Research group - Anders Sönnerborg

Translational research on HIV and other chronic infections.

Our research group consists of five major research teams from Division of Clinical Microbiology, Department of Laboratory Medicine and Division of Infectious Diseases, Department of Medicine Huddinge. The researchers interact closely and integrate experimental, translational and clinical research with focus of solving key problems related to HIV treatment, HIV cure, long-term consequences and the spread of HIV. The Multi-omics team headed by Dr Ujjwal Neogi, PhD, integrates multi-omics techniques and clinical data to understand the disease control mechanisms in HIV-1 infected Elite controllers, who control their infection, without any therapy, applying the molecular data-first approach, using genomics, transcriptomics, proteomics, metabolomics and clinical phenotypes. The driving question of the Microbiota-inflammation team, headed by Dr Piotr Nowak, MD, PhD, is the role of the microbiome in chronic infections like HIV/HCV and Mycobacterium tuberculosis. Also the mechanisms behind success of microbiome modulation in the clinic are investigated. The Antiviral team performs clinical research on antiretroviral therapy including academic and industry-sponsored in vivo studies. It is also involved in cohort studies of ART in low-middle income countries. The experimental antiviral research is focused on HIV drug resistance, methods for quantification and elimination of latent HIV and the antiretroviral sensitivity of different subtypes. Team Register studies is headed by Associate Professor Veronica Svedhem, MD, PhD whose research is based on data from the national InfCareHIV database, covering all Swedish patients. These cohort studies are focused on evaluating new treatment outcomes, long-term side effects, non-HIV related morbidity and life quality over time. InfCareHIV is then connected to other national databases like Statistics Sweden, Cause of Death and Cancer Registers. Team HIV epidemiology and Molecular phylogenetics, headed by Dr Johanna Brännström, MD, PhD is divided into a clinical oriented unit with focus on the undiagnosed population, late testers and HIV continuum of care and an experimental unit with focus on molecular epidemiology, phylogenetics and phylogeography. The two units interact extensively.

Research Teams

Team Multi-omics Research 

Team Microbiota-Inflammation

Team Register studies

Team Antivirals

Team HIV epidemiology and Molecular phylogenetics

Group members

Lab unit

Assistant professor

Ujjwal Neogi

Organizational unit: Division of Clinical Microbiology
E-mail: ujjwal.neogi@ki.se

Senior forskare

Piotr Nowak

Organizational unit: Division of Infection and Dermatology
E-mail: Piotr.Nowak@ki.se

Postdoc

Robert Van Domselaar

Organizational unit: Division of Infection and Dermatology
E-mail: robert.van.domselaar.1@ki.se

Bioinformatician

Anoop Ambikan

Organizational unit: Division of Clinical Microbiology
E-mail: anoop.ambikan@ki.se

PhD student

Kajsa Noyan

Organizational unit: Division of Clinical Microbiology
E-mail: kajsa.noyan@ki.se

PhD student

Nigus Fikrie Telele

Organizational unit: Division of Clinical Microbiology
E-mail: nigus.fikrie.telele@ki.se

PhD student

Amare Worku Kalu

Organizational unit: Division of Clinical Microbiology
E-mail: amare.worku.kalu@ki.se

Associated

Kamlendra Singh

Organizational unit: Division of Clinical Microbiology
E-mail: kamlendra.singh@ki.se

Graduate Student

Wang Zhang

Organizational unit: Division of Clinical Microbiology
E-mail: wang.zhang@ki.se

PhD student

Duncan Njenda

Organizational unit: Division of Clinical Microbiology
E-mail: duncan.njenda@ki.se

Associated

Maike Sperk

Organizational unit: Division of Clinical Microbiology
E-mail: maike.sperk@ki.se

Associated

Anxiong Long

E-mail: anxiong.long@ki.se

Associated

Anna-Lena Spetz

Organizational unit: Division of Clinical Microbiology
E-mail: Anna-Lena.Spetz@ki.se

Clinical unit

Senior forskare

Piotr Nowak

Organizational unit: Division of Infection and Dermatology
E-mail: Piotr.Nowak@ki.se

Division of Infectious Diseases

Anders Thalme

E-mail: anders.thalme@sll.se

Statistician

Gaetano Marrone

Organizational unit: Global health (IHCAR)
E-mail: Gaetano.Marrone@ki.se

PhD student

Christina Carlander

Organizational unit: Division of Infection and Dermatology
E-mail: christina.carlander@ki.se

PhD student

Emmi Andersson

Organizational unit: Division of Clinical Microbiology
E-mail: Emmi.Andersson@ki.se

 

Techniques and infrastructure

Techniques

  • High throughput sequencing; Transcriptomics; Proteomics; Metabolomics; RNAscope; Microfludics; miRNA profiling; Integrated system biology; Cell cultures; Large databases; Real-time PCR

Infrastructure

  • The clinical HIV unit is fully equipped for phase IIa-IV studies fulfilling GCP criteria. It has also a biobank of 4 freezers (-20ºC, -70ºC), computers, servers, access to IT-infrastructure of the hospital. Infrastructure at the HIV unit includes clinical examination rooms, dressing room, library etc. For all patients there are clinical electronic patient records. Selected clinical and laboratory data are once a night automatically transferred to the research InfCare HIV database.
     
