Clinical impact of respiratory virus in pulmonary exacerbations of children with Cystic Fibrosis.

BackgroundsCystic Fibrosis (CF) is a genetic, multisystemic, progressive illness that causes chronic suppurative lung disease. A major cause of morbimortality in this condition are pulmonary exacerbations. Although classically attributed to bacterial infections, respiratory virus have been increasingly recognized in its ethiopathogeny.MethodsNasopharyngeal swab samples were collected from children ResultsOut of 70 samples collected from 48 patients, 35.7% were positive for respiratory viruses. Rhinovirus were the most common (28% of all positive samples), followed by RSV. The virus positive group was associated with change in sinus discharge (p = 0.03). Considering only patients younger than five years old, positive virus detection was also associated with fever (p = 0.01). There was no significant difference in clinical severity or in bacterial colonization between virus positive and negative groups.ConclusionsProspective studies are still needed to assess the long term impact of viral infections in patients with CF, and their interaction with the bacterial microbiome in these patients

Whole-Genome Characterization of a Novel Human Influenza A(H1N2) Virus Variant, Brazil

We report the characterization of a novel reassortant influenza A(H1N2) virus not previously reported in humans. Recovered from a a pig farm worker in southeast Brazil who had influenza-like illness, this virus is a triple reassortant containing gene segments from subtypes H1N2 (hemagglutinin), H3N2 (neuraminidase), and pandemic H1N1 (remaining genes)

Molecular findings from influenza A(H1N1)pdm09 detected in patients from a Brazilian equatorial region during the pandemic period

After the World Health Organization officially declared the end of the first pandemic of the XXI century in August 2010, the influenza A(H1N1)pdm09 virus has been disseminated in the human population. In spite of its sustained circulation, very little on phylogenetic data or oseltamivir (OST) resistance is available for the virus in equatorial regions of South America. In order to shed more light on this topic, we analysed the haemagglutinin (HA) and neuraminidase (NA) genes of influenza A(H1N1)pdm09 positive samples collected during the pandemic period in the Pernambuco (PE), a northeastern Brazilian state. Complete HA sequences were compared and amino acid changes were related to clinical outcome. In addition, the H275Y substitution in NA, associated with OST resistance, was investigated by pyrosequencing. Samples from PE were grouped in phylogenetic clades 6 and 7, being clustered together with sequences from South and Southeast Brazil. The D222N/G HA gene mutation, associated with severity, was found in one deceased patient that was pregnant. Additionally, the HA mutation K308E, which appeared in Brazil in 2010 and was only detected worldwide the following year, was identified in samples from hospitalised cases. The resistance marker H275Y was not identified in samples tested. However, broader studies are needed to establish the real frequency of resistance in this Brazilian region

Epidemiological aspects of influenza A related to climatic conditions during and after a pandemic period in the city of Salvador, northeastern Brazil

Made available in DSpace on 2015-06-12T13:57:52Z (GMT). No. of bitstreams: 2 license.txt: 1914 bytes, checksum: 7d48279ffeed55da8dfe2f8e81f3b81f (MD5) marilda_siqueiraetal_IOC_2014.pdf: 584526 bytes, checksum: 73786a4075afec1fddd39db2a23a8a06 (MD5) Previous issue date: 2014Complexo Hospitalar Professor Edgard Santos. Laboratório de Pesquisa em Infectologia. BA, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Virus Respiratório e Sarampo. Rio de Janeiro, RJ, Brasil.Complexo Hospitalar Professor Edgard Santos. Laboratório de Pesquisa em Infectologia. BA, Brasil.Complexo Hospitalar Professor Edgard Santos. Laboratório de Pesquisa em Infectologia. BA, Brasil.Faculdade de Medicina da Bahia. Departamento de Pediatria. Salvador, BA, Brasil.Universidade Federal da Bahia. Programa de Pós-Graduação em Ciências da Saúde. Salvador, BA, Brasil. .Universidade Federal da Bahia. Programa de Pós-Graduação em Ciências da Saúde. Salvador, BA, Brasil. .Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Virus Respiratório e Sarampo. Rio de Janeiro, RJ, Brasil.Complexo Hospitalar Professor Edgard Santos. Laboratório de Pesquisa em Infectologia. BA, Brasil.During the influenza pandemic of 2009, the A(H1N1)pdm09, A/H3N2 seasonal and influenza B viruses were observed to be co-circulating with other respiratory viruses. To observe the epidemiological pattern of the influenza virus between May 2009-August 2011, 467 nasopharyngeal aspirates were collected from children less than five years of age in the city of Salvador. In addition, data on weather conditions were obtained. Indirect immunofluorescence, real-time transcription reverse polymerase chain reaction (RT-PCR), and sequencing assays were performed for influenza virus detection. Of all 467 samples, 34 (7%) specimens were positive for influenza A and of these, viral characterisation identified Flu A/H3N2 in 25/34 (74%) and A(H1N1)pdm09 in 9/34 (26%). Influenza B accounted for a small proportion (0.8%) and the other respiratory viruses for 27.2% (127/467). No deaths were registered and no pattern of seasonality or expected climatic conditions could be established. These observations are important for predicting the evolution of epidemics and in implementing future anti-pandemic measures

