Exploring the urban arbovirus landscape in Rio de Janeiro, Brazil: transmission dynamics and patterns of disease spread.

Background: 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.

Differential expression analyses and detection of SNP loci associated with environmental variables: Are salinity and temperature factors involved in population differentiation and speciation in Odontesthes?

Environmental factors play a key role in individual adaptation to different local conditions. Because of this, studies about the physiological and genetic responses of individuals exposed to different natural environments offer clues about mechanisms involved in population differentiation, and as a subsequent result, speciation. Marine environments are especially suited to survey this kind of phenomena because they commonly harbor species adapted to different local conditions along a geographic continuum. Silversides belonging to Odontesthes are commonly distributed in tropical and temperate regions of South America and exhibit noticeable phenotypic plasticity, which allows them to adapt to contrasting environments. In this study, the genetic expression of O. argentinensis sampled along the Uruguayan Atlantic coast and estuarine adjacent areas was investigated. In addition, the correlation between individual genotypes and environmental variables was also analysed in O. argentinensis and O. bonariensis. Results obtained suggest a differential expression pattern of low magnitude among individuals from the different areas sampled and a correlation between several SNP loci and environmental variables. The analyses carried out did not show a clear differentiation among individuals sampled along different salinity regimens, but enriched GOTerms seem to be driven by water oxygen content. On the other hand, a total of 46 SNPs analysed in O. argentinensis and O. bonariensis showed a correlation with salinity and temperature. Although none of the correlated SNPs and corresponding genes from our both analyses were directly associated with hypoxia, genes related to the cardiovascular system and muscle cell differentiation were found. All these genes are interesting candidates for future studies since they are closely related to the differentially expressed genes. Although salinity was also mentioned as an important parameter limiting introgression between O. argentinensis and O. bonariensis, it was found that salinity does not drive differential expression in O. argentinensis, but rather oxygen levels. Moreover, salinity does not directly affect the structure and genetic divergence of the populations, they appear to be structured based on their degree of isolation and geographical distance between them. Further studies, like genome-wide analyses, could help to elucidate additional genes adapted to the different environments in these silverside species.

Characterisation of the novel HLA-C*15:274 allele using short and long-read sequencing technologies.

The novel HLA-C*15:274 allele, first described in a potential bone marrow donor from Brazil.

Rare Earth Element Accumulation in Fiddler Crabs (Minuca rapax) from the Rio Doce Tropical Estuary Strongly Affected by Mine Tailings Following the Fundão Disaster.

A mining tailing dam rupture in Brazil in November 2015 released millions of tons of mining waste into the Rio Doce ecosystem, leading to long-term aquatic ecosystem impacts. Although multiple lines of evidence indicate tailings associations with potentially toxic elements in estuarine sediments and biological impact and bioaccumulation pathways in fishes, the extent of contamination in base benthic species is still largely unknown. Moreover, Rare Earth Elements (REE) have not received any attention in this regard. This study assessed REE in fiddler crabs (Minuca rapax) sampled from the Rio Doce estuary in 2017, nearly 2 years after the disaster. The ΣREE in crab hepatopancreas and muscle were high (327.83 mg kg-1 w.w. and 33.84 mg kg-1 w.w., respectively, compared to other assessments in crabs, indicating a preference for REE bioaccumulation in the hepatopancreas compared to muscle. Neodimium, La, and Ce were detected at the highest concentrations. The REE from the Rio Doce Basin were, thus, transported and deposited in the estuary with the mine tailings slurry, leading to bioaccumulation in crabs. This may lead to trophic effects and other ecological impacts not readily measured by typical impact assessment studies, revealing an invisible and not typically acknowledged damage to the Rio Doce estuary.

Antimicrobial resistance, virulence genes, and ESBL (Extended Spectrum Beta-Lactamase) production analysis in E. coli strains from the Rio Grande/Rio Bravo River in Tamaulipas, Mexico.

The Rio Grande/Rio Bravo River is used as a major water supply for diverse recreational, household, and industrial activities in Northeast Tamaulipas, Mexico, and South Texas. In this study, we sampled surface water from 38 sites along Rio Grande/Rio Bravo River (Díaz Ordaz, Reynosa and Matamoros). We isolated 105 E. coli strains that were molecularly and phenotypically characterized. The percentage of virulence genes detected in E. coli were: hlyA (15.23%), stx2 (11.42%), stx1 (9.52%), bfp (0.95%), and eae (0.0) and combinations of stx1/stx2 (2.85%), stx2/hlyA (1.90%), stx1/bfp (0.95%) and stx2/bfp (0.95%) were detected in these strains. Resistance to more than one antibiotic was detected in 85.71%, and 5.71% of strains were extended-spectrum ß-lactamase-E. coli (ESBL-EC). These results indicate the presence of potentially pathogenic E. coli strains in the Rio Grande/Rio Bravo River; therefore, it can be considered a reservoir of pathogenic strains and represents a health risk for the population.