  • Laboratory at Division of Clinical Microbiology consists of four physically separated biosafety level 2 rooms handing of infectious materials and dedicated four room PCR- set up (sample preparation, reagent preparation, template and post PCR gel documentation) with unidirectional movement. The main lab also has bench spaces as well as separate space for laboratory equipments and chemical storage. Standard equipment is available in the laboratory including six -20ºC freezers dedicated for each room for storage of reagents and samples, ten minus 80°C freezers dedicated for long term storages of samples. The lab also has four BSL Class2A biosafety cabinets and two PCR stations for reagent preparation and template mixing. There is a refrigerated centrifuge with swing out rotor (Eppendorf 5810R), refrigerated Microcentrifuge 5417R (Eppendorf) and a MiniSpin (Eppendorf). The lab also has five thermal cyclers (gradient and non-gradient) and NanoDrop to quantitate nucleic acids/proteins. Lab has two gel documentation system (GeneGenom and Genei) and six electrophoresis units with power packs. The laboratory also have two mono-chromator based ELISA reader of wavelength range 340-850 nm (Techcan) and automated plate washer. The lab as access to one BSL Class3 laboratory.
     
  • Specialized equipment’s like flow cytometers,  Applied Biosystems® 7500 Real-Time PCR Systems, VictorX3 Luminometer, CASY cell counter, Agilent 2100 platform, fluorscent microscope unit,  PCR set-up as per GLP recommendation (separate Pre-Amplification, Amplification and Post-Amplification areas) liquid scintillation counters, inverted phase contrast microscopes with fluorescence, automated ELISpot reader, PCR thermal cyclers, double distillation unit, Gel doc systems, ELISA Reader (3).
     
  • Laboratory has access to the Illumina HiSeq 2500 and MiSeq through centralized facilities and access to the for long-term storage of data sets to store data in a high-availability and high-security system based on iRODS through BILS (Bioinformatics Infrastructure for Life Sciences) is a distributed national research infrastructure supported by the Swedish Research Council (Vetenskapsrådet). The storage system automatically replicates data sets to two different data centers, and there is fine-grained access-control to share data to specific users.
     
  • Apart from that research group has access to Karolinska Institutet Core Facilities for proteomics, genomics and imaging required for the study, that is an umbrella definition for service laboratories, resources and competence centres whose activities are coordinated, supervised and partly financed by the Board of Research (FS) in collaboration with the local committees for Research and Education (FoUU) of the associated hospitals.
     
  • A top modern laboratory is presently built at Alfred Nobels Alle, Campus Flemingsberg, Huddinge, KI. The research group has already moved into the new offices. The lab.space will be inaugurated in Autumn 2018. The equipment will be top modern and the decision process is presently ongoing. 

Collaborations

Researchers

Prof Maurizio Zazzi, University of Sienna, Italy

Prof Andrea de Luca, University of Sienna, Italy

Dr Francesca Incardona, InformaPro, Rome, Italy

Prof Rolf Kaiser, University of Cologne, Germany

Prof Thomas Lengauer, Max Planck Institute for Bioinformatics, Saarbrucken Germany

Dr Roger Paredes, Microbial Genomics Group at the IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain

Prof Thomas Klimkait, PhD, University of Basel, Switzerland

Prof Marius Troseid, University of Oslo, Norway

Prof Stefan Sarafianos, Emory University, USA  

Dr Kamal Singh, University of Missouri, USA

Prof Andrew Badley, Mayo Clinic, USA

Prof Yiming Shao, Division of Research on Virology and Immunology of NCAIDS, China CDC

Prof Susan Engelbrecht, Stellenbosch University, South Africa

Dr  Amogne Wondwossen, Addis Ababa University, Ethiopia

Dr Sabina Mugusi, Muhimbili University of Health and Allied sciences, Dar-es-Salaam, Tanzania

Dr Steve Sarfo, Kwame Nkrumah University of Science & Technology, Kumasi, Ghana

Luke Elisabeth Hanna, NIRT, Chennai, India

 

