GeneXpert^® (Cepheid) is the only WHO prequalified platform for hepatitis C virus (HCV) nucleic acid amplification testing that is suitable for point-of-care use in resource-limited contexts. However, its application is constrained by the lack of evidence on genotype 6 (GT6) HCV. We evaluated its field performance among a patient population in Cambodia predominantly infected with GT6. Between August and September 2017, we tested plasma samples obtained from consenting patients at Médecins Sans Frontières' HCV clinic at Preah Kossamak Hospital for HCV viral load (VL) using GeneXpert^® and compared its results to those obtained using COBAS^® AmpliPrep/Cobas^® TaqMan^® HCV Quantitative Test, v2.0 (Roche) at the Institut Pasteur du Cambodge. Among 769 patients, 77% of the seropositive patients (n = 454/590) had detectable and quantifiable VL using Roche and 43% (n = 195/454) were GT6. The sensitivity and specificity of GeneXpert^® against Roche were 100% (95% CI 99.2, 100.0) and 98.5% (95% CI 94.8, 99.8). The mean VL difference was -0.01 (95% CI -0.05, 0.02) log₁₀ IU/mL for 454 samples quantifiable on Roche and -0.07 (95% CI -0.12, -0.02) log₁₀ IU/mL for GT6 (n = 195). The limit of agreement (LOA) was -0.76 to 0.73 log₁₀ IU/mL for all GTs and -0.76 to 0.62 log₁₀ IU/mL for GT6. Twenty-nine GeneXpert^® results were outside the LOA. Frequency of error and the median turnaround time (TAT) for GeneXpert^® were 1% and 0 days (4 days using Roche). We demonstrated that the GeneXpert^® HCV assay has good sensitivity, specificity, quantitative agreement, and TAT in a real-world, resource-limited clinical setting among GT6 HCV patients.

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