ABSTRACT
Introdução: Considerado um material nobre em laboratório clínico, o líquor (LCR) se assemelha a um ultrafiltrado de plasma e tem como principais funções o fornecimento de nutrientes essenciais ao cérebro e proteção mecânica. Os setores rotineiramente envolvidos na análise laboratorial do LCR são a bioquímica, a microbiologia e a citologia. Objetivo: Avaliar os principais agentes etiológicos associados à ocorrência de meningites e identificar as alterações laboratoriais mais prevalentes nas amostras liquóricas analisadas em laboratório de um hospital da região metropolitana de Porto Alegre. Métodos: Estudo transversal retrospectivo (01/2013 a 12/2017) em banco de dados. Resultados: Foi observada maior ocorrência de meningites bacterianas (35,53%), seguida por infecções virais (26,31%), fúngicas (25%) e parasitárias (13,16%). Os principais agentes infecciosos identificados foram Cryptococcus sp (n=18), Herpes Simples Vírus I e II (n=12), Toxoplasma gondii (n=10) e Streptococcus pneumoniae (n=9), e as principais alterações laboratoriais estiveram associadas à hiperproteinorraquia e à elevação no número de leucócitos. Nas meningites bacterianas, observaram-se hipoglicorraquia, hiperproteinorraquia e importante elevação de lactato desidrogenase (LDH); as fúngicas apresentaram discreta diminuição na glicorraquia e LDH moderadamente elevado, enquanto os agentes virais e parasitários apresentaram maior alteração na dosagem de proteínas (hiperproteinorraquia). Conclusão: Com perfil predominantemente masculino e adulto, a identificação de casos infecciosos na análise laboratorial liquórica representou 8,32% do total das análises, sendo as meningites bacterianas as mais prevalentes, podendo ser laboratorialmente reconhecidas por alterações bioquímicas e celulares. Os achados possibilitam o conhecimento epidemiológico e laboratorial, podendo embasar estudos posteriores.
Introduction: Considered a noble material in the clinical laboratory, CSF is similar to a plasma ultrafiltrate and its main functions are the supply of essential nutrients to the brain and mechanical protection. The sectors routinely involved in the laboratory analysis of CSF are biochemistry, microbiology and cytology. Objective: To evaluate the main etiological agents associated with the occurrence of meningitis and to identify the most prevalent alterations in CSF samples analyzed in the laboratory of a hospital in the metropolitan region of Porto Alegre. Methods: A retrospective cross-sectional study (01/2013 to 12/2017) in a database. Results: A higher occurrence of bacterial meningitis (35.53%) was observed, followed by viral (26.31%), fungal (25%) and parasitic (13.16%) infections. The main infectious agents identified were Cryptococcus sp (n=18), Herpes Simplex Virus I and II (n=12), Toxoplasma gondii (n=10) and Streptococcus pneumoniae (n=9) and the main laboratory alterations were associated with hyperproteinorrhachia and elevation in the number of leukocytes. In bacterial meningitis, hypoglycorrhachia, hyperproteinorrhachia and a significant increase in lactate dehydrogenase (LDH) relawere observed; fungal meningitis showed a slight decrease in glycorrhachia and moderately high LDH, while viral and parasitic agents showed greater change in protein level (hyperproteinorrhachia). Conclusion: With a predominantly male and adult profile, the identification of infectious cases in the CSF laboratory analysis represented 8.32% of the total analyses, with bacterial meningitis being the most prevalent, which can be recognized by biochemical and cellular alterations through laboratory testing. The findings allow for epidemiological and laboratory knowledge, which may support further studies.