Centre for HIV Research, Karolinska Institutet

Swedish National InfCareHIV cohort

EuResist Network, https://www.euresist.org/

ESAR, http://www.esar-society.eu/

Public Health Sweden

Public Health England

European Center for Disease Control 

External fundings

Swedish Research Council, Stockholm County Council, Swedish Physicians Against AIDS Foundation, Karolinska Institutet Research Foundation Grants, NIH, European and Developing Countries Clinical Trial Partnership, China Scholarship Council Fellowship, Govt. of China

Links

InfCare HIV and Hepatitis:

InfCare

EuResist:

EuResist mainpage

EuResist Wikipedia

EuResist Network video

EuResist case study video

EuResist case study

Referensgruppen för AntiViral terapi:

RAV

European and Developing Countries Clinical Trials Partnership:

EDCTP project

HIV in Europe:

hiveurope

CHIP:

https://www.chip.dk/

Alumni

Selected publications

Publications 2016- 2018

Evaluating the Impact of Functional Genetic Variation on HIV-1 Control.
McLaren P, Pulit S, Gurdasani D, Bartha I, Shea P, Pomilla C, et al
J. Infect. Dis. 2017 Nov;216(9):1063-1069

PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context.
Libin P, Vanden Eynden E, Incardona F, Nowé A, Bezenchek A, , et al
Bioinformatics 2017 Dec;33(24):3993-3995

Prediction of coreceptor usage by five bioinformatics tools in a large Ethiopian HIV-1 subtype C cohort.
Kalu A, Telele N, Gebreselasie S, Fekade D, Abdurahman S, Marrone G, et al
PLoS ONE 2017 ;12(8):e0182384

HIV incidence in the Estonian population in 2013 determined using the HIV-1 limiting antigen avidity assay.
Soodla P, Simmons R, Huik K, Pauskar M, Jõgeda E, Rajasaar H, et al
HIV Med. 2018 Jan;19(1):33-41

Recent increased identification and transmission of HIV-1 unique recombinant forms in Sweden.
Neogi U, Siddik A, Kalaghatgi P, Gisslén M, Bratt G, Marrone G, et al
Sci Rep 2017 Jul;7(1):6371

Richer gut microbiota with distinct metabolic profile in HIV infected Elite Controllers.
Vesterbacka J, Rivera J, Noyan K, Parera M, Neogi U, Calle M, et al
Sci Rep 2017 Jul;7(1):6269

Effect of therapy switch on time to second-line antiretroviral treatment failure in HIV-infected patients.
Häggblom A, Santacatterina M, Neogi U, Gisslen M, Hejdeman B, Flamholc L, et al
PLoS ONE 2017 ;12(7):e0180140

Drug resistance testing through remote genotyping and predicted treatment options in human immunodeficiency virus type 1 infected Tanzanian subjects failing first or second line antiretroviral therapy.
Svärd J, Mugusi S, Mloka D, Neogi U, Meini G, Mugusi F, et al
PLoS ONE 2017 ;12(6):e0178942

Quantitative humoral profiling of the HIV-1 proteome in elite controllers and patients with very long-term efficient antiretroviral therapy.
Zhang W, Morshed M, Noyan K, Russom A, Sönnerborg A, Neogi U
Sci Rep 2017 Apr;7(1):666

The Human Immunodeficiency Virus Continuum of Care in European Union Countries in 2013: Data and Challenges.
Gourlay A, Noori T, Pharris A, Axelsson M, Costagliola D, Cowan S, et al
Clin. Infect. Dis. 2017 Jun;64(12):1644-1656

Letter to the editor: Pre-exposure prophylaxis for HIV in Europe: The need for resistance surveillance.
van Tienen C, van de Vijver D, Noori T, Sönnerborg A, Boucher C
Euro Surveill. 2017 Mar;22(11):

Perturbed CD8T cell TIGIT/CD226/PVR axis despite early initiation of antiretroviral treatment in HIV infected individuals.
Tauriainen J, Scharf L, Frederiksen J, Naji A, Ljunggren H, Sönnerborg A, et al
Sci Rep 2017 Jan;7():40354

Monophylogenetic HIV-1C epidemic in Ethiopia is dominated by CCR5-tropic viruses-an analysis of a prospective country-wide cohort.
Kalu A, Telele N, Gebreselasie S, Fekade D, Abdurahman S, Marrone G, et al
BMC Infect. Dis. 2017 01;17(1):37

Impact of peer support on virologic failure in HIV-infected patients on antiretroviral therapy - a cluster randomized controlled trial in Vietnam.
Cuong D, Sönnerborg A, Van Tam V, El-Khatib Z, Santacatterina M, Marrone G, et al
BMC Infect. Dis. 2016 12;16(1):759

Antiretroviral treatment for HIV infection: Swedish recommendations 2016.
Eriksen J, Albert J, Blaxhult A, Carlander C, Flamholc L, Gisslén M, et al
Infect Dis (Lond) 2017 Jan;49(1):1-34

