A new coronavirus [severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)] is currently causing a life-threatening pandemic. In this study, we report the complete genome sequencing and genetic characterisation of a SARS-CoV-2 detected in Manaus, Amazonas, Brazil, and the protocol we designed to generate high-quality SARS-CoV-2 full genome data. The isolate was obtained from an asymptomatic carrier returning from Madrid, Spain. Nucleotide sequence analysis showed a total of nine mutations in comparison with the original human case in Wuhan, China, and support this case as belonging to the recently proposed lineage A.2. Phylogeographic analysis further confirmed the likely European origin of this case. To our knowledge, this is the first SARS-CoV-2 genome obtained from the North Brazilian Region. We believe that the information generated in this study may contribute to the ongoing efforts toward the SARS-CoV-2 emergence.

Abstract INTRODUCTION: The Culicoides transmit a variety of pathogens. Our aim was to survey the Culicoides species occurring in an Amazonian rural settlement, comparing abundance, richness, and diversity in different environments. METHODS: Culicoides were captured using CDC light traps. The Shannon-Wiener (H’) and Rényi indices were used to compare species diversity and evenness between environments, the equitability (J’) index was used to calculate the uniformity of distribution among species, and similarity was estimated using the Jaccard similarity index. A permutational multivariate analysis of variance was applied to assess the influence of environment on species composition. A non-metric dimensional scale was used to represent the diversity profiles of each environment in a multidimensional space. RESULTS: 6.078 Culicoides were captured, representing 84 species (45 valid species/39 morphotypes). H’ values showed the following gradient: forest > capoeira > peridomicile > forest edge. The equitability J’ was greater in capoeira and forests compared to peridomiciles and the forest edge. The population compositions of each environment differed statistically, but rarefaction estimates indicate that environments of the same type possessed similar levels of richness. Species of medical and veterinary importance were found primarily in peridomiciles: C. paraensis, vector of Oropouche virus; C. insignis and C. pusillus, vectors of Bluetongue virus; C. filariferus, C. flavivenula, C. foxi, and C. ignacioi, found carrying Leishmania DNA. CONCLUSIONS: This study indicates that diversity was higher in natural environments than in anthropized environments, while abundance and richness were highest in the most anthropized environment. These findings suggest that strictly wild Culicoides can adapt to anthropized environments.

Resumo Apesar da região amazônica abrigar a maior reserva de água doce do planeta, a falta de saneamento e de tratamento de água, sobretudo na zona rural, causa problemas ambientais e de saúde. Em assentamentos rurais isolados, o abastecimento geralmente é feito por poços rasos (cacimbões) e a qualidade da água é uma preocupação dos moradores. Nestes casos, as opções de tratamento de água são restritas. O objetivo deste estudo foi avaliar o uso de cloradores simplificados por difusão como método alternativo de tratamento de água. Foram realizadas análises bacteriológicas de 100 amostras de água dos poços, antes e após a aplicação dos cloradores, no Assentamento Rural do Rio Pardo, Presidente Figueiredo (AM). As fontes analisadas foram consideradas inadequadas para consumo sem tratamento prévio, e o uso dos cloradores zerou a contaminação por coliformes termotolerantes, na grande maioria dos casos. Além disso, o método teve boa receptividade pelos moradores por não conferir sabor à água de consumo, por ter relativo baixo custo e ser de fácil manuseio. Discutimos as vantagens e as limitações do uso deste método de tratamento para esse contexto socioambiental e apresentamos sugestões de melhoria e adaptação para a aplicação desta metodologia em outros assentamentos.

Abstract While the Amazon region has the world’s largest reserve of fresh water, the lack of water services and water treatment, especially in non-urban regions, causes environmental and health problems. In isolated rural settlements supply is usually by shallow wells, and the quality of water is a concern for residents. These are situations where there are restricted options for water treatment. This study aimed to assess the use of simplified diffusion chlorinators as an alternative water treatment method. Bacteriological analyses were made of 100 samples of water from the wells, before and after application of the chlorinators, in the Rural Settlement of Rio Pardo, Presidente Figueiredo in the Brazilian State of Amazonas. The sources that were analyzed were considered inappropriate for consumption without prior treatment, and the use of the chlorinators eliminated all contamination by thermotolerant coliforms in the great majority of cases. Also, the method was well received by residents, because it does not leave a taste in the water, is relatively low-cost and handling is easy. We discuss the advantages and limitations of the use of this method of treatment for this social-environmental context and present suggestions for improvement and adaptation, for application of this methodology in other settlements.