Characterisation of the novel HLA-A*02:1140 allele, first identified in a Brazilian individual.

The novel HLA-A*02:1140 allele, first described in a potential bone marrow donor from Brazil.

Metabolic organization of pregnant freshwater stingray and their offspring.

The elucidation of energetic patterns in adult viviparous elasmobranchs and their offspring can contribute to understanding ecophysiological questions, such as maternal-fetal metabolism and group life-history traits. We characterized the energetic substrates in pregnant individuals and stages of offspring development in the freshwater stingray Potamotrygon amandae. Our results show that the energetic distribution of the yolk is composed of more lipids than proteins, whereas the inverse pattern is observed in the egg and uterus, proving the plasticity of the energy provision of the species. As a novelty, we describe that yolk/intestine transfer occurs in this species.

Characterisation of the novel HLA-B*35:593 allele using short and long-read sequencing technologies.

The novel HLA-B*35:593 allele, first described in a potential bone marrow donor from Brazil.

Characterisation of the novel HLA-C*08:275 allele, first identified in a Brazilian individual.

The novel HLA-C*08:275 allele, first described in a potential bone marrow donor from Brazil.

Mining tailings alter insects: revealing fluctuating asymmetry in the caddisfly Smicridea coronata.

The Samarco/Vale/BHP mine tailing dam breach that took place in Minas Gerais, southeastern Brazil, in 2015, deposited high concentrations of metals and metalloids in the Rio Doce basin, severely impacting freshwater and riverine forest ecosystems. To assess developmental instability of caddisflies in response to the environmental impacts of the dam breach, we investigated the fluctuating asymmetry (FA) in the species Smicridea (Rhyacophylax) coronata (Trichoptera: Hydropsychidae). FA was assessed at individual and populational scales using geometric morphometric methods in the cephalic capsule and mandibles of larvae and also on the forewings of adults, both collected under the impacted condition, and under the least disturbed condition. The levels of FA increased in response to stressors on the forewings at the populational scale, and on the mandibles, at individual scale. These morphological variations in the larval and adult stages may lead to detrimental effects and result in high mortality rates as well as lower adult fitness. Trichoptera forewings are revealed as suitable traits for assessing FA, holding potential for applications in biomonitoring programs. Directional asymmetry levels were higher than FA levels for all traits, and this correlation could be explained by a transition from fluctuating to directional asymmetry in the presence of heightened disturbance. Our results validate the relationship between the impacts from the dam breach and increased developmental instability in this species with likely cascade effects on the insect community.

Characterisation of the novel HLA-A*30:218 allele using two different sequencing technologies.

The novel HLA-A*30:218 allele, first described in a potential bone marrow donor from Brazil.

Nature-based solutions potential for flood risk reduction under extreme rainfall events.

Climate change will substantially increase extreme rainfall events, especially in the Tropics, enhancing flood risks. Such imminent risks require climate adaptation strategies to endure extreme rainfall and increase drainage systems. Here, we evaluate the potential of nature-based solutions by using an ecosystem service modeling approach, evaluating the impact of extreme rainfall events on flood risks in a large urban area and with a real-world land recovery plan. We evaluate the cost-effectiveness of four different land recovery scenarios and associated co-benefits, based on a gradient increase in area recovered and cost of implementation. Although the scenarios reveal increasing flood risk reduction and co-benefits along with greater proportion of land recovery, the most cost-effective scenario was the one with an intermediate land recovery where 30% of the study area would be reforested. We emphasize the striking benefits of nature-based solutions for flood risk reduction in cities, considering landscape scale and stakeholders' needs.

Piroplasmid Infections Among Domestic Dogs in the Mountain City of Rio de Janeiro, Brazil.

