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Background: Two antigenically and genetically distinct lineages of influenza B viruses (B/Victoria and B/Yamagata) have been co-circulating worldwide since 2002. Virological surveillance is essential to differentiate between both lineages with a view to the annual updating of the B component for the trivalent or quadrivalent influenza vaccine composition. Methods: The samples analyzed in the present study were collected by influenza sentinel units located in the Southeast, Midwest, North, and Northeast regions of Brazil, part of the National Influenza Virus Surveillance Network, coordinated by the Ministry of Health of Brazil. A total of 870 influenza B positive samples by reverse transcription real - time polymerase chain reaction (RT-qPCR), collected during 2014, 2015, and 2016 influenza seasons, were submitted to the influenza B lineage genotyping panel for characterization as B/Yamagata or Victoria lineages using RT-qPCR. Results: Of the 197 samples analyzed in 2014, a total of 160 (81 %) corresponded to the B/Yamagata lineage, 19 (10 %) to the B/Victoria lineage, and 18 (9 %) to indeterminate lineages. Of the 190 samples analyzed in 2015, a total of 124 (65 %) corresponded to the B/Yamagata lineage; 55 (29 %) to the B/Victoria lineage, whereas 11 (6 %) were of indeterminate lineages. Of the 483 samples analyzed in 2016, a total of 297 (62 %) corresponded to the B /Victoria lineage; 174 (36 %) to the B/Yamagata lineage and 12 (2 %) to indeterminate lineages. This cross-sectional study revealed influenza B virus (IBV) infection in all age groups, and among them, the highest prevalence was observed in individuals between 11 and 49 years of age Our findings demonstrate the match between influenza B virus lineages recommended by the World Health Organization (WHO) for the trivalent vaccine composition to be used in the Southern Hemisphere (SH) and the predominant circulating viruses during the 2014, 2015, and 2016 seasons.

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We conducted the genome sequencing and analysis of the first confirmed COVID-19 infections in Brazil. Rapid sequencing coupled with phylogenetic analyses in the context of travel history corroborate multiple independent importations from Italy and local spread during the initial stage of COVID-19 transmission in Brazil.

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We conducted the genome sequencing and analysis of the first confirmed COVID-19 infections in Brazil. Rapid sequencing coupled with phylogenetic analyses in the context of travel history corroborate multiple independent importations from Italy and local spread during the initial stage of COVID-19 transmission in Brazil. (AU)

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The aims of this study were to investigate the human bocavirus (HBoV) frequency and genotypes in hospitalized children <5 years presenting acute respiratory infections (ARI) within the São Paulo metropolitan area. Nasopharyngeal samples from 300 patients, previously screened for common respiratory viruses, were tested by qPCR for the NSP1 and NP-1 genes. The VP1/2 gene in positive samples was then amplified by PCR and sequenced. A total of 49 positive HBoV cases (16.3%; mean Ct value of 34.41) were detected with the mean age being 18.1 months (range 1 month to 5 years) and the median age being 1 year of age. Children aged between 0 and 12 months had higher detection rates of HBoV (69.4%; 34/49; mean Ct = 34.45) than children from other age groups (30.6%; 15/49; mean Ct = 34.34). No significant differences were observed between HBoV Ct levels and clinical illness. The occurrence was more frequently associated with fall (38.8%; 19/49) and spring (36.7%; 18/49). All 12 sequenced isolates were identified as HBoV-1, displaying minor genetic variation compared to the Swedish reference strains ST1 and ST2 (99.1-99.7% nt). The sole identification of HBoV-1 supports the hypothesis that this particular genotype is strongly related to ARI, and contributes to the role of this virus in the aetiology of respiratory diseases.

