Molecular Characterization of Hepatitis A Virus Isolates from Nigeria

Forbi, Joseph C.; Esona, Mathew D.; Agwale, Simon M

doi:10.1159/000341612

Cited by 7 publications

(7 citation statements)

References 25 publications

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“…Indeed, our results obtained from the stool sample extract demonstrated that all seven confirmed SNVs fell within the polyprotein coding region and with only one SNV (at position 2864 nt) located in the VP1-P2A junction region. These results are consistent with the previous finding that, besides the VP1-P2A junction, other regions across the genome also display nucleotide variability [ 19 ]. Interestingly, our results of the cultured F4-c1 samples indicated that SNVs are distributed along the whole genome, in both UTRs and coding regions.…”

Section: Discussionsupporting

confidence: 93%

“…Traditionally, a highly variable region of 168 nucleotides within the viral genome encoding the VP1/P2A junction has been used for identifying and discriminating between different HAV strains [ 18 ]. However, several alternative regions within the genome including those encoding for VP1, 2C, and 3D also display high nucleotide variability and have offered limited alternative regions for strain identification [ 19 ]. Thus, whether tracking HAV strain(s) as they circulate through a given population or region, or linking a contaminated food item to an outbreak of illness, it is necessary and critical to accurately identify HAV strains by as few as one nucleotide variation along the entire viral genome.…”

Section: Introductionmentioning

confidence: 99%

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

Yang

Mammel

Whitehouse

et al. 2018

Viruses

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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.

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Section: Discussionsupporting

confidence: 93%

Section: Introductionmentioning

confidence: 99%

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

Yang

Mammel

Whitehouse

et al. 2018

Viruses

View full text Add to dashboard Cite

show abstract

“…Indeed, our results obtained from the stool sample extract demonstrated that all seven confirmed SNVs fell within the polyprotein coding region and with only one SNV (at position 2864 nt) located in the VP1-P2A junction region. These results are consistent with the previous finding that, besides the VP1-P2A junction, other regions across the genome also display nucleotide variability [19]. Interestingly, our as well as RNA synthesis [44,45].…”

Section: Discussionsupporting

confidence: 92%

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

Yang¹,

Mammel²,

Whitehouse³

et al. 2018

Preprint

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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.

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“…The extracted RNA samples for NoV were facilitated thru the reagent exchange program as a partner institution with the USDA-NIFA Food Virology Collaborative (North Carolina State University, Raleigh, NC, USA) [ 56 ]. HAV RNA samples were extracted from clinical stool specimens, subjected to RT-PCR following established procedures [ 57 , 58 , 59 ], and were kindly provided by Dr. G. Vaughan with the Molecular Epidemiology & Bioinformatics Laboratory, Division of Viral Hepatitis, CDC. All clinical stool specimens were obtained from patients suffering typical gastrointestinal symptoms including nausea, vomiting, low-grade fever and non-bloody diarrhea [ 5 , 23 ].…”

Section: Methodsmentioning

confidence: 99%

“…The estimated median Ct values were 24 and 22 for the CaliciNet samples from symptomatic specimens containing NoV GI and GII genotypes, respectively [ 60 ]. Positive specimens were subjected to RT-PCR followed by DNA sequencing to determine the genotype [ 7 , 58 , 60 ]. All RNA samples were stored at −80 °C until further use.…”

Section: Methodsmentioning

confidence: 99%

Sensitive Genotyping of Foodborne-Associated Human Noroviruses and Hepatitis A Virus Using an Array-Based Platform

Quiñones

Lee

Martinsky³

et al. 2017

Sensors

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Human noroviruses (NoV) are the leading cause of human gastroenteritis in populations of all ages and are linked to most of the foodborne outbreaks worldwide. Hepatitis A virus (HAV) is another important foodborne enteric virus and is considered the most common agent causing acute liver disease worldwide. In the present study, a focused, low-density DNA microarray was developed and validated for the simultaneous identification of foodborne-associated genotypes of NoV and HAV. By employing a novel algorithm, capture probes were designed to target variable genomic regions commonly used for typing these foodborne viruses. Validation results showed that probe signals, specific for the tested NoV or HAV genotypes, were on average 200-times or 38-times higher than those detected for non-targeted genotypes, respectively. To improve the analytical sensitivity of this method, a 12-mer oligonucleotide spacer sequence was added to the capture probes and resulted in a detection threshold of less than 10 cRNA transcripts. These findings have indicated that this array-based typing sensor has the accuracy and sensitivity for identifying NoV and HAV genotypic profiles predominantly linked to food poisoning. The implementation of this typing sensor would thus provide highly relevant and valuable information for use in surveillance and outbreak attribution.

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Molecular Characterization of Hepatitis A Virus Isolates from Nigeria

Cited by 7 publications

References 25 publications

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

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

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

Sensitive Genotyping of Foodborne-Associated Human Noroviruses and Hepatitis A Virus Using an Array-Based Platform

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