PURPOSE: The aim of the present study was to analyze the frequency of the piroplasmids in blood from dogs and ticks recovered from these animals in Teresópolis city, located in the mountain region of Rio de Janeiro state, Brazil. In addition to the clinical and hematological profile. METHODS: A total of 400 dogs attended in a veterinary clinic in this city between 2020 and 2021 were included. The blood was collected from the dogs, along with ticks and information on these dogs was obtained through a questionnaire applied to the owners. Thin-smear analyses and complete blood counts were performed. All forms characteristic of piroplasmids were measured and classified morphologically. The blood was also subjected to PCR assays based on the genes 18S rRNA and hsp70. In addition, the ixodid ticks were classified morphologically and subjected to PCR for piroplasmids research. The amplified products were sent for gene sequencing. RESULTS: Piroplasmids were detected in 2.3% of the dogs. The variables statistically associated with infections in these animals were hemorrhage/bleeding, jaundice, anisocytosis, activated monocytes and macroplatelets (p ≤ 0.05). Piriform, ring-shaped, oval and aberrant structures were viewed in erythrocytes, neutrophils and monocytes, with lengths greater than and less than 2.5 µm. The nine positive samples from these dogs were characterized as due to Rangelia vitalii. However, one sequence from B. vogeli was detected in a single adult specimen of R. sanguineus. CONCLUSION: Although circulation of two species of piroplasmids potentially infective for domestic dogs has been observed in the mountain city of Rio de Janeiro, infection due to R. vitalii was mostly seen in the dogs of the present study.

Assessment of the performance of cruise ship waste management: Case study of the Rio de Janeiro port, Brazil.

The significant growth of the cruise ship industry has resulted in economic benefits, but there are also waste management-related challenges. The aim of this case study was to contribute to the research of cruise ship waste management at the Port of Rio de Janeiro. A3 methodology, applied for the first time in this context, was used to create questionnaires to assess the stakeholders involved, revealing that institutional bureaucracy has a negative effect on waste management. In addition, secondary data on unloaded waste, obtained from the transport manifests, showed that 56 % contained reliable information. The main wastes were plastics (57 %), glass (17 %), metal (9 %), and others. With respect to destinations, 41 % were sent to landfills, 55 % recycled and 4 % thermally treated. Only 5 % of cruise ship moorings removed waste at the Port of Rio de Janeiro, attributed to factors such as high costs.

Wastewater surveillance to assess cocaine and methylenedioxymethamphetamine use trends during a major music festival in Brazil.

Wastewater-based epidemiology was applied in northeastern Brazil during a dance festival, revealing that cocaine consumption doubled during the event days. The daily drug loads were 0.95 ± 0.03 to 11.4 ± 0.4 g/day for BE, 1.8 ± 0.4 to 7.6 ± 0.3 g/day for COC, 0.04 ± 0.02 to 0.19 ± 0.02 g/day for COE, and 0.08 ± 0.02 to 0.80 ± 0.02 g/day for MDMA.

This study employed the wastewater­based epidemiology (WBE) strategy to investigate cocaine (COC) and ecstasy (MDMA) usage during Carnatal festival in Rio Grande do Norte, Brazil. Wastewater samples were collected over the four festival days (December 12­15, 2019), as well as during corresponding days before and after the event. The samples underwent filtration, acidification, solid­phase extraction (SPE) for pre­concentration, and analysis using ultra­high­performance liquid chromatography­tandem mass spectrometry (UHPLC­MS/MS) with calibration using deuterated internal standards. The measured concentration ranges in the wastewater samples were as follows: benzoylecgonine (BE, a metabolite of COC use) ranged from 760 ± 30 to 8914 ± 252 ng/L, COC (non­metabolized or directly discharged) ranged from 1182 ± 25 to 6,760 ± 95 ng/L, cocaethylene (COE, a metabolite of alcohol­COC use) ranged from 21 ± 10 to 161 ± 10 ng/L, and MDMA (ecstasy) ranged from 18 ± 5 to 613 ± 15 ng/L. Daily wastewater loads were estimated as 0.81 ± 0.03 to 11.69 ± 0.33 g/day for BE, 1.42 ± 0.03 to 8.06 ± 0.11 g/day for COC, 0.02 ± 0.01 to 0.21 ± 0.01 g/day for COE, and 0.02 ± 0.01 to 0.80 ± 0.02 g/day for MDMA. Notably, COE and MDMA were only detected above the quantification limit during the festival days. The data enable estimating that COC consumption doubled during the event days. The COC/BE ratio indicated likely drug disposals on the event's last day and the subsequent week. The study's findings shed light on illicit substance consumption, assisting in public health programs and combating drug trafficking efforts.

