The appearance of this sneaky “BA.2” sub-variant – “subline” is the scientific term – is the latest development in the still-developing crisis that the BA.1 Omicron baseline triggered after officials health officials in South Africa confirmed the new lineage, with its dozens of key mutations, two weeks ago.
The difficult to distinguish BA.2 subline is also a powerful reminder to the unvaccinated to get vaccinated and to the unboosted to get a boost. There is a lot we don’t know about Omicron and its sublines, but the first signs are that the major vaccines are still working very well against them. And, of course, all jabs work even better with a boost.
Scientists first detected the devious BA.2 days ago after genetically sequencing a batch of test samples collected by officials in South Africa, Australia and Canada. So far, the sub-variant has been identified in 30 countries and six continents.
“You can still detect it by PCR, but you cannot distinguish it from the dominant Delta strain,” Rob Knight, head of a genetic computation lab at the University of California at San Diego, told The Daily Beast. In other words, a PCR test can tell you that you have COVID, but it could not tell you that you specifically caught BA.2.
To be fair, this indistinguishability could be a problem. If Omicron and its sublines prove to be more dangerous than Delta and its sublines, then it would be very important to know exactly how many Omicron cases there are as a subset of all COVID infections. That is, how far into the population Omicron has “penetrated”, to borrow the term epidemiological.
“It is possible that this so-called ‘stealth variant’ means that there is more penetration of these disturbing variants in circulation than we realize,” said Lawrence Gostin, a global health expert at the University. from Georgetown, to the Daily Beast. This does not mean that we are powerless to assess the potential surge being fueled by Omicron in cases that already appear to be underway in much of the world. This Is means we’re catching up as we fine-tune our PCR tests and perform more detailed genetic sequencing of samples.
To understand how BA.2 could be hiding behind Delta, potentially obscuring the true extent of Omicron’s spread, you need to understand how PCR testing works. PCR involves a sample of the potential virus and a “primer” that the test creators adapted to encourage the virus to replicate. Expose the sample to the primer and wait a bit. If the virus replicates, you have a positive test result.
Here is the trap. PCR tests cannot distinguish one line of a particular virus from another. You can design the primer to match some unique attributes of the lineage that worries you the most, but since many lineages share genetic characteristics, the test may be positive for the virus but inconclusive for the lineage.
Experts initially hoped that we could use the same PCR test we used to detect the older SARS-CoV-2 Alpha line to find Omicron as well. This is because Alpha and Omicron share a genetic marker. “A deletion of amino acids 69 and 70 in the Spike gene,” according to Niema Moshiri, a geneticist at the University of California, San Diego.
Here is the problem. “Omicron’s new sub-line, BA.2, doesn’t have this deletion,” Moshiri told The Daily Beast. Guess which lineage too omit this deletion? That’s right: Delta. So lab technicians who use old Alpha tests to search for Omicron might miss the BA.2 cases. Meanwhile, techs looking for Delta could also accidentally count a bunch of BA.2 cases.
The ambiguity of the tests could slow us down as we try to understand how bad Omicron is and where and how fast it is spreading. But that will not really prevent us from understanding or approaching the new lines and his sub-lines.
After all, we still rely on detailed genetic sequencing, as opposed to rapid PCR tests, to really scrutinize and track the novel coronavirus. “With sequencing, we would be able to determine the lineage anyway, regardless of BA.1 or BA.2,” Moshiri explained.
But sequencing costs more than testing and takes longer. “It’s a significant problem,” Knight said.
Yet BA.2’s inability to hide from sequencing is why University of Washington virologist Keith Jerome said he wasn’t so worried. Jerome’s lab detected the first three cases of Omicron in Washington state last week. Washington is sequencing 14% of the tests, Jerome said, so BA.2 cannot stay hidden for long. “This Omicron sub-variant might go into hiding for a day or two, but if it becomes common, we’ll find it through random sequencing. “
All that to say, yes BA.2 is a problem. The extent of a problem depends, to a large extent, on how serious Omicron is after further study. “It could be that these variants could be considered a new post-pandemic normal, just like the flu, in which case the tests – while important for detecting hot spots and for assessing or projecting likely loads – may not be. too vital, ”Edwin Michael, an epidemiologist with the Center for Global Health Infectious Disease Research at the University of South Florida, told The Daily Beast.
Either way, BA.2 is a problem with obvious solutions. New PCR primers. No more sequencing. And, as always, masks, vaccines and boosters. “I know everyone is ‘excited’ about Omicron,” Stephanie James, head of a COVID testing lab at Regis University in Colorado, told The Daily Beast. “But variations are expected by the scientific community. The advice is the same–get vaccinated and wear a mask.