Comparative analysis of SARS-CoV-2 variants Alpha (B.1.1.7), Gamma (P.1), Zeta (P.2) and Delta (B.1.617.2) in Vero-E6 cells: ultrastructural characterization of cytopathology and replication kinetics

Abstract This study compares the effects of virus-cell interactions among SARS-CoV-2 variants of concern (VOCs) isolated in Brazil in 2021, hypothesizing a correlation between cellular alterations and mortality and between viral load and transmissibility. For this purpose, reference isolates of Alpha, Gamma, Zeta, and Delta variants were inoculated into monolayers of Vero-E6 cells. Viral RNA was quantified in cell supernatants by RT‒PCR, and infected cells were analyzed by Transmission Electron Microscopy (TEM) for qualitative and quantitative evaluation of cellular changes 24, 48, and 72 hours postinfection (hpi). Ultrastructural analyses showed that all variants of SARS-CoV-2 altered the structure and function of mitochondria, nucleus, and rough endoplasmic reticulum of cells. Monolayers infected with the Delta variant showed the highest number of modified cells and the greatest statistically significant differences compared to those of other variants. Viral particles were observed in the cytosol and the cell membrane in 100 % of the cells at 48 hpi. Alpha showed the highest mean particle diameter (79 nm), and Gamma and Delta were the smallest (75 nm). Alpha and Gamma had the highest particle frequency per field at 48 hpi, while the same was observed for Zeta and Delta at 72 hpi and 24 hpi, respectively. The cycle threshold of viral RNA varied among the target protein, VOC, and time of infection. The findings presented here demonstrate that all four VOCs evaluated caused ultrastructural changes in Vero-E6 cells, which were more prominent when infection occured with the Delta variant.

Perfil epidemiológico dos casos suspeitos de sarampo e rubéola notificados no SINAN, Brasil, 2007 a 2016 / Epidemiological profile of suspected cases of measles and rubella notified on SINAN, Brazil, 2007 to 2016

Descrever os casos suspeitos de sarampo e rubéola notificados no Sistema de Informação de Agravos de Notificação (Sinan), Brasil, 2007 a 2016. Métodos: Os dados foram extraídos do Sinan, referentes aos anos de 2007 a 2016. As variáveis utilizadas foram os números de notificações de casos de sarampo e rubéola por regiões e ano, idade, sexo, hospitalização, estado gestacional, histórico vacinal, realização de bloqueio vacinal, coletas sorológicas (S1 e S2), sinais e sintomas, investigação adequada, critério de confirmação ou descarte e classificação final do caso. Resultados: Entre 2007 e 2016 houve 127.802 casos suspeitos de sarampo e rubéola notificados. Aproximadamente 92% dos casos foram investigados, a maioria em menores de cinco anos. Os sintomas mais frequentes foram tosse (40%) e coriza (38%). Como instrumento de vigilância foi coletado sangue para confirmação laboratorial em 87% das notificações. A maioria dos casos de sarampo ocorreu entre os anos de 2011 e 2015, relacionados a casos importados, totalizando 1.443 casos; para rubéola, 10.125 casos foram confirmados. Foram descartados 1,3% (1.698/127.802) e 5,1% (6.555/127.802) das notificações de sarampo e rubéola, respectivamente. Foram ignorados 9% (11.523/127.802) para sarampo e 49% (62.978/127.802) para rubéola. Conclusão: A vigilância dos casos de doenças exantemáticas permitiu demonstrar a situação dos casos de doenças exantemáticas circulantes no país como importante ferramenta de saúde pública. O grande número de casos descartados classificados como ignorados merece atenção, no sentido de melhorar o encerramento dos casos suspeitos notificados