Entre territórios pandêmicos: cartografia de um Consultório na Rua durante a pandemia de covid-19 / Exploring pandemic territories: cartography of a street clinic during the covid-19 pandemic / Entre territorios pandémicos: cartografía de un Consultorio en la Calle durante la pandemia de covid-19

O objetivo do presente artigo foi realizar uma cartografia de um Consultório na Rua, durante o período da pandemia de covid-19. A cartografia foi produzida por uma vivência no consultório de um município de grande porte no sul do Brasil, de agosto de 2021 a janeiro de 2022. Foi perceptível que a locomoção e o funcionamento do serviço reconhecem outros territórios das Pessoas em Situação de Rua, muitas vezes não percebidos por outros pontos do Sistema Único de Saúde. Foram encontradas tanto as barreiras já estabelecidas historicamente quanto as emergentes da pandemia. Foi vivenciado que a esta população não utiliza o território do modo que a cidade racionalizada planeja, sendo, portanto, singular. O reconhecimento do serviço, aliado à compreensão de como as Pessoas em Situação de Rua vivem no território urbano, em cada realidade, mostrou-se essencial para a produção de cuidado.

The objective of this article was to conduct a cartographic study of a street clinic during the covid-19 pandemic. The cartography was based on an experiential approach in a street clinic located in a major city in southern Brazil, between August 2021 and January 2022. It became evident that the flows and operation of the service acknowledged the alternative territories inhabited by the homeless population, often overlooked by other parts of Brazil's Unified Health System. Both historically established barriers and those emerging from the pandemic were encountered. It was observed that the homeless population does not conform to rationalized urban plans, displaying unique patterns of engagement with the urban territory. Recognizing the significance of the service, coupled with a comprehensive understanding of the unique living conditions of homeless individuals, proved indispensable for the provision of effective care.

El objetivo de este artículo fue realizar una cartografía de un Consultorio en la Calle durante el período de la pandemia del covid-19. La cartografía fue producida por una experiencia en un Consultorio en la Calle en una gran ciudad del sur de Brasil, de agosto de 2021 a enero de 2022. Se pudo observar que la locomoción y operación del servicio reconocen otros territorios habitados por personas en situación de calle, a menudo no percibidos por otros puntos del Sistema Único de Salud. Se encontraron barreras, tanto históricamente establecidas como emergentes debido a la pandemia. Se constató que la población en situación de calle no utiliza el territorio de la forma planificada por la ciudad racionalizada. El reconocimiento del servicio, junto con la comprensión de cómo viven las personas en situación de calle en el territorio urbano en cada realidad, se mostró fundamental para la producción del cuidado.

A cidade não pode parar: a Maratona do Rio de Janeiro em 2020 na era da pandemia / The city cannot stop: the Rio de Janeiro Marathon in the era of the pandemic / La ville ne peut pas s'arrêter: le Marathon de Rio de Janeiro à l'ère de la pandémie

Neste artigo, iremos apresentar como ocorreu a edição virtual da Maratona do Rio de Janeiro em 2020, ainda sem autorizações sanitárias para a realização de grandes eventos. Para isso, analisaremos o Guia do corredor, apresentado aos corredores na época. A competição é realizada por meio de uso de aplicativos, mas o atleta é estimulado a correr com o slogan "Não correr nunca foi uma opção". Abordamos os conceitos de necrodemografia e necropolítica. Entende-se que a Maratona do Rio pratica uma espécie de necropolíti-ca ao organizar a competição em pleno período pandêmico do Brasil, apesar de valorizar a paisagem da rua em suas plataformas comunicacionais.

In this article, we will present how the virtual edition of the Rio de Janeiro Marathon took place in 2020 in the middle of the pandemic, still without health permits to hold major events. For this, we will analyze the Runner's Guide presented to the runners at the time. The competition is carried out using applications, but the athlete is encouraged to run with the slogan "Not running was never an option". We approach the concepts of necrodemography and necropolitics. It is understood that the Rio Marathon practices a kind of necropolitics when organizing the competition in the middle of the pandemic period in Brazil, despite valuing the street landscape in its communication platforms.

Dans cet article, nous allons vous présenter comment s'est déroulée l'édition virtuelle du Marathon de Rio de Janeiro en 2020, toujours sans autorisations sanitaires pour les grands événements. Pour cela, nous analyserons le Guide du marathonien, présenté aux marathoniens à l'époque. La compétition se déroule à l'aide d'applications, mais l'athlète est encouragé à courir avec le slogan "Ne pas courir n'a jamais été une option". Nous abordons les concepts de nécrodémographie et de nécropolitique. Il est entendu que le Marathon de Rio pratique une sorte de nécropolitique en organisant la compétition en pleine pandémie au Brésil, malgré la valorisation du paysage de rue dans ses plateformes de communication.

Community composition of black flies during and after the 2020 vesicular stomatitis virus outbreak in Southern New Mexico, USA.

