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Missing the Match Might Not Cost You the Game: Primer-Template Mismatches Studied in Different Hepatitis A Virus Variants
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infection medicine. Natl Food Agcy, European Union Reference Lab EURL Foodborne Viru, Hamnesplanaden 5, S-45323 Uppsala, Sweden.ORCID iD: 0000-0003-2611-3030
Stockholm Univ, Dept Math, Stockholm, Sweden.ORCID iD: 0000-0001-9662-507X
Southern Roslagen Environm & Hlth Author, Taby, Sweden.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infection medicine.ORCID iD: 0000-0001-8920-6061
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2019 (English)In: Food and Environmnetal Virology, ISSN 1867-0334, E-ISSN 1867-0342, Vol. 11, no 3, p. 297-308Article in journal (Refereed) Published
Abstract [en]

Mismatches between template sequences and reverse transcription (RT) or polymerase chain reaction (PCR) primers can lead to underestimation or false negative results during detection and quantification of sequence-diverse viruses. We performed an in silico inclusivity analysis of a widely used RT-PCR assay for detection of hepatitis A virus (HAV) in food, described in ISO 15216-1. One of the most common mismatches found was a single G (primer) to U (template) mismatch located at the terminal 3 '-end of the reverse primer region. This mismatch was present in all genotype III sequences available in GenBank. Partial HAV genomes with common or potentially severe mismatches were produced by in vitro transcription and analysed using RT-ddPCR and RT-qPCR. When using standard conditions for RT-qPCR, the mismatch identified resulted in underestimation of the template concentration by a factor of 1.7-1.8 and an increase in 95% limit of detection from 8.6 to 19 copies/reaction. The effect of this mismatch was verified using full-length viral genomes. Here, the same mismatch resulted in underestimation of the template concentration by a factor of 2.8. For the partial genomes, the presence of additional mismatches resulted in underestimation of the template concentration by up to a factor of 232. Quantification by RT-ddPCR and RT-qPCR was equally affected during analysis of RNA templates with mismatches within the reverse primer region. However, on analysing DNA templates with the same mismatches, we found that ddPCR quantification was less affected by mismatches than qPCR due to the end-point detection technique.

Place, publisher, year, edition, pages
SPRINGER , 2019. Vol. 11, no 3, p. 297-308
Keywords [en]
Digital PCR, Real-time PCR, Reverse transcription, Primer, Mismatch, Hepatitis A virus
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-393645DOI: 10.1007/s12560-019-09387-zISI: 000480501400011PubMedID: 31004336OAI: oai:DiVA.org:uu-393645DiVA, id: diva2:1354777
Available from: 2019-09-26 Created: 2019-09-26 Last updated: 2019-09-26Bibliographically approved

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