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Ability of COVID-19 tests to detect emerging genetic variants of SARS-CoV-2

13 January 2021

The Therapeutic Goods Administration (TGA) is undertaking a post-market review of all Point of Care (PoC) and Laboratory tests included in the Australian Register of Therapeutic Goods (ARTG), which are intended to identify patients with COVID-19, to ensure they can detect the emerging SARS-CoV-2 genetic variants and remain accurate. This review is in addition to the on-going review of the overall performance of PoC tests.

This web page will be updated during the course of the post-market review.

Emerging variants

The SARS-CoV-2 virus can mutate over time, like all viruses, resulting in genetic variation in the circulating viral strains. Two new, potentially more virulent SARS-CoV-2 variants, have been identified and are referred to as:

  • SARS-CoV-2 VUI 202012/01 (Variant Under Investigation, year 2020, month 12, variant 01) or B.1.1.7 lineage, identified through viral genomic sequencing in the United Kingdom (UK). This variant is defined by multiple specific spike protein mutations. The UK has identified that this mutation may impact performance characteristics of SARS-CoV-2 diagnostics. More information about this variant can be found in the European Centre for Disease Prevention and Control's Threat Assessment Brief (pdf,648kb).
  • The South African variant of SARS-CoV-2, known as 20C/501Y.V2 or B.1.351 lineage, shares some mutations with the UK variant but is also reported to carry other mutations. Further information can be found on the Centre of Disease Control (CDC) website

Information for laboratories and health professionals

The presence of SARS-CoV-2 genetic variants in a patient sample can potentially change the performance of a COVID-19 test. Tests that rely on the detection of multiple regions of the genome may be less impacted by genetic variation in the SARS-CoV-2 genome than tests that rely on detection of only a single region.

These variants have also been associated with higher viral loads compared with existing variants in preliminary analyses. This can result in lower cycle threshold (Ct) values for genetic testing undertaken by polymerase chain reaction (PCR).

Laboratory and health professionals should be aware that genetic variants of SARS-CoV-2 may yield false negative test results and that the use of PCR tests that utilise multiple genetic targets to determine a final result are less likely to be impacted by increased prevalence of genetic variants. The majority of PCR tests approved by the TGA detect multiple genetic targets. The TGA recommends that negative results be considered in combination with clinical observations, patient history, and epidemiological information and to consider repeat testing with a different test (with different genetic targets) if COVID-19 is still suspected after receiving a negative test result.

Reporting problems

Consumers and health professionals are encouraged to report problems with medical devices. Your report will contribute to the TGA's monitoring of these products. For more information see the TGA Incident Reporting and Investigation Scheme (IRIS).

The TGA cannot give advice about an individual's medical condition. You are strongly encouraged to talk with a health professional if you are concerned about a possible adverse event associated with a medical device.