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HSL Virology: Specialities

Within the Virology Department, there are four main diagnostic sections; Virus Detection, Virus Serology, Molecular HIV and Hepatitis, and Anti-viral Drug Resistance.

Molecular Virology (Floor 5)

This section uses Real-time PCR techniques for the detection of viral nucleic acid in clinical samples. PCRs routinely performed in the Virology Department are for the detection of:

  • Adenovirus (Qualitative & Quantitative)
  • Herpesviruses (HSV 1 & 2, VZV, (Qualitative), CMV, EBV (Qualitative & Quantitative), HHV6 (Quantitative), HHV8 (Qualitative & Quantitative)
  • Enterovirus
  • Parvovirus B19
  • Respiratory viruses (RSV, Influenza A/B, Parainfluenza 1/2/3/4, Rhinovirus, Human Metapnuemovirus, Enterovirus, Adenovirus, and Coronavirus, parechovirus)
  • Influenza A typing
  • MERS-CoV
  • COVID-19 PCR (SARS-CoV-2)
  • Gastroenteritis (Sapovirus, Norovirus type I and II, Rotavirus, Astrovirus, Adenovirus and Adenovirus Group F)
  • BK PCR Quantitative
  • Qualitative JC PCR
  • HIV-1 Proviral DNA
  • HIV-2 genome detection and viral load
  • Hepatitis E RNA Quantification
  • Hepatitis D RNA Quantification
  • Viral CSF panel (available viruses: CMV, HHV6, Enterovirus, Parechovirus, VZV PCR, HSV 1 & 2 PCR)
  • 16 & 18S sequencing
  • Genital Ulcer PCR (Syphilis, HSV 1 & 2)

Viral Serology (Floors 1 and 2)

This section detects viral antibodies (IgG and IgM) and antigens in patient serum using manual and automated assays and are split over two floors depending on whether it is a manual or automated process:

Floor 1 Automated

  • COVID-19 Total Antibodies (SARS-CoV-2)
  • HIV 1&2 Ag/Ab screening, HIV 1&2 Ag/Ab confirmation
  • HBsAg screening, HBsAg confirmation and HBsAg quantification
  • HB ‘e’ markers Ag and Ab
  • HB core Total and IgM
  • HBsAb
  • HCV Ab screening, HCV Ab confirmation
  • HCV Ag screening
  • Hepatitis D total antibody
  • Hepatitis A Total and IgM
  • CMV IgM, IgG and Avidity
  • Rubella IgM and IgG
  • Human T-lymphotropic virus (HTLV) 1 & 2 IgG
  • VZV IgG
  • HSV 1&2 IgG
  • Epstein Barr Virus (EBV) VCA IgG, IgM and EBNA IgG
  • Parvovirus IgM and IgG
  • Measles IgM and IgG
  • Mumps IgM and IgG

Floor 2 Manual

  • HSV type specific IgG
  • Hepatitis E IgM and IgG

Blood-borne Virus Laboratory, floor 2

This section detects either RNA or DNA in patient samples allowing the quantification of virus levels.

  • Hepatitis B viral load
  • Hepatitis C viral load
  • Hepatitis C Genotyping (performed on floor 5) 
  • HIV-1 viral load in Plasma and CSF
  • HIV-1 qualitative PCR

Anti-viral Drug Resistance, floor 5

This section looks for mutations that confer resistance to specific types of drugs in the viruses present in patient samples.

  • HIV drug resistance (NRTIs, NNRTIs, PIs, Fusion inhibitors, Integrase inhibitors)
  • HIV genotypic tropism assay
  • Hepatitis B genotyping and drug resistance
  • Hepatitis C genotyping and drug resistance, including NS3, NS5a and NS5b
  • CMV Ganciclovir resistance. UL97 and UL54

Molecular microbiology (Sexual health)

The department tests for DNA from:

  • Chlamydia trachomatis
  • Chlamydia trachomatis serovars L1, L2 & L3 (lymphogranuloma venereum)
  • Mycoplasma genitalium
  • Neisseria gonorrhoea
  • Trichomonas vaginalis

And mRNA from:

  • Human Papillomavirus

For Ureaplasma urealyticum/parvum and Gardnerella vaginalis, see the TDL Lab Guide. For Herpes Simplex Virus 1 and 2, and syphilis, see above.



Testing cannot be performed on swabs which have charcoal or gel additives in the tubes or Roche PCR swabs, as these are inhibitory to the PCR processes.

Acceptable samples types are swabs (preferably in Aptima tubes) from appropriate body sites, 1st catch urines in sterile containers and Thinprep.

Chlamydia trachomatis

Allow 6 weeks before re-testing to avoid picking up the DNA from a previous infection.

Lymphogranuloma venereum (LGV)

Investigation for possible LGV symptoms is by PCR swab taken from the rectum and penis. If LGV infection is suspected in female patients, cervical and vaginal PCR swabs should be taken. Samples are first tested for chlamydia. If chlamydia is detected, LGV is suspected and if requested, the same swab samples can be tested for LGV as an additional test. Sexual contact partners should also be checked.

Mycoplasma genitalium

M. genitalium cannot be cultured for diagnostic testing. Partner testing is advised for current partners only.

Rectal infections are common, and appear to be an important reservoir for resistance. BASHH guidance is that all patients must return for test of cure at 3–5 weeks. BASHH also recommends treatment with Resistance Guided Therapy – testing for M. genitalium with macrolide resistance determination.

Neisseria gonorrhoea

Individual PCR swabs from each site should be taken to screen for gonorrhoea. Partners should be treated at the same time with retesting after two weeks to confirm clearance – test of cure is recommended following treatment for gonococcal infections.

Trichomonas vaginalis

Infected women who are sexually active have a high rate of reinfection, thus re-screening at 3 month post treatment could be considered.

Human papillomavirus

The Human papillomavirus test helps healthcare providers detect the presence of abnormal cervical cells, and the HPV assays identify high-risk HPV mRNA that is indicative of the HPV infections most likely to lead to cervical disease. ThinPrep samples are the only samples which can be processed for HPV.