Reliable resolution of ambiguous hepatitis C virus genotype 1 results with the Abbott HCV Genotype Plus RUO assay

Abstract

Accurate subtyping of hepatitis C virus genotype 1 (HCV-1) remains clinically and epidemiologically relevant. The Abbott HCV Genotype Plus RUO (GT Plus ) assay, targeting the core region, was evaluated as a reflex test to resolve ambiguous HCV-1 results in a challenging sample collection. 198 HCV-1 specimens were analysed with GT Plus (38 specimens with and 160 without subtype assigned by the Abbott RealTi me Genotype II (GT II) assay targeting the 5’NC and NS5B regions). Sanger sequencing of the core and/or NS5B regions were performed in 127 specimens without subtype assignment by GT II, with “not detected” results by GT Plus , or with mixed genotypes/subtypes. The remaining GT Plus results were compared to LiPA 2.0 ( n = 45) or just to GT II results if concordant ( n = 26). GT Plus successfully assigned the subtype in 142/160 (88.8%) samples. “Not detected” results indicated other HCV-1 subtypes/genotypes or mismatches in the core region in subtype 1b. The subtyping concordance between GT Plus and either sequencing or LiPA was 98.6% (140/142). Therefore, combined use of GT II and GT Plus assays represents a reliable and simple approach which considerably reduced the number of ambiguous HCV-1 results and enabled a successful subtyping of 98.9% of all HCV-1 samples.

HCV microelimination in harm reduction centres has benefits beyond HCV cure but is hampered by high reinfection rates

“…NS5B amplification was performed by heminested-PCR, followed by Sanger sequencing and phylogenetic analysis along with reference sequences were performed as previously described. 15 When this methodology failed to provide a valid sequence as a result of low viral loads, the Abbott HCV Genotype II assay Abbott Laboratories (Abbott Park, IL, USA) was used from the RNA previously extracted from DBS samples.…”

“…For HCV genotyping, RNA previously extracted from DBS samples was subjected to reverse-transcription. NS5B amplification was performed by heminested-PCR, followed by Sanger sequencing and phylogenetic analysis along with reference sequences was performed as previously described [15]. When this methodology J o u r n a l P r e -p r o o f failed to provide a valid sequence due to low viral loads, the Abbott HCV Genotype II assay (Abbott Molecular Inc.) was used from the RNA previously extracted from DBS samples.…”

Pilot hepatitis C micro‐elimination strategy in Pakistani migrants in Catalonia through a community intervention

“…For this purpose, all Ab‐positive participants were contacted for a medical appointment at the IHU, located in a predominantly migrant neighbourhood. Additionally, HCV genotyping was performed from DBS samples by amplification, Sanger sequencing and phylogenetic analysis of a fragment of the NS5B region, as previously described 24 …”

“…Additionally, HCV genotyping was performed from DBS samples by amplification, Sanger sequencing and phylogenetic analysis of a fragment of the NS5B region, as previously described. 24…”

Characterization of Acute HCV Infection and Transmission Networks in People Who Currently Inject Drugs in Catalonia: Usefulness of Dried Blood Spots

“…A 1,534‐bp fragment covering the core, the E1, and the beginning of the E2 regions (nucleotide positions 278‐1811 of the HCV H77 reference genome) was amplified and sequenced as described, ( 28 ) with slight modifications (Supporting Text ). Maximum likelihood phylogenetic analysis was then performed as described, ( 23 ) including reference sequences obtained from the International Committee on Taxonomy of Viruses database (version 1.6.17; https://talk.ictvonline.org). Genetic pairs/clusters were identified using a bootstrap threshold of 90% and a genetic distance threshold of 0.05, ( 20 ) and identified clusters were individually assessed.…”