Resumo Apesar da região amazônica abrigar a maior reserva de água doce do planeta, a falta de saneamento e de tratamento de água, sobretudo na zona rural, causa problemas ambientais e de saúde. Em assentamentos rurais isolados, o abastecimento geralmente é feito por poços rasos (cacimbões) e a qualidade da água é uma preocupação dos moradores. Nestes casos, as opções de tratamento de água são restritas. O objetivo deste estudo foi avaliar o uso de cloradores simplificados por difusão como método alternativo de tratamento de água. Foram realizadas análises bacteriológicas de 100 amostras de água dos poços, antes e após a aplicação dos cloradores, no Assentamento Rural do Rio Pardo, Presidente Figueiredo (AM). As fontes analisadas foram consideradas inadequadas para consumo sem tratamento prévio, e o uso dos cloradores zerou a contaminação por coliformes termotolerantes, na grande maioria dos casos. Além disso, o método teve boa receptividade pelos moradores por não conferir sabor à água de consumo, por ter relativo baixo custo e ser de fácil manuseio. Discutimos as vantagens e as limitações do uso deste método de tratamento para esse contexto socioambiental e apresentamos sugestões de melhoria e adaptação para a aplicação desta metodologia em outros assentamentos.

Abstract While the Amazon region has the world’s largest reserve of fresh water, the lack of water services and water treatment, especially in non-urban regions, causes environmental and health problems. In isolated rural settlements supply is usually by shallow wells, and the quality of water is a concern for residents. These are situations where there are restricted options for water treatment. This study aimed to assess the use of simplified diffusion chlorinators as an alternative water treatment method. Bacteriological analyses were made of 100 samples of water from the wells, before and after application of the chlorinators, in the Rural Settlement of Rio Pardo, Presidente Figueiredo in the Brazilian State of Amazonas. The sources that were analyzed were considered inappropriate for consumption without prior treatment, and the use of the chlorinators eliminated all contamination by thermotolerant coliforms in the great majority of cases. Also, the method was well received by residents, because it does not leave a taste in the water, is relatively low-cost and handling is easy. We discuss the advantages and limitations of the use of this method of treatment for this social-environmental context and present suggestions for improvement and adaptation, for application of this methodology in other settlements.

In a recent issue of Memórias do Instituto Oswaldo Cruz, published in Rio de Janeiro in February 2014 (109: 87-92), Adami et al. have published a survey reporting Mansonella parasite prevalence in the Amazon Region. This report makes a useful contribution to the existing knowledge of filarial parasite distribution within the Amazon area, parasite prevalence rates in relation to age and occupation and provides observations on the possible clinical impact of Mansonella ozzardi. Their publication also provides an account of what appears to be a novel ELISA that has recently been used in the Simuliidae and Onchocerciasis Laboratory of the Oswaldo Cruz Institute, Rio de Janeiro, Brazil. We are concerned that the publication of this ELISA may have created an excessively positive impression of the effectiveness of the onchocerciasis recrudescence serological surveillance tools that are presently available for use in the Amazonia onchocerciasis focus. In this letter we have, thus, sought to highlight some of the limitations of this ELISA and suggest how continuing insecurities concerning the detection of antibodies to Onchocerca volvulus within the Amazonia onchocerciasis focus might be minimised.

We present filaria-nested polymerase chain reaction (PCR), which is based on amplification of first internal transcribed spacer rDNA to distinguish three parasitic filarial species (Onchocerca volvulus, Mansonella ozzardiand Mansonella perstans) that can be found in the Amazon Region. Nested PCR-based identifications yielded the same results as those utilizing morphological characters. Nested PCR is highly sensitive and specific and it detects low-level infections in both humans and vectors. No cross-amplifications were observed with various other blood parasites and no false-positive results were obtained with the nested PCR. The method works efficiently with whole-blood, blood-spot and skin biopsy samples. Our method may thus be suitable for assessing the efficacy of filaria control programmes in Amazonia by recording parasite infections in both the human host and the vector. By specifically differentiating the major sympatric species of filaria, this technique could also enhance epidemiological research in the region.

Simulium cauchense Floch & Abonnenc and Simulium quadrifidum Lutz are widely distributed in the Amazon region and are morphologically similar at the larval and pupal stages. Chromosomally, these species are readily distinguished by the position of the nucleolar organizer, which is in the short arm of chromosome I in S. cauchense and in the long arm of chromosomes III in S. quadrifidum. They also differ by three fixed inversions. Sex chromosomes are undifferentiated in both species. Chromosomal resolution of the two species allowed us to evaluate four structural features previously used as diagnostic aids at the larval stage. Characters that distinguish larvae of the two species are the number of branches and branching patterns of the dorsal abdominal setae and the dark band on each primary fan. Branching patterns of the gill histoblasts were often diagnostic, with S. quadrifidum exhibiting more proximal branching and S. cauchense more distal branching. Sites where both species occurred sometimes had larvae with one petiole branching proximally and the other distally; in these cases examination of the chromosomes permitted assignment of the specimen to species. Pigmentation patterns of larvae, on the other hand, are highly variable. Color typically is sex linked in both species.

Five species are included in the Simulium siolii group, which is placed in the subgenus Psaroniocompsa (Diptera: Simuliidae). Of these five species, only two (Simulium siolii Py-Daniel and Simulium tergospinosum Hamada) have been described in all their life stages, except eggs. Knowledge of the taxonomic characters of all life stages of a species is important in order to clarify interspecific and higher-level taxonomic relationships. The objectives of the present study are to describe the male of Simulium damascenoi Py-Daniel, to provide a list of black-fly species their bionomics and distributions in the state of Amapá, Brazil, and to provide an identification key for larvae and pupae for these species.