UK circulating strains of human parainfluenza 3: an amplicon based next generation sequencing method and phylogenetic analysis.

ABSTRACT: Background: Human parainfluenza viruses type 3 (HPIV3) are a prominent cause of respiratory infection with a significant impact in both pediatric and transplant patient cohorts.  Currently there is a paucity of whole genome sequence data that would allow for detailed epidemiological and phylogenetic analysis of circulating strains in the UK. Although it is known that HPIV3 peaks annually in the UK, to date there are no whole genome sequences of HPIV3 UK strains available.  Methods: Clinical strains were obtained from HPIV3 positive respiratory patient samples collected between 2011 and 2015.  These were then amplified using an amplicon based method, sequenced on the Illumina platform and assembled using a new robust bioinformatics pipeline. Phylogenetic analysis was carried o

SUBMITTER: Smielewska A 

PROVIDER: S-EPMC6281019 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature