Research group - Anders Sönnerborg (Labmed)

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 HIV

InfCare Hepatitis

EuResist:

EuResist mainpage

EuResist Wikipedia

EuResist Network video

EuResist case study video

EuResist case study

Referensgruppen för AntiViral terapi:

RAV

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 PJ, Pulit SL, Gurdasani D, Bartha I, Shea PR, Pomilla C, et al
J Infect Dis 2017 11;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 AW, Telele NF, 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 EL, Rajasaar H, et al
HIV Med 2018 01;19(1):33-41

Recent increased identification and transmission of HIV-1 unique recombinant forms in Sweden.
Neogi U, Siddik AB, Kalaghatgi P, Gisslén M, Bratt G, Marrone G, et al
Sci Rep 2017 07;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 07;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 MM, Noyan K, Russom A, Sönnerborg A, Neogi U
Sci Rep 2017 04;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 03;22(11):

Perturbed CD8+ T cell TIGIT/CD226/PVR axis despite early initiation of antiretroviral treatment in HIV infected individuals.
Tauriainen J, Scharf L, Frederiksen J, Naji A, Ljunggren HG, Sönnerborg A, et al
Sci Rep 2017 01;7():40354

Monophylogenetic HIV-1C epidemic in Ethiopia is dominated by CCR5-tropic viruses-an analysis of a prospective country-wide cohort.
Kalu AW, Telele NF, 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 DD, 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 SG, Winner D, Singh K, Sarafianos SG, Quiñones-Mateu ME, Sönnerborg A, et al
J Med Virol 2017 01;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 DM, Butler K, Costagliola D, et al
HIV Med 2017 03;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 Ö, 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 SG, Siddik AB, Manickam A, Ambikan AT, Kumar MM, Fernandes SJ, 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 LM, 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 LC, Rao SD, 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 GB, van Zyl G, Preiser W, et al
AIDS Res Hum Retroviruses 2016 Jan;32(1):80-4