National SARS-CoV-2 Whole Genome Sequencing (WGS) Surveillance Programme

Introduction
In 2021, an expert group was established to develop a proposal for a National SARS-CoV-2 Whole Genome Sequencing (WGS) Surveillance Programme in Ireland. The expert group’s proposal recommended that the Programme be developed and implemented, led by HSE-Health Protection Surveillance Centre (HPSC), with UCD National Virus Reference Laboratory (NVRL) as the lead partner laboratory. The primary aim of the Programme is to track the molecular epidemiology of SARS-CoV-2 in Ireland to inform and enhance the public health response to the COVID-19 pandemic. Associated programme goals include contributing to the global knowledge on SARS-CoV-2 WGS to inform the global public health response and developing the programme to facilitate expansion and diversification, beyond SARS-CoV-2, to surveillance of other priority pathogens.

Funding for the phase I of Programme was provided by the European Centre for Disease Prevention and Control (ECDC) and the Health Service Executive (HSE).

Phase II of the Programme is funded by the European Union EU4Health Programme and the HSE. This phase aims to ensure sustainability of WGS in the Programme and to integrate WGS into routine public health practice. 

How is the Programme structured?
The Programme is led by HPSC with NVRL as the lead laboratory partner. The Programme Steering Group agreed a hub and spoke model for the Programme, incorporating NVRL (hub), six regional acute hospital laboratories (spokes), one national paediatric hospital spoke laboratory (Children’s Health Ireland-Crumlin) and HPSC as the surveillance partner. The following seven regional acute hospital laboratories are designated as spokes:

• University Hospital Limerick (UHL)
• St James’s Hospital (SJH)
• Galway University Hospitals (GUH)
• Beaumont Hospital
• Cork University Hospital (CUH)
• St Vincent’s University Hospital (SVUH)
• CHI-Crumlin paediatric hospital

These acute hospital spokes and CHI- Crumlin were selected to represent each of the six Regional Health Areas (RHA) in line with public health reform and Sláintecare. 

What are the Objectives of the National SARS-CoV-2 WGS Surveillance Programme?
The objectives of the National SARS-CoV-2 WGS Surveillance Programme, are:

1. To collect WGS typed data i.e. Pango lineage (and mutations of interest/concern) on confirmed SARS-CoV-2 cases whose specimens have undergone WGS, and to record the data on the national Computerised Infectious Disease Reporting System (CIDR)
2. To deposit SARS-CoV-2 genetic sequence data to GISAID - the global sequence repository
3. To provide timely reporting on the epidemiology of SARS-CoV-2 lineages, variants of concern or interest (and mutations of concern or interest) in Ireland, in order to inform public health policy and actions. Reporting includes:
1. national reporting on variants (and mutations) in Ireland which will:
1. describe the molecular epidemiology of SARS-CoV-2 nationally by time/place/demography
2. highlight the emergence of variants or mutations - particularly those that may have characteristics that affect transmissibility, immune evasion, vaccine escape, clinical presentation, antiviral resistance or diagnostic performance
2. weekly reporting on variants (and mutations of concern or interest) to the European Centre for Disease Prevention and Control (ECDC) Tessy surveillance system
3. relevant information to EU member States via the European Early Warning and Response System (EWRS) and the ECDC EpiPulse system as needed or requested
4. To use the data to:
1. provide up to date information on the molecular epidemiology of SARS-CoV-2 for local incident and outbreak management and for informing public health policy at a national level
2. add to the global knowledge of SARS-CoV-2 epidemiology.  

In addition, the second phase of the Programme aims to:

1. Provide education and training opportunities to increase the knowledge and capacity for WGS in Ireland, ensuring sustainability and robustness of the system
2. Expand WGS use in the Programme to pathogens other than SARS-CoV-2. 

How does the Programme work?
The Programme aims to sequence SARS-CoV-2 samples to monitor circulating variants, particularly those causing illness and severe disease, and to detect any variants with unusual characteristics and potential for increased transmissibility and outbreaks

• The WGS Programme implements a SARS-CoV-2 WGS surveillance programme that is based on two complementary data flows/streams: National Surveillance Stream and Targeted Sequencing Stream
• It facilitates the timely reporting of SARS-CoV-2 WGS data to ECDC and/or other supra-national institutions, as well as sharing data in the public domain (e.g. in genetic sequence databases and repositories or epidemiological reports). 

Figure 1: Overview of SARS-C0V-2 sequencing framework in Ireland.

Who governs the Programme?
The overall governance of the Programme is with HPSC which reports to the Director of National Health Protection.     

How is the information shared?
The NVRL and spoke laboratories upload the SARS-CoV-2 sequences they generate to the Global initiative on sharing all influenza Data (GISAID) platform. GISAID is the world’s largest repository for SARS-CoV-2 sequences. The uploaded data include; sequence data, patient age, patient gender, patient county, laboratory name, pseudonymised specimen ID, specimen type and information on the sequencing technology and assembly method used.

GISAID uses the Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) software tool to compare the sequence to other sequences in its repository and to classify it into a SARS-CoV-2 lineage (Pango lineage). These are reported to the submitting laboratory with a GISAID generated accession number. The NVRL and spoke laboratories may also use additional software to assign Pango lineage and obtain detailed information on their sequences (e.g. Biomérieux Episeq).

All participating laboratories report the assigned Pango lineage and GISAID Accession number to HPSC. The results file also includes sufficient patient identifiers for the sequencing result to be matched to SARS-CoV-2 cases reported on the CIDR system. Once the sequencing results have been matched by HPSC, the Pango lineage and GISAID ID are added to the case-based information recorded on the CIDR system and the sequencing result can be accessed by HPSC staff and the local Departments of Public Health.

HPSC report nationally on the Pango lineage data in conjunction with epidemiological data on SARS-CoV-2 cases from the CIDR system. HPSC, the local Departments of Public Health and hospitals can also link with the NVRL and spoke laboratories in relation to more detailed analyses of the sequencing results where this is needed (e.g. specific mutations of interest or relatedness of cases in a suspected outbreak). HPSC is also responsible for uploading COVID-19 data to the European Centre for Disease Prevention and Control (ECDC) TESSy system. The data uploaded to TESSy include Pango lineage and GISAID ID in addition to epidemiological data. Access to TESSy is controlled and patient names, addresses and dates of birth are not included in the files uploaded. 

More information

You can contact the WGS Programme at WGS.programme@hpsc.ie

Last Updated: 15 August 2023