To describe the suspected cases of measles and rubella notified in the Notifiable Diseases Information System (Sinan), Brazil, from 2007 to 2016. Methods: Data were extracted from Sinan referring to the years 2007 to 2016. The variables used were the number of notifications of measles and rubella cases by region and year, age, gender, hospitalization, gestational status, vaccination history, vaccination blockade, serological collections (S1 and S2), signs and symptoms, adequate investigation, confirmation criteria or disposal and final case classification. Results: Between 2007 and 2016, there were 127,802 suspected cases of measles and rubella reported. Approximately 92% of cases were investigated, mostly in children under five years of age. The most frequent symptoms were cough (40%) and runny nose (38%). As a surveillance tool, blood was collected for laboratory confirmation in 87% of notifications. Most Measles cases occurred between 2011 and 2015, related to imported cases, totaling 1,443 cases; for Rubella 10,125 cases were confirmed. 1.3% (1,698/127,802) and 5.1% (6,555/127,802) of measles and rubella notifications, respectively, were discarded. 9% (11,523/127,802) for measles and 49% (62,978/127,802) for rubella were ignored. Conclusion: Surveillance of cases of exanthematous diseases allowed demonstrating the situation of cases of exanthematous diseases circulating in the country as an important public health tool. The large number of discarded cases classified as ignored deserves attention, in order to improve the closing of notified suspected cases

Long COVID-19 syndrome associated with Omicron XBB.1.5 infection: a case report

BACKGROUND There is interest in lingering non-specific symptoms after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, referred to as Long coronavirus disease 2019 (Long COVID-19). It remains unknown whether the risk of Long COVID-19 is associated with pre-existing comorbidities or initial COVID-19 severity, including infections due to new Omicron lineages which predominated in 2023. OBJECTIVES The aim of this case report was to characterize the clinical features of acute XBB.1.5 infection followed by Long COVID-19. METHODS We followed a 73-year old female resident of Rio de Janeiro with laboratory-confirmed SARS-CoV-2 during acute infection and subsequent months. The SARS-CoV-2 lineage was determined by genome sequencing. FINDINGS The participant denied comorbidities and had completed a two-dose vaccination schedule followed by two booster doses eight months prior to SARS-CoV-2 infection. Primary infection by viral lineage XBB.1.5. was clinically mild, but the participant subsequently reported persistent fatigue. MAIN CONCLUSIONS This case demonstrates that Long COVID-19 may develop even after mild disease due to SARS-CoV-2 in fully vaccinated and boosted individuals without comorbidities. Continued monitoring of new SARS-CoV-2 lineages and associated clinical outcomes is warranted. Measures to prevent infection should continue to be implemented including development of new vaccines and antivirals effective against novel variants.

A straightforward one-step strategy for SARS-CoV-2 diagnosis and screening of variants of concern: a multicentre study

BACKGROUND The prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) has changed unevenly over time around the world. Although whole genome sequencing is the gold standard for virus characterisation, the discovery of alpha VOC causing spike gene target failure (SGTF) result, when tested using an reverse transcription real-time polymerase chain reaction (RT-qPCR) assay, has provided a simple tool for tracking the frequencies of variants. OBJECTIVES The aim of this study was to investigate if a multiplex RT-qPCR assay (BioM 4Plex VOC) could be used to detect SARS-CoV-2 and to perform a VOC screening test in a single reaction tube. Here, we present the multicentre study evaluating this assay. METHODS Twelve laboratories have participated in the multicentre study. The BioM 4Plex VOC was distributed to them with detailed instructions of how to perform the test. They were asked to test the BioM 4Plex VOC in parallel with their routine Commercial SARS-CoV-2 diagnostic assay. Additionally, they were requested to select SARS-CoV-2-positive samples with genome sequenced and lineage definition according to PANGO lineage classification. FINDINGS The BioM 4Plex VOC and commercial RT-PCR assay are equally effective in detecting SARS-CoV-2. Results revealed a specificity of 96.5-100% [95% confidence interval (CI)], a sensitivity of 99.8-100% (95% CI), and an accuracy of 99.8-100% (95% CI). A 99% concordance rate was found between results from the BioM 4Plex VOC and that from available genome sequencing data. MAIN CONCLUSIONS The BioM 4Plex VOC provides an effective solution to detect SARS-CoV-2 infections and screening for VOCs in a single reaction. It is a straightforward method to help us monitor the frequency and distribution of VOCs and develop strategies to better cope with the pandemics.

