Spatiotemporal transmission of SARS-CoV-2 lineages during 2020-2021 in Pernambuco-Brazil.

SARS-CoV-2 virus emerged as a new threat to humans and spread around the world, leaving a large death toll. As of January 2023, Brazil is among the countries with the highest number of registered deaths. Nonpharmacological and pharmacological interventions have been heterogeneously implemented in the country, which, associated with large socioeconomic differences between the country regions, has led to distinct virus spread dynamics. Here, we investigate the spatiotemporal dispersion of SARS-CoV-2 lineages in the Pernambuco state (Northeast Brazil) throughout the distinct epidemiological scenarios that unfolded in the first 2 years of the pandemic. We generated a total of 1,389 new SARS-CoV-2 genomes from June 2020 to August 2021. This sampling captured the arrival, communitary transmission, and the circulation of the B1.1, B.1.1.28, and B.1.1.33 lineages; the emergence of the former variant of interest P.2; and the emergence and fast replacement of all previous variants by the more transmissible variant of concern P.1 (Gamma). Based on the incidence and lineage spread pattern, we observed an East-to-West to inner state pattern of transmission, which is in agreement with the transmission of more populous metropolitan areas to medium- and small-size country-side cities in the state. Such transmission patterns may be partially explained by the main routes of traffic across municipalities in the state. Our results highlight that the fine-grained intrastate analysis of lineages and incidence spread can provide actionable insights for planning future nonpharmacological intervention for air-borne transmissible human pathogens.IMPORTANCEDuring the COVID-19 pandemic, Brazil was one of the most affected countries, mainly due its continental-size, socioeconomic differences among regions, and heterogeneous implementation of intervention methods. In order to investigate SARS-CoV-2 dynamics in the state of Pernambuco, we conducted a spatiotemporal dispersion study, covering the period from June 2020 to August 2021, to comprehend the dynamics of viral transmission during the first 2 years of the pandemic. Throughout this study, we were able to track three significant epidemiological waves of transmission caused by B1.1, B.1.1.28, B.1.1.33, P.2, and P.1 lineages. These analyses provided valuable insights into the evolution of the epidemiological landscape, contributing to a deeper understanding of the dynamics of virus transmission during the early years of the pandemic in the state of Pernambuco.

Urban schistosomiasis: An ecological study describing a new challenge to the control of this neglected tropical disease.

Background: Social and environmental vulnerabilities contribute to the persistence and increase of Schistosomiasis, which has been a public health problem in Brazil and worldwide. In this study, we aimed to monitor the entry, installation, and maintenance of schistosomiasis transmission in an urban area on the Brazilian coast over two decades (2000-2010/2010-2020). Methods: This population-based cross-sectional study was conducted in Porto de Galinhas, state of Pernambuco, Brazil, to investigate the dynamics of schistosomiasis transmission in the urban area. Through 3 malacological and parasitological surveys and using geoprocessing technologies, schistosomiasis transmission foci (STF), as well as cases of the disease were identified and quantified. Statistical and geoprocessing tools were used to analyse the data. Findings: Overall, the number of STF decreased from 15 (2000) to 11 (2010) and then to 9 (2020). Although the infection ratio of snails in 2000 has decreased from 16·1% to 5·8% in 2010, we observed an increase to 7·2% in 2020. Additionally, 6,499 individuals were analysed (2012 in 2000; 2459 in 2010, and 2028 in 2020) and the prevalence of human infection has decreased over years, from 32·5% (2000), 16·6% (2010) to 8·8% (2020). The disorderly urbanization process was directly related to the spatial distribution of STF and schistosomiasis cases, causing a new scenario where people became infected by walking on unpaved and flooded streets. Interpretation: Although we observed a decreasing in schistosomiasis cases and STF, this NTD became a health problem related to urbanization in the study area. The challenge to overcome this new sort of transmission will require a greater understanding of the disorderly migration, spatial occupation, and degradation of the environment. Funding: National Council for Scientific and Technological Development (CNPq), Ministry of Science, Technology, Innovations and Communications, Brazil.

Gas chromatography-mass spectrometry (GC/MS) reveals urine metabolites associated to light and heavy infections by Schistosoma mansoni in mice.

