Arrow icon

SARS-CoV-2 Variants and the Detect Covid-19 Test™

BA.2, BA.2.12.1, BA.4, and BA.5 Omicron “subvariants” make up essentially all infections in the U.S. today. The Detect Covid-19 Test is expected to recognize them all (in addition to the older variants they have replaced). The increased sensitivity of molecular tests compared to antigen tests is important for accurate detection of Omicron and its subvariants, which are more likely to be associated with samples with low viral loads, as recently reported by FDA.

July 7, 2022

Currently circulating variants

Essentially all Covid-19 infections in the U.S. today are caused by 1 of 4 “subvariants” of the infamous Omicron variant that itself swept through the U.S. in December 2021. These 4 Omicron subvariants are BA.2, BA.2.12.1, BA.4 and BA.5. This analysis from the CDC's national genomic surveillance system shows the proportion of each variant found among infections in the US each week over the the period of March through June 2022.

Variants likely to dominate in the near future

The proportion of Covid-19 infections in the U.S. caused by BA.4 and BA.5 subvariants can be seen from the above analysis to be increasing over recent weeks, while the proportion of infections caused by BA.2 and BA.2.12.1 has been decreasing. Combined with observation of their rapid rise in other parts of the world, and with an apparent ability to infect people who are immune to earlier forms of Omicron and other variants (whether from natural infection or vaccination), it’s likely that BA.4 and BA.5 will soon cause most infections in the U.S. – with BA.5 likely to ultimately outcompete BA.4.

Detect Covid-19 Test performance against variants

The Detect Covid-19 Test is designed to maximize its chances of continuing to recognize new SARS-CoV-2 variants as they emerge. 

The Detect Covid-19 Test functions by targeting a unique region of the SARS-CoV-2 genome with nucleic acid amplification reagents called primers. As for all organisms, mutations (small changes in the genome sequence) occur spontaneously across the SARS-CoV-2 genome, and may end up rising in frequency in particular geographical regions, or globally, due to either simple chance or to positive selection in the case where the mutation incurs a functional “fitness” advantage, such as increased transmissibility or immune escape. Positively selected mutations are more likely to occur in some genes or parts of the genome than others.

The part of the SARS-CoV-2 genome targeted by the Detect Covid-19 Test is a highly stable or conserved (less likely to be mutated) region of the ORF1ab gene, unlike the genome regions where proliferation-enhancing mutations are most quickly appearing (eg. the S gene encoding the famous Spike protein). The ORF1ab gene encodes several nonstructural proteins (i.e. proteins that are not part of the viral particle structure) necessary for the SARS-CoV-2 viral life cycle. Mutations have not persisted within our target region to date, so it’s less likely that we'll see mutations that could impact test performance emerge in the future.

In addition to targeting a genetically stable region of the genome, the nucleic acid amplification chemistry used by the Detect Covid-19 Test (RT-LAMP) is known to be largely unaffected by chance single mutations even if they did occur in the precise region of the SARS-CoV-2 genome targeted by the test. 

The superior sensitivity of molecular tests like the Detect Covid-19 Test over rapid antigen tests helps the Detect Covid-19 Test remain accurate even in the face of variants with new behaviors, such as lowered abundance of the virus in the nasal tissue analyzed by the majority of tests. This lowered viral load appears to be the case for Omicron and its subvariants, noted the Director of the Food and Drug Administration’s Office of In Vitro Diagnostics and Radiological Health this week, explaining that a single antigen test may only be able to correctly identify the virus 60% of the time in symptomatic patients infected with the Omicron variant. 

We continuously monitor public SARS-CoV-2 genomic surveillance data for the emergence of new variants that could affect Detect Covid-19 Test performance. 

We run software-based analyses that regularly check for mutations within the Detect Covid-19 Test target region of new SARS-CoV-2 genome sequences. If a significant number of SARS-CoV-2 genome sequences are found by these analyses to have a mutation posing a potential risk to the test’s performance, its impact is verified in the lab. From these analyses, the Detect Covid-19 Test is expected to recognize every Variant of Concern and Variant of Interest declared to date, including more specifically the currently circulating BA.2, BA.2.12.1, BA.4 and BA.5 Omicron sub-variants described above.


Harry Kemble, Ph.D.

Informatics & Nucleic Acids Group Lead

Detect Blog image

Partner with Detect™ to get back to business