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Compared to previous years, seasonal influenza activity commenced early in São Paulo State, Brazil, Southern hemisphere during the 2016 year. In order to investigate the genetic pattern of influenza A(H1N1)pdm09 in the State of Sao Paulo a total of 479 respiratory samples, collected in January by Sentinel Surveillance Units, were screened by real-time RT-PCR. A total of 6 Influenza viruses A(H1N1)pdm09 presenting ct values ≤ 30 were sequenced following phylogenetic analysis. The present study identified the circulation of the new 6B.1 subgroup (A/Sao Paulo/10-118/2016 and A/Sao Paulo/3032/2016). In addition, influenza A(H1N1)pdm09 group 6B has also been identified during January in the State of Sao Paulo. Despite amino acid changes and changes in potential glycosylation motifs, 6B.1 viruses were well inhibited by the reference ferret antiserum against A/California/07/2009 virus, the A(H1N1)pdm09 component of the vaccine for the 2016 influenza season.

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In São Paulo the mumps virus (MuV) outbreaks have been increasing from In São Paulo the mumps virus (MuV) outbreaks have been increasing from 2011 to nowadays. MuV epidemiological surveillance has been improving by using the polymerase chain reaction in real time (rRT-PCR) in addition to the specific IgM antibody (IgM-Ab) detection; in some cases,genome sequencing studies were performed. Increased virus transmission and recent outbreakshave raised interest on MuV genotyping, as a means to understand the transmission pathways andto identify the vaccine-associated cases. From January 2011 to August 2016, MuV infection was analyzed at Institute Adolfo Lutz. A total of 232 (77.33 %) throat wash samples showed positivity to mumps genome, and 68 (22.66 %) were negative when analyzed by rRT-PCR. Among 15 samples for molecular analysis, 10 serum samples from respective patients were also available for detecting anti-MuV IgM-Ab; and from these, four (40%) samples were seropositive. Vaccination statuswas available only for patients from Cedral and Araraquara. Phylogenetic analysis revealed the circulation of the following mumps virus genotypes in the investigated periods: 2011(M), 2012, and 2013 (K); 2014 (N); 2015 (G, K, and N); 2016 (G). Knowledge on MuV molecular epidemiology in São Paulo-Brazil could contribute to the surveillance and epidemiological program in Brazil, and globally as well.

No estado de São Paulo têm ocorrido surtos de caxumba desde 2011. O diagnóstico laboratorialtem sido realizado no Instituto Adolfo Lutz utilizando-se a técnica de identificação de material genético viral por meio de reação de cadeia de polimerase-em tempo real (rRT-PCR) e peladetecção de anticorpos IgM (Ac-IgM) específicos circulantes. Os recentes surtos de caxumbatêm aumentado o interesse em investigar os genótipos dos vírus prevalentes para identificaros casos associadas à vacina. De janeiro de 2011 a agosto de 2016, 300 amostras de lavadosda orofaringe coletadas de pacientes suspeitos de infecção foram analisadas. O material genéticoviral específico foi detectado em 232 (77,33 %) amostras e 68 (22,66 %) foram negativas.Das 10 amostras analisadas pelo teste sorológico, quatro (40 %) demonstraram positividadepara Ac-IgM específicos anti-vírus da caxumba e seis foram negativas. Somente os municípios Cedral e Araraquara forneceram os dados referentes à vacinação. Análise filogenética mostroua circulação dos seguintes genótipos do vírus da caxumba no período investigado: 2011 (M),2012 e 2013 (K); 2014 (N); 2015 (GKN); 2016 (G). A vigilância virológica é mundialmente imprescindível, para identificar a diversidade e a distribuição dos diferentes genótipos, com vistasà composição de vacinas específicas.

