Novel variants of SARS-CoV-2 and the impact on diagnostic testing

Novel variants of SARS-CoV-2 and the impact on diagnostic testing

Two SARS-CoV-2 variants of potential concern have recently been identified, characterized by a number of novel genetic mutations.1,2 Although mutations in viral genetic sequences have the potential to alter the performance of diagnostic tests, based on analysis of the specific mutations carried by the two novel variants, it is expected that the majority of tests currently used in primary detection of SARS-CoV-2 will be unaffected. However, laboratories should be aware of potential effects on certain diagnostic tests.

Variant designation VOC-202012/01 (or B.1.1.7) 501Y.V2

Location first identified

United Kingdom1 South Africa2

Mutations

23 mutations, of which 17 are of concern (13 non-synonymous, 4 deletions)1

Majority in S gene; ORF1ab, ORF8 and N also affected1

19 lineage-defining mutations, including eight in the S gene (three at key sites in the receptor binding domain)2

Mutations in ORF1ab, ORF3a, N and E genes also reported2

Impact on performance of molecular diagnostics

Minimal impact

69–70 deletion causes S gene dropout1

Minimal impact

No data on impact of mutations on assay performance but may impact assays that target S gene sequences

PCR assays targeting the S gene are not widely used for primary detection, and many assays target multiple genes.3 Laboratories using S-gene based assays should monitor for dropout and consider implementing assays specific for other genomic targets (e.g. E or RdRP genes) if not already included as part of existing panel

Impact on performance of antigen-based tests (including rapid lateral flow devices)

Most antigen-based tests target the C-terminus of the viral nucleocapsid protein, encoded by the N gene

Minimal impact

The N gene mutations in this variant are located at the N-terminal. A UK government assessment found that all five SARS-CoV-2 rapid antigen tests evaluated were able to successfully detect the variant4*

*Tests evaluated were Abbott Panbio, Fortress, Innova, Roche/SD Biosensor nasal swab, and Surescreen

Minimal impact anticipated

To date, no evaluation studies have been carried out to confirm that test performance is not affected but no major performance deficits are anticipated

Impact on performance of serological antibody tests

No data No data
There is potential for the performance of assays detecting antibodies to viral spike protein or nucleocapsid to be affected, but to date no evaluations have been performed

Notably, both variants have been associated with higher viral loads compared with existing variants in preliminary analyses,5,6 resulting in lower cycle threshold (Ct) values for PCR testing. Detection rates with antigen-based tests may increase due to increased concentration of antigen in samples.

While the full significance of these mutations is yet to be determined, both novel variants have been associated with higher transmission rates compared with existing variants, suggesting that they carry a selective advantage.2,7 There is currently no evidence to suggest that the mutations carried by these novel variants lead to increased pathogenicity or confer resistance to antibodies or vaccines.8 However, their rapid emergence clearly demonstrates the need for continued, robust and widespread SARS-CoV-2 surveillance, to ensure that other novel mutations are identified as early as possible.

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  1. Public Health England. Investigation of novel SARS-COV-2 variant: Technical briefing 1. https://www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201. Accessed 4 January 2021
  2. Tegally H et al. Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. medRxiv 2020. doi: 10.1101/2020.12.21.20248640
  3. World Health Organization (WHO). Molecular assays to diagnose COVID-19: Summary table of available protocols. https://www.who.int/publications/m/item/molecular-assays-to-diagnose-covid-19-summary-table-of-available-protocols. Accessed 4 January 2021
  4. Public Health England. SARS-CoV-2 lateral flow antigen tests: evaluation of VUI-202012/01. https://www.gov.uk/government/publications/sars-cov-2-lateral-flow-antigen-tests-evaluation-of-vui-20201201/sars-cov-2-lateral-flow-antigen-tests-evaluation-of-vui-20201201. Accessed 5 January 2021
  5. New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG). NERVTAG meeting on SARS-CoV-2 variant under investigation VUI-202012/01. https://khub.net/documents/135939561/338928724/SARS-CoV-2+variant+under+investigation%2C+meeting+minutes.pdf/962e866b-161f-2fd5-1030-32b6ab467896?t=1608491166921. Accessed 4 January 2021
  6. Karim SA. Presentation on the 18 December 2020 describing the new SARS-CoV-2 variant (501Y.V2) in South Africa.https://www.krisp.org.za/ngs-sa/ngs-sa_updates_covid-19_analysis_narratives_reports/token/19. Accessed 6 January 2021
  7. Davies NG et al. Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England. medRxiv 2020. doi: 10.1101/2020.12.24.20248822
  8. World Health Organization (WHO). SARS-CoV-2 Variants. https://www.who.int/csr/don/31-december-2020-sars-cov2-variants/en/. Accessed 4 January 2021

Last updated: 6 January 2021


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