About that BA.2.86 COVID variant
There has been some head-scratching about the recent COVID variant, BA.2.86, which has 34 amino acid changes in the spike protein compared to its closest reference sequence. Commenter rjs asks: “how can one virus suddenly wake up one morning and find it had mutated 30 times overnight? And that all 30 of its mutations were viable? ..it’s difficult for me to understand how such a major change could have possibly occurred as part of what should naturally be a slow-moving evolutionary process…”
Let’s unpack this comment, since I think doing so can clarify virus population biology, how variants arise and what they mean.
First of all, we’re not talking about “one virus” acquiring 34 mutations “overnight.” It is estimated each infected person carries 10^9–10^11 SARS-CoV-2 virions* during peak infection and that the genetic diversity of virions in an infected host covers all possible single nucleotide substitutions. So the BA.2.86 variant emerged from an immense, evolving population. What likely happened is that BA.2.86 arose from a chronically infected host who harbored orders of magnitude more virus particles over the course of infection than would be carried by most people. This could be someone who is immunocompromised, either by age, disease or medication, and thus (a) was delayed in clearing the virus and (b) wasn’t providing strong immunological selection. So what happened over time (timespan of weeks, not geological time) is that sequence changes accumulated in the population of virus particles, one family of which emerged as BA.2.86.
Secondly, a useful distinction can be made between “variants” and “mutations.” Those 34 differences are probably not all functionally significant—some are probably neutral, both for virus entry and for immunogenicity. In the event, it looks like there might be less than meets the eye in the case of BA.2.86:
“Two independent labs have basically shown that BA.2.86 essentially is not a further immune escape compared with current variants,” Dr. Dan Barouch, director of the Center for Virology and Vaccine Research at Beth Israel Deaconess Medical Center and leader of one of the labs, told CNN.
“Their results align with earlier experiments by labs in China and Sweden. Taken together, the data suggests that BA.2.86 will not be as troublesome as experts had feared. In short, this one seems to be a “scariant.””
* for comparison, it is estimated that the total number of humans that have ever lived is 117 billion, or 1.17×10^11, and the coronavirus genome is a tiny fraction of the size of the human genome.
BA.2.86 is a COVID scariant
New study led by Boston scientists finds latest COVID-19 variant is less of a threat than feared
Boston Globe – just in
US lab tests suggest new Covid-19 variant BA.2.86 may be less contagious and less immune-evasive than feared
CNN – Sep 4
@Fred,
This CNN link is identical to the one I posted. The Globe link you posted says the same thing and also quotes Barouch.
Fun fact: ‘Scariant’ (Urban Dictionary)
A new variant of COVID imagined by governments to scare the public into complying with new regulations.
In other words, a scary variant.
A good friend, in his mid-80’s, is dealing with covid, has had it for going on one month now. Still in good spirits, at least, says he’s ‘on the mend.’
@Fred,
Let’s hope he doesn’t get long COVID, although after one month, he may have it already.
Yeah, I know. He’s under the watchful eye of his daughter, a physician.
Covid Continues to Rise, but Experts Remain Optimistic
NY Times – September 7
Yeah, right.
Mrs Fred & I, heavily immunized & boosted for covid, have avoided contracting covid ever.
Our elderly friends, less boosted than us, have also. But were visited by relatives from Europe with their two teenage sons, and the visitors did intense touristy stuff during their stay, all around Boston, Cape Cod & NH, came down with covid before leaving and infected our friends. We also had spent time with our friends two days before they became infected, (un?)fortunately. (‘Before’ being critical here.)
I would say the latest variants (‘scariants’) are indeed more infectious.
@Fred,
“I would say the latest variants (‘scariants’) are indeed more infectious.”
That’s not what I’m reading. What’s your evidence?
However… WebMD (via Medscape)
What no doubt IS going on is that hardly anyone is ‘masking up’ these days.
from the UK Health Security Agency:
SARS-CoV-2 variant surveillance and assessment: technical briefing 53 – Updated 8 September 2023
Excerpt:
There are 34 confirmed cases of BA.2.86 in England, with 3 low-quality sequences being further investigated.
Of the 34 sequenced cases, 28 cases are part of a care home outbreak in the East of England.
There are an additional 6 cases identified through routine surveillance: 4 in London, one in the North West, and one in the East of England. None of these cases are known to be epidemiologically linked and none have recent travel history.
Of 34 cases, 5 cases were hospitalised, 2 cases had unknown hospitalisation status, and there were no deaths due to COVID-19 among these cases (note that this will not be representative of all BA.2.86 cases as most genomic surveillance is among people tested in hospital).
Scotland have reported 2 confirmed cases of BA.2.86, further information about Scottish cases is published on the Public Health Scotland webpages.
Care home outbreak
On 21 August 2023 UKHSA was notified of an outbreak in a care home in the East of England with reports of an increased number of cases and increased severity compared to previous outbreaks at the home. All residents and symptomatic or lateral flow device (LFD) positive staff members were polymerase chain reaction (PCR) tested and PCR positive samples were referred to UKHSA for sequencing.
As of 5 September 2023, 33 out of 38 residents have tested positive for SARS-CoV-2 (attack rate 86.6%). Of the 33 positive residents, 19 (57.6%) were symptomatic with symptom onset between the 20 August 2023 and 28 August 2023; 29 of the residents have now recovered, while 4 remain unwell. One resident was hospitalised as a result of their illness (hospitalisation rate, 3.0%), and no deaths due to COVID-19 have been reported. Twelve staff tested positive either by LFD and/or PCR, and all have now recovered. No staff members were hospitalised.
A total of 43 samples were sent for sequencing (33 care home samples and 10 staff samples) of which 28 of the samples were identified as BA.2.86 (22 care home residents and 6 staff). Of the remaining 15 samples sent for sequencing, 11 were not suitable for sequencing, one failed and 3 are low quality and being further investigated.
At least 29 out of 33 the residents who tested positive had received a dose of COVID-19 vaccination as part of the spring booster campaign around 4 months prior to the outbreak and all 4 of the residents who tested negative had received a spring booster. Known information about confirmed cases among care home residents is summarised in table 1.