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Whole Genome Sequence Analysis for SARS-CoV-2

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Whole Genome Sequence Analysis for SARS-CoV-2

Whole-genome sequencing (WGS) has emerged as an increasingly important tool in the effort to contain COVID-19 and has led to many important findings about the virus.

Enfer Medical is proud to support the national COVID-19 pandemic response and the work of the National SARS-CoV-2 Surveillance & Whole Genome Sequencing Programme. Working with partners in the Health Protection Surveillance Centre, we continue to provide timely genomic data on circulating SARS-CoV-2 strains in Ireland to our public health colleagues. Our emphasis is on rapid detection of variants of concern and the evolution of these viruses in our population.

Our service also enables guided public health responses to outbreak management in real time. Our team are on hand to discuss how this service might support your decision making in a rapidly evolving outbreak situation.

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Clinical Details

Viruses like SARS-CoV-2 continuously evolve as changes in the genetic code (caused by genetic mutations or viral recombination) occur during replication of the genome. Most changes have little to no impact on the viral properties. However, some changes may affect how easily the virus spreads, the associated disease severity, or the performance of vaccines, therapeutics or diagnostic tools etc. During late 2020, the emergence of SARS-CoV-2 variants that posed an increased risk to global public health prompted the WHO to characterise specific Variants of Interest (VOIs) and Variants of Concern (VOCs). Details on how these variants are designated etc can be found here https://www.who.int/activities/tracking-SARS-CoV-2-variants. To date (Sept. 2022) cases of all five VOCs (B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta) and B.1.1.529 (Omicron)) have been detected in Ireland. Several sublineages of Delta and Omicron variants have also been identified in Ireland.

The interim case definition for variants of concern (VOC) for public health response and an overview of the procedures for the laboratory detection of mutations or variants of concern are available here.

Case Study

Delivering True Innovation

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At Enfer Medical, we have integrated a cutting-edge and fully automated WASPLab® (Walk Away Specimen Processor) that has significantly enhanced our testing capabilities to ensure the highest of quality when processing patient samples.
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WASPLab® at Enfer Medical
Our entire microbiology workflow has been optimized using automation and highly sophisticated robots to ensure uninterrupted incubation for rapid bacterial growth and improved turnaround times for patients.
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Our Services

Service
Health & Wellness
General health and wellness testing can include a variety of tests, depending on the needs of the individual or recommendations of
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Service
Sexual Health
Regular STI screening facilitates early treatment and reduces the long-term consequences of infection.
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Service
Respiratory Health
Rapid early pathogen identification has important treatment and infection control implications. See our range of tests here.
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Reproductive & Female Health
Hormonal analysis is hugely beneficial to identifying problems that can arise during the reproductive years.
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Sample Type &
Volume Required

Nasopharyngeal and/or oropharyngeal swabs placed in up to 3 mL of viral transport media. Samples will be pre-screened by SARS-CoV-2 PCR to determine the quantity of viral RNA in the sample. Samples with Ct values <25 will be processed for WGS. Samples with Ct values >25 can be processed upon request.

Alternatively, extracted RNA from a SARS-CoV-2 positive sample can be processed directly for WGS.

Enfer Medical

Tests/Assays

The assay offered by Enfer Medical is the llumina, CovidSeq assay for patients with PCR confirmed COVID-19 infection. The amplicon-based next generation amplicon sequencing (NGS) assay leverages a modified version of the publicly available ARTIC multiplex PCR protocol to help identify novel strains of SARS-CoV-2.  The service is clinically validated for nasopharyngeal and oropharyngeal swabs with detectable SARS-CoV-2 RNA.

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Patient

Request Form

For clients using the Enfer Medical Client Portal, the Enfer Medical Patient Request Form (PRF) will be generated when you have completed your “Test Request” within the portal linked below.

Enfer Medical Portal

Please note that samples suspected of containing high risk pathogens such as Mycobacterium tuberculosis should be clearly identified on the form and packed separately from other samples.

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72 hours

Results are available within three working days.

7 Days a Week

This assay is available seven days a week.

Packaging

The packaging/preparation of samples for delivery to the laboratory are required to be in adherence to all national regulations for the safe transport of biological materials. HSE guidance can be reviewed HERE.
There are specific packaging instructions and labelling requirements requiring triple packaging including:

  • Primary leak-proof container – tube or vial containing the sample.
  • Secondary watertight container, with absorbent material, intended to protect the primary container.
  • Outer container protects the secondary container.
  • Patient Request forms must be placed between the secondary container and the outer shipping container.


Further information on the packaging/preparation of samples for delivery to the laboratory is contained within the Enfer Medical Laboratory User Manual which clients are provided with.

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Storage & Stability

Samples must be tested within 1 week of collection and stored at 2-8°C.

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Transporting
Samples

In addition to the packaging of samples, the transport/delivery of clinical samples to the laboratory is required to be in adherence to all national regulations for the safe transport of biological materials. Enfer Medical provides a fully compliant logistics service, aligned with clients’ testing requirements.

Prompt transport of specimens:
To ensure prompt testing of samples and release of results within the published test turnaround times, samples should arrive to the laboratory by 18:00. Test turnaround time is measured from receipt of the sample at the laboratory until the time the authorised results are reported to users.

Acceptance/Rejection
of Samples

In rare cases specimens may not be suitable for testing on arrival to the laboratory. In that case the sample will be rejected at the receipt stage and the service user will be notified immediately and an explanation as to why the sample could not be processed will be provided. Reasons why samples cannot be processed include but are not limited to:

  • Samples received beyond the stability limits and/or not at the correct temperature indicated for each test.
  • Incorrect sample type received.
  • Leaking samples, sample not received or sample insufficient for analysis as stated below within sample requirements.
  • Non-compliant samples or request forms i.e. those missing sample date information, missing sample test request and/or missing sample site/type information.
  • Samples received without the necessary patient identifiers.
Clients will be provided with guidance on Sample Receipt Anomalies.

Our Services

Service
Health & Wellness
General health and wellness testing can include a variety of tests, depending on the needs of the individual or recommendations of
Find Out More
Service
Sexual Health
Regular STI screening facilitates early treatment and reduces the long-term consequences of infection.
Find Out More
Service
Respiratory Health
Rapid early pathogen identification has important treatment and infection control implications. See our range of tests here.
Find Out More
Service
Reproductive & Female Health
Hormonal analysis is hugely beneficial to identifying problems that can arise during the reproductive years.
Find Out More
Service
All Services
View the full suite of services at Enfer Medical here.......
Find Out More
Result Values:
Whole genome sequence results are reported at the SARS-CoV-2 lineage and clade level.
WGS Results:
  • Standard result reports are presented in a “line list” format. Details include but are not limited to SARS-CoV-2 lineage and clade, a list of substitutions, deletions and insertions present at the nucleic acid and amino acid level in the sample.
Phylogenetic analysis of patient samples in the context of locally circulating strains can also be provided on request. Our team can provide a consultation on the service and tailor the report output to your individual needs.

 

 

Accessing

Your Results

Following receipt at the Laboratory, results should be available within three workings days from time of receipt at the laboratory and will be reported to the referring clinician via the Enfer Medical Client Portal or in a format agreed with clients.

Client Login

Established clients can login to the portal using the link above.

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