Low prevalence of influenza A strains with resistance markers in Brazil during 2017–2019 seasons

This project was supported by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES); Programa Estratégico de Apoio à Pesquisa em Saúde (PAPES), Fundação Oswaldo Cruz, CNPq, and Coordenação Geral de Laboratórios de Saúde Pública (CGLAB) from the Brazilian Ministry of Health.Fiocruz Fundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brazil.Fiocruz Fundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brazil.Fiocruz Fundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brazil.Fiocruz Fundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brazil.Fiocruz Fundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brazil.Fiocruz Fundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brazil.Fiocruz Fundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brazil.Fiocruz Fundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brazil.Fiocruz Fundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brazil.Fiocruz Fundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brazil.Laboratório Central de Saúde Pública de Sergipe. Aracaju, SE, Brazil.Laboratório Central de Saúde Pública de Sergipe. Aracaju, SE, Brazil.Laboratório Central do Estado do Paraná. Curitiba, PR, Brazil.Laboratório Central do Estado do Paraná. Curitiba, PR, Brazil.Secretaria de Saúde do Estado do Espírito Santo. Laboratório de Saúde Pública do Estado do Espírito Santo. Vitória, ES, Brazil / Universidade Federal do Espírito Santo. Núcleo de Doenças Infecciosas. Vitória, ES, Brazil.Secretaria de Saúde do Estado do Espírito Santo. Laboratório de Saúde Pública do Estado do Espírito Santo. Vitória, ES, Brazil / Universidade Federal do Espírito Santo. Núcleo de Doenças Infecciosas. Vitória, ES, Brazil.Laboratório Central de Saúde Pública do Rio de Janeiro. Rio de Janeiro, RJ, Brazil.Laboratório Central de Saúde Pública do Rio de Janeiro. Rio de Janeiro, RJ, Brazil.Secretaria de Saúde do estado do Rio Grande do Sul. Laboratório Central de Saúde Pública. Porto Alegre, RS, Brazil.Secretaria de Saúde do estado do Rio Grande do Sul. Laboratório Central de Saúde Pública. Porto Alegre, RS, Brazil.Fundação Ezequiel Dias. Laboratório Central de Saúde Pública de Minas Gerais. Belo Horizonte, MG, Brazil.Fundação Ezequiel Dias. Laboratório Central de Saúde Pública de Minas Gerais. Belo Horizonte, MG, Brazil.Laboratório Central da Saúde Pública do estado da Bahia. Salvador, BA, Brazil.Laboratório Central da Saúde Pública do estado da Bahia. Salvador, BA, Brazil.Laboratório Central de Santa Catarina. Florianópolis, SC, Brazil.Laboratório Central de Santa Catarina. Florianópolis, SC, Brazil.Ministério da Saúde. Secretaria de Ciência, Tecnologia, Inovação e Insumos Estratégicos. Instituto Evandro Chagas. Ananindeua, PA. Brasil.Ministério da Saúde. Secretaria de Ciência, Tecnologia, Inovação e Insumos Estratégicos. Instituto Evandro Chagas. Ananindeua, PA. Brasil.Instituto Adolfo Lutz. Laboratório Central de Saúde Pública do