BACKGROUND: Vesicular stomatitis virus (VSV), a vector-borne pathogen of livestock, emerges periodically in the western US. In New Mexico (NM), US, most cases occur close to the Rio Grande River, implicating black flies (Simulium spp.) as a possible vector. In 2020, VS cases were reported in NM from April to May, although total black fly abundance remained high until September. We investigated the hypothesis that transience of local VSV transmission results from transient abundance of key, competent black fly species. Additionally, we investigated whether irrigation canals in southern NM support a different community of black flies than the main river. Lastly, to gain insight into the source of local black flies, in 2023 we collected black fly larvae prior to the release of water into the Rio Grande River channel. METHODS: We randomly sub-sampled adult black flies collected along the Rio Grande during and after the 2020 VSV outbreak. We also collected black fly adults along the river in 2021 and 2022 and at southern NM farms and irrigation canals in 2022. Black fly larvae were collected from dams in the area in 2023. All collections were counted, and individual specimens were subjected to molecular barcoding for species identification. RESULTS: DNA barcoding of adult black flies detected four species in 2020: Simulium meridionale (N = 158), S. mediovittatum (N = 83), S. robynae (N = 26) and S. griseum/notatum (N = 1). Simulium robynae was only detected during the VSV outbreak period, S. meridionale showed higher relative abundance, but lower absolute abundance, during the outbreak than post-outbreak period, and S. mediovittatum was rare during the outbreak period but predominated later in the summer. In 2022, relative abundance of black fly species did not differ significantly between the Rio Grande sites and farm and irrigation canals. Intriguingly, 63 larval black flies comprised 56% Simulium vittatum, 43% S. argus and 1% S. encisoi species that were either extremely rare or not detected in previous adult collections. CONCLUSIONS: Our results suggest that S. robynae and S. meridionale could be shaping patterns of VSV transmission in southern NM. Thus, field studies of the source of these species as well as vector competence studies are warranted.

Ciliate diversity in rodrigo de freitas lagoon (Rio de Janeiro, Brazil) from an integrative standpoint.

The Rodrigo de Freitas Lagoon is a highly eutrophic lacustrine system and has one of the longest histories of exploration and anthropic alteration in Brazil. Despite its relevance, limited studies explored the diversity of micro-eukaryotes in the lagoon. Ciliates (Alveolata, Ciliophora) are overlooked in environmental microbiology, especially in tropical and subtropical ecosystems, resulting in limited knowledge about their diversity and functional relevance in South American habitats, particularly in coastal lagoons. To fill this gap, here we investigated the diversity of ciliates in a brackish coastal lagoon in an urban area of Rio de Janeiro, Brazil, applying and comparing the performance of morphological and metabarcoding approaches. The metabarcoding analysis, based on high-throughput sequencing of the hipervariable region V4 of the 18S rRNA genes detected 37 molecular operational taxonomic units (MOTUs) assigned to Ciliophora, representing only about a half (56.9%) of the diversity detected by microscopy, which counted 65 ciliate morphotypes. The most representative classes in both approaches were Spirotrichea and Oligohymenophorea. The metabarcoding analysis revealed that 35.3% of the ciliate MOTUs had less than 97% similarity to available sequences in the NCBI database, indicating that more than one-third of these MOTUs potentially represents still not represented or undescribed ciliate species in current databases. Our findings indicate that metabarcoding techniques can significantly enhance the comprehension of ciliate diversity in tropical environments, but the scarcity of reference sequences of brackish ciliates in molecular databases represents a challenge to the taxonomic assignment of the MOTUs. This study provides new insights into the diversity of ciliates in a threatened coastal lagoon, revealing a vast array of still unknown and rare ciliate taxonomic units in tropical environments.

Patterns of genetic divergence in the Rio Grande cooter (Pseudemys gorzugi), a riverine turtle inhabiting an arid and anthropogenically modified system.

The lower Rio Grande and Pecos River of the southwest United States have been heavily modified by human activities, profoundly impacting the integrity of their aquatic wildlife. In this context, we focused our study on the population genomics of the Rio Grande Cooter (Pseudemys gorzugi), a freshwater turtle of increasing conservation concern, residing in these two rivers and their tributaries. The genetic data revealed two distinct populations: one in the Pecos and Black Rivers of New Mexico and another in the Rio Grande and Devils River of Texas, with admixed individuals identified at the confluence of the Rio Grande and Pecos River. In addition to having a smaller geographic range, we found lower observed heterozygosity, reduced nucleotide diversity, and a smaller effective population size (Ne) in New Mexico population. Our results depict a significant isolation-by-distance pattern across their distribution, with migration being notably infrequent at river confluences. These findings are pivotal for future conservation and restoration strategies, emphasizing the need to recognize the unique needs of each population.