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.
| Original language | English |
|---|---|
| Article number | 641 |
| Number of pages | 11 |
| Journal | Viruses |
| Volume | 13 |
| Issue number | 4 |
| DOIs | |
| Publication status | Published - Apr 2021 |
Bibliographical note
Funding Information:Funding: This paper is based on independent research commissioned and funded by the National Institute for Health Research (NIHR) Policy Research Programme (NIBSC Regulatory Science Research Unit). The views expressed in the publication are those of the author(s) and not necessarily those of the NHS, the NIHR, the Department of Health, arm’s length bodies, or other government departments.
Funding Information:
This paper is based on independent research commissioned and funded by the National Institute for Health Research (NIHR) Policy Research Programme (NIBSC Regulatory Science Research Unit). The views expressed in the publication are those of the author(s) and not necessarily those of the NHS, the NIHR, the Department of Health, arm?s length bodies, or other government departments.
Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.
Keywords
- Clinical diagnosis
- Direct detection
- Enterovirus surveillance
- Human enterovirus
- Next generation sequencing (NGS)
- Whole-genome sequencing
- clinical diagnosis
- human enterovirus
- direct detection
- whole-genome sequencing
- next generation sequencing (NGS)
- enterovirus surveillance
