In silico analysis of non-structural protein 12 sequences from SARS-COV-2 found in Manaus, Amazonas, Brazil, reveals mutations linked to higher transmissibility.

The disease coronavirus COVID-19 has been the cause of millions of deaths worldwide. Among the proteins of SARS-CoV-2, non-structural protein 12 (NSP12) plays a key role during COVID infection and is part of the RNA-dependent RNA polymerase complex. The monitoring of NSP12 polymorphisms is extremely important for the design of new antiviral drugs and monitoring of viral evolution. This study analyzed the NSP12 mutations detected in circulating SARS-CoV-2 during the years 2020 to 2022 in the population of the city of Manaus, Amazonas, Brazil. The most frequent mutations found were P323L and G671S. Reports in the literature indicate that these mutations are related to transmissibility efficiency, which may have contributed to the extremely high numbers of cases in this location. In addition, two mutations described here (E796D and R914K) are close and have RMSD that is similar to the mutations M794V and N911K, which have been described in the literature as influential on the performance of the NSP12 enzyme. These data demonstrate the need to monitor the emergence of new mutations in NSP12 in order to better understand their consequences for the treatments currently used and in the design of new drugs.

SARS-CoV-2 intra-host diversity, antibody response, and disease severity after reinfection by the variant of concern Gamma in Brazil.

The rapid spread of the SARS-CoV-2 Variant of Concern (VOC) Gamma in Amazonas during early 2021 fueled a second large COVID-19 epidemic wave and raised concern about the potential role of reinfections. Very few cases of reinfection associated with the VOC Gamma have been reported to date, and their potential impact on clinical, immunological, and virological parameters remains largely unexplored. Here we describe 25 cases of SARS-CoV-2 reinfection in Brazil. SARS-CoV-2 genomic analysis confirmed that individuals were primo-infected with distinct viral lineages between March and December 2020 (B.1.1, B.1.1.28, B.1.1.33, B.1.195, and P.2) and reinfected with the VOC Gamma between 3 to 12 months after primo-infection. We found a similar mean cycle threshold (Ct) value and limited intra-host viral diversity in both primo-infection and reinfection samples. Sera of 14 patients tested 10-75 days after reinfection displayed detectable neutralizing antibodies (NAb) titers against SARS-CoV-2 variants that circulated before (B.1.*), during (Gamma), and after (Delta and Omicron) the second epidemic wave in Brazil. All individuals had milder or no symptoms after reinfection, and none required hospitalization. These findings demonstrate that individuals reinfected with the VOC Gamma may display relatively high RNA viral loads at the upper respiratory tract after reinfection, thus contributing to onward viral transmissions. Despite this, our study points to a low overall risk of severe Gamma reinfections, supporting that the abrupt increase in hospital admissions and deaths observed in Amazonas and other Brazilian states during the Gamma wave was mostly driven by primary infections. Our findings also indicate that most individuals analyzed developed a high anti-SARS-CoV-2 NAb response after reinfection that may provide some protection against reinfection or disease by different SARS-CoV-2 variants.

Structural analysis of SARS-Cov-2 nonstructural protein 1 polymorphisms found in the Brazilian Amazon.

The coronavirus disease COVID-19 has been the cause of millions of deaths worldwide. Among the SARS-CoV-2 proteins, the non-structural protein 1 (NSP1) has great importance during the virus infection process and is present in both alpha and beta-CoVs. Therefore, monitoring of NSP1 polymorphisms is crucial in order to understand their role during infection and virus-induced pathogenicity. Herein, we analyzed how mutations detected in the circulating SARS-CoV-2 in the population of the city of Manaus, Amazonas state, Brazil could modify the tertiary structure of the NSP1 protein. Three mutations were detected in the SARS-CoV-2 NSP1 gene: deletion of the amino acids KSF from positions 141 to 143 (delKSF), SARS-CoV-2, lineage B.1.195; and two substitutions, R29H and R43C, SARS-CoV-2 lineage B.1.1.28 and B.1.1.33, respectively. The delKSF was found in 47 samples, whereas R29H and R43C were found in two samples, one for each mutation. The NSP1 structures carrying the mutations R43C and R29H on the N-terminal portion (e.g. residues 10 to 127) showed minor backbone divergence compared to the Wuhan model. However, the NSP1 C-terminal region (residues 145 to 180) was severely affected in the delKSF and R29H mutants. The intermediate variable region (residues 144 to 148) leads to changes in the C-terminal region, particularly in the delKSF structure. New investigations must be carried out to analyze how these changes affect NSP1 activity during the infection. Our results reinforce the need for continuous genomic surveillance of SARS-CoV-2 to better understand virus evolution and assess the potential impact of the viral mutations on the approved vaccines and future therapies.

COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence.

