(P31) High throughput sequencing for in depth analysis of pre-treatment HIV-1 drug resistance in Sweden


Emmi Andersson [1,2], Anoop Ambikan [1], Johanna Brännström [3,4], Shambhu Aralaguppe [1], Aylin Yilmaz [5], Jan Albert [2,6], Ujjwal Neogi [1], Anders Sönnerborg [1,2,3,7]


1. Division of Clinical Microbiology, Department of Laboratory Medicine, ANA Futura Laboratory, Karolinska Institute, Stockholm, Sweden 2. Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden 3. Division of Infection and Dermatology, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden 4. Department of Infectious Diseases/Venhälsan, South Hospital, Stockholm, Sweden 5. Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden 6. Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden 7. Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden


The success of antiretroviral treatment (ART) to treat and prevent new infections with HIV-1 is challenged by the emergence of drug resistance (HIVDR). Introduction of cost-effective and sensitive high-throughput sequencing assays (HTS) for genotypic resistance testing has the potential to improve diagnostics and surveillance of HIVDR also including resistance to integrase strand transfer inhibitors (INSTI). However, assays need to be properly validated, especially in countries like Sweden, where many subtypes and variants of HIV-1 coexist. Additionally, interpretation of minor viral variants remains a challenge in HTS-based resistance testing.
To investigate pre-treatment resistance (PDR) in a representative cohort of individuals presenting for HIV-1 care in Sweden with an in house HTS assay.
Individuals newly diagnosed with HIV-1 (n= 158) in Sweden who entered HIV care in Stockholm and Gothenburg from November 1st 2017 until March 7th, 2019 were recruited prospectively. Also, a retrospective cohort (n= 66) of individuals presenting for HIV-1 care in Stockholm in Stockholm January 1st 2017 until October 31st 2017 were included.
HTS of the HIV-1 pol gene (cut off 1% for intra-patient polymorphisms) was performed and drug resistance mutations (DRM) were identified according to a modified Stanford HIVdb list. Relationships between DRM and epidemiological and clinical data were investigated.

Of 224 samples from 224 unique individuals, HTS resulted in interpretable genotypes in 195 samples (87%) and subtype was determined in 188 (84%). Sequencing failures were explained by low virus levels (viral load <3000 copies/ml) in 16/29 (55%) of cases. A majority, 139 of the 224 (62%) patients were born abroad and previous ART exposure was self-reported in 24 individuals (11% of the total cohort). As expected, the subtype distribution was wide and in addition 32 cases (14%) unique recombinant forms (URF) were identified. The commonest subtypes were B (n=41; 18%) and CRF01_AE (n=35; 16%). In 96 individuals (49%) pre-treatment DRM at levels ≥1% were detected in protease or reverse transcriptase (PR/RT). In 36 individuals (18%) PR/RT DRM ≥20% were detected and this finding was strongly associated to previous ART exposure (p50%) was found in the virus populations of 37 individuals (19%).
Our HTS approach and bioinformatics pipeline allows detection of PDR in newly diagnosed individuals in Sweden with diverse HIV-1 subtypes, but has reduced success for low viral loads. The prevalence of DRM polymorphisms ≥20% in PR/RT was 18% and low level DRM polymorphisms (1-19%) were found in 38% of remaining individuals. Detection of PR/RT DRM at ≥20% but not at lower levels was associated to reported ART exposure prior to first presentation for care in Sweden. No INSTI DRMs ≥20% were detected, but the finding of major INSTI DRM in minor viral populations in some patients and the high presence of L74M/I, especially in combination with low frequency major INSTI mutations, warrants further investigations.