Abstract
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.
Highlights
Human influenza represents a major public health concern, especially in south-east Asia where the risk of emergence and spread of novel influenza viruses is high
Within Indonesia, the island province of Bali might be a particular hotspot for the mixing of influenza viruses from different geographic regions and host species and potential genomic reassortment thereof, due to high densities and close proximity of humans, poultry and pigs, along with its status as a popular tourist destination with continuous, high numbers of a transient population. [13, 14] Importantly the preliminary results from the Molecular Epidemiology of Influenza in Bali (BaliMEI) study allow us to assess the degree of agreement between epidemiologically and genetically inferred information, understand the extent of mutation observed between genetically clustered cases and to improve estimates of the extent of diversity within the circulating, clinically presented influenza
Sequence de novo assembly Genome assembly and construction of consensus sequences was performed at Indonesia using the Infection response through virus genomics (ICONIC) bioinformatics pipeline for de novo viral sequence assembly [16] developed at University College London (UCL) with phylogenetic analyses to infer transmission performed at the Farr institute of Health Informatics Research
Summary
Human influenza represents a major public health concern, especially in south-east Asia where the risk of emergence and spread of novel influenza viruses is high. NGS data were subjected to quality control using Trimmomatic 0.33 to remove any primer sequences and trim reads, reads mapped with SMALT version 0.7.6 (http://www.sanger.ac.uk/science/tools/smalt-0) to the human genome were removed. Quality controlled and filtered read sets were de novo assembled using IVA version 1.0.0 [17]; SAMtools 1.2 [18] and custom scripts were used to create a consensus genome from the assembled fragments (“contigs”).
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