CLINICAL SCIENCEHigh-throughput sequencing reveals a high prevalence of pretreatment HIV-1 drug resistance in SwedenAndersson, Emmia,b; Ambikan, Anoopa; Brännström, Johannac,d; Aralaguppe, Shambhu G.a; Yilmaz, Ayline; Albert, Janb,f; Neogi, Ujjwala; Sönnerborg, Andersa,b,c,gAuthor Information aDivision of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute bDepartment of Clinical Microbiology, Karolinska University Hospital cDivision of Infection and Dermatology, Department of Medicine Huddinge, Karolinska Institute dDepartment of Infectious Diseases/Venhälsan, South Hospital, Stockholm eDepartment of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg fDepartment of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm gDepartment of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden. Correspondence to Emmi Andersson, Tel: +46 8737039293; e-mail: [email protected] Received 20 May, 2020 Revised 21 September, 2020 Accepted 13 October, 2020 Supplemental digital content is available for this article. Direct URL citations appear in the printed text and are provided in the HTML and PDF versions of this article on the journal's Website (http://www.AIDSonline.com). AIDS: February 2, 2021 - Volume 35 - Issue 2 - p 227-234 doi: 10.1097/QAD.0000000000002740 Buy SDC Metrics Abstract Objectives: HIV-1 pretreatment drug resistance (PDR) is a global concern. Our aim was to evaluate high-throughput sequencing (HTS) for HIV-1 resistance testing and describe PDR in Sweden, where 75% of diagnosed individuals are foreign-born. Design: Cross-sectional study. Methods: Individuals entering HIV-1 care in Sweden 2017 to March 2019 (n = 400) were included if a viremic sample was available (n = 220). HTS was performed using an in-house assay. Drug resistance mutations (DRMs) (based on Stanford HIV DB vs. 8.7) at levels 1–5%, 5–19% and at least 20% of the viral population were described. Results from HTS and routine Sanger sequencing were compared. Results: HTS was successful in 88% of patients, 92% when viral load was at least 1000 copies/ml. DRMs at any level in protease and/or reverse transcriptase were detected in 95 individuals (49%), whereas DRMs at least 20% in 35 (18%) individuals. DRMs at least 20% correlated well to findings in routine Sanger sequencing. Protease/reverse transcriptase (PR/RT) DRMs at least 20% were predicted by treatment exposure; adjusted OR 9.28 (95% CI 2.24–38.43; P = 0.002) and origin in Asia; adjusted OR 20.65 (95% CI 1.66–256.24; P = 0.02). Nonnucleoside reverse transcriptase inhibitor (NNRTI) DRMs at least 20% were common (16%) and over-represented in individuals originating from sub-Saharan Africa or Asia. Low-level integrase strand transfer inhibitor (INSTI) DRMs less than 20% were detected in 15 individuals (8%) with no association with INSTI exposure. Conclusion: Our HTS can efficiently detect PDR and findings of DRMs at least 20% compare well to routine Sanger sequencing. The high prevalence of PDR was because of NNRTI DRMs and associated with migration from areas with emerging PDR. Copyright © 2020 Wolters Kluwer Health, Inc. All rights reserved.