 Increased replication capacity following evolution of PYxE insertion in Gag-p6 is associated with enhanced virulence in HIV-1 subtype C from East Africa.
Aralaguppe S, Winner D, Singh K, Sarafianos S, Quiñones-Mateu M, Sönnerborg A, et al
J. Med. Virol. 2017 Jan;89(1):106-111

 HIV-1 transmission between MSM and heterosexuals, and increasing proportions of circulating recombinant forms in the Nordic Countries.
Esbjörnsson J, Mild M, Audelin A, Fonager J, Skar H, Bruun Jørgensen L, et al
Virus Evol 2016 Jan;2(1):vew010

Higher rates of triple-class virological failure in perinatally HIV-infected teenagers compared with heterosexually infected young adults in Europe.
Judd A, Lodwick R, Noguera-Julian A, Gibb D, Butler K, Costagliola D, et al
HIV Med. 2017 Mar;18(3):171-180

Symptomatic Patients without Epidemiological Indicators of HIV Have a High Risk of Missed Diagnosis: A Multi-Centre Cross Sectional Study.
Brännström J, Svedhem V, Marrone G, Andersson , Azimi F, Blaxhult A, et al
PLoS ONE 2016 ;11(9):e0162503

Multiplexed next-generation sequencing and de novo assembly to obtain near full-length HIV-1 genome from plasma virus.
Aralaguppe S, Siddik A, Manickam A, Ambikan A, Kumar M, Fernandes S, et al
J. Virol. Methods 2016 10;236():98-104

Viral blips during suppressive antiretroviral treatment are associated with high baseline HIV-1 RNA levels.
Sörstedt E, Nilsson S, Blaxhult A, Gisslén M, Flamholc L, Sönnerborg A, et al
BMC Infect. Dis. 2016 06;16():305

The global spread of HIV-1 subtype B epidemic.
Magiorkinis G, Angelis K, Mamais I, Katzourakis A, Hatzakis A, Albert J, et al
Infect. Genet. Evol. 2016 12;46():169-179

Impact of immunosuppression and region of birth on risk of cervical intraepithelial neoplasia among migrants living with HIV in Sweden.
Carlander C, Wagner P, Svedhem V, Elfgren K, Westling K, Sönnerborg A, et al
Int. J. Cancer 2016 10;139(7):1471-9

Gut Microbiota Linked to Sexual Preference and HIV Infection.
Noguera-Julian M, Rocafort M, Guillén Y, Rivera J, Casadellà M, Nowak P, et al
EBioMedicine 2016 Mar;5():135-46

Virological failure in patients with HIV-1 subtype C receiving antiretroviral therapy: an analysis of a prospective national cohort in Sweden.
Häggblom A, Svedhem V, Singh K, Sönnerborg A, Neogi U
Lancet HIV 2016 Apr;3(4):e166-74

Phylogenetic Analysis of Ethiopian HIV-1 Subtype C Near Full-Length Genomes Reveals High Intrasubtype Diversity and a Strong Geographical Cluster.
Amogne W, Bontell I, Grossmann S, Aderaye G, Lindquist L, Sönnerborg A, et al
AIDS Res. Hum. Retroviruses 2016 May;32(5):471-4

Transmission of HIV Drug Resistance and the Predicted Effect on Current First-line Regimens in Europe.
Hofstra L, Sauvageot N, Albert J, Alexiev I, Garcia F, Struck D, et al
Clin. Infect. Dis. 2016 Mar;62(5):655-663

Factors influencing the efficacy of rilpivirine in HIV-1 subtype C in low- and middle-income countries.
Neogi U, Häggblom A, Singh K, Rogers L, Rao S, Amogne W, et al
J. Antimicrob. Chemother. 2016 Feb;71(2):367-71

Six-week follow-up after HIV-1 exposure: a position statement from the Public Health Agency of Sweden and the Swedish Reference Group for Antiviral Therapy.
Gaines H, Albert J, Axelsson M, Berglund T, Gisslén M, Sönnerborg A, et al
Infect Dis (Lond) 2016 Feb;48(2):93-8

Mutational Heterogeneity in p6 Gag Late Assembly (L) Domains in HIV-1 Subtype C Viruses from South Africa.
Neogi U, Engelbrecht S, Claassen M, Jacobs G, van Zyl G, Preiser W, et al
AIDS Res. Hum. Retroviruses 2016 Jan;32(1):80-4

Publications 2005-2015

Multidimensional Clusters of CD4+ T Cell Dysfunction Are Primarily Associated with the CD4/CD8 Ratio in Chronic HIV Infection.
Frederiksen J, Buggert M, Noyan K, Nowak P, Sönnerborg A, Lund O, et al
PLoS ONE 2015 ;10(9):e0137635

