Diagnostic Virology 
The range of tests available, particularly those that can provide a rapid result have increased greatly in recent years. Diagnosis of acute hepatitis B, respiratory syncitial virus infection, varicella immunity in a pregnant contact, etc. can all be made within hours of receiving the specimen. In many cases perceived delays are due to specimen transport and postal services rather than the investigation itself. While batching of non-urgent tests is necessary for economic reasons, stat tests are usually possible when required. 


General principles

In general, 5-10 ml of blood should be sent in gold topped vacutainer tubes for all serological investigations (except where indicated on the test listing) and paired sera where indicated.  

Adequate clinical information must be given to ensure appropriate tests are performed, particularly onset date. Acute samples will be held to await receipt of convalescent samples (at least 10 days into illness.) 

Guidelines for investigation of specific conditions are given below, however useful points to remember are: 

Onset date - many investigations will give false-negative results if performed on a specimen collected too early or too late in the course of the illness. Onset dates are also crucial in the management of susceptible contacts, where treatment may be of benefit within the incubation period of the illness 

Clinical details - without basic information about the patient it is likely that inappropriate or no investigations will be performed. When unusual infections are suspected investigation can be expedited by early discussion with the laboratory. Please remember to add relevant clinical information when requesting tests electronically via ICM, to ensure appropriate tests are done

Appropriate specimens - this is not always obvious, e.g. a useful specimen for determining the cause of viral meningitis is faeces for virus culture.


Viral swabs from skin, vulval lesions, etc:
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

Legionella urine antigen ASAP where compatible clinical or epidemiological features



Enterovirus IgM


Myocarditis / Cardiomyopathy


Enterovirus IgM

HSV, CMV and respiratory CFT panel if Enterovirus IgM negative

Culture negative endocarditis

Chlamydia & C. burnetti CFT

Bartonella investigations not available in the UK.


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



Parvovirus IgM

Rubella IgM

Hepatitis B surface antigen,

Lyme serology only if suggestive history, Mycoplasma agglutination

Chronic fatigue syndrome


Virological investigations are rarely helpful




EBV, Toxoplasma, CMV, Respiratory CFT’s

Further investigations will be guided by clinical features

Acute hepatitis  



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:

List of Molecular PCR Tests



CSF Viral screen (VZV,HSV and Enterovirus)

mumps and parechovirus


Respiratory viral screen

UTM (Virus Transport Medium) or NPA


Stool samples

HIV viral load

EDTA Blood tube


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 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).

Review Status

Reviewed March 2019 
This page will be updated June 2019

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