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Viruses 2018, 10(11), 619; https://doi.org/10.3390/v10110619

Inter- and Intra-Host Nucleotide Variations in Hepatitis A Virus in Culture and Clinical Samples Detected by Next-Generation Sequencing

1
Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
2
Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD 20708, USA
*
Author to whom correspondence should be addressed.
Received: 20 September 2018 / Revised: 23 October 2018 / Accepted: 5 November 2018 / Published: 9 November 2018
(This article belongs to the Section Animal Viruses)
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Abstract

The accurate virus detection, strain discrimination, and source attribution of contaminated food items remains a persistent challenge because of the high mutation rates anticipated to occur in foodborne RNA viruses, such as hepatitis A virus (HAV). This has led to predictions of the existence of more than one sequence variant between the hosts (inter-host) or within an individual host (intra-host). However, there have been no reports of intra-host variants from an infected single individual, and little is known about the accuracy of the single nucleotide variations (SNVs) calling with various methods. In this study, the presence and identity of viral SNVs, either between HAV clinical specimens or among a series of samples derived from HAV clone1-infected FRhK4 cells, were determined following analyses of nucleotide sequences generated using next-generation sequencing (NGS) and pyrosequencing methods. The results demonstrate the co-existence of inter- and intra-host variants both in the clinical specimens and the cultured samples. The discovery and confirmation of multi-viral RNAs in an infected individual is dependent on the strain discrimination at the SNV level, and critical for successful outbreak traceback and source attribution investigations. The detection of SNVs in a time series of HAV infected FRhK4 cells improved our understanding on the mutation dynamics determined probably by different selective pressures. Additionally, it demonstrated that NGS could potentially provide a valuable investigative approach toward SNV detection and identification for other RNA viruses. View Full-Text
Keywords: inter- and intra-host nucleotide variations; Hepatitis A virus; next-generation sequencing; pyrosequencing inter- and intra-host nucleotide variations; Hepatitis A virus; next-generation sequencing; pyrosequencing
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Yang, Z.; Mammel, M.; Whitehouse, C.A.; Ngo, D.; Kulka, M. Inter- and Intra-Host Nucleotide Variations in Hepatitis A Virus in Culture and Clinical Samples Detected by Next-Generation Sequencing. Viruses 2018, 10, 619.

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