la calidad del LIRAa. El análisis comparativo de los valores de los IIP y las respectivas TI en el período indicó correlación significativa entre esas variables solamente en 2011/2012 (rs = 0,479; p < 0,01). Asimismo, se observó correlación entre los IIP e IB. Es urgente repensar los parámetros establecidos por la metodología LIRAa, e invertir en metodologías alternativas de vigilancia entomoepidemiológica, que midan de forma confiable el riesgo de transmisión en el territorio y así delinear estrategias más efectivas para el control de esas arbovirosis.