The ability of COVID-19 tests to detect emerging genetic variants of SARS-CoV-2
The TGA is undertaking a post-market review of all Point of Care and Laboratory tests included in the 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.
The Therapeutic Goods Administration (TGA) has undertaken a post-market review of all point-of-care (POC) and laboratory tests included in the Australian Register of Therapeutic Goods (ARTG) that are intended to identify individuals with COVID-19. The review verified whether these tests could accurately detect emerging genetic variants of the SARS-CoV-2 virus.
Like all viruses, SARS-CoV-2 can mutate over time, resulting in genetic variation among the viral strains circulating in the community. The aim of the post-market review was to ensure all viral diagnostic tests continued to be able to detect known and emerging genetic variants. If the kits were not able to do so, they could have potentially led to false negatives and delayed the treatment or isolation of individuals with COVID-19.
Although this post-market review has been completed, the TGA will continue to monitor the emerging variants of SARS-CoV-2 with at least 5% prevalence in the global population, such as mutations that occur in at least 5% of each viral variant. The TGA may reopen the review or commence additional testing if there is an indication that new variants are impacting the performance of the tests.
Variants' impact on test performance can be influenced by the variant's prevalence in the population and the design of the test kit.
Variants
Multiple variants of SARS-CoV-2 have been emerging and circulating globally since the start of the pandemic.
The nomenclature system and a list of the variants are maintained by the World Health Organisation (WHO) and the Communicable Diseases Genomics Network (CDGN).
The variants are broken down into classifications, including:
- variants of concern (VOC)
- variants of interest (VOI)
- variants under monitoring (VUM)
- formerly monitored variants (FMV).
During the pandemic, the understanding of the impacts of SARS-CoV-2 variants on public health improved and – based on the phenotypic characteristics (transmissibility, disease severity, risk of reinfection, and impacts on diagnostics and vaccine performance) – variants were reclassified.
As of 15 March 2023, the WHO has updated its definitions for variants of SARS-CoV-2, to consider sublineages of Omicron independently, as opposed to treating all sublineages as part of the Omicron VOC.
The updated WHO definition for VOCs is more specific than the old definition, requiring the variants to possess major evolutionary steps when compared to previous variants that would require major public health interventions.
All current VOIs and VUMs are sublineages of Omicron and have been found to have similar mutations and phenotypes.
WHO/CDGN variant classifications
Currently circulating variants of concern (VOCs)
As of 15 March 2023, there are currently no VOCs, as the Omicron parent variant has now been designated a previously circulating VOC.
Currently circulating variants of interest (VOIs)
As of 21 April 2023, the WHO has listed the following VOIs
| Classification | Pango Lineage | Genetic features | Nextstrain clade | First identified |
|---|---|---|---|---|
| VOI | XBB.1.5 | Recombinant of BA.2.10.1 and BA.2.75 sublineages, i.e. BJ1 and BM.1.1.1, with a breakpoint in S1 XBB.1 + S:F486P (similar Spike genetic profile as XBB.1.9.1) | 23A | 5 January 2022 |
| VOI | XBB.1.16 | Recombinant of BA.2.10.1 and BA.2.75 sublineages, i.e. BJ1 and BM.1.1.1 XBB.1 + S:E180V, S:K478R and S:F486P | 23B | 9 January 2022 |
Currently circulating variants under monitoring (VUMs)
As of 17 May 2023, the WHO has listed the following VUMs
| Classification | Pango Lineage | Genetic features | Nextstrain clade | First identified |
|---|---|---|---|---|
| VUM | BA.2.75 | BA.2 + S:K147E, S:W152R, S:F157L, S:I210V, S:G257S, S:D339H, S:G446S, S:N460K, S:Q493R reversion | 22D | 31 December 2021 |
| VUM | CH.1.1 | BA.2.75 + S:L452R, S:F486S | 22D | 27 July 2022 |
| VUM | BQ.1 | BA.5 + S:R346T, S:K444T, S:N460K | 22E | 7 February 2022 |
| VUM | XBB* *excludes XBB sublineages listed here as VOIs and VUMs | BA.2+ S:V83A, S:Y144-, S:H146Q, S:Q183E, S:V213E, S:G252V, S:G339H, S:R346T, S:L368I, S:V445P, S:G446S, S:N460K, S:F486S, S:F490S | 22F | 13 August 2022 |
| VUM | XBB.1.9.1 | Recombinant of BA.2.10.1 and BA.2.75 sublineages, i.e. BJ1 and BM.1.1.1 XBB.1 + S:F486P (similar Spike genetic profile as XBB.1.5) | Not assigned | 5 December 2022 |
| VUM | XBB.1.9.2 | Recombinant of BA.2.10.1 and BA.2.75 sublineages, i.e. BJ1 and BM.1.1.1 XBB.1 + S:F486P, S:Q613H | Not assigned | 5 December 2022 |
| VUM | XBB.2.3 | Recombinant of BA.2.10.1 and BA.2.75 sublineages, i.e. BJ1 and BM.1.1.1 XBB + S:D253G, S:F486P, S:P521S | Not assigned | 9 December 2022 |
