Metagenomics Pathogen Detection – Service Summary

Metagenomics is a broad-range test that utilises deep sequencing to sequence total RNA and total DNA in a clinical specimen; this has the potential for un-targeted pan-pathogen detection.


Metagenomics is particularly useful in difficult-to-diagnose syndromes, such as encephalitis, in which an infectious aetiology is suspected but cannot be identified by routine methods.


In CSF, the sensitivity is similar to targeted real-time PCR for both RNA and DNA pathogens.


In tissue, the sensitivity for RNA viruses is similar to targeted real-time PCR. For DNA viruses, bacteria and fungi the sensitivity in tissue is reduced (approximately 100-fold) compared to targeted real-time PCR but comparable to pan-bacterial and pan-fungal PCR (16S and 18S). Low level DNA pathogens in tissue may not be detected.


Please note this test is under on-going validation and as such is not yet accredited by UKAS against ISO 15189:2012.


Test Description

Specimen required

NHS Price

Turnaround Time

Request Form


Tissue biopsy (fresh/frozen or FFPE)







2-4 weeks

Click here for request form


Specimen Requirements

Metagenomics is currently offered for tissue biopsies and CSF. The recommended specimen type is fresh tissue collected directly into RNALater.


See below for collection and storage requirements.



500 µl whole CSF (not filtered or centrifuged). We recommend CSFs are stored at −80 °C within 24 hours of collection (maximum 72 hours) to minimise RNA degradation. CSF is not stable at room temperature.


CSF collected with RNALater (1:4 ratio of RNALater:CSF) is stable for up to 1 week at ambient temperature and at least 1 week at +4 °C. CSF in RNALater can be shipped at ambient temperature or with ice packs.


Smaller volumes, sub-optimal storage or any pre-processing (e.g. filtering or centrifugation) will reduce ability to detect pathogens.


Fresh tissue - RNALater

Specimens must be collected directly into RNALater at the point of collection (e.g. in theatre); this is to rapidly stabilise RNA and prevent degradation. Specimens stabilised in RNALater can be stored at room temperature for up to 1 week or at +4 °C for up to one month prior to shipping.


Aliquots of RNALater are available on request from GOSH Microbiology/Virology labs or from laboratory reagent suppliers.


Fresh tissue - Frozen

Specimens that are not stabilised in RNALater should be immediately collected onto dry ice (e.g. in theatre) and stored at −80 °C prior to shipping. It is important to avoid any freeze-thaw cycles.


Fresh tissue - unstabilised

Tissue that has not been immediately stabilised in RNALater nor frozen is not recommended for metagenomics due to rapid degradation of RNA. Tissue in saline is not suitable.


Please be aware sub-optimal specimen collection, storage or transport will result in RNA degradation which will significantly reduce ability to detect RNA pathogens.


FFPE (formalin fixed paraffin embedded) tissue

4x 10 µm or 2 x 20 µm rolled sections


Please be aware the ability to detect low-level pathogens will be reduced in FFPE tissue compared to fresh tissue due to degradation of nucleic acid during formalin fixation. FFPE is a sub-optimal specimen type but can be processed in the absence of fresh tissue.


Specimen Transport


Tissue in RNALater: Ambient temperature
FFPE: Ambient temperature
Frozen tissue: Dry ice
CSF: Dry ice


Coming Soon

Metagenomics for other body fluids; including blood, urine and respiratory specimens



Please send samples accompanied by request form to:

Virology Laboratory

Level 4, Camelia Botnar Laboratories
Great Ormond Street Hospital for Children
Great Ormond Street
London WC1N 3JH

Hays Dx: GOSH DX 6640203, Bloomsbury 91 WC

General and Technical Enquiries:  

Dr Julianne Brown

Tel: 020 7405 9200 Ext 5929


Clinical Enquiries:

Professor Judy Breuer

Tel: 020 7405 9200 Ext 42129 / 020 3108 2130


Relevant publications arising from metagenomics service in our laboratory

1. Brown JR, Bharucha T and Breuer J (2018). Encephalitis diagnosis using metagenomics: application of next generation sequencing for undiagnosed cases. Journal of Infection, 76 (3): 225-240.

2. Bucciol G, Moens L, Payne K, Wollants E, Mekahli D, Levtchenko E, Vermeulen F, Tousseyn T, Gray P, Ma CS, Tangye SG, Van Ranst M, Brown JR, Breuer J and Meyts I (2018). Chronic Aichi virus infection in a patient with X-linked Agammaglobulinemia, Journal of Clinical Immunology, 38 (7): 748-752.

3. Morfopoulou S, Mee ET, Connaughton SM, Brown JR, Gilmour K, Chong WK, Duprex WP, Ferguson D, Hubank M, Hutchinson C, Kaliakatsos M, McQuaid S, Paine S, Plagnol V, Ruis C, Virasami A, Zhan H, Jacques TS, Schepelmann S, Qasim W, Breuer J (2016). Deep sequencing reveals persistence of cell-associated mumps vaccine virus in chronic encephalitis, Acta Neuropathologica, 133 (1): 139-147.

4. Lum SH, Turner A, Guiver M, Bonney D, Martland T, Davies E, Newbould M, Brown J, Morfopoulou S, Breuer J, Wynn R (2016). An emerging opportunistic infection: fatal astrovirus (VA1/HMO-C) encephalitis in a pediatric stem cell transplant recipient, Transplant Infectious Disease, 18(6): 960-964

5. Morfopoulou S,  Brown JR,  Davies EG,  Anderson G,  Virasami A,  Qasim W, Chong WK, Hubank M,  Plagnol V, Desforges M,  Jacques TS,  Talbot PJ,  Breuer J (2016). Coronavirus HCoV-OC43 Associated with Fatal Encephalitis, New England Journal of Medicine, 375(5): 497-8.

6. Duncan JAD, Mohamad SMB, Young DF, Skelton AJ, Leahy TR, Munday DC, Butler KM, Morfopoulou S, Brown JR, Hubank M, Connell J, Gavin PJ, McMahon C, Dempsey E, Lynch NE, Jacques TS, Valappil M, Cant AJ, Beuer J, Engelhardt KR, Randall RE and Hambleton S (2015). Human IFNAR2 deficiency: Lessons for antiviral immunity, Science Translational Methods, 7 (307).

7. Brown JR, Morfopoulou S, Hubb J, Emmett WA, Ip W, Shah D, Brooks T, Paine SML, Anderson G, Virasami A, Tong  CY W, Clark DA, Plagnol V, Jacques TS, Qasim W, Hubank M, Breuer J (2015). Astrovirus VA1/HMO-C: an increasingly recognised neurotropic pathogen in immunocompromised patients. Clinical Infectious Diseases, 60 (6): 881-888.



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