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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

Docent

Ujjwal Neogi

Enhet: Ujjwal Neogis grupp
E-post: ujjwal.neogi@ki.se

Senior forskare

Piotr Nowak

Enhet: Enheten för infektion och hud
E-post: Piotr.Nowak@ki.se

Postdoc

Robert Van Domselaar

Enhet: Enheten för infektion och hud
E-post: robert.van.domselaar.1@ki.se

Forskarstuderande

Anoop Ambikan

Enhet: Institutionen för laboratoriemedicin (LABMED), H5
E-post: anoop.ambikan@ki.se

Anknuten

Kamlendra Singh

Enhet: Anders Sönnerborgs grupp
E-post: kamlendra.singh@ki.se

Postdoc

Wang Zhang

E-post: wang.zhang@ki.se

Doktorand

Duncan Njenda

Enhet: Avdelningen för klinisk mikrobiologi
E-post: duncan.njenda@ki.se

Doktorand

Maike Sperk

Enhet: Institutionen för laboratoriemedicin (LABMED), H5
E-post: maike.sperk@ki.se

Anknuten

Anna-Lena Spetz

Enhet: Avdelningen för klinisk mikrobiologi
E-post: Anna-Lena.Spetz@ki.se

Clinical unit

Senior forskare

Piotr Nowak

Enhet: Enheten för infektion och hud
E-post: Piotr.Nowak@ki.se

Division of Infectious Diseases

Anders Thalme

E-post: anders.thalme@sll.se

Forskare

Gaetano Marrone

Enhet: Institutionen för folkhälsovetenskap (PHS), K9
E-post: Gaetano.Marrone@ki.se

Doktorand

Emmi Andersson

Enhet: Avdelningen för klinisk mikrobiologi
E-post: 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

28968755

28961923

28841646

28762652

28744024

28740260

28727795

28582463

28386076

28369283

28333614

28084312

28061826

27986077

27804313

 27328744

 27774303

27625109

27603207

27448822

27329293

27262355

27177207

27077120

27036992

26881451

26620652

26518047

26414596

26413747

Publications 2005-2015

26402620

26355675

26344864

26322977

26295709

25966339

25574966

25512631

25397534

25333961

25254383

25102091

25085657

25073537

25047543

25032686

25000302

24984040

24951853

24922326

24872130

24798766

24754479

24219163

23533618

23383047

22719767

23031662

23016535

22792193

22768132

22719767

22719767

22200100

22122590

21913053

21794106

21708049

21624929

21587341

21438788

21429803

21198433

21060792

20455766

20200191

20140263

19922061

19835478

19474477

19430102

19239365

18586740

18584531

18434556

18427210

17577810

17509807

17314518

17159658

16766244

16697213

15893572

15308569

Publications before 2005

15167626

15000572

12824784

12799551

12448313

11964524