Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time, and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space. While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes, vast areas of the tropics remain understudied. In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity, but it remains among the least known forests in America and is often underrepresented in biodiversity databases. To worsen this situation, human-induced modifications may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge, it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost

Efeito fotodinâmico da curcumina em micelas de cetrimida sobre cepas de candida susceptíveis e resistentes a fluconazol

Nos últimos anos o aumento na incidência da candidose superficial ou invasiva causada por espécies emergentes e resistentes aos medicamentos tem sido atribuído a disseminação do uso de antibióticos e/ou agentes imunossupressores. A candidose é considerada uma doença oportunista de alta incidência em pacientes que utilizam medicamentos imunossupressores após transplante de órgãos, antibióticos de amplo espectro, terapias antineoplásicas e nos que possuem imunossupressão relacionada à síndrome da imunodeficiência adquirida. A Terapia Fotodinâmica (Photodynamic Therapy ou PDT) utiliza a combinação de luz (visível) e um composto fotossensível. A maior aplicação da PDT ocorre no tratamento de câncer, entretanto, a técnica está difundindo-se para o tratamento de outras doenças como infecções microbianas. O objetivo desse trabalho foi avaliar o efeito da PDT mediada pela Curcumina, na ausência e na presença do surfactante brometo de cetiltrimetilamônio (CTAB), com uma fonte de luz do tipo LED, sobre suspensões planctônicas de isolados clínicos das espécies C. albicans e C. glabrata fluconazol-resistentes, bem como de cepas ATCC. Após a PDT, foram obtidas diluições seriadas de cada amostra e alíquotas foram plaqueadas para a contagem das células viáveis (ufc/mL). O metabolismo celular para todas as condições experimentais também foi avaliado por meio do ensaio de redução do 2,3-bis[2-methoxy-4-nitro-5-sulphophenyl]2H-tetrazolium-carboxanilida (XTT). Também foi avaliada a capacidade de adesão/formação de biofilme dessas cepas após a PDT. Para isso, amostras obtidas da fase de adesão e da fase madura dos biofilmes foram monitoradas pela contagem de células viáveis (ufc/mL). Os resultados permitem observar que a utilização da PDT com curcumina em micelas de CTAB em suspensões planctônicas...In recent years the increase in the incidence of superficial or invasive candidiasis caused by species emerging drug-resistant and has been attributed to widespread use of antibiotics and/or immunosuppressive agents. Candidiasis is considered an opportunistic disease of high incidence in patients taking immunosuppressive drugs after organ transplantation, broad-spectrum antibiotics, anticancer therapies and who has immunosuppression related to acquired immunedeficiency syndrome. Photodynamic Therapy (PDT) uses a combination of (visible) light and a photosensitive compound. The largest application of PDT occurs in the treatment of cancer, however, the technique is diffusing in the treatment of other diseases such microbial infections. The aim of this study was to evaluate the effect of PDT mediated by Curcumin, in the absence and presence of surfactant cetyltrimethylammonium bromide (CTAB) with a light source type LED on planktonic suspensions of clinical isolates of the species C. albicans and C. glabrata Fluconazole-resistant strains as well as strains ATCC. After PDT, serial dilutions were collected and aliquots of each sample were plated for viable cell count (cfu/ml). Cellular metabolism for all experimental conditions was also assessed by reduction assay of 2,3-bis [2-methoxy-4-nitro-5-sulphophenyl]-2H-tetrazolium carboxanilide (XTT). It was also evaluated the ability of adhesion/biofilm formation of these strains after PDT. For this, samples of the accession and the mature phase biofilms were monitored by viable cell count (cfu/mL). The results allow to observe that the use of PDT with curcumin in CTAB micelles in planktonic suspensions was able to decrease metabolism (XTT) strains of C. albicans and C. glabrata susceptible and resistant to fluconazole, however, the reduction in viable cell count... (Complete abstract click electronic access below

Efeito fotodinâmico da curcumina em micelas de cetrimida sobre cepas de candida susceptíveis e resistentes a fluconazol