The northern state of Amazonas is among the regions in Brazil most heavily affected by the COVID-19 epidemic and has experienced two exponentially growing waves, in early and late 2020. Through a genomic epidemiology study based on 250 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from different Amazonas municipalities sampled between March 2020 and January 2021, we reveal that the first exponential growth phase was driven mostly by the dissemination of lineage B.1.195, which was gradually replaced by lineage B.1.1.28 between May and June 2020. The second wave coincides with the emergence of the variant of concern (VOC) P.1, which evolved from a local B.1.1.28 clade in late November 2020 and replaced the parental lineage in <2 months. Our findings support the conclusion that successive lineage replacements in Amazonas were driven by a complex combination of variable levels of social distancing measures and the emergence of a more transmissible VOC P.1 virus. These data provide insights to understanding the mechanisms underlying the COVID-19 epidemic waves and the risk of dissemination of SARS-CoV-2 VOC P.1 in Brazil and, potentially, worldwide.

Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region.

Zika virus (ZIKV) has caused an explosive epidemic linked to severe clinical outcomes in the Americas. As of June 2018, 4,929 ZIKV suspected infections and 46 congenital syndrome cases had been reported in Manaus, Amazonas, Brazil. Although Manaus is a key demographic hub in the Amazon region, little is known about the ZIKV epidemic there, in terms of both transmission and viral genetic diversity. Using portable virus genome sequencing, we generated 59 ZIKV genomes in Manaus. Phylogenetic analyses indicated multiple introductions of ZIKV from northeastern Brazil to Manaus. Spatial genomic analysis of virus movement among six areas in Manaus suggested that populous northern neighborhoods acted as sources of virus transmission to other neighborhoods. Our study revealed how the ZIKV epidemic was ignited and maintained within the largest urban metropolis in the Amazon. These results might contribute to improving the public health response to outbreaks in Brazil.

Analysis of the immunological biomarker profile during acute Zika virus infection reveals the overexpression of CXCL10, a chemokine linked to neuronal damage.

BACKGROUND: Infection with Zika virus (ZIKV) manifests in a broad spectrum of disease ranging from mild illness to severe neurological complications and little is known about Zika immunopathogenesis. OBJECTIVES: To define the immunologic biomarkers that correlate with acute ZIKV infection. METHODS: We characterized the levels of circulating cytokines, chemokines, and growth factors in 54 infected patients of both genders at five different time points after symptom onset using microbeads multiplex immunoassay; comparison to 100 age-matched controls was performed for statistical analysis and data mining. FINDINGS: ZIKV-infected patients present a striking systemic inflammatory response with high levels of pro-inflammatory mediators. Despite the strong inflammatory pattern, IL-1Ra and IL-4 are also induced during the acute infection. Interestingly, the inflammatory cytokines IL-1ß, IL-13, IL-17, TNF-α, and IFN-γ; chemokines CXCL8, CCL2, CCL5; and the growth factor G-CSF, displayed a bimodal distribution accompanying viremia. While this is the first manuscript to document bimodal distributions of viremia in ZIKV infection, this has been documented in other viral infections, with a primary viremia peak during mild systemic disease and a secondary peak associated with distribution of the virus to organs and tissues. MAIN CONCLUSIONS: Biomarker network analysis demonstrated distinct dynamics in concurrence with the bimodal viremia profiles at different time points during ZIKV infection. Such a robust cytokine and chemokine response has been associated with blood-brain barrier permeability and neuroinvasiveness in other flaviviral infections. High-dimensional data analysis further identified CXCL10, a chemokine involved in foetal neuron apoptosis and Guillain-Barré syndrome, as the most promising biomarker of acute ZIKV infection for potential clinical application.

Analysis of the immunological biomarker profile during acute Zika virus infection reveals the overexpression of CXCL10, a chemokine linked to neuronal damage

BACKGROUND Infection with Zika virus (ZIKV) manifests in a broad spectrum of disease ranging from mild illness to severe neurological complications and little is known about Zika immunopathogenesis. OBJECTIVES To define the immunologic biomarkers that correlate with acute ZIKV infection. METHODS We characterized the levels of circulating cytokines, chemokines, and growth factors in 54 infected patients of both genders at five different time points after symptom onset using microbeads multiplex immunoassay; comparison to 100 age-matched controls was performed for statistical analysis and data mining. FINDINGS ZIKV-infected patients present a striking systemic inflammatory response with high levels of pro-inflammatory mediators. Despite the strong inflammatory pattern, IL-1Ra and IL-4 are also induced during the acute infection. Interestingly, the inflammatory cytokines IL-1β, IL-13, IL-17, TNF-α, and IFN-γ; chemokines CXCL8, CCL2, CCL5; and the growth factor G-CSF, displayed a bimodal distribution accompanying viremia. While this is the first manuscript to document bimodal distributions of viremia in ZIKV infection, this has been documented in other viral infections, with a primary viremia peak during mild systemic disease and a secondary peak associated with distribution of the virus to organs and tissues. MAIN CONCLUSIONS Biomarker network analysis demonstrated distinct dynamics in concurrence with the bimodal viremia profiles at different time points during ZIKV infection. Such a robust cytokine and chemokine response has been associated with blood-brain barrier permeability and neuroinvasiveness in other flaviviral infections. High-dimensional data analysis further identified CXCL10, a chemokine involved in foetal neuron apoptosis and Guillain-Barré syndrome, as the most promising biomarker of acute ZIKV infection for potential clinical application.