Estado de São Paulo. São Paulo, SP, Brazil.Instituto Adolfo Lutz. Laboratório Central de Saúde Pública do Estado de São Paulo. São Paulo, SP, Brazil.Fiocruz Fundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brazil.Fiocruz Fundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brazil.Fiocruz Fundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brazil.Fiocruz Fundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Departamento de Imunização e Doenças Transmissíveis. Brasília, DF, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Departamento de Imunização e Doenças Transmissíveis. Brasília, DF, Brazil.Fiocruz Fundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brazil.Fiocruz Fundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brazil.Fiocruz Fundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brazil.Fiocruz Fundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brazil.The influenza A virus (IAV) is of a major public health concern as it causes annual epidemics and has the potential to cause pandemics. At present, the neuraminidase inhibitors (NAIs) are the most widely used anti-influenza drugs, but, more recently, the drug baloxavir marboxil (BXM), a polymerase inhibitor, has also been licensed in some countries. Mutations in the viral genes that encode the antiviral targets can lead to treatment resistance. Worldwide, a low prevalence of antiviral resistant strains has been reported. Despite that, this situation can change rapidly, and resistant strain surveillance is a priority. Thus, the aim of this was to evaluate Brazilian IAVs antiviral resistance from 2017 to 2019 through the identification of viral mutations associated with reduced inhibition of the drugs and by testing the susceptibility of IAV isolates to oseltamivir (OST), the most widely used NAI drug in the country. Initially, we analyzed 282 influenza A(H1N1)pdm09 and 455 A(H3N2) genetic sequences available on GISAID. The amino acid substitution (AAS) NA:S247N was detected in one A(H1N1)pdm09 strain. We also identified NA:I222V (n = 6) and NA:N329K (n = 1) in A(H3N2) strains. In addition, we performed a molecular screening for NA:H275Y in 437 A(H1N1)pdm09 samples, by pyrosequencing, which revealed a single virus harboring this mutation. Furthermore, the determination of OST IC50 values for 222 A(H1N1)pdm09 and 83 A(H3N2) isolates revealed that all isolates presented a normal susceptibility profile to the drug. Interestingly, we detected one A(H3N2) virus presenting with PA:E119D AAS. Moreover, the majority of the IAV sequences had the M2:S31N adamantanes resistant marker. In conclusion, we show a low prevalence of Brazilian IAV strains with NAI resistance markers, in accordance with what is reported worldwide, indicating that NAIs still remain an option for the treatment of influenza infections in Brazil. However, surveillance of influenza resistance should be strengthened in the country for improving the representativeness of investigated viruses and the robustness of the analysis

