A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B 1 1 33 Circulating in Brazil

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in Brazil was dominated by two lineages designated as B.1.1.28 and B.1.1.33. The two SARS-CoV-2 variants harboring mutations at the receptor-binding domain of the Spike (S) protein, designated as lineages P.1 and P.2, evolved from lineage B.1.1.28 and are rapidly spreading in Brazil. Lineage P.1 is considered a Variant of Concern (VOC) because of the presence of multiple mutations in the S protein (including K417T, E484K, N501Y), while lineage P.2 only harbors mutation S:E484K and is considered a Variant of Interest (VOI). On the other hand, epidemiologically relevant B.1.1.33 deriving lineages have not been described so far. Here we report the identification of a new SARS-CoV-2 VOI within lineage B.1.1.33 that also harbors mutation S:E484K and was detected in Brazil between November 2020 and February 2021. This VOI displayed four non-synonymous lineage-defining mutations (NSP3:A1711V, NSP6:F36L, S:E484K, and NS7b:E33A) and was designated as lineage N.9. The VOI N.9 probably emerged in August 2020 and has spread across different Brazilian states from the Southeast, South, North, and Northeast regions.

More than just a common cold: endemic coronaviruses OC43, HKU1, NL63, and 229E associated with severe acute respiratory infection and fatality cases among healthy adults

Respiratory viral infection can cause severe disease and hospitalization, especially among children, the elderly, and patients with comorbidities. In Brazil, the official surveillance system of severe acute respiratory infection (SARI) investigates influenza A (IAV) and B (IBV) viruses, respiratory syncytial virus (RSV), adenovirus (HAdV), and parainfluenza viruses (hPIV 1­3). In Rio Grande do Sul (RS), Brazil, many fatalities associated with SARI between 2013 and 2017 occurred among patients without underlying diseases and for whom the causative agent had not been identified using official protocols. This cross­sectional study analyzed the presence of coronaviruses (HCoV), bocavirus (HBoV), metapneumovirus (hMPV), and rhinovirus in patients who died of SARI despite not having comorbidities, and that were negative for IAV, IBV, RSV, HAdV, and hPIV. Nasopharyngeal aspirates/swabs from patients were used for nucleic acid extraction. The presence of HCoVs OC43, HKU1, NL63, and 229E; HBoV; hMPV; and rhinovirus was assessed by quantitative reverse transcription­polymerase chain reaction. Clinical data were also analyzed. Between 2013 and 2017, 16 225 cases of SARI were reported in RS; 9.8% of the patients died; 20% of all fatal cases were patients without comorbidities and for whom no pathogen was detected using standard protocols. Analysis of 271 of these cases identified HCoV in nine cases; HBoV, hMPV, and rhinovirus were detected in 3, 3, and 10 cases, respectively. Of note, patients infected with HCoV were adults. Results reinforce the importance of including coronaviruses in diagnostic panels used by official surveillance systems because besides their pandemic potential, endemic HCoVs are associated to severe disease in healthy adults.

Enterovirus and herpesviridae family as etiologic agents of lymphomonocytary meningitis, Southern Brazil / Enterovirus e família herpesviridae como agentes etiológicos de meningites linfomonocitárias, no sul do Brasil

Viral meningitis is a common infectious disease of the central nervous system (CNS) that occurs worldwide. The aim of this study was to identify the etiologic agent of lymphomonocytary meningitis in Curitiba, PR, Brazil. During the period of July 2005 to December 2006, 460 cerebrospinal fluid (CSF) samples with lymphomonocytary meningitis were analyzed by PCR methodologies. Fifty nine (12.8 percent) samples were positive. Enteroviruses was present in 49 (83 percent) samples and herpes virus family in 10 (17 percent), of these 6 (10 percent) herpes simplex virus, 1 (2 percent) Epstein Barr virus, 2 (3 percent) human herpes virus type 6 and 1 (2 percent) mixed infection of enterovirus and Epstein Barr virus. As conclusion enterovirus was the most frequent virus, with circulation during summer and was observed with higher frequency between 4 to 17 years of age. PCR methodology is an important method for rapid detection of RNA enterovirus and DNA herpesvirus in CSF.

A meningite viral é uma síndrome infecciosa comum do sistema nervoso central (SNC), que ocorre no mundo inteiro. O objetivo deste estudo foi identificar o agente etiológico de meningite linfomonocitária em Curitiba, PR, Brasil. Durante o período de julho de 2005 a dezembro de 2006, 460 amostras com meningite linfomonocitária foram analisadas por metodologias de PCR. Cinquenta e nove (12,8 por cento) amostras foram positivas. Enterovirus estava presente em 49 (83 por cento) amostras e herpes vírus em 10 (17 por cento), destas 6 (10 por cento) HSV, 1 (2 por cento) EBV, 2 (3 por cento) HHV- 6 e 1 (2 por cento) infecção mista de enterovírus e EBV. Conclui-se que o enterovirus foi o vírus mais frequente, com a circulação durante o verão. Houve maior número de amostras positivas entre 4 a 17 anos. A metodologia de PCR é um importante método para a detecção rápida de RNA de enterovirus e DNA do herpesvirus no LCR.

