Integrating patient and whole genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) viruses
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PROVIDER: PRJEB23363 | ENA |
REPOSITORIES: ENA
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Project description:Integrating patient and whole genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) viruses
| PRJEB23104 | ENA
Project description:Genetic surveillance of seasonal influenza is largely focused on sequencing of the haemagglutinin gene. Consequently, our understanding of the contribution of the remaining seven gene segments to the evolution and epidemiological dynamics of seasonal influenza is relatively limited. The increased availability of next-generation sequencing technologies allows rapid and economic whole-genome sequencing (WGS) of influenza virus. Here, 150 influenza A(H3N2) positive clinical specimens with linked epidemiological data, from the 2014/15 season in Scotland, were sequenced directly using both Sanger sequencing of the HA1 region and WGS using the Illumina MiSeq platform. Sequences generated by the two methods were highly correlated, and WGS provided on average >90?%?whole genome coverage. As reported in other European countries during 2014/15, all strains belonged to genetic group 3C, with subgroup 3C.2a predominating. Multiple inter-subgroup reassortants were identified, including three 3C.3 viruses descended from a single reassortment event, which had persisted in the population. Cases of severe acute respiratory illness were significantly clustered on phylogenies of multiple gene segments indicating potential genetic factors warranting further investigation. Severe cases were also more likely to be associated with reassortant viruses and to occur later in the season. These results suggest that WGS provides an opportunity to develop our understanding of the relationship between the influenza genome and disease severity and the epidemiological consequences of within-subtype reassortment. Therefore, increased levels of WGS, linked to clinical and epidemiological data, could improve influenza surveillance.
| S-EPMC5857367 | biostudies-literature
Project description:In this study, we performed a miRNA global profiling in human lung epithelial cells (A549) infected by two different subtypes of human influenza A viruses (H1N1 and H3N2).
2013-04-03 | GSE42003 | GEO
Project description:In this study, we performed a miRNA global profiling in human lung epithelial cells (A549) infected by two different subtypes of human influenza A viruses (H1N1 and H3N2). A549 cells were either mock-infected or infected at a multiplicity of infection (MOI) of 1 with H1N1 or H3N2 viruses, and total RNAs were isolated at 24 hours post-infection (hpi). An MOI of 1 was performed to ensure that 100% of the cells were infected at 24 hpi, a strategy that we have previously validated and used for a transcriptional profiling study of infected cells (Josset et al. , 2010). The purified RNAs were subjected to reverse transcription using a pool of miRNA RT primers (Human pool A v2.1, Applied Biosystems) and subsequently amplified and quantified by RT-qPCR in a TaqMan array MicroRNA card (Applied biosystems).
2013-04-03 | E-GEOD-42003 | biostudies-arrayexpress
Project description:Binding profile of H3N2 hemagglutinin (HA) reactive antibodies for various H3N2 and H7 HA proteins
2014-11-14 | GSE63249 | GEO
Project description:The increasing availability of complete influenza virus genomes is deepening our understanding of influenza evolutionary dynamics and facilitating the selection of vaccine strains. However, only one complete African influenza virus sequence is available in the public domain. Here we present a complete genome analysis of 59 influenza A/H3N2 viruses isolated from humans in Uganda during the 2008 and 2009 season. Isolates were recovered from hospital-based sentinel surveillance for influenza-like illnesses and their whole genome sequenced. The viruses circulating during these two seasons clearly differed from each other phylogenetically. They showed a slow evolution away from the 2009/10 recommended vaccine strain (A/Brisbane/10/07), instead clustering with the 2010/11 recommended vaccine strain (A/Perth/16/09) in the A/Victoria/208/09 clade, as observed in other global regions. All of the isolates carried the adamantane resistance marker S31N in the M2 gene and carried several markers of enhanced transmission; as expected, none carried any marker of neuraminidase inhibitor resistance. The hemagglutinin gene of the 2009 isolates differed from that of the 2008 isolates in antigenic sites A, B, D, and to a lesser extent, C and E indicating evidence of an early phylogenetic shift from the 2008 to 2009 viruses. The internal genes of the 2009 isolates were similar to those of one 2008 isolate, A/Uganda/MUWRP-050/2008. Another 2008 isolate had a truncated PB1-F2 protein. Whole genome sequencing can enhance surveillance of future seasonal changes in the viral genome which is crucial to ensure that selected vaccine strains are protective against the strains circulating in Eastern Africa. This data provides an important baseline for this surveillance. Overall the influenza virus activity in Uganda appears to mirror that observed in other regions of the southern hemisphere.