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In São Paulo the mumps virus (MuV) outbreaks have been increasing from 2011 to nowadays. MuV epidemiological surveillance has been improving by using the polymerase chain reaction in real time (rRT-PCR) in addition to the specific IgM antibody (IgM-Ab) detection; in some cases, genome sequencing studies were performed. Increased virus transmission and recent outbreaks have raised interest on MuV genotyping, as a means to understand the transmission pathways and to identify the vaccine-associated cases. From January 2011 to August 2016, MuV infection was analyzed at Institute Adolfo Lutz. A total of 232 (77.33 %) throat wash samples showed positivity to mumps genome, and 68 (22.66 %) were negative when analyzed by rRT-PCR. Among 15 samples for molecular analysis, 10 serum samples from respective patients were also available for detecting anti-MuV IgM-Ab; and from these, four (40%) samples were seropositive. Vaccination status was available only for patients from Cedral and Araraquara. Phylogenetic analysis revealed the circulation of the following mumps virus genotypes in the investigated periods: 2011(M), 2012, and 2013 (K); 2014 (N); 2015 (G, K, and N); 2016 (G). Knowledge on MuV molecular epidemiology in São Paulo-Brazil could contribute to the surveillance and epidemiological program in Brazil, and globally as well.

No estado de São Paulo têm ocorrido surtos de caxumba desde 2011. O diagnóstico laboratorial tem sido realizado no Instituto Adolfo Lutz utilizando-se a técnica de identificação de material genético viral por meio de reação de cadeia de polimerase-em tempo real (rRT-PCR) e pela detecção de anticorpos IgM (Ac-IgM) específicos circulantes. Os recentes surtos de caxumba têm aumentado o interesse em investigar os genótipos dos vírus prevalentes para identificar os casos associadas à vacina. De janeiro de 2011 a agosto de 2016, 300 amostras de lavados da orofaringe coletadas de pacientes suspeitos de infecção foram analisadas. O material genético viral específico foi detectado em 232 (77,33 %) amostras e 68 (22,66 %) foram negativas. Das 10 amostras analisadas pelo teste sorológico, quatro (40 %) demonstraram positividade para Ac-IgM específicos anti-vírus da caxumba e seis foram negativas. Somente os municípios Cedral e Araraquara forneceram os dados referentes à vacinação. Análise filogenética mostrou a circulação dos seguintes genótipos do vírus da caxumba no período investigado: 2011 (M), 2012 e 2013 (K); 2014 (N); 2015 (GKN); 2016 (G). A vigilância virológica é mundialmente imprescindível, para identificar a diversidade e a distribuição dos diferentes genótipos, com vistas à composição de vacinas específicas.

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In São Paulo the mumps virus (MuV) outbreaks have been increasing from 2011 to nowadays. MuV epidemiological surveillance has been improving by using the polymerase chain reaction in real time (rRT-PCR) in addition to the specific IgM antibody (IgM-Ab) detection; in some cases, genome sequencing studies were performed. Increased virus transmission and recent outbreaks have raised interest on MuV genotyping, as a means to understand the transmission pathways and to identify the vaccine-associated cases. From January 2011 to August 2016, MuV infection was analyzed at Institute Adolfo Lutz. A total of 232 (77.33 %) throat wash samples showed positivity to mumps genome, and 68 (22.66 %) were negative when analyzed by rRT-PCR. Among 15 samples for molecular analysis, 10 serum samples from respective patients were also available for detecting anti-MuV IgM-Ab; and from these, four (40%) samples were seropositive. Vaccination status was available only for patients from Cedral and Araraquara. Phylogenetic analysis revealed the circulation of the following mumps virus genotypes in the investigated periods: 2011(M), 2012, and 2013 (K); 2014 (N); 2015 (G, K, and N); 2016 (G). Knowledge on MuV molecular epidemiology in São Paulo-Brazil could contribute to the surveillance and epidemiological program in Brazil, and globally as well.(AU)