Nos últimos anos o aumento na incidência da candidose superficial ou invasiva causada por espécies emergentes e resistentes aos medicamentos tem sido atribuído a disseminação do uso de antibióticos e/ou agentes imunossupressores. A candidose é considerada uma doença oportunista de alta incidência em pacientes que utilizam medicamentos imunossupressores após transplante de órgãos, antibióticos de amplo espectro, terapias antineoplásicas e nos que possuem imunossupressão relacionada à síndrome da imunodeficiência adquirida. A Terapia Fotodinâmica (Photodynamic Therapy ou PDT) utiliza a combinação de luz (visível) e um composto fotossensível. A maior aplicação da PDT ocorre no tratamento de câncer, entretanto, a técnica está difundindo-se para o tratamento de outras doenças como infecções microbianas. O objetivo desse trabalho foi avaliar o efeito da PDT mediada pela Curcumina, na ausência e na presença do surfactante brometo de cetiltrimetilamônio (CTAB), com uma fonte de luz do tipo LED, sobre suspensões planctônicas de isolados clínicos das espécies C. albicans e C. glabrata fluconazol-resistentes, bem como de cepas ATCC. Após a PDT, foram obtidas diluições seriadas de cada amostra e alíquotas foram plaqueadas para a contagem das células viáveis (ufc/mL). O metabolismo celular para todas as condições experimentais também foi avaliado por meio do ensaio de redução do 2,3-bis[2-methoxy-4-nitro-5-sulphophenyl]2H-tetrazolium-carboxanilida (XTT). Também foi avaliada a capacidade de adesão/formação de biofilme dessas cepas após a PDT. Para isso, amostras obtidas da fase de adesão e da fase madura dos biofilmes foram monitoradas pela contagem de células viáveis (ufc/mL). Os resultados permitem observar que a utilização da PDT com curcumina em micelas de CTAB em suspensões planctônicas...In recent years the increase in the incidence of superficial or invasive candidiasis caused by species emerging drug-resistant and has been attributed to widespread use of antibiotics and/or immunosuppressive agents. Candidiasis is considered an opportunistic disease of high incidence in patients taking immunosuppressive drugs after organ transplantation, broad-spectrum antibiotics, anticancer therapies and who has immunosuppression related to acquired immunedeficiency syndrome. Photodynamic Therapy (PDT) uses a combination of (visible) light and a photosensitive compound. The largest application of PDT occurs in the treatment of cancer, however, the technique is diffusing in the treatment of other diseases such microbial infections. The aim of this study was to evaluate the effect of PDT mediated by Curcumin, in the absence and presence of surfactant cetyltrimethylammonium bromide (CTAB) with a light source type LED on planktonic suspensions of clinical isolates of the species C. albicans and C. glabrata Fluconazole-resistant strains as well as strains ATCC. After PDT, serial dilutions were collected and aliquots of each sample were plated for viable cell count (cfu/ml). Cellular metabolism for all experimental conditions was also assessed by reduction assay of 2,3-bis [2-methoxy-4-nitro-5-sulphophenyl]-2H-tetrazolium carboxanilide (XTT). It was also evaluated the ability of adhesion/biofilm formation of these strains after PDT. For this, samples of the accession and the mature phase biofilms were monitored by viable cell count (cfu/mL). The results allow to observe that the use of PDT with curcumin in CTAB micelles in planktonic suspensions was able to decrease metabolism (XTT) strains of C. albicans and C. glabrata susceptible and resistant to fluconazole, however, the reduction in viable cell count... (Complete abstract click electronic access below

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1, acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7-2.4-fold more transmissible, and that previous (non-P.1) infection provides 54-79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness

Evolution and epidemic spread of SARS-CoV-2 in Brazil

Detailed metadata on all 1,182 sequences used in this study. File contains information on epidemiology, demography, location, diagnostics, sequencing statistics and evolution of 427 SARS-CoV-2 sequences generated in this study and 755 sequences downloaded from GISAID