The Pathogen Genomic Unit offers access to this cutting edge technology to UCL/UCLH researchers but also importantly to explore the clinical applications and interpretation of pathogen genomic data for patients with a variety of infections. It is currently based at UCLH Virology, 307 Euston Road, London, hosted by Health Services Laboratories in a clinically accredited laboratory (full CPA accreditation).

The unit has optimised the use of Illumina’s Nextera XT protocols for the generation of library preparations from clinical samples for pathogen genome sequencing.

We are able to undertake Next Generation Sequencing (NGS) for whole viral pathogen genomes and sub-genomic amplicons, from culture samples or direct clinical and/or residual diagnostic specimens.

The unit is also equipped with Qiagen Symphony robots for extraction of nucleic acids, multiple ABI PCR units and a BRC-funded Illumina MiSeq sequencer.

General enquiries


UCLH PGU Manager and bookings
HSL, Ground Floor
307 Euston Road
London, NW1 3AD

This service is suitable for whole genome sequencing of pathogens directly from clinical samples. There are three options for using this service:

1. Customers use PCR primer sets already optimised by UCLH-PGU for clinical diagnostic and/or clinical research use. Pathogens that can currently be sequenced readily using the targeted sequencing and Nextera XT library preparation are shown in the table below:




Resistance detection

Human Immunodeficiency virus-1 (HIV-1)*

Influenza A virus (FluA)


Influenza B virus (FluB)

Hepatitis B virus (HBV)

Hepatitis C virus (HCV)

Hepatitis D virus (HDV)


Hepatitis E virus (HEV)


Zika virus (ZKV)



2. Customers use their own PCR primers for Nextera XT library preparation and sequencing. In this case, the library preparation would be preferably by the user – SOPs and directions will be provided and per sample charges will be lowered accordingly.

3. Customers collaborate with the UCLH-PGU to design and optimise a new PCR primer set. This option is available if customers wish to utilise UCLH-PGU’s clinically relevant expertise and develop new primer sets for pathogens that are not already held by the UCLH PGU. For further details please email Dr Bridget Ferns.