Evolutionary Dynamics and Dissemination Pattern of the SARS-CoV-2 Lineage B.1.1.33 During the Early Pandemic Phase in Brazil.

A previous study demonstrates that most of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Brazilian strains fell in three local clades that were introduced from Europe around late February 2020. Here we investigated in more detail the origin of the major and most widely disseminated SARS-CoV-2 Brazilian lineage B.1.1.33. We recovered 190 whole viral genomes collected from 13 Brazilian states from February 29 to April 31, 2020 and combined them with other B.1.1 genomes collected globally. Our genomic survey confirms that lineage B.1.1.33 is responsible for a variable fraction of the community viral transmissions in Brazilian states, ranging from 2% of all SARS-CoV-2 genomes from Pernambuco to 80% of those from Rio de Janeiro. We detected a moderate prevalence (5-18%) of lineage B.1.1.33 in some South American countries and a very low prevalence (<1%) in North America, Europe, and Oceania. Our study reveals that lineage B.1.1.33 evolved from an ancestral clade, here designated B.1.1.33-like, that carries one of the two B.1.1.33 synapomorphic mutations. The B.1.1.33-like lineage may have been introduced from Europe or arose in Brazil in early February 2020 and a few weeks later gave origin to the lineage B.1.1.33. These SARS-CoV-2 lineages probably circulated during February 2020 and reached all Brazilian regions and multiple countries around the world by mid-March, before the implementation of air travel restrictions in Brazil. Our phylodynamic analysis also indicates that public health interventions were partially effective to control the expansion of lineage B.1.1.33 in Rio de Janeiro because its median effective reproductive number (R e ) was drastically reduced by about 66% during March 2020, but failed to bring it to below one. Continuous genomic surveillance of lineage B.1.1.33 might provide valuable information about epidemic dynamics and the effectiveness of public health interventions in some Brazilian states.

Human virome in nasopharynx and tracheal secretion samples.

BACKGROUND: In Brazil the implementation of the Sentinel Surveillance System of Influenza began in 2000. Central public health laboratories use reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for diagnosis of respiratory viruses, but this protocol identifies only specific targets, resulted in inconclusive diagnosis for many samples. Thus, high-throughput sequencing (HTS) would be complementary method in the identification of pathogens in inconclusive samples for RT-qPCR or other specific detection protocols. OBJECTIVES: This study aimed to detect unidentified viruses using HTS approach in negative samples of nasopharynx/tracheal secretions by the standard RT-qPCR collected in the Federal District, Brazil. METHODS: Nucleic acids were extracted from samples collected in winter period of 2016 and subjected to HTS. The results were confirmed by the multiplex PR21 RT-qPCR, which identifies 21 respiratory pathogens. FINDINGS: The main viruses identified by HTS were of families Herpesviridae, Coronaviridae, Parvoviridae and Picornaviridae, with the emphasis on rhinoviruses. The presence of respiratory viruses in the samples was confirmed by the PR21 multiplex RT-qPCR. Coronavirus, enterovirus, bocavirus and rhinovirus were found by multiplex RT-qPCR as well as by HTS analyses. MAIN CONCLUSIONS: Wide virus diversity was found by different methodologies and high frequency of rhinovirus occurrence was confirmed in population in winter, showing its relevance for public health.

Validation and reliability of the rapid diagnostic test 'SD Bioeasy Dengue Duo' for dengue diagnosis in Brazil: a phase III study.

