Gatherer, D. | bioRxiv Science

bioRxiv2018

Phylodynamic analysis of the historical spread of Toscana virus around the Mediterranean

All available sequences of the three genome segments of Toscana virus with date and location of sampling were analysed using Bayesian phylodynamic methods. We estimate that extant Toscana virus strains had a common ancestor in the late 16th to early 17th century AD, in territories controlled by the Ottoman Empire, giving rise to an ancestral genotype A/B in north Africa and to genotype C in the Balkans. Subsequent spread into western Europe may have occurred during the period of European colonization of north Africa in the 19th and early 20th centuries AD, establishing genotypes A and B in Italy and Spain respectively. Very little positive evolutionary selection pressure is detectable in Toscana virus, suggesting that the virus has become well adapted to its human hosts. There is also no convincing evidence of reassortment between genome segments, despite genotypes A and B now co-circulating in several countries.

microbiology↗

bioRxiv2016

Influenza C incidence and herd immunity in Lancaster, UK, in the winter of 2014-2015

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 estimated a 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 is 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. We calculate that this level of herd immunity would be sufficient to suppress epidemics of influenza C and restricts the virus to sporadic endemic spread.

microbiology↗