A straightforward one-step strategy for SARS-CoV-2 diagnosis and screening of variants of concern: a multicentre study

BACKGROUND The prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) has changed unevenly over time around the world. Although whole genome sequencing is the gold standard for virus characterisation, the discovery of alpha VOC causing spike gene target failure (SGTF) result, when tested using an reverse transcription real-time polymerase chain reaction (RT-qPCR) assay, has provided a simple tool for tracking the frequencies of variants. OBJECTIVES The aim of this study was to investigate if a multiplex RT-qPCR assay (BioM 4Plex VOC) could be used to detect SARS-CoV-2 and to perform a VOC screening test in a single reaction tube. Here, we present the multicentre study evaluating this assay. METHODS Twelve laboratories have participated in the multicentre study. The BioM 4Plex VOC was distributed to them with detailed instructions of how to perform the test. They were asked to test the BioM 4Plex VOC in parallel with their routine Commercial SARS-CoV-2 diagnostic assay. Additionally, they were requested to select SARS-CoV-2-positive samples with genome sequenced and lineage definition according to PANGO lineage classification. FINDINGS The BioM 4Plex VOC and commercial RT-PCR assay are equally effective in detecting SARS-CoV-2. Results revealed a specificity of 96.5-100% [95% confidence interval (CI)], a sensitivity of 99.8-100% (95% CI), and an accuracy of 99.8-100% (95% CI). A 99% concordance rate was found between results from the BioM 4Plex VOC and that from available genome sequencing data. MAIN CONCLUSIONS The BioM 4Plex VOC provides an effective solution to detect SARS-CoV-2 infections and screening for VOCs in a single reaction. It is a straightforward method to help us monitor the frequency and distribution of VOCs and develop strategies to better cope with the pandemics.

Condições socioeconômicas e impactos da pandemia da Covid-19 na região da Sub-Bacia do Canal do Cunha, Rio de Janeiro / Socioeconomic conditions and impacts of the COVID-19 pandemic in the Canal do Cunha Sub-Basin region, Rio de Janeiro municipality

RESUMO O Município do Rio de Janeiro (MRJ) estava entre as cidades com altas taxas de mortalidade ao longo da pandemia de Covid-19. Neste estudo, analisamos as taxas de incidência, de mortalidade e letalidade por Covid-19 nas áreas com predominância de Aglomerados Subnormais (ASN). Foram considerados todos os 36 bairros da Sub-Bacia do Canal do Cunha (SBCC) associadas às características demográficas, socioeconômicas e epidemiológicas, com estatística espacial de Moran. A taxa de incidência nos bairros da SBCC foi de 621,5/10.000 habitantes. Complexo do Alemão, Mangueira, e Maré tiveram maiores proporções de casos e mortes. A menor incidência (33,6/10.000 habitantes) e mortalidade (8,3/10.000 habitantes), mas com maior taxa de letalidade (24,7%) foi registrada no Complexo do Alemão. Foi observado correlação negativa entre a taxa de mortalidade e a proporção de habitantes nos bairros com ASN (rho= -0,433; p=0,023). Na estatística espacial, houve correlação inversa para a incidência da Covid-19 (índice Moran, -0,155863; p=0,02). Conclui-se que incidência e mortalidade nas áreas de ASN estão significativamente relacionadas com as estruturas sociodemográficas, demandando o reforço dos sistemas de vigilância e de controle da Covid-19 em territórios de favelas. As recomendações não farmacológicas e a Atenção Primária à Saúde em favelas desempenham relevante papel na redução da transmissão, mortalidade e iniquidades em saúde.