BACKGROUND: The diagnosis of dengue is complex. Until recently, only specialised laboratories were able to confirm dengue infection. However, this has changed with the newly available immunochromatographic rapid tests. Early diagnosis is of great interest, and point-of-care rapid tests have been increasingly used in Brazil. Most of those tests have not undergone validation in the Brazilian population. In this context, we decided to evaluate a rapid test introduced in the Federal District (FD). OBJECTIVES: To estimate the accuracy and reliability of the SD Bioeasy Dengue Duo rapid test and its components to detect dengue infections in a consecutive sample of symptomatic residents in the FD, Brazil. METHODS: In total, 1353 venous blood samples were collected between 2013 and 2014. Two hundred and six positive samples (cases) and 246 negative samples (non cases) were required for sensitivity and specificity estimation, respectively; for agreement evaluation, we used 401 samples. The reference standard used was a composite of MAC-ELISA, virus isolation and real-time polymerase chain reaction (RT-qPCR). The evaluation was conducted prospectively under field conditions in the public health units of the FD. FINDINGS: The results for the overall accuracy of the rapid test (NS1/IgM combined) showed 76% sensitivity and 98% specificity. The sensitivity for the NS1 component (67%) was better than that for the IgM component (35%). The positive likelihood ratio was 46, and the negative likelihood ratio was 0.24. The reliability of the test (NS1/IgM combined) demonstrated crude agreement of 98% (Kappa index 0.94). MAIN CONCLUSIONS: The present phase III, large-scale validation study demonstrates that the rapid test SD Bioeasy Dengue Duo has moderate sensitivity (NS1/IgM combined) and high specificity. Therefore, the test is useful in confirming the diagnosis of dengue, but not enough to rule out the diagnosis. Our results also suggest that Dengue virus (DENV) viral load estimated through the RT-qPCR and antibody level measured through the MAC-ELISA could have had a direct influence on the accuracy of the rapid test.

Validation and reliability of the rapid diagnostic test 'SD Bioeasy Dengue Duo' for dengue diagnosis in Brazil: a phase III study

BACKGROUND The diagnosis of dengue is complex. Until recently, only specialised laboratories were able to confirm dengue infection. However, this has changed with the newly available immunochromatographic rapid tests. Early diagnosis is of great interest, and point-of-care rapid tests have been increasingly used in Brazil. Most of those tests have not undergone validation in the Brazilian population. In this context, we decided to evaluate a rapid test introduced in the Federal District (FD). OBJECTIVES To estimate the accuracy and reliability of the SD Bioeasy Dengue Duo rapid test and its components to detect dengue infections in a consecutive sample of symptomatic residents in the FD, Brazil. METHODS In total, 1353 venous blood samples were collected between 2013 and 2014. Two hundred and six positive samples (cases) and 246 negative samples (non cases) were required for sensitivity and specificity estimation, respectively; for agreement evaluation, we used 401 samples. The reference standard used was a composite of MAC-ELISA, virus isolation and real-time polymerase chain reaction (RT-qPCR). The evaluation was conducted prospectively under field conditions in the public health units of the FD. FINDINGS The results for the overall accuracy of the rapid test (NS1/IgM combined) showed 76% sensitivity and 98% specificity. The sensitivity for the NS1 component (67%) was better than that for the IgM component (35%). The positive likelihood ratio was 46, and the negative likelihood ratio was 0.24. The reliability of the test (NS1/IgM combined) demonstrated crude agreement of 98% (Kappa index 0.94). MAIN CONCLUSIONS The present phase III, large-scale validation study demonstrates that the rapid test SD Bioeasy Dengue Duo has moderate sensitivity (NS1/IgM combined) and high specificity. Therefore, the test is useful in confirming the diagnosis of dengue, but not enough to rule out the diagnosis. Our results also suggest that Dengue virus (DENV) viral load estimated through the RT-qPCR and antibody level measured through the MAC-ELISA could have had a direct influence on the accuracy of the rapid test.

Effects of an anticarcinogenic Bowman-Birk protease inhibitor on purified 20S proteasome and MCF-7 breast cancer cells.

Proteasome inhibitors have been described as an important target for cancer therapy due to their potential to regulate the ubiquitin-proteasome system in the degradation pathway of cellular proteins. Here, we reported the effects of a Bowman-Birk-type protease inhibitor, the Black-eyed pea Trypsin/Chymotrypsin Inhibitor (BTCI), on proteasome 20S in MCF-7 breast cancer cells and on catalytic activity of the purified 20S proteasome from horse erythrocytes, as well as the structural analysis of the BTCI-20S proteasome complex. In vitro experiments and confocal microscopy showed that BTCI readily crosses the membrane of the breast cancer cells and co-localizes with the proteasome in cytoplasm and mainly in nucleus. Indeed, as indicated by dynamic light scattering, BTCI and 20S proteasome form a stable complex at temperatures up to 55°C and at neutral and alkaline pHs. In complexed form, BTCI strongly inhibits the proteolytic chymotrypsin-, trypsin- and caspase-like activities of 20S proteasome, indicated by inhibition constants of 10(-7) M magnitude order. Besides other mechanisms, this feature can be associated with previously reported cytostatic and cytotoxic effects of BTCI in MCF-7 breast cancer cells by means of apoptosis.