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A summation of what is known about Omicron’s BA.2 variant

Omicron BA.2 is inherently substantially more transmissible than BA, and  possesses immune-evasive properties but does not increase its transmissibility from vaccinated individuals with breakthrough infections, found a Danish analysis.

Paul Griffin, Associate Professor, Infectious Diseases and Microbiology at University of Queensland, provides a summation of what is so far know about the variant in The Conversation:

Cases of the SARS-CoV-2 variant Omicron have escalated globally over the past two months, with many countries experiencing peaks higher than previous variants. Now we’re seeing cases of a sub-variant of Omicron, known as BA.2, emerge. Rather than a daughter of the Omicron variant BA.1 (or B.1.1.529), it’s more helpful to think of BA.2 as Omicron’s sister.

What is the Omicron lineage?

A lineage, or sub-variant, is a genetically closely related group of virus variants derived from a common ancestor. The Omicron variant comprises three sub-lineages: B.1.1.529 or BA.1, BA.2 and BA.3.

While the WHO has not given BA.2 a separate classification, the United Kingdom has labelled BA.2 a variant “under investigation”. So not yet a variant of interest or concern, based on WHO definitions, but one that is being watched closely.

This is not the first variant to have sub-lineages. Late last year, Delta “plus” or AY.4.2 was reported widely, then Omicron came along.

What’s different about BA.2?

While the first sequences of BA.2 were submitted from the Philippines – and we have now seen thousands of cases, including in the United States, the UK and some in Australia – its origin is still unknown.

The Conversation adds that the exact properties of BA.2 are also still being investigated. While there is no evidence so far that it causes more severe disease, scientists do have some specific concerns.

1. It’s harder to differentiate

A marker that helped differentiate Omicron (BA.1) from other SARS-CoV-2 variants on PCR tests is the absence of the the S gene, known as “S gene target failure”. But this is not the

The inability to detect this lineage in this way has led some to label it the “stealth sub-variant”. But it doesn’t mean we can’t diagnose BA.2 with PCR tests. It just means when someone tests positive for SARS-CoV-2, it will take us a little longer to know which variant is responsible, through genome sequencing. This was the case with previous variants.

2. It may be more infectious

Perhaps most concerning is emerging evidence that BA.2 may be more infectious than the original Omicron, BA.1.

A preliminary study from Denmark, posted on medRxiv, where BA.2 has largely replaced BA.1, suggests BA.2 increases unvaccinated people’s susceptibility of infection by just more than two times when compared with BA.1.

The researchers suggest fully vaccinated people are 2.5 times more susceptible to BA.2 than BA.1, and those who were booster vaccinated are nearly three times more susceptible

The study examined more than 2,000 primary household cases of BA.2 to determine the number of cases that arose during a seven-day follow up period.

The researchers also estimated the secondary attack rate (basically, the probability infection occurs) to be 29% for households infected with BA.1 versus 39% for those infected with BA.2.

This Danish study is still a preprint, meaning it’s yet to be checked by independent scientists, so more research is needed to confirm if BA.2 is truly more infectious than BA.1.

We’re likely to see new variants

We should expect new variants, sub-variants and lineages to continue to emerge. With such high levels of transmission, the virus has abundant opportunity to reproduce and for errors or mutations to continue to arise.

The way to address this, of course, is to try to slow transmission and reduce the susceptible pool of hosts in which the virus can freely replicate.

Strategies such as social distancing and mask-wearing, as well as increasing vaccination rates globally, will slow the emergence of new variants and lineages.

Study details

Transmission of SARS-CoV-2 Omicron VOC subvariants BA.1 and BA.2: Evidence from Danish Households

Plesner Lyngse, Carsten Thure Kirkeby, Matthew Denwood, Lasse Engbo Christiansen, Kåre Mølbak, Camilla Holten Møller, Robert Leo Skov, Tyra Grove Krause, Morten Rasmussen, Raphael Niklaus Sieber, Thor Bech Johannesen, Troels Lillebaek, Jannik Fonager, Anders Fomsgaard, Fredrik Trier Møller, Marc Stegger, Maria Overvad, Katja Spiess, Laust Hvas Mortensen.

Posted on medRxiv on 28 January 2022


The Omicron SARS-CoV-2 variant of concern (VOC lineage B.1.1.529), which became dominant in many countries during early 2022, includes several subvariants with strikingly different genetic characteristics. Several countries, including Denmark, have observed the two Omicron subvariants: BA.1 and BA.2. In Denmark the latter has rapidly replaced the former as the dominant subvariant.

Based on nationwide Danish data, we estimate the transmission dynamics of BA.1 and BA.2 following the spread of Omicron VOC within Danish households in late December 2021 and early January 2022.

Among 8,541 primary household cases, of which 2,122 were BA.2, we identified a total of 5,702 secondary infections among 17,945 potential secondary cases during a 1-7 day follow-up period. The secondary attack rate (SAR) was estimated as 29% and 39% in households infected with Omicron BA.1 and BA.2, respectively.

We found BA.2 to be associated with an increased susceptibility of infection for unvaccinated individuals (Odds Ratio (OR) 2.19; 95%-CI 1.58-3.04), fully vaccinated individuals (OR 2.45; 95%-CI 1.77-3.40) and booster-vaccinated individuals (OR 2.99; 95%-CI 2.11-4.24), compared to BA.1. We also found an increased transmissibility from unvaccinated primary cases in BA.2 households when compared to BA.1 households, with an OR of 2.62 (95%-CI 1.96-3.52). The pattern of increased transmissibility in BA.2 households was not observed for fully vaccinated and booster-vaccinated primary cases, where the OR of transmission was below 1 for BA.2 compared to BA.1.

We conclude that Omicron BA.2 is inherently substantially more transmissible than BA.1, and that it also possesses immune-evasive properties that further reduce the protective effect of vaccination against infection, but do not increase its transmissibility from vaccinated individuals with breakthrough infections.


The Conversation article – BA.2 is like Omicron’s sister. Here’s what we know about it so far (Creative Commons Licence)


medRxiv article – Transmission of SARS-CoV-2 Omicron VOC subvariants BA.1 and BA.2: Evidence from Danish Households (Open access)


See more from MedicalBrief archives:


Increased risk of SARS-CoV-2 reinfection associated with Omicron — South African study


Discovery Health’s large real-world analysis of Omicron


SA-German study shows boosters protect but unlikely to prevent Omicron


WHO: Omicron more transmissible but not necessarily milder



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