High-throughput profiling of metabolites has been used to identify metabolic changes in murine models as a response to the infection by the parasitic trematode Schistosoma. These investigations have contributed to our understanding on the pathogenesis of this tropical neglected disease, with a potential of helping diagnosis. Here, our study aimed to investigate the application of gas chromatography-mass spectrometry (GC/MS) on the profiling of urine metabolites from mice carrying infections by Schistosoma mansoni. Two larval infection doses created distinctive infection intensities in mice, whereby the heavily infected animals were found to release 25 times more eggs in faeces than lightly infected animals. Over 200 urine metabolites were identified from these animals by GC/MS, following two complementary derivatisation methods. A list of 14 individual metabolites with altered relative abundances between groups were identified. Most of the altered metabolites showed a trend of increased abundances in response to infection intensity, indicating host-specific metabolic alterations as a result of the disease. Hippurate, a metabolite which concentration is intimately modulated by the gut microbiota, was found to be highly correlated to infection intensity. Our study showed that urine metabolic profiling by GC/MS can distinguish non-infected animals from those carrying light and heavy infections by S. mansoni, revealing metabolites associated to the infection and providing insights on the pathogenesis of schistosomiasis.

Investigation of schistosomiasis cases and deaths in the city of Recife, Pernambuco, Brazil, 2005-2013. / Investigação sobre os casos e óbitos por esquistossomose na cidade do Recife, Pernambuco, Brasil, 2005-2013.

OBJECTIVE: to describe schistosomiasis cases and deaths among residents of the city of Recife, Pernambuco, Brazil, from 2005 to 2013. METHODS: this was a descriptive epidemiological study using data from the Mortality Information System (SIM) (2005-2013) and the Notifiable Diseases Information System (SINAN) (2007-2013); active tracing of the relatives of the dead was undertaken and probabilistic linkage of the databases (2007-2013) was performed using the Reclink program. RESULTS: 297 schistosomiasis deaths were recorded on the SIM system; through active tracing, 130 relatives were contacted and 20.8% autochthony was identified; 388 cases resident in Recife were registered on the SINAN system; through probabilistic linkage, 23 matching records were identified on SIM and SINAN. CONCLUSION: investigation of deaths showed that some individuals had never traveled outside Recife and progressed to the chronic stage of the disease; 23.8% of the cases registered on SINAN had Recife as the municipality in which infection occurred.

The Geographic Information System applied to study schistosomiasis in Pernambuco.

OBJECTIVE: Diagnose risk environments for schistosomiasis in coastal localities of Pernambuco using geoprocessing techniques. METHODS: A coproscopic and malacological survey were carried out in the Forte Orange and Serrambi areas. Environmental variables (temperature, salinity, pH, total dissolved solids and water fecal coliform dosage) were collected from Biomphalaria breeding sites or foci. The spatial analysis was performed using ArcGis 10.1 software, applying the kernel estimator, elevation map, and distance map. RESULTS: In Forte Orange, 4.3% of the population had S. mansoni and were found two B. glabrata and 26 B. straminea breeding sites. The breeding sites had temperatures of 25ºC to 41ºC, pH of 6.9 to 11.1, total dissolved solids between 148 and 661, and salinity of 1,000 d. In Serrambi, 4.4% of the population had S. mansoni and were found seven B. straminea and seven B. glabrata breeding sites. Breeding sites had temperatures of 24ºC to 36ºC, pH of 7.1 to 9.8, total dissolved solids between 116 and 855, and salinity of 1,000 d. The kernel estimator shows the clusters of positive patients and foci of Biomphalaria, and the digital elevation map indicates areas of rainwater concentration. The distance map shows the proximity of the snail foci with schools and health facilities. CONCLUSIONS: Geoprocessing techniques prove to be a competent tool for locating and scaling the risk areas for schistosomiasis, and can subsidize the health services control actions.

Modelling of the distribution of Biomphalaria glabrata and Biomphalaria straminea in the metropolitan region of Recife, Pernambuco, Brazil.

