Whole genome sequencing identifies influenza A H3N2 transmission and offers superior resolution to classical typing methods

Infection
Dominik M MeinelAndreas Sing

Abstract

Influenza with its annual epidemic waves is a major cause of morbidity and mortality worldwide. However, only little whole genome data are available regarding the molecular epidemiology promoting our understanding of viral spread in human populations. We implemented a RT-PCR strategy starting from patient material to generate influenza A whole genome sequences for molecular epidemiological surveillance. Samples were obtained within the Bavarian Influenza Sentinel. The complete influenza virus genome was amplified by a one-tube multiplex RT-PCR and sequenced on an Illumina MiSeq. We report whole genomic sequences for 50 influenza A H3N2 viruses, which was the predominating virus in the season 2014/15, directly from patient specimens. The dataset included random samples from Bavaria (Germany) throughout the influenza season and samples from three suspected transmission clusters. We identified the outbreak samples based on sequence identity. Whole genome sequencing (WGS) was superior in resolution compared to analysis of single segments or partial segment analysis. Additionally, we detected manifestation of substantial amounts of viral quasispecies in several patients, carrying mutations varying from the dominant virus in each pat...Continue Reading

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Citations

Feb 6, 2020·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Martina SansoneJohan Westin
Nov 2, 2019·Journal of Clinical Microbiology·Kuiama LewandowskiPhilippa C Matthews
Jun 7, 2018·The Journal of Infectious Diseases·Catherine F HoulihanEleni Nastouli
Nov 16, 2018·Frontiers in Microbiology·Cyril BarbezangeSylvie van der Werf

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