Barcoding analysis of HIV drug resistance mutations using Oxford Nanopore MinION (ONT) sequencing

Abstract Determination of HIV drug resistance (HIVDR) is becoming an integral baseline HIV evaluation for newly infected subjects, as the level of pre-treatment resistance is increasing worldwide. Moreover, surveys to assess levels of acquired drug resistance are giving insight to a better selection of the most efficient first line ARV drug schemes in specific population groups. Until now, the gold standard for monitoring ART mutations is the Sanger sequencing method, however, next-generation sequencing technologies (NGS) because high-throughput capability, are gaining attention as a method for detection of HIVDR. Nevertheless, the cost of both methodologies is interdictory for some economies. In the present work, we evaluated the use of the Oxford Nanopore Technologies (ONT) MinION as an alternative method for detection of drug resistance mutations in pre-treatment HIV positive subjects. A percentage of similarity greater than 95% was observed among the sequences when compared against the gold standard. These results encourage the evaluation of the ONT methodology with a wider number of samples to assess its suitability for HIVDR testing.