BA.2 Now Dominant in South Africa: Could New ‘Stealth’ Sub-Variant Delay Hoped-For Pandemic Reprieve?
A molecular model of the Omicron subvariant BA.2

The BA.2 sub-variant of Omicron is now the dominant COVID-19 variant in South Africa, the head of Africa’s Centers for Disease Control and Prevention (CDC) confirmed on Thursday – raising questions about whether the continued global creep of the new SARS-CoV2 sub-variant could dash hopes of a much-needed COVID-19 reprieve.

“We have data from South Africa that the BA.2 lineage has now become the predominant variant in South Africa,” said Africa CDC director John Nkengasong at a regular online media briefing.

He added that the variant had already been detected in Botswana, Kenya, Malawi, Mauritius and Mozambique – and is likely present in other parts of the continent, as well.  That follows earlier reports from Europe, notably Denmark, and India where BA.2 is also overtaking the BA.1 version of the Omicron variant – becoming the latest variant to watch around the globe.

BA.2: Omicron’s ‘stealth’ sub-variant

Artist’s rendition of SARS-CoV2

The World Health Organization began monitoring BA.2 weeks ago, alongside other “sister” or “daughter” variants of the Omicron: BA.1.1 and BA.3. But BA.2 has been referred to as the “stealth” sub-variant because it has genetic mutations that could make it harder to distinguish from the earlier Delta variant, as compared to the original Omicron, according to the American Medical Association.

WHO already classified Omicron as a SARS-CoV2 variant of concern – alongside Alpha, Beta and Delta. Since BA.2 is “related” to Omicron, it is also a variant of concern.

Variants of concern, otherwise known as VOCs, are those variants about which WHO has enough data or signs to be concerned and warn the public to take extra care, explained Dr. Dorit Nitzan, former Coordinator of the Health Emergencies for WHO’s European region. 

“I would probably call it a sister,” Prof William Moss, Executive Director of the International Vaccine Access Center at Johns Hopkins University in Baltimore, told Health Policy Watch. “This sub-variant has actually been around for a long time. It was identified around the same time as BA.1 and so they are obviously genetically related like siblings. But we don’t really know the temporal sequence in which these variants evolved.”

What scientists do understand is that BA.2 is more transmissible, based on evidence that has emerged from India, Denmark and now South Africa, where BA.2 is becoming dominant in these settings – countries where BA.1 was most prevalent.

Last month, Danish scientists reported that BA.2 was around 33% more transmissible than the original Omicron strain.

“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,” the study’s researchers said.

BA.2: More transmissible, not deadlier

Other studies have found the variant to be as much as 50% transmissible, Nitzan said, though she added that the percentage does not really matter. What is important to know is that you can get infected faster.

Before WHO labels a variant a VOC, it first classifies it as a “Variant of Interest” or VOI, meaning that scientists are tracking the variant, but still learning about it.

“WHO is following many variants in many different lineages,” Nitzan told Health Policy Watch. “We know that many of them are not going to be developed.”

Omicron, however, is a variant that did develop and “it now appears to have its own little family,” she added:

“I think it could happen that just about everyone will have COVID,” Nitzan said. “It can happen if we cannot protect ourselves with masks, social distancing and good hygiene.”

And, of course, vaccination.

Moss said that while BA.2 is more transmissible, the good news is that it does not appear to cause more severe disease than the original Omicron strain, especially in people who have been inoculated. While vaccine effectiveness against Omicron infection appears much lower than what was seen against previous variants, it does still seem to be keeping most people out of the hospital.

He added that “the emergence and spread of BA.2 is not going to dramatically impact the course of the pandemic in the United States or European Union. It may just prolong it a bit.”

NeoCoV: ‘More attention than it deserves’

The research team prepares to gather samples from a dromedary camel in surveillance of MERS.

Another coronavirus discovered in bats last month has raised the eyebrows of some scientists: NeoCoV, a new bat coronavirus, was identified in South Africa.  It is of concern because it is closely related to the deadly MERS-CoV virus that has caused limited outbreaks since 2012 in countries around the Arabian Peninsula, where the virus is typically transmitted to humans from camels.

However, unlike MERS,  NeoCoV uses an ACE-2 receptor to infect cells  – the same mechanisms that has made SARS-CoV2 so infectious.

To date, no cases of NeoCoV have been reported in humans.

However, one pre-print study led by scientists associated with Wuhan’s Institute of Virology, warns that the NeoCoV virus could be on the threshold of human infectivity – due to its uptake of the ACE-2 receptor gene.

“Our study demonstrates the first case of ACE2 usage in MERS-related viruses, shedding light on a potential bio-safety threat of the human emergence of an ACE2 using “MERS-CoV-2” with both high fatality and transmission rate,” states the study, published in late January 2022.

“Notably, the infection could not be cross-neutralized by antibodies targeting SARS-CoV-2 or MERS-CoV,” the paper also adds.

The study also notes that NeoCoV has certain genomic characteristics of MERS-CoV, which was 20 times more deadly than the SARS-CoV2 Delta variant, for example –although much less transmissible.

“This unexpected ACE2 usage of these MERS-CoV close relatives highlights a latent biosafety risk, considering a combination of two potentially damaging features of high fatality observed for MERS-CoV and the high transmission rate noted for SARS-CoV-2,” the report said. “Furthermore, our studies show that the current COVID-19 vaccinations are inadequate to protect humans from any eventuality of the infections caused by these viruses.”

Notably, Wuhan’s Institute of Virology has been under international scrutiny for months due to suggestions from some international virus experts that a biosafety lapse at the laboratory that studies bat coronaviruses could have been the cause of the original Wuhan SARS-CoV2 leap into human populations.  That narrative has been  disputed by other experts who point to wild food chain sources as the  more likely original cause of infection – and even more adamantly by official Chinese sources, who have also sought to point attention to SARS and SARS-like virus threats elsewhere in the world.

A new WHO SAGO group of experts began meeting late last year to explore the narratives further – although China has not agreed to allow a second expert mission to enter the country  to further investigate the SARS-CoV2 virus origins.

Moss, however, said that in his view, NeoCoV is getting more attention than it deserves.

“There is no evidence that it can be transmitted from bats to humans,” Moss said. “My takeaway from NeoCoV is just a reminder that there are a wide-range of potential viruses with potential to cause spillover events.”

Image Credits: Delthia Ricks/Twitter, Trinity Care Foundation/Flickr, NIAID/Flickr.

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