Detection and Typing of Human Enteroviruses from Clinical Samples by Entire-Capsid Next Generation Sequencing.

Manasi Majumdar,Cristina Celma,Jake Dunning,Elaine Pegg,Krunal Polra,Javier Martin

doi:10.3390/v13040641

Manasi Majumdar, Cristina Celma + Show 4 more

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https://doi.org/10.3390/v13040641

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Abstract

There are increasing concerns of infections by enteroviruses (EVs) causing severe disease in humans. EV diagnostic laboratory methods show differences in sensitivity and specificity as well as the level of genetic information provided. We examined a detection method for EVs based on next generation sequencing (NGS) analysis of amplicons covering the entire capsid coding region directly synthesized from clinical samples. One hundred and twelve clinical samples from England; previously shown to be positive for EVs, were analyzed. There was high concordance between the results obtained by the new NGS approach and those from the conventional Sanger method used originally with agreement in the serotypes identified in the 83 samples that were typed by both methods. The sensitivity and specificity of the NGS method compared to those of the conventional Sanger sequencing typing assay were 94.74% (95% confidence interval, 73.97% to 99.87%) and 97.85% (92.45% to 99.74%) for Enterovirus A, 93.75% (82.80% to 98.69%) and 89.06% (78.75% to 95.49%) for Enterovirus B, 100% (59.04% to 100%) and 98.10% (93.29% to 99.77%) for Enterovirus C, and 100% (75.29% to 100%) and 100% (96.34% to 100%) for Enterovirus D. The NGS method identified five EVs in previously untyped samples as well as additional viruses in some samples, indicating co-infection. This method can be easily expanded to generate whole-genome EV sequences as we show here for EV-D68. Information from capsid and whole-genome sequences is critical to help identifying the genetic basis for changes in viral properties and establishing accurate spatial-temporal associations between EV strains of public health relevance.

Highlights

Virus outbreaks are a constant threat to our health systems and monitoring circulating strains is extremely relevant for contingency planning, outbreak management, and containment response
The recent evidence of increased detection of enterovirus D68 (EV-D68) in respiratory samples and the temporal and geographical association of these outbreaks with an increase in acute flaccid myelitis (AFM) cases observed in the United States and Europe [4,5], as well as periodic outbreaks of EV71 in Asia, demonstrates the significant morbidity and mortality that can be caused by EVs [6]
2 EV-A, 7 EV-B, and 2 EV-C strains were identified by the next generation sequencing (NGS) method in samples that were not positive for these viruses by Sanger sequencing

Summary

Introduction

Virus outbreaks are a constant threat to our health systems and monitoring circulating strains is extremely relevant for contingency planning, outbreak management, and containment response. Conventional Sanger sequencing of part of the gene encoding VP1 capsid protein has been the gold standard for genomic analysis and genotyping of EVs in public health laboratories for decades [8,9]. This methodology has been shown to be far more sensitive than traditional virus isolation using cell cultures. These new NGS approaches have improved molecular epidemiology resolution, primer designing, studying genomic recombination events, pathogens identification and association with syndromes where etiologies often remain unknown like encephalitis, fulminant hepatitis, sepsis, etc., [10,11,12,13,14,15,16,17,18,19]

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