Previously circulating variants
| Classification | WHO / CGDN | Pango Lineage | GISAID clade/lineage | Nextstrain clade | First identified |
|---|---|---|---|---|---|
| VOC | Omicron | B.1.1.529 | GR/484A | 21K | Multiple countries, November 2021 |
| VOC | Alpha | B.1.1.7 | GRY (formerly GR/501Y.V1) | 20I (V1) | United Kingdom, Sep 2020 |
| VOC | Beta | B.1.351 | GH/501YV2 | 20H (V2) | South Africa, May 2020 |
| VOC | Gamma | P.1 | GR/501Y.V3 | 20J (V3) | Brazil, Nov 2020 |
| VOC | Delta | B.1.617.2 (+ AY lineages) | G/478K.V1 | 21A | India, Oct 2020 |
| VOI | Lambda | C.37 | GR/452Q.V1 | 21G | Peru, December 2020 |
| VOI | Mu | B.1.621 | GH | 21H | Colombia, January 2021 |
| VUM | Kappa | B.1.617.1 | G/452R.V3 | 21B | India, Oct 2020 |
| VUM | Iota | B.1.526 | GH/253G.V1 | 21F | United States, November 2020 |
| VUM | Eta | B.1.525 | G/484K.V3 | 21D | Multiple countries, December 2020 |
| FMV | Epsilon | B.1.427, B.1.429 | GH/452R.V1 | 21C | United States, California |
| FMV | Zeta | P.2 | GR/484K.V2 | 20B/S.484K | Brazil |
| FMV | Theta | P.3 | GR | 20B/S:265C | Philippines |
Information for laboratories and health professionals
The three main types of SARS-CoV-2 tests include:
- nucleic acid tests (NATs), which detect SARS-CoV-2 viral RNA
- rapid antigen tests (RATS), which detect antigen viral proteins from SARS-CoV-2
- serology tests, which detect IgM and/or IgG antibodies against SARS-CoV-2.
Laboratory and health professionals should be aware that:
- genetic variants of SARS-CoV-2 may yield false negative test results
- NATs that utilise multiple genetic targets to determine a final result are less likely to be impacted by increased prevalence of genetic variants.
The TGA recommends that negative results be considered in combination with clinical observations, person’s history and epidemiological information, and that repeat testing using a different test (with different genetic targets) be considered if COVID-19 is still suspected after a negative test result.
Post-market reviews
Post-market review of nucleic acid tests
The TGA continues to monitor all NAT kits included in the ARTG to determine whether they will be impacted by the known variants, with ongoing activity to assess their ability to detect all emerging variants of interest.
Information about each test kit's performance against the emerging variants of concern will be published as it becomes available.
Post-market review of antigen and RATs
The TGA has undertaken desktop analyses of all laboratory antigen and RATs included in the ARTG to determine whether they have been impacted by the current known variants, with ongoing activity to assess their ability to detect all emerging variants of interest.
The post-market review included laboratory testing of all PoC and self-test RAT kits included in the ARTG to validate their performance in detecting the Delta and Omicron variants.
Post-market review of serology tests
The post-market review monitored the ability of COVID-19 diagnostic test kits to detect emerging genetic variants of the SARS-CoV-2 virus. Serological assays fell outside of the scope of this review of viral variants. However, the TGA has undertaken a post-market review of all serology-based point-of-care tests included in the ARTG.
Serology tests detect the presence of antibodies in the blood from the body's adaptive immune response to an infection, like COVID-19. They generally provide historic information that indicates whether an individual has past exposure to SARS-CoV-2 but do not detect the virus itself. It is not yet evident that the detection of antibodies reflects the presence of protective immunity, so the detection of antibodies may not exclude remaining infectivity in a patient.
- Post-market review of all serology-based PoC tests included in the ARTG
- Post-market evaluation of serology-based PoC tests
Conditions imposed on all COVID-19 serology tests approved for ARTG inclusion
All COVID-19 tests that are included in the ARTG based on an expedited assessment process are subject to additional non-standard conditions that inform post-market validations as experience and knowledge around COVID-19 diagnostic testing grows.
The conditions require that additional evidence to support the ongoing safety and performance of the device be provided to the TGA within 12 months of approval.
Some states and territories have prohibited or restricted use of serology rapid screening tests. Please check the TGA website for further information about serology test kits and their legal supply.
- Non-standard condition on COVID-19 tests
- COVID-19 testing in states and territories
- Serology PoC test kits
- Legal supply of COVID-19 test kits
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. See the TGA Incident Reporting and Investigation Scheme (IRIS) for more information.
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.