Adenovirus respiratory infection: significant increase in diagnosis using PCR comparing with antigen detection and culture methods / Infecção respiratória aguda por adenovirus: comparação dos métodos de PCR e imunofluorescência indireta para o seu diagnóstico e dados clínicos dos pacientes infectados

Adenovirus (AdV) respiratory infections are usually described as being associated with high mortality rates. Laboratory diagnosis is essential for the establishment of the appropriate therapy, and for guiding the implementation of preventive measures in order to prevent the spread of the infection. Aiming to analyze the sensitivity and specificity of the laboratorial diagnosis methods available, we compared antigen detection by indirect immunofluorescence assay (IF), and a specific nested polymerase chain reaction (PCR), to detect AdV in respiratory samples collected from patients admitted to hospital with acute respiratory disease. Positive samples were inoculated into a cell culture to confirm the results. We analyzed 381 samples from the nasopharyngeal aspirates collected during the year 2008; of these, 2.6 percent tested were positive for adenovirus through IF and 10 percent through PCR; positive isolation was obtained in 40 percent and 26 percent of these cases, respectively. Most infected patients were children under six months of age, and despite of the fact that a significant number of patients required intensive care, the mortality rate was low (5 percent). In conclusion, molecular methods were found to be useful for rapid diagnosis of adenovirus infections with higher sensitivity than antigen detection; their introduction permitted a significant increase in diagnoses of adenovirus infections.

Infecções respiratórias por Adenovírus (ADV) são geralmente descritas associadas com alta mortalidade. O diagnóstico laboratorial é essencial para o estabelecimento da terapêutica adequada e para orientar a implantação de medidas preventivas evitando a propagação da infecção. Com o objetivo de analisar a sensibilidade e a especificidade dos métodos de avaliação de diagnóstico laboratorial, foi comparada a detecção de antígeno por imunofluorescência indireta (IF) com a reação em cadeia da polimerase específica (PCR) para detectar AdV em amostras respiratórias coletadas de pacientes internados com doença respiratória aguda. As amostras com resultados positivos foram inoculadas em cultura celular. Foram analisadas 381 amostras da secreção nasofaríngea coletadas durante o ano de 2008, das quais 2,6 por cento foram positivas pela IF e 10 por cento pela PCR, isolamento positivo foi obtido em 40 por cento e 26 por cento dos casos positivos pelos testes anteriores, respectivamente. A maioria dos pacientes infectados eram crianças com menos de seis meses de idade, e apesar do fato de que um número significativo de pacientes necessitou de cuidados intensivos, a taxa de mortalidade foi baixa (5 por cento). Em conclusão, os métodos moleculares são úteis para o diagnóstico rápido de infecções por adenovírus com maior sensibilidade do que a detecção do antígeno, a sua introdução na rotina permitiu um aumento significativo no diagnóstico de infecções por adenovírus.

Comparison of immunoperoxidase and immunofluorescence assays for pp65 cytomegalovirus antigen in immunocompromised patients

We compared the pp65 antigen detection by an in house method (immunoperoxidase assay) and by a commercial kit (immunofluorescence assay) available for cytomegalovirus infection diagnosis in immunocompromised patients. Sixty-four blood samples were analyzed in duplicate for both techniques. Eight-six percent of the samples had concordant qualitative results. The discordant results occurred more frequently in samples with low quantity of positive cells. There were no significant differences with qualitative and quantitative results of the methods.

The epidemiology and antigenic characterization of influenza viruses isolated in Curitiba, South Brazil

Several studies conducted all over the world have reported that the influenza virus is associated with great morbidity and mortality rates. In this study, we analyzed the incidence of the influenza virus between 2000 and 2003 in Curitiba. We studied 1621 samples obtained from outpatients and hospitalized patients of both sexes and all ages. The study was conducted at the local primary care health units (outpatients) and at the tertiary care unit (hospitalized) of the General Hospital of the Federal University in the state of Paraná, Brazil. Nasopharyngeal aspirates and, eventually, bronchoalveolar lavage were assayed for the presence of viral antigens, either by indirect immunofluorescence or cell culture. Of the samples studied, 135 (8.3 percent) were positive for influenza virus, and of those, 103 (76.3 percent) were positive for type A and 32 (23.7 percent) for type B. Additionally, positive samples were analyzed by reverse transcription followed by polymerase chain reaction and subtypes H1 and H3 were identified from this group. A high incidence of positive samples was observed mainly in the months with lower temperatures. Furthermore, outpatients showed a higher incidence of influenza viruses than hospitalized patients.

Characteres of the leaf and stem morpho-anatomy of Alternanthera brasiliana (L.) O. Kuntze, Amaranthaceae

Alternanthera brasiliana (L.) O. Kuntze, Amaranthaceae is a Brazilian perennial herb employed as analgesic and anti-inflammatory in the traditional medicine. This work has analysed the morpho-anatomy of the leaf and stem, in order to supply knowledge to the medicinal plant identification. The botanical material was fixed, freehand sectioned and stained according to usual microtechniques. The leaves are simple, entire, decussate, oval-lanceolate and purple, presenting uniseriate epidermis, pluricellular non-glandular trichomes coated by papillose cuticle, anomocytic and diacytic stomata on both surfaces; the mesophyll is dorsiventral, with collateral vascular bundles and druses. The stem, in secondary growth, has the dermal system similar to the leaf; the angular collenchyma alternates with the chlorenchyma; it occurs druses and a cambial variant, consisting of concentrical arcs of extra-cambia outside the first cambium and aligned vascular bundles in the pith