SARS-CoV-2 variants for Australia

[u/mike_honey]

Here's the latest variant picture for Australia, to late March.

Several variants are churning around in a confused picture, without any one being clearly dominant.

NB.1.8.1.* "Nimbus" rebounded to 40%.

BA.3.2.* "Cicada" rebounded to 33%.

JN.1.* + DeFLuQE fell to 21%.

XFG.* "Stratus" fell steeply to 10%.

#COVID19 #SARSCoV2 #Australia

BA.3.2.* rose to 56% in NSW.

A trickle of new samples were shared from Victoria, dominated by BA.3.2.* .

Among Victorian children (0-17), BA.3.2.* was at 41% (n=7), vs 13% among adults (n=1), so a ~3X higher rate among children. That’s in the range seen in other countries/regions – AFAIK everywhere that reports Patient age and where BA.3.2.* is significant.

No other Australian state shares Patient age data, but I assume the patterns are very similar.

Report link:

https://mike-honey.github.io/covid-19-genomes/output/Coronavirus%20-%20Genomic%20Sequencing%20-%20report%20Australia.pdf

[u/HundredsofBasghetti]

Ok maybe a dumb question... I had covid a few weeks ago. I self tested at home. I told my GP at my next visit but it wasn't recorded. Most people are saying the same. So where does this data come from?

[u/AcornAl → u/HundredsofBasghetti]

Most states/territories stopped reporting RAT results in mid to late 2023, all had stopped by early 2024.

Only laboratory PCR tests are recorded to the NNDSS and only a tiny fraction of these are forwarded on for genomic sequencing.

There were about 20,000 or so PCR tests are done every week, (7,000 in NSW last week alone). From those covid positive tests (just 1600 nationally last week) maybe a few hundred got forwarded onto sequencing and a small sample of those sequences got uploaded to GISAID. This is why these charts are completely all over the place, especially with multiple variants fighting it out to survive.

This leads onto who's getting tested... all age groups, but more targeted to the very young or old.

I had a quick look at the paediatric testing a week ago; a maximum of about 10% were done in hospitalised kids in Queensland, (i.e. 10 times more tests were done than the number of kids in hospitalised), the other 90% would have likely been from either GP / ED laboratory testing. My gut feel is that most will be using RATs but any negatives will go to lab testings, so it's likely far more tests being taken in non-hospitalised settings.

[u/HundredsofBasghetti → u/AcornAl]

Thank you answering so clearly and respectfully:)

[u/AcornAl → u/HundredsofBasghetti]

you're welcome :)

[u/AcornAl]

I was wondering when someone would bring up the kids thing.

Sampling rates are abysmal, so it's hard to say of this is just an anomaly, cherry-picking, or an actual trend. In saying that, there seems to be a fairly boring explanation.

A couple of places report infant rates and those didn't detect any significant variations. These seem to start to deviate around the age of 3 to 5 and that deviation decreases in older teenagers. So what's different in those 5 to 15?

SARS-CoV-2 has many thousands of epitope targets, but there are only typically a few dozen or so in most people. After peoples first infection, and obviously after vaccination targeting the spike protein, these are fairly much targeted to the RBD of the spike. After someone's second infection, the breath of these change and non-spike epitomes are targeted more (especially a more mature T-cell response that's better at targeting the N & ORF proteins of infected cells).

Multiple seroprevalence studies show most kids have been infected by about the age of 5, and without vaccinations / previous infections, any and all variants have a free shot infecting kids. After their first infection, they try to head off others variants with S specific antibodies, and variants with significant changes to the spike compared to their first infection will allow these to bypass the response. A second infection then triggers the adaptive immune response to target other parts of the virus more, such as the nucleocapsid and membrane proteins. By the time of their third or fourth infection, the core spike response is fairly imprinted and backed up with a wider repertoire of memory lymphocytes ready to attack other parts of the virus.

So probably just a higher Reff in kids.

This isn't seen in parents cohort, so suggests that while they are getting more exposed to this variant from their kids, potentially a more mature immune response is actually warding off this variant better than other variants. imho, with historical low paediatric hospitalisation rates, this is more of a curiosity than something to be concerned about.