Skin viral culture samples

If possible select a recently developed vesicle. Using a scalpel or needle gently incise/remove skin or crust over the top. Moisten the swab in virus transport medium and then rub the fluid exuding from the vesicle. Snap off the swab into virus transport medium.

Throat swabs

Diagnosis of viral pharyngitis and streptococcal pharyngitis depends on the culture of a throat swab.
virology – moisten the swab in virus transport medium before taking the specimen. Follow procedures as for the bacteriology throat swab. Snap off the swab into transport medium. If a respiratory virus is suspected a nose swab can also be taken

bacteriology – See Bacteriology section

Serology Test Profiles 

Diagnostic virology 

Immunity Screening:

Rubella – we screen by looking for IgG using an ELISA technique. It is important to remember that re-infection can occur, and may rarely cause foetal damage, so pregnant contacts should be followed up even if previously reported as immune. If sending specimens from pregnant contacts please give the gestation and date of contact, as this will influence the investigations performed.

Hepatitis B – post-vaccination screening is by measuring anti-HBs. A level >100 IU will provide protection for at least 5 years; levels between 10-100 are protective for an indeterminate period.

Varicella – we are regularly asked to check the immune status of pregnant contacts, and a rapid (though expensive) method is available for this. If the patient has had an antenatal screen at Plymouth, we can test the stored serum and provide the result within hours. Zoster immune globulin will be issued if required.

Needlestick injuries
See the latest copy of the Needlestick Injury Policy, which is available on all wards, and is also on the Trust’s intranet under clinical guidelines/communicable diseases.

The tables below summarise the investigations that may be performed for various clinical syndromes. They are open for modification depending upon clinical information provided.

Clinical Details Routine Investigations 2nd line Investigations
Atypical pneumonia onset date <10 days

(Nose and Throat swab in Virus transport medium)

Respiratory PCR viral screen (Influenza A, B and Swine flu variant, RSV, Parainfluenza types 1-4, Metapneumovirus, Adenovirus and Coronavirus)
Atypical pneumonia

Onset date > 10 days

(Convalescent Blood sample)

Respiratory CFT looking for antibodies to;

Flu A and B, Adenovirus, Chlamydia pneumoniae , RSV, Mycoplasma, Coxiella burnetti

This test is retrospective and not useful for acute management

Moderate to severe Pneumonia Urine antigen for Strep pneumoniae where compatible clinical or epidemiological features eg hyponatraemia Na <130 mmol/L, fever, diarrhoea, and recent travel
Pleurodynia Enterovirus IgM
Myocarditis / Cardiomyopathy Enterovirus IgM HSV, CMV and respiratory CFT panel if Enterovirus IgM negative
Culture negative endocarditis C. burnetti CFT and Bartonella investigation.
Lymphadenopathy EBV serology CMV IgM

Toxoplasma agglutination

Adenovirus CFT

Cat-scratch serology not available in the UK.

(Please describe the nature of the rash)

Rubella IgM

Parvovirus IgM


Mycoplasma agglutination

Adenovirus CFT

Measles CFT Quantitative

Lyme Antibody will be done if the symptoms are suggestive or if the history is compatible
Post transplant CMV monitoring CMV DNA on EDTA blood
Joint pain ASO

Parvovirus IgM

Rubella IgM

Hepatitis B surface antigen,

Lyme serology only if suggestive history, Mycoplasma agglutination

Chronic fatigue syndrome Virological investigations are rarely helpful
PUO  EBV, Toxoplasma, CMV, Respiratory CFT’s Further investigations will be guided by clinical features
Acute hepatitis HBsAg,

HAV IgM,  send serum 6/52 later for antiHCV CMV, (acute cases can be diagnosed by PCR after discussion with a consultant microbiologist.)


EBV, Toxoplasma, Hepatitis E, Leptospira, C.burnetti and

Chlamydia serology will be done for specific cases after discussion with the microbiologist

Chronic hepatitis Anti-HCV, HbsAg Anti-HCV, HbsAg
GI upset  None (serology is not helpful in this condition)

Molecular microbiology

The current repertoire of rapid molecular PCR Tests available in Microbiology includes:

Test Sample
CSF Viral screen (VZV,HSV and Enterovirus)

mumps and parechovirus

Respiratory viral screen UTM (Virus Transport Medium) or NPA
Norovirus Stool samples
HIV viral load EDTA Blood tube
MRSA Red top Nose swabs from participating wards
Varicella zoster lesion swabs in UTM (Virus Transport Medium)
Herpes simplex Genital swabs in UTM (Virus Transport Medium)
HCV viral load Clotted blood (Gold Top SST tube)
Chlamydia Chlamydia transport medium
CMV viral load EDTA Blood tube
Neisseria gonorrhoea Chlamydia transport medium

Chlamydia PCR (Sample types):

Self taken vulvo-vaginal swabs have been shown to be acceptable for Chlamydia testing on females, and ‘1st catch’ urine (rich in epithelial cells) samples are acceptable for Chlamydia testing on males (Also, see notes below for Urethral and cervical swabs).