Fact Check-COVID-19 variants are monitored by genomic sequencing of samples

Questions are appearing on social media about how we know there is a rise in certain COVID-19 variants if individual tests cannot detect specific variants. The U.S. Centers of Disease Control and Prevention (CDC) and several experts explained to Reuters that increases in COVID-19 variants are detected by analysing samples of cases through a process called genomic sequencing.

“How can a rise in certain variants be detected when test kits do not decipher between different variant strains??” ask the posts ( here , here , here ). "Since there is no “Delta Variant” test, how exactly are people being diagnosed with the “Delta Variant”?” say other posts (here).

Viruses constantly change through mutation, creating new variants, which may have different characteristics. Scientists monitor these changes so that they can learn how they might affect the way the virus spreads, the severity of its effects, how easy it is to detect and whether vaccines will be effective against it. At the time of publication there were multiple variants of the virus that causes COVID-19 (SARS-CoV-2) in the United States, including the Delta variant (B.1.617.2) (here).

Jade Fulce, a spokesperson for the CDC, told Reuters via email that it is correct that COVID-19 tests for current infection “will not be able to tell you which specific variant you (or a patient) might have.”

This does not mean that variants cannot be monitored. The CDC receives approximately 750 samples per week from state health departments and other public health agencies to be evaluated. The CDC then uses a process called genomic sequencing to analyse these samples to identify and characterize variants (here).

Genomic sequencing decodes the genes in the SARS-CoV-2 genome to tell scientists which variant might be present in the specimen, allowing them to monitor mutations and learn more about the virus (here).

“At this time, genomic sequencing is available for surveillance purposes only, not for individual diagnostic purposes,” Fulce told Reuters.

She said the amount of sequencing by public health laboratories has “generally increased over the course of the pandemic, ranging from about 2,000 to 15,000 sequences per week.”

“Genomic sequencing is the definitive method for identifying variants. As of now, it’s also the main way that new variants are identified when they appear”, Dr Stephen Morse, Professor of Epidemiology at the Columbia University Medical Center (here) confirmed to Reuters via email.

Asked whether he thought it was an accurate method, Morse said, “I think we should be doing more systematic virus testing in the general population to have better estimates of viral circulation in the community. But when 80%+ of the viruses tested (by doing genomic sequencing on samples from PCR+ tests) are Delta variant, there’s a very high statistical likelihood it’s true.”

Professor Nick Loman, Professor of Microbial Genomics and Bioinformatics at the University of Birmingham in Britain ( here , here ) told Reuters via email, “Generally speaking whole genome sequencing is required in order to detect new variants that have previously not been observed.”

Loman said that a test can be devised to identify a known variant using a process called ‘genotyping’ but the sequencing is still required even with the genotyping: “genotyping techniques can occasionally be fooled as the virus evolves and so have to be constantly monitored to compensate for this by comparing with sequencing results.”


Missing context. Although COVID-19 tests cannot detect a specific variant, the CDC tracks variants through genomic sequencing of samples.

This article was produced by the Reuters Fact Check team. Read more about our fact-checking work here .