2022-01-28 General


I don’t like to warn about variants before there’s data. (I didn’t sound alarms about Mu, for example.) Well, I think it’s time to talk about BA.2 — an Omicron variant. (The Omicron variant which sprouted up first is BA.1.) BA.2 doesn’t look like it is lot worse than BA.1 — not like Delta compared to Alpha, for example — and it is still very early, but it looks like it is a bit worse. This report says that BA.2 is a bit more transmissible than BA.1 but in initial assessments, it doesn’t look like it’s any more immune evasive. There’s not enough data to say if BA.2 infections are more or less severe.

The BA.2 virus, like Delta and COVID Classic, (but unlike Alpha and BA.1) has S-Gene Target Failure (explained in the next paragraph), which means it is easy to tell Omicron and BA.2 apart, but harder (more expensive) to tell BA.2 and Delta apart. This is not a big deal where Delta has been outcompeted into extinction, but it will make it more difficult in areas where there is both Delta and BA.2.

Explanation: Almost all (all?) PCR tests for COVID-19 look for three different genetic markers from COVID Classic: one from the spike protein, one from the nucleocapsid (the envelope that the virus’ mRNA is wrapped in), and one (ORF1ab) from a region which (I think) makes proteins which do things like suppress the immune system. The nucleocapsid (N) and ORF1ab haven’t changed much over time, so the PCR test designed for COVID Classic still recognizes them well. The spike gene (S), however, is different enough in the Alpha and BA.1 variants that the regular PCR tests can’t recognize it. This is called “S-Gene Target Failure” (SGTF), and means that (waves hands slightly) the signal in the PCR reading machine is only two-thirds as strong as expected (but still much stronger than zero). It is thus very easy (and cheap) to tell if something is in the set of {COVID Classic, Beta, Gamma, Delta, BA.2} or {Alpha, BA.1}.


WHOOHOO! This preprint reports that the NDV-HXP-S vaccine — the Thai version of the HexaPro vaccine — finished Phase 1 trials, and it looks like it is going to be an awesome vax. Its neutralizing antibody levels were slightly lower than Pfizer’s, but it had a higher proportion of neutralizing to binding antibodies. (Binding antibodies are ones which just attach like remoras to the virus, which acts as a signal to T-cells to eat them. Neutralizing antibodies are ones that not just stick to the outside but also jam up the mechanical workings of the virus. Neutralizing antibodies are better!)

I know, I know, I try not to give news prematurely, but this is a big f deal. I have been excited about the HexaPro vaccines for a long time. HexaPro is grown in chicken eggs with a really old, mature process (i.e. cheap and stupid easy to make). Not only that, but the inventors are giving free licenses to developing countries. (Mexico and Brazil are also making versions.)

This article reports that NACI says vulnerable teens in Canada — those with dangerous medical conditions or who live in congregate housing — should get booster doses.

This preprint says basically that the third time’s the charm: three vaccinations or two vax+infection give markedly better antibodies.

This report from the US says that a third dose took vaccine effectiveness against hospitalization from 82% to 97%. Among immunocompromised people, it went from 69% to 88%.

Mitigation Measures

This article reports that Canada has dropped additional entrance restrictions to visitors from India and Morocco.


This preprint found that pet Syrian hamsters imported into Hong Kong not only had the Delta strain of COVID-19, but they transmitted it to humans in at least two cases.

This is by no means the first time that animals have been found to catch COVID-19. Felines of all sizes, minks, ferrets, otters, primates, deer, dogs, and mice are some of the animals which have been observed to catch COVID-19.

Syrian hamsters catch COVID-19 so well, in fact, that hamsters are one of the most (if not the most) common lab animals I see in the (many) scientific papers I read about COVID-19. This is the first time I can recall, however, where a pet store was an infection vector for COVID-19, and it is a reminder that animals are not completely innocuous, even when they are cute.

This also gives a nudge towards the “COVID Classic jumped from humans to animals, mutated, then jumped back as Omicron” theory for where Omicron came from.


This large study in Denmark with a strong control group found that Long COVID in kids was rare and usually resolved in 1 to 5 months.


This preprint found that problems with particular interferons seem to lead to severe disease:

  • In young people, 1-5% of severe cases are in patients with genetic variants which mess up sepecific interferons.
  • In old people, 15-20% of severe cases are in patients who have antibodies to their own interferons (autoantibodies).

This preprint found that the number of children with Type 1 Diabetes increased by 57% during the pandemic. (Note: it’s not from getting fat from not going out, that’s Type 2 Diabetes.) There’s some speculation that the autoimmunity is triggered by COVID-19. This study did not have the ability to do seroprevalence studies, so more work is needed.

The kids were also sicker when their diabetes was discovered, which was seen also in this study from the western US and this study from Poland. This might be because of delaying treatment.

Recommended Reading

This article talks about the origins of Omicron. Yeah, I know, yawn right? But it’s got some things that were new to me.