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

Evolutionary dynamics and dissemination pattern of the SARS-CoV-2 lineage B.1.1.33 during the early pandemic phase in Brazil

We would like to thank the funding support from CGLab/MoH (General Laboratories Coordination of Brazilian Ministry of Health), CVSLR/FIOCRUZ (Coordination of Health Surveillance and Reference Laboratories of Oswaldo Cruz Foundation), CNPq COVID-19 MCTI 402457/2020-0, and INOVA VPPCB-005-FIO20-2Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brasil / Brazilian Ministry of Health. Pan-American Health Organization. SARS-CoV-2 National Reference Laboratory. Regional Reference Laboratory in Americas. Rio de Janeiro, RJ, Brazil.Universidade Federal do Espírito Santo - Campus de Alegre. Centro de Ciências Exatas, Naturais e da Saude. Departamento de Biologia. Vitória, ES, Brazil.Fundação Oswaldo Cruz. Gonçalo Moniz. Salvador, BA, Brazil.Universidad de la Republica. Centro Universitario Regional del Litoral Norte. Unidad de Genomica y Bioinformatica. Salto, Uruguay.Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brasil / Brazilian Ministry of Health. Pan-American Health Organization. SARS-CoV-2 National Reference Laboratory. Regional Reference Laboratory in Americas. Rio de Janeiro, RJ, Brazil.Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brasil / Brazilian Ministry of Health. Pan-American Health Organization. SARS-CoV-2 National Reference Laboratory. Regional Reference Laboratory in Americas. Rio de Janeiro, RJ, Brazil.Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brasil / Brazilian Ministry of Health. Pan-American Health Organization. SARS-CoV-2 National Reference Laboratory. Regional Reference Laboratory in Americas. Rio de Janeiro, RJ, Brazil.Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brasil / Brazilian Ministry of Health. Pan-American Health Organization. SARS-CoV-2 National Reference Laboratory. Regional Reference Laboratory in Americas. Rio de Janeiro, RJ, Brazil.Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brasil / Brazilian Ministry of Health. Pan-American Health Organization. SARS-CoV-2 National Reference Laboratory. Regional Reference Laboratory in Americas. Rio de Janeiro, RJ, Brazil.Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brasil / Brazilian Ministry of Health. Pan-American Health Organization. SARS-CoV-2 National Reference Laboratory. Regional Reference Laboratory in Americas. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhaes. Recife, PE, Brazil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhaes. Recife, PE, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Laboratorio Central de Saude Publica do Estado de Santa Catarina. Florianopolis, SC, Brazil.Laboratorio Central de Saude Publica do Estado Espirito Santo. Vitoria, ES, Brazil.Laboratorio Central de Saude Publica do Distrito Federal. Brasília, DF, Brazil.Laboratorio Central de Saude Publica de Alagoas. Maceio, AL, Brazil.Laboratorio Central de Saude Publica da Bahia. Salvador, BA, Brazil.Laboratorio Central de Saude Publica de Sergipe. Aracaju, SE, Brazil.Laboratorio Central de Saude Publica de Parana. Curitiba, PR, Brazil.Laboratorio Central de Saude Publica de Parana. Curitiba, PR, Brazil.Fundação Oswaldo Cuz - Mato Grosso do Sul. Campo Grande, MT, Brazil / Universidade Federal de Mato Grosso do Sul. Campo Grande, MT, Brazil.Ministério da Defesa. Hospital das Forças Armadas. Brasília, DF, Brazil.Ministério da Saude. Coordenadoria Geral de Laboratorios. Brasília, DF, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratorio de AIDS e Imunologia Molecular. Rio de Janeiro, RJ, Brazil.Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brasil / Brazilian Ministry of Health. Pan-American Health Organization. SARS-CoV-2 National Reference Laboratory. Regional Reference Laboratory in Americas. Rio de Janeiro, RJ, 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

Investigation of SARS-CoV-2 infection in dogs and cats of humans diagnosed with COVID-19 in Rio de Janeiro, Brazil.

BackgroundInfection by SARS-CoV-2 in domestic animals has been related to close contact with humans diagnosed with COVID-19. Objectives: To assess the exposure, infection, and persistence by SARS-CoV-2 of dogs and cats living in the same households of humans that tested positive for SARS-CoV-2, and to investigate clinical and laboratory alterations associated with animal infection.MethodsAnimals living with COVID-19 patients were longitudinally followed and had nasopharyngeal/oropharyngeal and rectal swabs collected and tested for SARS-CoV-2. Additionally, blood samples were collected for laboratory analysis, and plaque reduction neutralization test (PRNT90) to investigate specific SARS-CoV-2 antibodies.ResultsBetween May and October 2020, 39 pets (29 dogs and 10 cats) of 21 patients were investigated. Nine dogs (31%) and four cats (40%) from 10 (47.6%) households were infected with or seropositive for SARS-CoV-2. Animals tested positive from 11 to 51 days after the human index COVID-19 case onset of symptoms. Three dogs tested positive twice within 14, 30, and 31 days apart. SARS-CoV-2 neutralizing antibodies were detected in one dog (3.4%) and two cats (20%). In this study, six out of thirteen animals either infected with or seropositive for SARS-CoV-2 have developed mild but reversible signs of the disease. Using logistic regression analysis, neutering, and sharing bed with the ill owner were associated with pet infection.ConclusionsThe presence and persistence of SARS-CoV-2 infection have been identified in dogs and cats from households with human COVID-19 cases in Rio de Janeiro, Brazil. People with COVID-19 should avoid close contact with their pets during the time of their illness