The occurrence of schistosomiasis is directly linked to the presence of its snail intermediate host Biomphalaria spp. Knowledge of geographical distribution, habitats and behaviour of these snails in relation to the climate is essential for guiding measures for disease prevention and control. This study aims to model the distribution of B. glabrata and B. straminea in schistosomiasis non-endemic areas of the metropolitan region of Recife (MRR) based on environmental data and estimates of snail distributions in endemic and neighbouring areas. We applied Kriging with the aim of determining the spatial distribution of these two snail species and MaxEnt for modelling their ecological behaviour. Kriging showed that the North and the Centre of the MRR were generally either snail-free or contained only B. straminea, while both snail species could be found in the South. MaxEnt supported our observation that the northern and southern coastal regions were favoured by B. glabrata and diurnal mean temperature variation; July rainfall and November rainfall were the three variables favouring Biomphalaria breeding sites that contributed the most in the predictive model we developed. The study showed the location of areas suitable to Biomphalaria spp. and therefore at potential risk, first for invasion of these snails and later for the development of new schistosomiasis- endemic areas. This information should be useful, not only to estimate expansion possibilities of this disease in the MRR, but also to point out the climatic variables that would contribute to this expansion, thereby allowing timely application of prevention and control measures.

First report of schistosomiasis on Serrambi beach, Ipojuca, State of Pernambuco.

INTRODUCTION: The expansion of schistosomiasis to previously unaffected areas is being monitored by identifying new cases and georeferencing outbreaks of vector snails. METHODS: In 2014, the Laboratório de Esquistossomose began an epidemiological survey in Serrambi and registered 2,574 people living there. RESULTS: Of these subjects, 1,414 (54.9%) underwent feces examination and 63 (4.5%) were diagnosed with Schistosoma mansoni infection. At this locality, seven breeding sites each were identified for Biomphalaria straminea and Biomphalaria glabrata. At two sites, B. glabrata were shedding cercariae. CONCLUSIONS: Implementing preventive measures is necessary to avoid the establishment of schistosomiasis in yet another tourist locality, Pernambuco.

Investigação sobre os casos e óbitos por esquistossomose na cidade do Recife, Pernambuco, Brasil, 2005-2013 / Investigación sobre los casos y los óbitos por esquistosomiasis en la ciudad de Recife, Pernambuco, Brasil, 2005-2013 / Investigation of schistosomiasis cases and deaths in the city of Recife, Pernambuco, Brazil, 2005-2013

Objetivo: descrever os casos e óbitos por esquistossomose em residentes na cidade de Recife, Pernambuco, Brasil, no período 2005-2013. Métodos: estudo epidemiológico descritivo com dados do Sistema de Informações sobre Mortalidade (SIM) (2005-2013) e do Sistema de Informação de Agravos de Notificação (Sinan) (2007-2013); realizou-se a busca ativa dos familiares dos óbitos e o relacionamento probabilístico das bases de dados (2007-2013) pelo aplicativo Reclink. Resultados: no SIM, registraram-se 297 óbitos por esquistossomose no período estudado; pela busca ativa, 130 familiares foram contatados, identificando-se 20,8% de autoctonia; no Sinan, 388 casos foram registrados para residentes no Recife; pelo relacionamento probabilístico, identificaram-se 23 registros pareados entre SIM e Sinan. Conclusão: a investigação dos óbitos demonstrou que alguns indivíduos nunca viajaram para fora do Recife e evoluíram para a fase crônica da doença; 23,8% dos casos notificados no Sinan tiveram como município de infecção o Recife.

Objetivo: describir casos y óbitos por esquistosomiasis en residentes de la ciudad de Recife, Pernambuco, Brasil, en el período de 2005 a 2013. Métodos: estudio epidemiológico descriptivo con datos del Sistema Información sobre Mortalidad (SIM) (2005-2013) y del Sistema de Información de Agravamientos de Notificación (Sinan) (2007-2013); se realizó la búsqueda activa de los familiares de los fallecidos y la relación probabilística de los datos (2007-2013) en el aplicativo Reclink. Resultados: en el SIM, hubo 297 óbitos por esquistosomiasis; en la búsqueda activa, se identificaron 130 familiares y un 20,8% de autoctonía; en Sinan, 388 casos fueron registrados para residentes en Recife; en la relación probabilística, 23 registros pareados fueron identificados en el SIM y el Sinan. Conclusión: la investigación de los óbitos mostró que algunas personas nunca viajaron fuera de Recife y evolucionaron a la fase crónica de la enfermedad; 23,8% de los casos registrados en el Sinan tuvieron a Recife como municipio de la infección.

