Evaluation of A Reverse Transcriptase (Rt) Loop Mediated Isothermal Amplification Assay for Detection of Hepatitis C Genotypes 1-4 Viruses Under Limited Logistical Conditions

Abstract

The loop-amplification mediated isothermal amplification (LAMP) presents characteristics that overcome the limitations associated with the Current limitations of nucleic acid based technologies (NATs) hinder their use in the low resource settings hence overreliance on serological assays which miss hepatitis C virus (HCV) during the long seroconversion period. The LAMP assay would be ideal for early detection of HCV in routine diagnostics and blood transfusion setups in such settings drastically reducing transmission related transfusion. This study validated and tested a reverse transcriptase-LAMP for HCV detection under limited logistical conditions in a low resource setting. Under stringent laboratory conditions, analytical sensitivity and reproducibility were performed using a panel of HCV positive plasma of genotypes 1a, 1b, mixed 1a/1b, 2b, 3a and 4. Cell culture supernatants of HIV-1 B and plasma samples for Hepatitis B virus were used for specificity testing. Upto 227 plasma including 70 (40 RNA positive and 30 negative) from German patients and 157 (43 RNA positive and 114 negative) from Kenyan patients were tested. Kenyan samples were obtained from 121 sero-positive plasma screened from 1121 participants of various cohorts in Kenya. Although LAMP detected upto 102 IU/mL for genotypes 1a, 1b and 2b, a lower detection threshold was established at 103 IU/mL. Overall sensitivity was 94% (PPV 98%) and specificity was 98% (NPV 96%) for RT-LAMP. Sub optimal detection was noted for genotypes 2b, 3a and 4. Sequence analysis revealed mismatches affecting stringency of primer binding at the F1, B1 and the LB primer targets. RT-LAMP shows potential for early HCV diagnosis and screening in low resource settings. Its robustness is however genotype dependent and can be enhanced by designing primers targeting circulating and suspected genotypes. More studies should be done on the possibility of designing multiplex RT-LAMP primers to capture a wide variety of genotypes. The assay remains simple, rapid, and cost effective for nucleic acid detection and is ideal for use in the limited resource settings.