No estado de São Paulo têm ocorrido surtos de caxumba desde 2011. O diagnóstico laboratorial tem sido realizado no Instituto Adolfo Lutz utilizando-se a técnica de identificação de material genético viral por meio de reação de cadeia de polimerase-em tempo real (rRT-PCR) e pela detecção de anticorpos IgM (Ac-IgM) específicos circulantes. Os recentes surtos de caxumba têm aumentado o interesse em investigar os genótipos dos vírus prevalentes para identificar os casos associadas à vacina. De janeiro de 2011 a agosto de 2016, 300 amostras de lavados da orofaringe coletadas de pacientes suspeitos de infecção foram analisadas. O material genético viral específico foi detectado em 232 (77,33 %) amostras e 68 (22,66 %) foram negativas. Das 10 amostras analisadas pelo teste sorológico, quatro (40 %) demonstraram positividade para Ac-IgM específicos anti-vírus da caxumba e seis foram negativas. Somente os municípios Cedral e Araraquara forneceram os dados referentes à vacinação. Análise filogenética mostrou a circulação dos seguintes genótipos do vírus da caxumba no período investigado: 2011 (M), 2012 e 2013 (K); 2014 (N); 2015 (GKN); 2016 (G). A vigilância virológica é mundialmente imprescindível, para identificar a diversidade e a distribuição dos diferentes genótipos, com vistas à composição de vacinas específicas.(AU)

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In February 2012, an outbreak of respiratory illness occurred on the cruise ship MSC Armonia in Brazil. A 31-year-old female crew member was hospitalized with respiratory failure and subsequently died. To study the etiology of the respiratory illness, tissue taken at necropsy from the deceased woman and respiratory specimens from thirteen passengers and crew members with respiratory symptoms were analyzed. Influenza real-time RT-PCR assays were performed, and the full-length hemagglutinin (HA) gene of influenza-positive samples was sequenced. Influenza B virus was detected in samples from seven of the individuals, suggesting that it was the cause of this respiratory illness outbreak. The sequence analysis of the HA gene indicated that the virus was closely related to the B/Brisbane/60/2008-like virus, Victoria lineage, a virus contained in the 2011-12 influenza vaccine for the Southern Hemisphere. Since the recommended composition of the influenza vaccine for use during the 2013 season changed, an intensive surveillance of viruses circulating worldwide is crucial. Molecular analysis is an important tool to characterize the pathogen responsible for an outbreak such as this. In addition, laboratory disease surveillance contributes to the control measures for vaccine-preventable influenza.

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In February 2012, an outbreak of respiratory illness occurred on the cruise ship MSC Armonia in Brazil. A 31-year-old female crew member was hospitalized with respiratory failure and subsequently died. To study the etiology of the respiratory illness, tissue taken at necropsy from the deceased woman and respiratory specimens from thirteen passengers and crew members with respiratory symptoms were analyzed. Influenza real-time RT-PCR assays were performed, and the full-length hemagglutinin (HA) gene of influenza-positive samples was sequenced. Influenza B virus was detected in samples from seven of the individuals, suggesting that it was the cause of this respiratory illness outbreak. The sequence analysis of the HA gene indicated that the virus was closely related to the B/Brisbane/60/2008-like virus, Victoria lineage, a virus contained in the 2011-12 influenza vaccine for the Southern Hemisphere. Since the recommended composition of the influenza vaccine for use during the 2013 season changed, an intensive surveillance of viruses circulating worldwide is crucial. Molecular analysis is an important tool to characterize the pathogen responsible for an outbreak such as this. In addition, laboratory disease surveillance contributes to the control measures for vaccine-preventable influenza.

