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Analysis of hepatit...
Analysis of hepatitis C NS5A resistance associated polymorphisms using ultra deep single molecule real time (SMRT) sequencing
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- Bergfors, Assar (author)
- Uppsala universitet,Klinisk mikrobiologi och infektionsmedicin
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- Leenheer, Daniel (author)
- Uppsala universitet,Klinisk virologi,Univ Tsukuba, PhD Program Human Biol, Sch Integrat & Global Majors, Tsukuba, Ibaraki 3058577, Japan.
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- Bergqvist, Anders (author)
- Uppsala universitet,Klinisk mikrobiologi och infektionsmedicin
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- Ameur, Adam (author)
- Uppsala universitet,Institutionen för immunologi, genetik och patologi
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- Lennerstrand, Johan (author)
- Uppsala universitet,Klinisk virologi
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(creator_code:org_t)
- Elsevier BV, 2016
- 2016
- English.
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In: Antiviral Research. - : Elsevier BV. - 0166-3542 .- 1872-9096. ; 126, s. 81-89
- Related links:
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Subject headings
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- Development of Hepatitis C virus (HCV) resistance against direct-acting antivirals (DAAs), including NS5A inhibitors, is an obstacle to successful treatment of HCV when DAAs are used in sub-optimal combinations. Furthermore, it has been shown that baseline (pre-existing) resistance against DAAs is present in treatment naive-patients and this will potentially complicate future treatment strategies in different HCV genotypes (GTs). Thus the aim was to detect low levels of NS5A resistant associated variants (RAVs) in a limited sample set of treatment-naive patients of HCV GT1a and 3a, since such polymorphisms can display in vitro resistance as high as 60000 fold. Ultra-deep single molecule real time (SMRT) sequencing with the Pacific Biosciences (PacBio) RSII instrument was used to detect these RAVs. The SMRT sequencing was conducted on ten samples; three of them positive with Sanger sequencing (GT1a Q30H and Y93N, and GT3a Y93H), five GT1a samples, and two GT3a non-positive samples. The same methods were applied to the HCV GT1a H77-plasmid in a dilution series, in order to determine the error rates of replication, which in turn was used to determine the limit of detection (LOD), as defined by mean + 3SD, of minority variants down to 0.24%. We found important baseline NS5A RAVs at levels between 0.24 and 0.5%, which could potentially have clinical relevance. This new method with low level detection of baseline RAVs could be useful in predicting the most cost-efficient combination of DAA treatment, and reduce the treatment duration for an HCV infected individual.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Infektionsmedicin (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Infectious Medicine (hsv//eng)
Keyword
- Hepatitis C virus
- NS5A
- Resistance
- RAV
- Deep sequencing
- Pacific biosciences
Publication and Content Type
- ref (subject category)
- art (subject category)
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