ABSTRACT Along COVID-19 pandemics, Rio de Janeiro (MRJ) has figured among the Brazilian cities with the highest mortality rates. In this study, we explored COVID-19 incidence and mortality in areas with a predominance of subnormal population clusters (SNC) in MRJ. We analyzed 36 neighborhoods of Canal do Cunha Sub-basin (CCSB) and the associations between demographic, socioeconomic, and epidemiological features, and the cumulative incidence, mortality, and lethality rates, and Moran's spatial statistics were performed. The incidence rate in CCSB neighborhoods was 621.5/10,000 inhabitants. Complexo do Alemão, Mangueira, and Maré had the highest proportions of cases and deaths. And the lowest incidence (33.6/10,000 inhabitants), mortality (8.3/10,000 inhabitants), but with the highest lethality rate (24.7%) was recorded in Complexo do Alemão. There was a negative correlation between mortality and the proportion of inhabitants in neighborhoods with ASN (rho= -0.433; p=0.023). In spatial statistics, there was an inverse correlation for the incidence (Moran index, -0.155863; p=0.02). It is concluded that incidence and mortality in SNC areas are significantly related to their sociodemographic structures, highlighting the need to strengthen the surveillance and control systems of COVID-19 in slums territories. Non-pharmacological recommendations and suitable Primary Health Care in slums areas play a relevant role in reducing viral transmission, mortality, and health inequities.

Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon

BACKGROUND The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has become a major concern contributing to increased morbidity and mortality worldwide. OBJECTIVES Here we describe the replacement of the Gamma variant of concern (VOC) with Delta in the western Brazilian Amazon. METHODS In this study, we analysed 540 SARS-CoV-2 positive samples determined by qualitative real-time RT-PCR selected in the state of Rondônia between June and December 2021. The positive cohort was sequenced through next-generation sequencing (NGS) and each sample was quantified using real-time RT-qPCR, the whole genome sequence was obtained, SARS-CoV-2 lineages were classified using the system Pango and the maximum likelihood (ML) method was used to conduct phylogenetic analyses. FINDINGS A total of 540 high-quality genomes were obtained, where the Delta VOC showed the highest prevalence making up 72%, with strain AY.43 being the most abundant, while the Gamma VOC was present in 28%, where the P.1 strain was the most frequent. In this study population, only 32.96% (178/540) had completed the vaccination schedule. MAIN CONCLUSIONS This study highlighted the presence of Gamma and Delta variants of SARS-CoV-2 in RO. Furthermore, we observed the replacement of the Gamma VOC with the Delta VOC and its lineages.

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.

SARS-CoV-2 variant N. 9 identified in Rio de Janeiro, Brazil

BACKGROUND The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.33-derived lineage named N.9 was described recently in Brazil and it's considered a potential variant of interest (VOI) due to the presence of E484K substitution at the receptor-binding domain (RBD) of the Spike (S) protein. OBJECTIVE To describe the first detection of variant N.9 in Rio de Janeiro State. METHODS SARS-CoV-2 N.9 was confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR), whole-genome sequencing and phylogenetic analysis. FINDINGS Here, we report two SARS-CoV-2 N.9 lineage strains in Rio de Janeiro. One of them had only the E484K substitution of the six N.9 lineage-defining mutations. Other three strains pre-defined as N.9 have the same genomic profile. These four strains are grouped within the B.1.1.33 lineage and basal to the N.9 lineage in our phylogenetic analysis, and we call them "N.9-like/B.1.1.33 + E484K". MAIN CONCLUSIONS The phylogenetic analysis shows four independent introductions of N.9 in the state of Rio de Janeiro in October and December 2020, January and March 2021. SARS-CoV-2 N.9 dissemination in the Rio de Janeiro could have been limited by the emergence and dominance of other variants, mainly by the lineage P.2 VOI Zeta that emerged in the same period and co-circulated with N.9, as observed in the neighboring State of São Paulo.

