Clinical virology
The Department of Clinical Virology specializes in the diagnosis of infectious diseases caused by viruses. The department covers the fields of virus isolation, molecular diagnostics, genotyping and resistance, infection serology with detection of virus-specific antibodies, antigens and T-cells. The range of tests includes HIV, hepatitis A, B, C, D, E, herpes viruses (CMV, EBV, HSV, VZV, HHV6, HHV7, HHV8), polyomaviruses (BK, JC), measles, mumps, rubella, parvovirus B19, viruses in returning travelers (dengue, chikungunya, West Nile, Zika, yellow fever, Japan. Encephalitis), respiratory viruses (Influenza, RSV, PIV, HMPV, Corona, Adeno). We are a national WHO base for poliomyelitis, HIV confirmation laboratory and participate in relevant studies (Swiss HIV Cohort Study; Swiss Hepatitis C Cohort Study).
Our services are also used by other hospitals, doctors' surgeries and other diagnostic laboratories. Around 40,000 test materials are processed each year. Our laboratory works in close collaboration with the Clinic for Infectiology and Hospital Hygiene. We are also very actively involved in teaching and research at the University of Basel and the University Hospital Basel.
Address and contact
University Hospital Basel
Clinical Virology
Petersplatz 10
CH-4031 Basel
Phone +41 61 265 42 20
Fax +41 61 265 46 00
Opening hours
Monday - Sunday: 8.00 am - 5.00 pm
Management
Academic management
Team leader
Basic diagnostics
Viral infectious agents, virus-specific antibodies, antigens, genomes or T-cells are detected qualitatively or quantitatively from various test materials (blood, urine, stool, smears, secretions, lavage, punctates and tissue) in order to diagnose infection, replication, immunity, typing or antiviral resistance and, if necessary, dynamics.
Our most frequent requirements are quantitative detection of HIV in plasma, cytomegalovirus in plasma, Epstein-Barr virus in EDTA whole blood, hepatitis B virus in plasma, hepatitis C virus in plasma and BK polyomavirus in plasma.
For most viral infections, we offer the corresponding infection serology tests, which can be carried out initially for suspicion or screening or during the course or monitoring.
For urgent individual examinations from our basic range or special questions, it is helpful to contact the head of department on duty by telephone to determine the procedure and prioritization.
Specialist responsible
Team leader
Molecular diagnostics
Our most frequent requirements are quantitative detection of HIV in plasma, cytomegalovirus in plasma, Epstein-Barr virus in EDTA whole blood, hepatitis B virus in plasma, hepatitis C virus in plasma and BK polyomavirus in plasma.
Depending on the clinical question, epidemiology and manifestation (risk group HIV, transplantation, immunocompromised, travel returnees, systemic or localized, respiratory, gastrointestinal, neurological, cutaneous, genital), various test materials can be analysed.
Information on differential diagnosis, test material, collection and transportation can be found in the list of analyses or can also be discussed with the Clinical Virology team.
Specialist responsible
Team leader
Genotyping and resistance
We offer genotyping and resistance testing of the following viruses:
- HIV-1 genotyping (group M subtype A-K and CRFs, group O) and resistance interpretation according to Stanford for protease, reverse transcriptase and integrase
- HIV-1 tropism (CCR5/CXCR4) and patient genotype CCR5 / CCR5D32
- Cytomegalovirus resistance testing (UL97 serine/threonine kinase and UL54 DNA polymerase and UL56 terminase complex)
- Herpes simplex virus-1/-2 resistance testing (UL23 thymidine kinase and UL30 DNA polymerase)
- Hepatitis B virus resistance testing (genotype A-J; viral <s>pol </s>DNA polymerase)
- Hepatitis E virus genotyping (genotype 1-4)
- Enterovirus genotyping (genotype A-C)
- JC polyomavirus genotyping (genotype 1-8, NCCR rearrangements)
- BK Polyomavirus genotyping (genotype 1-4, NCCR rearrangements)
Information on differential diagnosis, test material, collection and transportation can be found in the list of analyses or can also be discussed with the Clinical Virology team.
Specialist responsible
Team leader
Virus isolation
Our most frequent requirements are the detection of cytomegalovirus and herpes simplex virus-1/-2 in broncho-alveolar lavage, herpes simplex virus-1/-2 in swabs or vesicle contents and varicella zoster virus in swabs or vesicle contents. Furthermore, we offer real-time phenotypic resistance testing of herpes simplex virus-1/-2 isolates against acyclovir.
As the WHO National Poliomyelitis Support Center, we receive stool samples for testing for polioviruses from doctors throughout Switzerland. It is important that two samples are taken 24 to 48 hours apart, as polioviruses can be excreted intermittently (link to order form | Formulaire d'envoi).
Depending on the clinical question, epidemiology and manifestation (respiratory, cutaneous, genital), different test materials can be analyzed.
Information on differential diagnosis, test material, collection and transportation can be found in the list of analyses or can also be discussed with the Clinical Virology team.
Specialist responsible
Team leader
Swiss HIV Cohort Study (SHCS)
In cooperation with the Clinical Chemistry Department, we currently offer the following daily antibody and antigen tests:
- Cytomegalovirus (CMV) IgG and IgM antibodies, IgG avidity
- Epstein-Barr virus (EBV) EBNA-1 IgG, VCA IgG, VCA IgM
- Total hepatitis A antibodies and IgM
- Hepatitis B virus
- HBs antigen
- HBe antigen
- HBe antibody
- HBs antibody quantitative
- HBc antibodies total and IgM
- Hepatitis C virus
- Hepatitis C antibodies
- Hepatitis D virus
- IgG and/or IgM antibodies
- HIV screening test (4th generation test with p24 antigen and HIV-1, HIV-2 antibodies IgG and IgM)
- HIV-1 immunoblot
- Herpes simplex virus (HSV)-1/-2 antibodies total and IgM, as well as HSV-2 specific antibodies (IgG)
- Measles IgG and/or IgM antibodies
- Mumps IgG and/or IgM antibodies
- Rubella IgG and/or IgM antibodies
- Parvovirus B19 IgG and/or IgM antibodies
- Varicella Zoster Virus (VZV) IgG and/or IgM antibodies
- Tick-borne encephalitis virus (IgG and/or IgM antibodies, intrathecal IgG antibodies)
- Viruses in tropical returnees incl. dengue, chikungunya, Zika, yellow fever, Japan. Encephalitis, flavirus panel (IgG and/or IgM)