Phylogenetic characterisation of circulating, clinical influenza isolates from Bali, Indonesia: preliminary report from the BaliMEI project

BMC Infectious Diseases

Research Article

T. Gallo Cassarino¹  Z. Kozlakidis¹  G. J. D. Smith²  J. W. Rudge³  R. Coker³  W. Adisasmito⁴  D. N. Aisyah⁵  S. N. Budayanti⁶  S. J. Watson⁷ 

[1] Division of Infection and Immunity, University College London, 222 Euston Road, NW1 2DA, London, UK;Duke Global Health Institue, Duke University, Durham, NC, USA;London School of Hygiene and Tropical Medicine, London, UK;Universitas Indonesia, Depok, Indonesia;Universitas Indonesia, Depok, Indonesia;Farr Institute of Health Informatics Research, University College London, London, UK;Universitas Udayana, Denpasar, Indonesia;Wellcome Trust Sanger Institute, Hinxton, UK;

关键词: Next generation sequencing;    Influenza;    Bali;    Indonesia;    Phylogeny;   

DOI  :  10.1186/s12879-017-2684-2

 received in 2016-10-04, accepted in 2017-08-15,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundHuman influenza represents a major public health concern, especially in south-east Asia where the risk of emergence and spread of novel influenza viruses is particularly high. The BaliMEI study aims to conduct a five year active surveillance and characterisation of influenza viruses in Bali using an extensive network of participating healthcare facilities.MethodsSamples were collected during routine diagnostic treatment in healthcare facilities. In addition to standard clinical and molecular methods for influenza typing, next generation sequencing and subsequent de novo genome assembly were performed to investigate the phylogeny of the collected patient samples.ResultsThe samples collected are characteristic of the seasonally circulating influenza viruses with indications of phylogenetic links to other samples characterised in neighbouring countries during the same time period.ConclusionsThere were some strong phylogenetic links with sequences from samples collected in geographically proximal regions, with some of the samples from the same time-period resulting to small clusters at the tree-end points. However this work, which is the first of its kind completely performed within Indonesia, supports the view that the circulating seasonal influenza in Bali reflects the strains circulating in geographically neighbouring areas as would be expected to occur within a busy regional transit centre.

【 授权许可】

CC BY   
© The Author(s). 2017