Iniquidades étnico-raciais nas hospitalizações por causas evitáveis em menores de cinco anos no Brasil, 2009-2014 / Ethnic and racial inequalities in hospital admissions due to avoidable causes in under-five Brazilian children, 2009-2014 / Inequidades étnico-raciales en las hospitalizaciones por causas evitables en menores de cinco años en Brasil, 2009-2014

Resumo: Internacionalmente, observa-se um incremento no uso das internações por condições sensíveis à atenção primária (ICSAP) como indicador de efetividade da atenção primária à saúde. Este artigo analisa as iniquidades étnico-raciais nas internações por causas em menores de cinco anos no Brasil e regiões, com ênfase nas ICSAP e nas infecções respiratórias agudas (IRA). Com dados do Sistema de Informações Hospitalares do Sistema Único de Saúde (SIH/SUS), 2009-2014, calcularam-se proporções por causas, taxas e razões de taxas de ICSAP ajustadas por sexo e idade após a imputação múltipla de dados faltantes de cor/raça. As principais causas de internação foram doenças do aparelho respiratório (37,4%) e infecciosas e parasitárias (19,3%), sendo as crianças indígenas as mais acometidas. As taxas brutas de ICSAP (por 1.000) foram mais elevadas em indígenas (97,3; IC95%: 95,3-99,2), seguidas das pardas (40,0; IC95%: 39,8-40,1), e as menores foram nas amarelas (14,8; IC95%: 14,1-15,5). As maiores razões de taxas ajustadas de ICSAP foram registradas entre crianças de cor/raça indígena e branca - 5,7 (IC95%: 3,9-8,4) no país, atingindo 5,9 (IC95%: 5,0-7,1) e 18,5 (IC95%: 16,5-20,7) no Norte e Centro-oeste, respectivamente. As IRA permanecem como importantes causas de hospitalização em crianças no Brasil. Foram observadas alarmantes iniquidades étnico-raciais nas taxas de ICSAP, com situação de desvantagem para indígenas. São necessárias melhorias nas condições de vida, saneamento e subsistência, bem como garantia de acesso oportuno e qualificado à atenção primária à saúde das populações mais vulneráveis, com destaque para os indígenas no Norte e no Centro-oeste, a fim de minimizar iniquidades em saúde e fazer cumprir as diretrizes do SUS e da Constituição do Brasil.

Abstract: There has been a global increase in hospital admissions for primary care-sensitive conditions (PCSCs) as an indicator of effectiveness in primary health care. This article analyzes ethnic and racial inequalities in cause-related hospitalizations in under-five children in Brazil as a whole and the country's five major geographic regions, with an emphasis on PCSCs and acute respiratory infections (ARIs). Using data from the Hospital Information Systems of the Brazilian Unified National Health System (SIH/SUS), 2009-2014, the authors calculated proportions, rates, and rate ratios for PCSCs, adjusted by sex and age after multiple imputation of missing data on color/race. The principal causes of hospitalization were respiratory tract infections (37.4%) and infectious and parasitic diseases (19.3%), and indigenous children were proportionally the most affected. Crude PCSC rates (per 1,000) were highest in indigenous children (97.3; 95%CI: 95.3-99.2), followed by brown or mixed-raced children (40.0; 95%CI: 39.8-40.1), while the lowest rates were in Asiandescendant children (14.8; 95%CI: 14.1-15.5). The highest adjusted rate ratios for PCSCs were seen among indigenous children compared to white children - 5.7 (95%CI: 3.9-8.4) for Brazil as a whole, reaching 5.9 (95%CI: 5.0-7.1) and 18.5 (95%CI: 16.5-20.7) in the North and Central, respectively, compared to white children. ARIs remained as important causes of pediatric hospitalizations in Brazil. Alarming ethnic and racial inequalities were observed in PCSCs, with indigenous children at a disadvantage. Improvements are needed in living conditions, sanitation, and subsistence, as well as guaranteed timely access to high-quality primary health care in the more vulnerable population groups, especially the indigenous peoples of the North and Central, in order to mitigate the health inequalities and meet the guidelines of the SUS and the Brazilian Constitution.