Gut microbiota diversity predicts immune status in HIV-1 infection.
Nowak P, Troseid M, Avershina E, Barqasho B, Neogi U, Holm K, et al
AIDS 2015 Nov;29(18):2409-18

Role of translocated bacterial flagellin in monocyte activation among individuals with chronic HIV-1 infection.
Svärd J, Paquin-Proulx D, Buggert M, Noyan K, Barqasho B, Sönnerborg A, et al
Clin. Immunol. 2015 Dec;161(2):180-9

HIV Testing and Diagnosis Rates in Kiev, Ukraine: April 2013-March 2014.
Simmons R, Malyuta R, Chentsova N, Medoeva A, Kruglov Y, Yurchenko A, et al
PLoS ONE 2015 ;10(8):e0137062

Arming of MAIT Cell Cytolytic Antimicrobial Activity Is Induced by IL-7 and Defective in HIV-1 Infection.
Leeansyah E, Svärd J, Dias J, Buggert M, Nyström J, Quigley M, et al
PLoS Pathog. 2015 Aug;11(8):e1005072

Efficacy and Safety of Antiretroviral Therapy Initiated One Week after Tuberculosis Therapy in Patients with CD4 Counts < 200 Cells/μL: TB-HAART Study, a Randomized Clinical Trial.
Amogne W, Aderaye G, Habtewold A, Yimer G, Makonnen E, Worku A, et al
PLoS ONE 2015 ;10(5):e0122587

Minor viral population with drug-resistant mutation and risk of persistent low-level viremia or 'blips' in HIV-1 subtype C.
Neogi U, Sonnerborg A
AIDS 2014 Nov;28(17):2635-6

Global Dispersal Pattern of HIV Type 1 Subtype CRF01_AE: A Genetic Trace of Human Mobility Related to Heterosexual Sexual Activities Centralized in Southeast Asia.
Angelis K, Albert J, Mamais I, Magiorkinis G, Hatzakis A, Hamouda O, et al
J. Infect. Dis. 2015 Jun;211(11):1735-44

Time on drug analysis based on real life data.
Schülter E, Kaiser R, Zazzi M, Sönnerborg A, Camacho R, Verheyen J
J Int AIDS Soc 2014 ;17(4 Suppl 3):19790

Minority drug-resistant HIV-1 variants in treatment naïve East-African and Caucasian patients detected by allele-specific real-time PCR.
Ekici H, Amogne W, Aderaye G, Lindquist L, Sönnerborg A, Abdurahman S
PLoS ONE 2014 ;9(10):e111042

Drug resistance in non-B subtype HIV-1: impact of HIV-1 reverse transcriptase inhibitors.
Singh K, Flores J, Kirby K, Neogi U, Sonnerborg A, Hachiya A, et al
Viruses 2014 Sep;6(9):3535-62

Novel tetra-peptide insertion in Gag-p6 ALIX-binding motif in HIV-1 subtype C associated with protease inhibitor failure in Indian patients.
Neogi U, Rao S, Bontell I, Verheyen J, Rao V, Gore S, et al
AIDS 2014 Sep;28(15):2319-22

Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: implications for use in low- and middle-income countries.
Ekici H, Rao S, Sönnerborg A, Ramprasad V, Gupta R, Neogi U
J. Antimicrob. Chemother. 2014 Dec;69(12):3349-55

Risk of HIV transmission from patients on antiretroviral therapy: a position statement from the Public Health Agency of Sweden and the Swedish Reference Group for Antiviral Therapy.
Albert J, Berglund T, Gisslén M, Gröön P, Sönnerborg A, Tegnell A, et al
Scand. J. Infect. Dis. 2014 Oct;46(10):673-7

Increase in transmitted resistance to non-nucleoside reverse transcriptase inhibitors among newly diagnosed HIV-1 infections in Europe.
Frentz D, Van de Vijver D, Abecasis A, Albert J, Hamouda O, Jørgensen L, et al
BMC Infect. Dis. 2014 Jul;14():407

T-bet and Eomes are differentially linked to the exhausted phenotype of CD8+ T cells in HIV infection.
Buggert M, Tauriainen J, Yamamoto T, Frederiksen J, Ivarsson M, Michaëlsson J, et al
PLoS Pathog. 2014 Jul;10(7):e1004251

Decreased phenotypic susceptibility to etravirine in patients with predicted genotypic sensitivity.
Agneskog E, Nowak P, Maijgren Steffensson C, Casadellà M, Noguera-Julian M, Paredes R, et al
PLoS ONE 2014 ;9(7):e101508