Em fevereiro de 2012, durante a temporada de verão no Brasil, um surto de doença respiratória ocorreu no navio de cruzeiro MSC Armonia. Mulher de 31 anos, membro da tripulação, foi internada com insuficiência respiratória e morreu. Com o objetivo de estudar a etiologia da doença foram investigadas necrópsia de tecido do caso fatal e secreções respiratórias de 13 passageiros e membros da tripulação com sintomas respiratórios. O teste de influenza por RT-PCR em tempo real foi realizado e o gene completo da hemaglutinina (HA) das amostras positivas foi sequenciado. O vírus influenza B foi detectado em sete indivíduos, sugerindo-o como a causa do surto de doença respiratória a bordo do navio. A análise da sequência do gene da HA indicou que os vírus estão fortemente relacionados com o vírus B/Brisbane/60/2008, linhagem Victoria, componente da vacina de influenza para 2011-2012 no hemisfério sul. Uma vez que a composição da vacina foi alterada para uso na temporada de 2012-2013, é essencial a vigilância ativa dos vírus circulantes em todo o mundo. A análise molecular é uma ferramenta importante para caracterização do patógeno responsável pelo surto. Além disso, a vigilância de doenças baseada em dados laboratoriais contribui para as medidas de controle da influenza, uma doença imunoprevinível.

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In this paper, we analysed the haemagglutinin (HA) gene identified by polymerase chain reaction from 90 influenza A H1N1 virus strains that circulated in Brazil from April 2009-June 2010. A World Health Organization sequencing protocol allowed us to identify amino acid mutations in the HA protein at positions S220T (71%), D239G/N/S (20%), Y247H (4.5%), E252K (3.3%), M274V (2.2%), Q310H (26.7%) and E391K (12%). A fatal outcome was associated with the D239G mutation (p < 0.0001). Brazilian HA genetic diversity, in comparison to a reference strain from California, highlights the role of influenza virus surveillance for study of viral evolution, in addition to monitoring the spread of the virus worldwide.

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In this paper, we analysed the haemagglutinin (HA) gene identified by polymerase chain reaction from 90 influenza A H1N1 virus strains that circulated in Brazil from April 2009-June 2010. A World Health Organization sequencing protocol allowed us to identify amino acid mutations in the HA protein at positions S220T (71 percent), D239G/N/S (20 percent), Y247H (4.5 percent), E252K (3.3 percent), M274V (2.2 percent), Q310H (26.7 percent) and E391K (12 percent). A fatal outcome was associated with the D239G mutation (p < 0.0001). Brazilian HA genetic diversity, in comparison to a reference strain from California, highlights the role of influenza virus surveillance for study of viral evolution, in addition to monitoring the spread of the virus worldwide.

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Em abril de 2009, um novo subtipo viral do vírus influenza A (H1N1) foi identificado em espécimes clínicos obtidos de dois pacientes nos Estados Unidos. A mesma cepa viral foi identificada no México, no Canadá e em outras partes do mundo. Esse evento foi considerado pela Organização Mundial de Saúde como de emergência em Saúde Pública de Interesse Internacional. O presente estudo descreve a ocorrência de casos notificados de influenza A (H1N1), novo subtipo viral, ao Centro de Vigilância Epidemiológica do Estado de São Paulo, no período de 22 de abril a 21 de maio de 2009, de acordo com sua distribuição no tempo e espaço, assim como a faixa etária e gênero acometidos, culminando com a classificação final dos casos e os critérios utilizados. Uma vigilância aprimorada de influenza foi implementada, com base no plano de preparação para pandemia do Estado, no sentido de identificar e investigar oportunamente os casos. As amostras respiratórias foram processadas no Instituto Adolfo Lutz, cujo método utilizado foi reação de polimerização em cadeia em tempo real (rRT-PCR). Um total de 87 casos notificados, maioria na Grande São Paulo, concentraram-se na faixa etária de 20 a 49 anos de idade (70,1%), provenientes de áreas com casos confirmados de influenza A (H1N1). Os sintomas mais frequentes foram febre e tosse (100%) e mialgia (70,1%); 40,2% foram hospitalizados e todos evoluíram para a cura com remissão dos sintomas. Cumpre ressaltar a necessidade de manter em alerta os sistemas de saúde com vistas à detecção precoce e resposta rápida frente aos casos e à adoção de medidas de prevenção e controle adequadas e de prover os profissionais de saúde e a população de informações concernentes ao atual estágio deste agravo.

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