HYDERABAD: The RT-PCR test is unlikely to identify the Omicron (B.1.1.529) sub-lineage
BA.2, top experts said on Wednesday. Since BA.2 does not have the S gene dropout unlike
the main sub-lineage BA.1, it escapes identification through RT-PCR tests, scientists said.

The RT-PCR test will still give a positive result for Covid even if the sample contains BA.2. To
know the presence of BA.2, one needs to go for genome sequencing.

Dr Emma Hodcroft, co-developer of Nextstrain, an open-source project to harness scientific
and public health potential of pathogen genome data, said there is need to design new PCRs
to identify this sub-lineage. “A new set of sequences closely related to Omicron have been
detected. We absolutely can detect cases with PCR. What we can’t tell as easily is that they
are Omicron or Omicron-like,” she said.

The lineage may also cause immune evasion and vaccine breakthrough infection.

Variant can cause immune evasion, says IGIB scientist

Commenting on a research finding on Omicron, Dr Vinod Scaria, senior scientist at Delhi’s
Institute of Genomics and Integrative Biology (IGIB), tweeted that the variant can indeed
cause immune (antibody) evasion.

“(The research study) corroborates with additional clinical/epidemiological evidence on reinfections and breakthrough infections as well as what was suggestive of mutational profile
and computational analyses,” he posted.

He said the Pfizer vaccine has better efficacy in hybrid immunity (vaccine plus previous
infection).

The Omicron lineage first identified on November 8 has now split into two sub-lineages –
BA.1 and BA.2.

The new sub-lineages were officially announced on December 7 by Phylogenetic Assignment
of Named Global Outbreak Lineages (PANGOLIN), which has been assigning nomenclature
to the novel coronavirus variants under PANGO lineage system.

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