High HCV treatment uptake in the Swedish HIV/HCV co-infected cohort.
Stenkvist J, Weiland O, Sönnerborg A, Blaxhult A, Falconer K
Scand. J. Infect. Dis. 2014 Sep;46(9):624-32

Occasional spontaneous clearance of chronic hepatitis C virus in HIV-infected individuals.
Stenkvist J, Nyström J, Falconer K, Sönnerborg A, Weiland O
J. Hepatol. 2014 Oct;61(4):957-61

Temporal trends in the Swedish HIV-1 epidemic: increase in non-B subtypes and recombinant forms over three decades.
Neogi U, Häggblom A, Santacatterina M, Bratt G, Gisslén M, Albert J, et al
PLoS ONE 2014 ;9(6):e99390

Evaluation of rapid progressors in HIV infection as an extreme phenotype.
Olson A, Guiguet M, Zangerle R, Gill J, Perez-Hoyos S, Lodi S, et al
J. Acquir. Immune Defic. Syndr. 2014 Sep;67(1):15-21

On the usefulness of circulating bacterial 16S rDNA as a marker of microbial translocation in HIV-1-infected patients.
Svärd J, Sönnerborg A, Vondracek M, Mölling P, Nowak P
J. Acquir. Immune Defic. Syndr. 2014 Aug;66(4):e87-9

Prophylaxis and treatment of HIV-1 infection in pregnancy: Swedish recommendations 2013.
Navér L, Albert J, Böttiger Y, Carlander C, Flamholc L, Gisslén M, et al
Scand. J. Infect. Dis. 2014 Jun;46(6):401-11

Superinfection with drug-resistant HIV is rare and does not contribute substantially to therapy failure in a large European cohort.
Bartha I, Assel M, Sloot P, Zazzi M, Torti C, Schülter E, et al
BMC Infect. Dis. 2013 Nov;13():537

Trends in antiretroviral therapy and prevalence of HIV drug resistance mutations in Sweden 1997-2011.
Bontell I, Häggblom A, Bratt G, Albert J, Sönnerborg A
PLoS ONE 2013 ;8(3):e59337

Kinetics of microbial translocation markers in patients on efavirenz or lopinavir/r based antiretroviral therapy.
Vesterbacka J, Nowak P, Barqasho B, Abdurahman S, Nyström J, Nilsson S, et al
PLoS ONE 2013 ;8(1):e55038

Impact of HMGB1/TLR Ligand Complexes on HIV-1 Replication: Possible Role for Flagellin during HIV-1 Infection.
Nowak P, Abdurahman S, Lindkvist A, Troseid M, Sönnerborg A
Int J Microbiol 2012 ;2012():263836

[pubmed:22768132​]

Treatment-associated polymorphisms in protease are significantly associated with higher viral load and lower CD4 count in newly diagnosed drug-naive HIV-1 infected patients.
Theys K, Deforche K, Vercauteren J, Libin P, van de Vijver D, Albert J, et al
Retrovirology 2012 Oct;9():81

Long-term efficacy and safety of atazanavir/ritonavir treatment in a real-life cohort of treatment-experienced patients with HIV type 1 infection.
Jansen K, Sönnerborg A, Brockmeyer N, Thalme A, Svedhem V, Dupke S, et al
AIDS Res. Hum. Retroviruses 2013 Mar;29(3):564-73

Characterization of HIV-specific CD4+ T cell responses against peptides selected with broad population and pathogen coverage.
Buggert M, Norström M, Czarnecki C, Tupin E, Luo M, Gyllensten K, et al
PLoS ONE 2012 ;7(7):e39874

Molecular epidemiology of HIV-1 subtypes in India: origin and evolutionary history of the predominant subtype C.
Neogi U, Bontell I, Shet A, De Costa A, Gupta S, Diwan V, et al
PLoS ONE 2012 ;7(6):e39819

Impact of HMGB1/TLR Ligand Complexes on HIV-1 Replication: Possible Role for Flagellin during HIV-1 Infection.
Nowak P, Abdurahman S, Lindkvist A, Troseid M, Sönnerborg A
Int J Microbiol 2012 ;2012():263836

Predicting response to antiretroviral treatment by machine learning: the EuResist project.
Zazzi M, Incardona F, Rosen-Zvi M, Prosperi M, Lengauer T, Altmann A, et al
Intervirology 2012 ;55(2):123-7

Use of InfCare HIV to identify and characterize suboptimally treated HIV patients at a Danish HIV clinic: a cross-sectional cohort study.
Dalgaard L, Søgaard O, Jensen-Fangel S, Larsen C, Sönnerborg A, Østergaard L
Scand. J. Infect. Dis. 2012 Feb;44(2):108-14