Resumen: Internacionalmente, se observa un incremento en las hospitalizaciones por condiciones sensibles a la atención primaria (ICSAP), como un indicador de efectividad de la atención primaria a la salud. Este artículo analiza las inequidades étnico-raciales en las hospitalizaciones por causas evitables em menores de cinco años en Brasil y sus regiones, con énfasis en las ICSAP y en las infecciones respiratorias agudas (IRA). Con datos del Sistema de Informaciones Hospitalarias del Sistema Único de Salud (SIH/SUS), 2009-2014, se calcularon porcentajes por causas, tasas y razones de tasas de ICSAP ajustadas por sexo y edad, tras la imputación múltiple de datos faltantes de color/raza. Las principales causas de hospitalización fueron enfermedades del aparato respiratório (37,4%) e infecciosas y parasitarias (19,3%), siendo los niños indígenas los más afectados. Las tasas brutas de ICSAP (por 1.000) fueron más elevadas en indígenas (97,3; IC95%: 95,3-99,2), seguidas de las mulatos/mestizos (40,0; IC95%: 39,8-40,1), mientras que las menores fueron en las de origen asiática (14,8; IC95%: 14,1-15,5). Las mayores razones de tasas ajustadas de ICSAP fueron en los niños indígenas comparados a los niños de color/raza blanca - 5,7 (IC95%: 3,9-8,4) en el país, alcanzando 5,9 (IC95%: 5,0-7,1) y 18,5 (IC95%: 16,5-20,7) en el Norte y Centro-oeste, respectivamente, en comparación con El color/raza blanca. Las IRA permanecen como importantes causas de hospitalización en niños em Brasil. Se observaron alarmantes inequidades étnico-raciales en las tasas de ICSAP, con situación de desventaja para los indígenas. Se necesitan mejoras en las condiciones de vida, saneamiento y subsistencia, así como la garantía de un acceso oportuno y cualificado a la atención primaria a La salud de las poblaciones más vulnerables, destacando los indígenas en el Norte y Centro-oeste, a fin de minimizar inequidades en salud y hacer cumplir las directrices del SUS y de la Constitución de Brasil.

Immunogenicity and safety of the combined vaccine for measles, mumps, and rubella isolated or combined with the varicella component administered at 3-month intervals: randomised study

BACKGROUND Field testing required to license the combined measles, mumps, and rubella (MMR) vaccine must take into account the current recommendation of the vaccine in Brazil: first dose at 12 months and second dose at 15 months of age in combination with a varicella vaccine. OBJECTIVES This study aimed to evaluate the clinical consistency, immunogenicity, and reactogenicity of three batches of MMR vaccine prepared with active pharmaceutical ingredients (API) from Bio-Manguinhos, Fiocruz (MMR-Bio), and compare it to a vaccine (MMR produced by GlaxoSmithKline) with different API. METHODS This was a phase III, randomised, double-blind, non-inferiority study of the MMR-Bio administered in infants immunised at health care units in Pará, Brazil, from February 2015 to January 2016. Antibody levels were titrated by immunoenzymatic assays. Adverse events were recorded in diaries. FINDINGS Seropositivity levels after MMR-Bio were 97.6% for measles, 84.7% for mumps, and 98.0% for rubella. After the MMRV vaccine, seroconversion rates and GMT increased substantially for mumps. In contrast, approximately 35% of the children had no detectable antibodies to varicella. Systemic adverse events were more frequent than local events. CONCLUSION The demonstration of batch consistency and non-inferiority of the Bio-MMR vaccine completed the technology transfer. This is a significant technological achievement with implications for immunisation programs.

