BackgroundrnSeveral studies were conducted in the past two decades in Ethiopia to understand the genotypicrncharacteristics of prevalent HIV subtypes in the country. However, the majority of the informationrngathered relied on sequencing of the envelope and a certain portion of the gag gene fragments of the HIVrngenome. Considering the facts that relying only on sequencing of the env and gag regions has inherentrninadequacy in characterizing HIV subtypes, that long time has elapsed since genomic characterization ofrnHIV isolates in Ethiopia, that non-C subtypes have expanded in the neighboring countries, and that a newrnselective pressure coming from the recently initiated ARV treatment has been introduce into current HIVrnisolates circulating in the country as a consequence of which newHIV subtypes might be currentlyrncirculating in the country, this PhD study was, therefore, undertaken to understand the genomicrncharacteristics of HIV isolates from ARV drug-naÃ¯ve and drug-experienced persons by sequencing thernprotease (PR) and reverse transcriptase (RT) genes using standard RT-PCR/PCR amplification andrngenome sequencing protocols. In addition, two test evaluation studies were carried out: one on use of Inhousernrnbrewed genotyping system, and the other on use of DBS as source of specimen for genotypic HIVrndrug resistance monitoring. rnMaterials and MethodsrnDifferent set of criteria were used to select eligible HIV-infected people to take part in three study groups:rnrecently infected drug-naÃ¯ve antenatal care (ANC) attendee pregnant women (recent drug-naÃ¯ve),rnchronically infected drug-naÃ¯ve but who were eligible to start ART (chronic drug-naÃ¯ve), and chronicallyrninfected heavily treated patients (chronic drug-experienced). For drug resistance assays, list of mutationsrnfrom three algorithms were utilized. For evaluations of the performance of In-house genotyping systemrnand DBS as source sample, the commercial genotyping system ViroSeqrnTMrn and plasma samples,rnrespectively, were used as standards. Mean nucleotide similarities of paired sequences generated from Inhouse/ViroSeqrnTM rngenotyping system and DBS/plasma were determined on pairwise alignment sequencesrnusing ClustalW multiple alignment program in BioEdit Version 7.0.9.0 software. For other purposes,rnFASTA-formatted nucleotide and amino acid sequences were aligned and analyzed using various on-linernand off-line software. Descriptive, Ï‡rn2rn test, and Student t test statistical data analyses were used asrnappropriate, with significant level of 0.05. rnResultsrnAmong chronically infected participant groups, 74% of drug-naÃ¯ve and 84% of drug-experiencedrnparticipants were in the advanced WHO clinical stages III and IV at baseline. Nearly 92% of chronic rndrug-naÃ¯ve patients had CD4+ count of