Survival and causes of death among HIV-infected patients starting antiretroviral therapy in north-eastern Vietnam.
Cuong D, Thorson A, Sönnerborg A, Hoa N, Chuc N, Phuc H, et al
Scand. J. Infect. Dis. 2012 Mar;44(3):201-8

Bilirubin-a potential marker of drug exposure in atazanavir-based antiretroviral therapy.
Rekić D, Clewe O, Röshammar D, Flamholc L, Sönnerborg A, Ormaasen V, et al
AAPS J 2011 Dec;13(4):598-605

HIV-1 mutational pathways under multidrug therapy.
Lawyer G, Altmann A, Thielen A, Zazzi M, Sönnerborg A, Lengauer T
AIDS Res Ther 2011 Jul;8():26

Rebound of residual plasma viremia after initial decrease following addition of intravenous immunoglobulin to effective antiretroviral treatment of HIV.
Mellberg T, Gonzalez V, Lindkvist A, Edén A, Sönnerborg A, Sandberg J, et al
AIDS Res Ther 2011 Jun;8():21

Detection of drug resistance mutations at low plasma HIV-1 RNA load in a European multicentre cohort study.
Prosperi M, Mackie N, Di Giambenedetto S, Zazzi M, Camacho R, Fanti I, et al
J. Antimicrob. Chemother. 2011 Aug;66(8):1886-96

European recommendations for the clinical use of HIV drug resistance testing: 2011 update.
Vandamme A, Camacho R, Ceccherini-Silberstein F, de Luca A, Palmisano L, Paraskevis D, et al
AIDS Rev ;13(2):77-108

Prophylaxis and treatment of HIV-1 infection in pregnancy: Swedish recommendations 2010.
Navér L, Albert J, Belfrage E, Flamholc L, Gisslén M, Gyllensten K, et al
Scand. J. Infect. Dis. 2011 Jul;43(6-7):411-23

European guidelines on the clinical management of HIV-1 tropism testing.
Vandekerckhove L, Wensing A, Kaiser R, Brun-Vézinet F, Clotet B, De Luca A, et al
Lancet Infect Dis 2011 May;11(5):394-407

High mobility group box protein-1 in HIV-1 infection.
Trøseid M, Sönnerborg A, Nowak P
Curr. HIV Res. 2011 Jan;9(1):6-10

Antiretroviral therapy optimisation without genotype resistance testing: a perspective on treatment history based models.
Prosperi M, Rosen-Zvi M, Altmann A, Zazzi M, Di Giambenedetto S, Kaiser R, et al
PLoS ONE 2010 Oct;5(10):e13753

Differential effects of efavirenz, lopinavir/r, and atazanavir/r on the initial viral decay rate in treatment naïve HIV-1-infected patients.
Edén A, Andersson L, Andersson O, Flamholc L, Josephson F, Nilsson S, et al
AIDS Res. Hum. Retroviruses 2010 May;26(5):533-40

Implications of the release of high-mobility group box 1 protein from dying cells during human immunodeficiency virus type 1 infection in vitro.
Barqasho B, Nowak P, Abdurahman S, Walther-Jallow L, Sönnerborg A
J. Gen. Virol. 2010 Jul;91(Pt 7):1800-9

Only slight impact of predicted replicative capacity for therapy response prediction.
Weisser H, Altmann A, Sierra S, Incardona F, Struck D, Sönnerborg A, et al
PLoS ONE 2010 Feb;5(2):e9044

Treatment of HIV infection: Swedish recommendations 2009.
Josephson F, Albert J, Flamholc L, Gisslén M, Karlström O, Moberg L, et al
Scand. J. Infect. Dis. 2009 ;41(11-12):788-807

Transmission of drug-resistant HIV-1 is stabilizing in Europe.
Vercauteren J, Wensing A, van de Vijver D, Albert J, Balotta C, Hamouda O, et al
J. Infect. Dis. 2009 Nov;200(10):1503-8

Investigation of expert rule bases, logistic regression, and non-linear machine learning techniques for predicting response to antiretroviral treatment.
Prosperi M, Altmann A, Rosen-Zvi M, Aharoni E, Borgulya G, Bazso F, et al
Antivir. Ther. (Lond.) 2009 ;14(3):433-42

Advantages of predicted phenotypes and statistical learning models in inferring virological response to antiretroviral therapy from HIV genotype.
Altmann A, Sing T, Vermeiren H, Winters B, Van Craenenbroeck E, Van der Borght K, et al
Antivir. Ther. (Lond.) 2009 ;14(2):273-83

Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database.
Altmann A, Däumer M, Beerenwinkel N, Peres Y, Schülter E, Büch J, et al
J. Infect. Dis. 2009 Apr;199(7):999-1006

