Differentiation of influenza B lineages circulating in different regions of Brazil, 2014 – 2016, using molecular assay

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.

Importation and early local transmission of COVID-19 in Brazil, 2020

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.

Human bocavirus in hospitalized children under 5 years with acute respiratory infection, São Paulo, Brazil, 2010

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.

Molecular epidemiology of influenza A(H1N1)PDM09 hemagglutinin gene circulating in São Paulo State , Brazil: 2016 anticipated influenza season

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.

Molecular characterization of influenza B virus outbreak on a cruise ship in Brazil 2012

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.