How 'stealth Omicron' goes undetected by RT-PCR test; here's all you need to know

A sub-variant of Omicron known as BA.2 is already outpacing the original strain of Omicron in some European countries, raising fears that it will lead to even higher caseloads worldwide. BA.2 has been designated as a "variant under investigation" by the UK Health Security Agency, which means we know it exists but aren't sure how dangerous it will be just yet. The BA.2 sub-strain, commonly called the "stealth Omicron", reportedly, can even elude detection from RT-PCR test, which is where the 'stealth' bit comes in.

The World Health Organization (WHO) classifies the Omicron variant into three sub-strains: BA.1, BA.2, and BA.3. It went on to say that the BA.1 sub strain was found in up to 99 percent of the cases sequenced.

Where have the cases of 'stealth Omicron' been detected?

Aside from the UK and Denmark, cases of the BA.2 sub strain have been reported in Sweden, Norway, and India. Scientists in India and France have also expressed concern about the sub-strain, fearing that it will outmatch the BA.1 sub-strain.

The situation is particularly bad in Denmark. The country has reported over 30,000 cases this week, ten times the peak in the previous COVID-19 wave.

Why does one need to worry about the sub-variant?

According to researchers, the BA.3 sub-strain is probably antigenically similar to BA.1, as it shares many similar mutations. However, Denmark has stated that it is too early to tell what the BA.2 mutations mean. Denmark's government also stated that preliminary analysis shows no difference in hospitalizations between BA.2 and BA.1. As the number of people requiring intensive care decreases, the government announced that it is loosening restrictions.

What is the relevance behind the name 'stealth Omicron'?

The researchers say that the BA.1 has a mutation — a deletion in the "S" or spike gene — that shows up on PCR tests, making Omicron detection simple. BA.2 on the other hand, lacks the same mutation, making it difficult to detect, which is why it was called 'stealth Omicron'.

But in recent weeks, many experts have claimed that the sub-strain does show up on PCR tests. Accordingly, the gold standard test is the lab RT-PCR test, and there is no difference in the detection rate between Omicron and the previous Delta when using this test.

When reading about BA.2 and other new variants, it's important to keep the larger COVID-19 landscape in mind. For the time being, however, the good news outweighs the bad: vaccines continue to protect most people from the worst effects of COVID-19, and the virus itself appears to be mutating into a less lethal form.