Objective: to describe schistosomiasis cases and deaths among residents of the city of Recife, Pernambuco, Brazil, from 2005 to 2013. Methods: this was a descriptive epidemiological study using data from the Mortality Information System (SIM) (2005-2013) and the Notifiable Diseases Information System (SINAN) (2007-2013); active tracing of the relatives of the dead was undertaken and probabilistic linkage of the databases (2007-2013) was performed using the Reclink program. Results: 297 schistosomiasis deaths were recorded on the SIM system; through active tracing, 130 relatives were contacted and 20.8% autochthony was identified; 388 cases resident in Recife were registered on the SINAN system; through probabilistic linkage, 23 matching records were identified on SIM and SINAN. Conclusion: investigation of deaths showed that some individuals had never traveled outside Recife and progressed to the chronic stage of the disease; 23.8% of the cases registered on SINAN had Recife as the municipality in which infection occurred.

The Geographic Information System applied to study schistosomiasis in Pernambuco / Os Sistemas de Informação Geográfica em estudo sobre a esquistossomose em Pernambuco

ABSTRACT OBJECTIVE Diagnose risk environments for schistosomiasis in coastal localities of Pernambuco using geoprocessing techniques. METHODS A coproscopic and malacological survey were carried out in the Forte Orange and Serrambi areas. Environmental variables (temperature, salinity, pH, total dissolved solids and water fecal coliform dosage) were collected from Biomphalaria breeding sites or foci. The spatial analysis was performed using ArcGis 10.1 software, applying the kernel estimator, elevation map, and distance map. RESULTS In Forte Orange, 4.3% of the population had S. mansoni and were found two B. glabrata and 26 B. straminea breeding sites. The breeding sites had temperatures of 25ºC to 41ºC, pH of 6.9 to 11.1, total dissolved solids between 148 and 661, and salinity of 1,000 d. In Serrambi, 4.4% of the population had S. mansoni and were found seven B. straminea and seven B. glabrata breeding sites. Breeding sites had temperatures of 24ºC to 36ºC, pH of 7.1 to 9.8, total dissolved solids between 116 and 855, and salinity of 1,000 d. The kernel estimator shows the clusters of positive patients and foci of Biomphalaria, and the digital elevation map indicates areas of rainwater concentration. The distance map shows the proximity of the snail foci with schools and health facilities. CONCLUSIONS Geoprocessing techniques prove to be a competent tool for locating and scaling the risk areas for schistosomiasis, and can subsidize the health services control actions.

RESUMO OBJETIVO Diagnosticar ambientes de risco para esquistossomose em localidades litorâneas de Pernambuco utilizando técnicas de geoprocessamento. MÉTODOS Foi realizado inquérito coproscópico e malacológico nas localidades Forte Orange e Serrambi. Foram coletadas variáveis ambientais (temperatura, salinidade, pH, sólidos totais dissolvidos e dosagem de coliformes fecais da água) relacionadas aos criadouros ou focos de Biomphalaria. A análise espacial foi realizada no software ArcGis 10.1, aplicando-se o estimador kernel, mapa de elevação e mapa de distância. RESULTADOS No Forte Orange, 4,3% da população estava com S. mansoni e existem dois criadouros de B. glabrata e 26 de B. straminea. Os criadouros apresentaram temperaturas de 25ºC a 41ºC, pH de 6,9 a 11,1, sólidos totais dissolvidos de 148 a 661 e salinidade de 1.000 d. Em Serrambi, 4,4% da população estava com S. mansoni e há sete criadouros de B. straminea e sete de B. glabrata. Os criadouros apresentaram temperaturas de 24ºC a 36ºC, pH de 7,1 a 9,8, sólidos totais dissolvidos de 116 a 855 e salinidade de 1.000 d. O estimador de kernel mostra os aglomerados de pacientes positivos e de focos de Biomphalaria, e o mapa de elevação digital indica áreas de concentração de águas pluviais. O mapa de distância mostra a proximidade dos focos dos caramujos em relação às escolas e unidades de saúde. CONCLUSÕES As técnicas de geoprocessamento se mostraram como importantes ferramentas para a localização e dimensionamento das áreas de risco para esquistossomose, podendo subsidiar as ações de controle por parte dos serviços de saúde.