Copa do mundo 2014: diferentes opiniões sobre as obras públicas / World Cup 2014: different opinions on public works

Este artigo trata de assunto muito polêmico e atual: as obras da copa do mundo e suas repercussões na mídia e na opinião de pessoas comuns, que sofreram por mais de dois anos coma construção das obras de mobilidade urbana e viram a construção de estádios grandiosos para o mundial de futebol, e que acham que o dinheiro deveria ser mais bem investido, como na saúde,na educação e na segurança. Notamos que opiniões existem de diferentes formas, e que os problemas no Brasil não surgiram somente depois do início das obras, eles são mais antigos. (AU)

This article is related to a very current and controversial issue: the works of the world cup and its repercussions in the media and in the public opinion, who have suffered for more than two years with the constructions related to urban mobility and watched the construction of massive stadiums for the World Cup. People who think that the money invested could be of better use, as in health, education and security. We notice that opinion may vary, and that problems in Brazil did not arise only after the commencement of works, they are older. (AU)

Copa do mundo 2014: diferentes opiniões sobre as obras públicas / World Cup 2014: different opinions on public works

Este artigo trata de assunto muito polêmico e atual: as obras da copa do mundo e suas repercussões na mídia e na opinião de pessoas comuns, que sofreram por mais de dois anos coma construção das obras de mobilidade urbana e viram a construção de estádios grandiosos para o mundial de futebol, e que acham que o dinheiro deveria ser mais bem investido, como na saúde,na educação e na segurança. Notamos que opiniões existem de diferentes formas, e que os problemas no Brasil não surgiram somente depois do início das obras, eles são mais antigos.

This article is related to a very current and controversial issue: the works of the world cup and its repercussions in the media and in the public opinion, who have suffered for more than two years with the constructions related to urban mobility and watched the construction of massive stadiums for the World Cup. People who think that the money invested could be of better use, as in health, education and security. We notice that opinion may vary, and that problems in Brazil did not arise only after the commencement of works, they are older.

Dor na criança internada: a percepção da equipe de enfermagem / Pain in hospitalized children: nursing team perception

JUSTIFICATIVA E OBJETIVOS: A dor é um fenômeno complexo e subjetivo que marca de forma singular a vida da criança. O objetivo deste estudo foi compreende ra percepção da equipe de enfermagem com relação ao manuseio e avaliação da dor na criança internada.MÉTODO: Trata-se de um estudo descritivo, de natureza qualitativa. Os dados foram coletados por meio de entrevista semiestruturada no mês de maio de 2011. Participaram do estudo 11 profissionais da equipe de enfermagem que atuavam na pediatria de um hospital-escola.RESULTADOS: Foram analisadas quatro categorias:"O significado do choro na criança internada"; "Avaliaçãoda dor pela equipe de enfermagem"; "Percebendo as situações de dor na criança internada" e "Minimizando a dor na criança internada". Evidenciou-se que os profissionais reconhecem a dor na criança, todavia, não utilizam métodos validados para mensurá-las. O controle farmacológico da dor foi colocado pelos profissionais como principal maneira de alívio desse sintoma.CONCLUSÃO: Os profissionais de enfermagem são comprometidos na identificação da dor nas crianças, porém, existe fragilidade quanto ao conhecimento relacionado ao seu controle, pois a maior parte se restringe aos métodos farmacológicos e não visualiza o problema de forma mais ampla, impossibilitando melhor assistência.

BACKGROUND AND OBJECTIVES: Pain is a complex and subjective phenomenon which marks children's lives in a unique manner. This study aimed at understanding the nursing team perception with regard to managing and evaluating pain in hospitalized children.METHOD: This is a descriptive and qualitative study.Data were collected by means of semi-structured surveyin the month of May 2011. Participated in this study 11 nursing team professionals working in the pediatric department of a teaching hospital.RESULTS: Four categories were analyzed: "The meaning of hospitalized children crying"; "Pain evaluationby the nursing team"; "Perceiving pain situations in hospitalized children"; and "Minimizing pain in hospitalized children". It was evidenced that professionals do recognize children's pain, however they do not use validated methods to measure it. Pharmacological pain control was considered by the professionals as the primary method to relieve this symptom.CONCLUSION: Nursing professionals are committed to the identification of children's pain, however pain control-related knowledge is fragile because most professionals are limited to pharmacological methods and do not see the problem in a broader way, thus making impossible a better assistance.