Selecting anti-HIV therapies based on a variety of genomic and clinical factors.
Rosen-Zvi M, Altmann A, Prosperi M, Aharoni E, Neuvirth H, Sönnerborg A, et al
Bioinformatics 2008 Jul;24(13):i399-406

Prophylaxis and treatment of HIV-1 infection in pregnancy: Swedish Recommendations 2007.
Navér L, Bohlin A, Albert J, Flamholc L, Gisslén M, Gyllensten K, et al
Scand. J. Infect. Dis. 2008 ;40(6-7):451-61

Quality control assessment of human immunodeficiency virus type 2 (HIV-2) viral load quantification assays: results from an international collaboration on HIV-2 infection in 2006.
Damond F, Benard A, Ruelle J, Alabi A, Kupfer B, Gomes P, et al
J. Clin. Microbiol. 2008 Jun;46(6):2088-91

Similar hepatitis C virus RNA kinetics in HIV/hepatitis C virus monoinfected genotype 2 or 3 matched controls during hepatitis C virus combination therapy.
Karlström O, Sönnerborg A, Weiland O
AIDS 2008 Apr;22(7):899-901

Antiretroviral treatment of HIV infection: Swedish recommendations 2007.
Josephson F, Albert J, Flamholc L, Gisslén M, Karlström O, Lindgren S, et al
Scand. J. Infect. Dis. 2007 ;39(6-7):486-507

A structural equation modeling approach to the concepts of adherence and readiness in antiretroviral treatment.
Södergård B, Höfer S, Halvarsson M, Sönnerborg A, Tully M, Lindblad A
Patient Educ Couns 2007 Jul;67(1-2):108-16

Early immune activation in gut-associated and peripheral lymphoid tissue during acute HIV infection.
Nilsson J, Kinloch-de-Loes S, Granath A, Sönnerborg A, Goh L, Andersson J
AIDS 2007 Mar;21(5):565-74

Early virologic rebound in a pilot trial of ritonavir-boosted atazanavir as maintenance monotherapy.
Karlström O, Josephson F, Sönnerborg A
J. Acquir. Immune Defic. Syndr. 2007 Apr;44(4):417-22

Assessing and achieving readiness to initiate HIV medication.
Nordqvist O, Södergård B, Tully M, Sönnerborg A, Lindblad A
Patient Educ Couns 2006 Jul;62(1):21-30

HMGB1 activates replication of latent HIV-1 in a monocytic cell-line, but inhibits HIV-1 replication in primary macrophages.
Nowak P, Barqasho B, Treutiger C, Harris H, Tracey K, Andersson J, et al
Cytokine 2006 Apr;34(1-2):17-23

Discrimination of lamivudine resistant minor HIV-1 variants by selective real-time PCR.
Bergroth T, Sönnerborg A, Yun Z
J. Virol. Methods 2005 Jul;127(1):100-7

Publications before 2005

Expansion of CD7(low) and CD7(negative) CD8 T-cell effector subsets in HIV-1 infection: correlation with antigenic load and reversion by antiretroviral treatment.
Aandahl E, Quigley M, Moretto W, Moll M, Gonzalez V, Sönnerborg A, et al
Blood 2004 Dec;104(12):3672-8

Efavirenz plasma concentrations in HIV-infected patients: inter- and intraindividual variability and clinical effects.
Ståhle L, Moberg L, Svensson J, Sönnerborg A
Ther Drug Monit 2004 Jun;26(3):267-70

Use of genotypic assays for the detection of antiretroviral resistance: a legal proceeding, Rome, 22-23 April 2002.
Sönnerborg A
Scand J Infect Dis Suppl 2003 ;106():5

[pubmed:14604962]

Use of HIV-1 reverse transcriptase recovered from human plasma for phenotypic drug susceptibility testing.
Shao X, Malmsten A, Lennerstrand J, Sönnerborg A, Unge T, Gronowitz J, et al
AIDS 2003 Jul;17(10):1463-71

Suppression of leukemia inhibitor factor in lymphoid tissue in primary HIV infection: absence of HIV replication in gp130-positive cells.
Tjernlund A, Fleener Z, Behbahani H, Connick E, Sönnerborg A, Broström C, et al
AIDS 2003 Jun;17(9):1303-10

[Swedish guidelines for antiretroviral treatment of HIV. Good compliance is crucial for a good result].
Gisslén M, Sönnerborg A
Lakartidningen 2002 Oct;99(43):4263-6

Accumulation of DC-SIGN+CD40+ dendritic cells with reduced CD80 and CD86 expression in lymphoid tissue during acute HIV-1 infection.
Loré K, Sönnerborg A, Broström C, Goh L, Perrin L, McDade H, et al
AIDS 2002 Mar;16(5):683-92

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