Viral detection profile in children with severe acute respiratory infection

ABSTRACT Objectives: The role of viral co-detection in children with severe acute respiratory infection is not clear. We described the viral detection profile and its association with clinical characteristics in children admitted to the Pediatric Intensive Care Unit (PICU) during the 2009 influenza A(H1N1) pandemic. Method: Longitudinal observational retrospective study, with patients aged 0-18 years, admitted to 11 PICUs in Rio de Janeiro, with suspected H1N1 infection, from June to November, 2009. The results of respiratory samples which were sent to the Laboratory of Fiocruz/RJ and clinical data extracted from specific forms were analyzed. Results: Of 71 samples, 38% tested positive for H1N1 virus. Of the 63 samples tested for other viruses, 58 were positive: influenza H1N1 (43.1% of positive samples), rhinovirus/enterovirus (41.4%), respiratory syncytial vírus (12.1%), human metapneumovirus (12.1%), adenovirus (6.9%), and bocavirus (3.5%). Viral codetection occured in 22.4% of the cases. H1N1-positive patients were of a higher median age, had higher frequency of fever, cough and tachypnea, and decreased leukometry when compared to H1N1-negative patients. There was no difference in relation to severity outcomes (number of organic dysfunctions, use of mechanical ventilation or amines, hospital/PICU length of stay or death). Comparing the groups with mono-detection and co-dection of any virus, no difference was found regarding the association with any clinical variable. Conclusions: Other viruses can be implicated in SARI in children. The role of viral codetection has not yet been completely elucidated.

Molecular diversity of human parvovirus B19 during two outbreaks of erythema infectiosum in Brazil

Abstract This study was conducted to provide information on the genetic diversity of human parvovirus B19 (B19V) circulating in the municipality of Niterói, Rio de Janeiro, Southeast Brazil during 1996-2006, a period with two distinct outbreaks of B19V infection: 1999-2000 and 2004-2005. A total of 27 sera from patients with erythema infectiosum and five sera from HIV-infected patients that tested positive for B19V DNA during the study period were analyzed. To genotype B19V strains, a semi-nested PCR for partial amplification of the capsid gene was performed and sequence analysis revealed that 31 sequences belonged to subgenotype 1a (G1a) of the main genotype 1 and one sequence was characterized as subgenotype 3b (G3b). The phylogenetic tree supported the division of the G1a into two well-defined clades with 1.3% of divergence. The low diversity of the G1a strains may be explained by the fact that all patients had acute B19V infection and 30/32 sera were collected during two distinct outbreaks. The G3b strain was from an HIV-infected patient who seroconverted to anti-B19 IgG antibodies in September/2005. This is the first report of G3b in the state of Rio de Janeiro.

Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance

The 2009 pandemic influenza A virus outbreak led to the systematic use of the neuraminidase (NA) inhibitor oseltamivir (OST). Consequently, OST-resistant strains, carrying the mutation H275Y, emerged in the years after the pandemics, with a prevalence of 1-2%. Currently, OST-resistant strains have been found in community settings, in untreated individuals. To spread in community settings, H275Y mutants must contain additional mutations, collectively called permissive mutations. We display the permissive mutations in NA of OST-resistant A(H1N1)pdm09 virus found in Brazilian community settings. The NAs from 2013 are phylogenetically distinct from those of 2012, indicating a tendency of positive selection of NAs with better fitness. Some previously predicted permissive mutations, such as V241I and N369K, found in different countries, were also detected in Brazil. Importantly, the change D344N, also predicted to compensate loss of fitness imposed by H275Y mutation, was found in Brazil, but not in other countries in 2013. Our results reinforce the notion that OST-resistant A(H1N1)pdm09 strains with compensatory mutations may arise in an independent fashion, with samples being identified in different states of Brazil and in different countries. Systematic circulation of these viral strains may jeopardise the use of the first line of anti-influenza drugs in the future. (AU)

Whole-genome sequences of influenza A(H3N2) viruses isolated from Brazilian patients with mild illness during the 2014 season

