Molecular diversity and biennial circulation of enterovirus D68: a systematic screening study in Lyon, France, 2010 to 2016

Abstract

BackgroundUnderstanding enterovirus D68 (EV-D68) circulation patterns as well as risk factors for severe respiratory and neurological illness is important for developing preventive strategies. Methods: Between 2010 and 2016, 11,132 respiratory specimens from hospitalised patients in Lyon, France, were screened for EV-D68 by PCR. Phylogenetic relationships of the viral-protein-1 sequences were reconstructed using maximum-likelihood and Bayesian-Markov-Chain-Monte-Carlo approaches. Results: Overall, 171 infections with a biennial pattern were detected, including seven, one, 55, none, 42, one and 65 cases annually during 2010-16. Children (< 16 years-old; n = 150) were mostly affected and 71% (n = 121) of the total patients were under 5 years-old. In 146 patients with medical reviews, 73% (n = 107) presented with acute respiratory distress. Among paediatric patients with medical reviews (n = 133), 55% (n=73) had an asthma/wheezing history, while among adults (n = 13), 11 had underlying diseases. In total, 45 patients had severe infections and 28 patients needed intensive care unit stays. No acute flaccid myelitis (AFM) was detected. We found genotypes A, B1, B2 B3 and D circulating, and no associations between these and clinical presentations. During the study, new genotypes continuously emerged, being replaced over time. We estimated that ancestors of currently circulating genotypes emerged in the late-1990s to 2010. Rises of the EV-D68 effective population size in Lyon coincided with infection upsurges. Phylogenetic analyses showed ongoing diversification of EV-D68 worldwide, coinciding with more infections in recent years and increases of reported AFM paediatric cases. Conclusions: Reinforcement of diagnostic capacities and clinical-based surveillance of EV-D68 infections is needed in Europe to assess the EV-D68 burden.

Keywords: EV-D68; clinic; enteroviruses; laboratory surveillance; respiratory infections; typing.

Figure 1

Screening for enterovirus-D68 (EV-D68)-positive samples in Lyon, and selection of subsets for clinical analyses, or for sequencing and phylogenetic analyses together with French or global EV-D68 sequence collections, 2010–2016

Figure 2

A. Distribution of enterovirus D68 (EV-D68) infections (n = 171) and B. Clinical presentation of a subset of infected patients (n = 146), Lyon, France, 2010–2016

Figure 3

A. Phylogenetic analyses and B. Date of emergence of enterovirus D68 clades based on a worldwide viral-protein-1 (VP1) gene sequence dataset, 2000–2016 (n = 1,212 sequences)

Figure 4

Time tree based on Bayesian Markov-Chain-Monte-Carlo analysis of the French viral-protein-1 gene sequence dataset of enterovirus D68, 2010–2016

Figure 5

Bayesian skyline plots showing the effective population size fluctuations of enterovirus D68 in the French and global viral-protein-1 (VP1) gene sequence datasets, 2010–2016