| S-EPMC3221667 | biostudies-literature
Project description:The close contact between cats and humans poses a threat to public health because of the potential zoonotic transmission of influenza viruses to humans. Therefore, we examined the seroprevalence of pandemic H1N1/09, canine H3N2, and human H3N2 viruses in pet cats in northern China from 2010 to 2014.Of 1794 serum samples, the seropositivity rates for H1N1/09, canine H3N2, and human H3N2 were 5.7%, 0.7%, and 0.4%, respectively. The seropositivity rate for H1N1/09 in cats was highest in 2010 (8.3%), and then declined continuously thereafter. Cats older than 10 years were most commonly seropositive for the H1N1/09 virus.Our findings emphasize the need for continuous surveillance of influenza viruses in cats in China.
| S-EPMC4391672 | biostudies-other
Project description:Determining the role of interferons in the host defence against influenza A virus Methods: Tumor-free human lung explants were obtained from patients undergoing lung surgery at the University Hospital Muenster on the day of surgery. Tissue blocks were individually placed in a 12-well plate in RPMI medium. Virus infection of human lung tissue was performed with seasonal IV H3N2 strain A/Panama/2007/1999. RNA was prepared from tissue homogenates. Results: RNA sequencing revealed significant transcriptional upregulation of genes encoding IFN-α subtypes α1, α2, α8, α14 and α17, which we identified to possess only low to intermediate antiviral activity. In contrast, our experiments provide evidence that subtypes α16, α5 and α4 suppress H3N2 replication 40 – 231 fold more efficiently compared to clinically approved IFN-α2. We detected significantly higher induction of IV restriction factors MxA, RIG-I, OAS1 and PKR by these subtypes compared to the non-active IFN-α1 but correlation of antiviral activity with the expression levels of these restriction factors was not observed. Conclusions: Our results show that IFN-α subtypes differ in their ability to repress H3N2 replication in human lung tissue and emphasize that IFN-α subtypes α16, α5 and α4 have high therapeutic potential and should be further investigated for the prevention and treatment of severe infections with seasonal H3N2.
2019-12-31 | GSE135069 | GEO
Project description:Seasonal influenza virus A/H3N2 is a major cause of death globally. Vaccination remains the most effective preventative. Rapid mutation of hemagglutinin allows viruses to escape adaptive immunity. This antigenic drift necessitates regular vaccine updates. Effective vaccine strains need to represent H3N2 populations circulating one year after strain selection. Experts select strains based on experimental measurements of antigenic drift and predictions made by models from hemagglutinin sequences. We developed a novel influenza forecasting framework that integrates phenotypic measures of antigenic drift and functional constraint with previously published sequence-only fitness estimates. Forecasts informed by phenotypic measures of antigenic drift consistently outperformed previous sequence-only estimates, while sequence-only estimates of functional constraint surpassed more comprehensive experimentally-informed estimates. Importantly, the best models integrated estimates of both functional constraint and either antigenic drift phenotypes or recent population growth.
| S-EPMC7553778 | biostudies-literature
Project description:Under selective pressure from the host immune system, antigenic epitopes of influenza virus hemagglutinin (HA) have continually evolved to escape antibody recognition, termed antigenic drift. We analyzed the genomes of influenza A(H3N2) and A(H1N1)pdm09 virus strains circulating in Thailand between 2010 and 2014 and assessed how well the yearly vaccine strains recommended for the southern hemisphere matched them. We amplified and sequenced the HA gene of 120 A(H3N2) and 81 A(H1N1)pdm09 influenza virus samples obtained from respiratory specimens and calculated the perfect-match vaccine efficacy using the pepitope model, which quantitated the antigenic drift in the dominant epitope of HA. Phylogenetic analysis of the A(H3N2) HA1 genes classified most strains into genetic clades 1, 3A, 3B, and 3C. The A(H3N2) strains from the 2013 and 2014 seasons showed very low to moderate vaccine efficacy and demonstrated antigenic drift from epitopes C and A to epitope B. Meanwhile, most A(H1N1)pdm09 strains from the 2012-2014 seasons belonged to genetic clades 6A, 6B, and 6C and displayed the dominant epitope mutations at epitopes B and E. Finally, the vaccine efficacy for A(H1N1)pdm09 (79.6-93.4%) was generally higher than that of A(H3N2). These findings further confirmed the accelerating antigenic drift of the circulating influenza A(H3N2) in recent years.
| S-EPMC4594909 | biostudies-literature