Influenza C in Lancaster, UK, in the winter of 2014–2015

Abstract

Influenza C is not included in the annual seasonal influenza vaccine, and has historically been regarded as a minor respiratory pathogen. However, recent work has highlighted its potential role as a cause of pneumonia in infants. We performed nasopharyngeal or nasal swabbing and/or serum sampling (n = 148) in Lancaster, UK, over the winter of 2014–2015. Using enzyme-linked immunosorbent assay (ELISA), we obtain seropositivity of 77%. By contrast, only 2 individuals, both asymptomatic adults, were influenza C-positive by polymerase chain reaction (PCR). Deep sequencing of nasopharyngeal samples produced partial sequences for 4 genome segments in one of these patients. Bayesian phylogenetic analysis demonstrated that the influenza C genome from this individual is evolutionarily distant to those sampled in recent years and represents a novel genome constellation, indicating that it may be a product of a decades-old reassortment event. Although we find no evidence that influenza C was a significant respiratory pathogen during the winter of 2014–2015 in Lancaster, we confirm previous observations of seropositivity in the majority of the population. (170 words).

Molecular Characterization of Influenza C Viruses from Outbreaks in Hong Kong SAR, China

“…Seroprevalence studies for ICV have shown high rates, with the virus being distributed worldwide in the human population and initial exposure (infection) occurring during childhood ( 2 – 8 ), while recurrent infection with this virus occurs in both children and adults ( 9 ). Overall, as summarized in Atkinson et al ( 10 ), seropositivity has been reported to be between 57 and 100%, being lower in children and rising in adulthood. ICV has been considered a pathogen of low significance, as it generally causes mild disease or clinically inapparent infection ( 9 , 11 , 12 ), but in recent years it has become increasingly apparent that the virus can be associated with severe disease, notably in children with lower respiratory tract infections ( 12 – 18 ).…”

Sequence Variation in Multidrug-Resistant Plasmid pLUH01, Isolated from Human Nasopharyngeal Swabs

“…Deep sequencing was performed using an Illumina Nextera XT library and HiSeq 2500 system (SRA accession number SRP092324 ) ( 4 , 5 ). The variant sequences were assembled from the following sequence pools: pLUH01/Lancaster/2015/1 from 2 pediatric patients with respiratory symptoms (BioSample accession number SAMN05954284 ) and from 10 asymptomatic adults ( SAMN05954287 ); pLUH01/Lancaster/2015/2 from 6 chronic obstructive pulmonary disease (COPD) patients ( SAMN05954289 ); and pLUH01/Lancaster/2015/3 from a single asymptomatic adult ( SAMN05954290 ).…”

Nasopharyngeal metagenomic deep sequencing data, Lancaster, UK, 2014–2015

“…Our project (ref. 7 ) initially focussed on the prevalence and severity of influenza C infection in Lancaster, UK, during the winter of 2014–2015. We performed Ilumina deep sequencing on 9 patient pools (Data Citations 1–9), as detailed in Table 1 .…”

“…Two of our 9 sequencing pools (Data Citations 8, 9) were from individuals diagnosed with influenza C infection via quantitative RT-PCR, from one of which we could partially assemble (ref. 7 ) the genome of a novel strain of influenza C, designated C/Lancaster/1/2015 (Data Citations 10–12). Within other sequencing pools we also detected the complete genomes of novel strains of human rhinovirus A22 (ref.…”