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Characterization of influenza A(H1N1)pdm09 viruses isolated from Nepalese and Indian outbreak patients in early 2015.

ABSTRACT: We characterized influenza A(H1N1)pdm09 isolates from large-scale outbreaks that occurred in Nepal and India in early 2015. Although no specific viral features, which may have caused the outbreaks, were identified, an S84N substitution in hemagglutinin was frequently observed. Chronological phylogenetic analysis revealed that these Nepalese and Indian viruses possessing the S84N substitution constitute potential ancestors of the novel genetic subclade 6B.1 virus that spread globally in the following (2015/16) influenza season. Thus, active surveillance of circulating influenza viruses in the Southern Asia region, including Nepal and India, would be beneficial for detecting novel variant viruses prior to their worldwide spread.

SUBMITTER: Nakamura K

PROVIDER: S-EPMC5596518 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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Characterization of influenza A(H1N1)pdm09 viruses isolated from Nepalese and Indian outbreak patients in early 2015.

Nakamura Kazuya K Shirakura Masayuki M Fujisaki Seiichiro S Kishida Noriko N Burke David F DF Smith Derek J DJ Kuwahara Tomoko T Takashita Emi E Takayama Ikuyo I Nakauchi Mina M Chadha Mandeep M Potdar Varsha V Bhushan Arvind A Upadhyay Bishnu Prasad BP Shakya Geeta G Odagiri Takato T Kageyama Tsutomu T Watanabe Shinji S

Influenza and other respiratory viruses 20170809 5

We characterized influenza A(H1N1)pdm09 isolates from large-scale outbreaks that occurred in Nepal and India in early 2015. Although no specific viral features, which may have caused the outbreaks, were identified, an S84N substitution in hemagglutinin was frequently observed. Chronological phylogenetic analysis revealed that these Nepalese and Indian viruses possessing the S84N substitution constitute potential ancestors of the novel genetic subclade 6B.1 virus that spread globally in the follo ...[more]

PMID: 28792671

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Project description:BackgroundWhen an outbreak of a novel pathogen occurs, some of the most pressing questions from a public-health point of view relate to its transmissibility, and the probabilities of different clinical outcomes following infection, to allow an informed response. Estimates of these quantities are often based on household data due to the high potential for transmission in this setting, but typically a rich spectrum of individual-level outcomes (from uninfected to serious illness) are simplified to binary data (infected or not). We address the added benefit from retaining the heterogeneous outcome information in the case of the 2009-10 influenza pandemic, which posed particular problems for estimation of key epidemiological characteristics due to its relatively mild nature and hence low case ascertainment rates.MethodsWe use mathematical models of within-household transmission and case ascertainment, together with Bayesian statistics to estimate transmission probabilities stratified by household size, the variability of infectiousness of cases, and a set of probabilities describing case ascertainment. This novel approach was applied to data we collected from the early "containment phase" stage of the epidemic in Birmingham, England. We also conducted a comprehensive review of studies of household transmission of influenza A(H1N1)pdm09.ResultsWe find large variability in the published estimates of within-household transmissibility of influenza A(H1N1)pdm09 in both model-based studies and those reporting secondary attack rates, finding that these estimates are very sensitive to how an infected case is defined. In particular, we find that reliance on laboratory confirmation alone underestimates the true number of cases, while utilising the heterogeneous range of outcomes (based on case definitions) for household infections allows a far more comprehensive pattern of transmission to be elucidated.ConclusionsDifferences in household sizes and how cases are defined could account for an appreciable proportion of the reported variability of within-household transmissibility of influenza A(H1N1)pdm09. Retaining and statistically analysing the full spectrum of individual-level outcomes (based on case definitions) rather than taking a potentially arbitrary threshold for infection, provides much-needed additional information. In a future pandemic, our approach could be used as a real-time analysis tool to infer the true number of cases, within-household transmission rates and levels of case ascertainment.

Dataset Information

Characterization of influenza A(H1N1)pdm09 viruses isolated from Nepalese and Indian outbreak patients in early 2015.

Publications

Characterization of influenza A(H1N1)pdm09 viruses isolated from Nepalese and Indian outbreak patients in early 2015.

Similar Datasets

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