The influenza A(H3N2) virus has circulated worldwide for almost five decades and is the dominant subtype in most seasonal influenza epidemics, as occurred in the 2014 season in South America. In this study we evaluate five whole genome sequences of influenza A(H3N2) viruses detected in patients with mild illness collected from January-March 2014. To sequence the genomes, a new generation sequencing (NGS) protocol was performed using the Ion Torrent PGM platform. In addition to analysing the common genes, haemagglutinin, neuraminidase and matrix, our work also comprised internal genes. This was the first report of a whole genome analysis with Brazilian influenza A(H3N2) samples. Considerable amino acid variability was encountered in all gene segments, demonstrating the importance of studying the internal genes. NGS of whole genomes in this study will facilitate deeper virus characterisation, contributing to the improvement of influenza strain surveillance in Brazil.

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.

Detection of respiratory viruses by real-time polymerase chain reaction in outpatients with acute respiratory infection

Viruses are the major contributors to the morbidity and mortality of upper and lower acute respiratory infections (ARIs) for all age groups. The aim of this study was to determine the frequencies for a large range of respiratory viruses using a sensitive molecular detection technique in specimens from outpatients of all ages with ARIs. Nasopharyngeal aspirates were obtained from 162 individuals between August 2007-August 2009. Twenty-three pathogenic respiratory agents, 18 respiratory viruses and five bacteria were investigated using multiplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) and indirect immunofluorescence assay (IIF). Through IIF, 33 (20.4%) specimens with respiratory virus were recognised, with influenza virus representing over half of the positive samples. Through a multiplex real-time RT-PCR assay, 88 (54.3%) positive samples were detected; the most prevalent respiratory viral pathogens were influenza, human rhinovirus and respiratory syncytial virus (RSV). Six cases of viral co-detection were observed, mainly involving RSV. The use of multiplex real-time RT-PCR increased the viral detection by 33.9% and revealed a larger number of respiratory viruses implicated in ARI cases, including the most recently described respiratory viruses [human bocavirus, human metapneumovirus, influenza A (H1N1) pdm09 virus, human coronavirus (HCoV) NL63 and HCoV HKU1].

Immune response to the mumps component of the MMR vaccine in the routine of immunisation services in the Brazilian National Immunisation Program

A non-controlled longitudinal study was conducted to evaluate the combined vaccine against measles, mumps and rubella (MMR) immunogenicity in 150 children vaccinated in the routine of three health units in the city of Rio de Janeiro, Brazil, 2008-2009, without other vaccines administered during the period from 30 days before to 30 days after vaccination. A previous study conducted in Brazil in 2007, in 1,769 children ranging from 12-15 months of age vaccinated against yellow fever and MMR simultaneously or at intervals of 30 days or more between doses, had shown low seroconversion for mumps regardless of the interval between administration of the two vaccines. The current study showed 89.5% (95% confidence interval: 83.3; 94.0) seroconversion rate for mumps. All children seroconverted for measles and rubella. After revaccination, high antibody titres and seroconversion rates were achieved against mumps. The results of this study and others suggest that two MMR doses confer optimal immunoresponses for all three antigens and the possible need for additional doses should be studied taking into account not only serological, but also epidemiological data, as there is no serological correlate of protection for mumps.

Clinical features and laboratory findings of human parvovirus B19 in human immunodeficiency virus-infected patients

Immunocompromised patients may develop severe chronic anaemia when infected by human parvovirus B19 (B19V). However, this is not the case in human immunodeficiency virus (HIV)-infected patients with good adherence to highly active antiretroviral treatment (HAART). In this study, we investigated the clinical evolution of five HIV-infected patients receiving HAART who had B19V infections confirmed by serum polymerase chain reaction. Four of the patients were infected with genotype 1a strains and the remaining patient was infected with a genotype 3b strain. Anaemia was detected in three of the patients, but all patients recovered without requiring immunoglobulin and/or blood transfusions. In all cases, the attending physicians did not suspect the B19V infections. There was no apparent relationship between the infecting genotype and the clinical course. In the HAART era, B19V infections in HIV-positive patients may be limited, subtle or unapparent.

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

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.