ABSTRACT
BackgroundP.1 lineage (Gamma) was first described in the State of Amazonas, northern Brazil, in the end of 2020, and has emerged as a very important variant of concern (VOC) of SARS-CoV-2 worldwide. P.1 has been linked to increased infectivity, higher mortality and immune evasion, leading to reinfections and potentially reduced efficacy of vaccines and neutralizing antibodies. MethodsThe samples of 276 patients from the State of Amazonas were sent to a central referral laboratory for sequencing by gold standard techniques, through Illumina MiSeq platform. Both global and regional phylogenetic analyses of the successfully sequenced genomes were conducted through maximum likelihood method. Multiple alignments were obtained including previously obtained unique human SARS-CoV-2 sequences. The evolutionary histories of spike and non-structural proteins from ORF1a of northern genomes were described and their molecular evolution was analyzed for detection of positive (FUBAR, FEL, and MEME) and negative (FEL and SLAC) selective pressures. To further evaluate the possible pathways of evolution leading to the emergence of P.1, we performed specific analysis for copy-choice recombination events. A global phylogenomic analysis with subsampled P.1 and B.1.1.28 genomes was applied to evaluate the relationship among samples. ResultsForty-four samples from the State of Amazonas were successfully sequenced and confirmed as P.1 (Gamma) lineage. In addition to previously described P.1 characteristic mutations, we find evidence of continuous diversification of SARS-CoV-2, as rare and previously unseen P.1 mutations were detected in spike and non-structural protein from ORF1a. No evidence of recombination was found. Several sites were demonstrated to be under positive and negative selection, with various mutations identified mostly in P.1 lineage. According to the Pango assignment, phylogenomic analyses indicate all samples as belonging to the P.1 lineage. ConclusionP.1 has shown continuous evolution after its emergence. The lack of clear evidence for recombination and the positive selection demonstrated for several sites suggest that this lineage emergence resulted mainly from strong evolutionary forces and progressive accumulation of a favorable signature set of mutations.
ABSTRACT
Almost a year after the COVID-19 pandemic had begun, The United Kingdom, South Africa, and Brazil became the epicenter of new lineages, the Variant of Concern (VOCs), B.1.1.7, B.1.351, and P.1, respectively. These VOCs are increasingly associated with enhanced transmissibility, immunity evasion, and mortality. The previous most prevalent lineages in the state of Rio Grande do South (Brazil), B.1.1.28 and B.1.1.33 were rapidly replaced by P.1 and P.2, two B.1.1.28-derived lineages harboring the E484K mutation. To perform a genomic characterization of SARS-CoV-2 samples from COVID-19 patients from the metropolitan region of Porto Alegre (Rio Grande do Sul, Southern Brazil), in this second pandemic wave, we sequenced viral samples from patients of this region to: (i) identify the prevalence of SARS-CoV-2 lineages in the region, the state and bordering countries/states, (ii) characterize the mutation spectra, and (iii) hypothesize possible viral dispersal routes by using phylogenetic and phylogeographic approaches. As results, we not only confirmed that 96.4% of the samples belonged to the P.1 lineage but also that approximately 20% of which could be assigned as the newer P.1.2 (a P.1 derived new sublineage harboring new signature substitutions recently described and present in other Brazilian states and foreign countries). Moreover, P.1 sequences from this study were allocated in several distinct branches (four clades and five clusters) of the P.1 phylogeny, suggesting multiple introductions of P.1 in Rio Grande do Sul still in 2020 and placing this state as a potential core of diffusion and emergence of P.1-derived clades. It is still uncertain if the emergence of P.1.2 and other P.1 clades are related to further virological, clinical, or epidemiological consequences. However, the clear signs of viral molecular diversification from recently introduced P.1 warrant further genomic surveillance.
ABSTRACT
Population-based prevalence surveys of COVID-19 contribute to establish the burden and epidemiology of infection, the role of asymptomatic and mild infections in transmission, and allow more precise decisions about reopen policies. We performed a systematic review to evaluate qualitative aspects of these studies, their reliability, and biases. The available data described 37 surveys from 19 countries, mostly from Europe and America and using antibody testing. They reached highly heterogeneous sample sizes and prevalence estimates. Disproportional prevalence was observed in minority communities. Important risk of bias was detected in four domains: sample size, data analysis with sufficient coverage, measurements in standard way, and response rate. The correspondence analysis showed few consistent patterns for high risk of bias. Intermediate risk of bias was related to American and European studies, blood samples and prevalence >1%. Low risk of bias was related to Asian studies, RT-PCR tests and prevalence <1%. One sentence summaryPopulation-based prevalence surveys of COVID-19 until September 2020 were mostly conducted in Europe and Americas, used antibody testing, and had important risks of bias.
