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Post Archive 2024

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My family decided (perhaps unwisely) to take a cruise over Christmas. There was lots of coughing on the ship and very little masking. I’m not surprised we all got sick. I AM surprised by what my PCR lab results showed!
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Me: Influenza A
My Son: COVID
My Daughter: RSV B
Despite sharing rooms and spending all our time together, we apparently didn’t infect each other! Were each of our infections protective against the others?
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We were hosting a party tonight, 18 people for dinner and fun. This morning I felt a little scratch in my throat but otherwise felt fine. 11am: negative Panbio, probably nothing to worry about. Panbio is a great test - reliably indicates contagiousness. But…
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At 9pm (prime party time) I did another one, and it was positive! Now I’m contagious! Did I infect my friends? Did I have to scramble to send everyone home with the hassle and worry of being exposed? [2/4]

No! Because before I even did the Panbio, I did a @CueHealth molecular test, and it was positive 22 hours ahead of the Panbio. We postponed the party and I wore a mask around my family well before becoming contagious.
Molecular tests predict future contagiousness! [3/4]

Few people have this luxury today. Cue tests are $77 each and I’m lucky to have an employer (Google) who provides them free-of-charge. But it’s just a matter of time and economies of scale before we all have multiplex molecular tests at our fingertips for a few bucks! [4/4]

Taken at the same time. This better sensitivity, combined with much nicer feeling swabs, is why I buy Abbot PanBio instead of using the crappy free BTNX tests from the grocery store.

Today BTNX shows very strong, maybe even stronger than what I saw from PanBio today:

In my freezer I now have (non-imfectious) RNA of:

  • Rhinovirus
  • SARS-CoV-2
  • Influenza A
  • RSV B
  • OC43
    I feel a bit like a kid collecting serial killer trading cards 😳

A triplex fluorescent probe assay prior to mixing. In this case:
Influenza A: “FAM” absorbs green, looks red
Influenza B: “Cy5” absorbs red, looks blue
RSV B: “TEX 615” absorbs amber, looks purple

Hey @DanteLabs, are you still doing business? I’ve had two samples stuck in “sequencing started” for half a YEAR and no response from repeated inquiries to your support email!

Here’s two different pluslife SARS-CoV-2 results from the same weakly positive sample.
In the first case it was classified as negative as the target was detected in only a single channel. In the second case it was strongly positive as the target was detected in all channels. 1/3

The only difference between these tests is that in the first case I spiked 20µL of my positive sample into a real negative sample from a fresh swab. In the second case I put 20µL of positive sample into buffer on it’s own. 2/3

This highlights a likely problem with lots of PCR sensitivity analysis in the literature: diluting a sample with buffer alone is not a good approximation of a weak sample. Likely the ratio of target to non-target nucleic acid in the sample matters to assay performance! 3/3

What a perfect PCR amplification plot for this one 😀. One positive sample from me, one from my son, and a negative from my wife and negative control.

I love all my COVID conscious friends here. I feel I must share that upon careful reflection, my family and I were definitely happier and healthier after deciding to accept the risks. For us, the fighting likely caused more lasting harm than the (well-vaxed) infections (so far).

I’m not going to go into details, but I will admit that I failed to appreciate how fragile mental health can be - for my teenagers, and also for us adults. I don’t regret the caution prior to vaccination, but I do regret pushing it on my family for too long afterwards.

I had to take a week off work and was up until 2am last night doing laborious “bead cleanup” on 21 samples. Now I have a few drops of clear liquid to show for my week of effort! 😂.

I’m heading to Ottawa for the weekend to drop my son off for his first year of University! With luck, when I get back I’ll have sequence from up to 30 viruses that have gone through my house in the past few years.

I had Rhinovirus-C11 in August last year, and then my daughter caught the same variant in November. But look, there’s one base (of the 390 I sequenced) different! A “G” became an “A. This is viral mutation in action, seen in my own family!

What’s the chances I gave it to her, eg. by the virus surviving in our house somewhere for months? I think it’s much more likely it’s spread around our community.

I guess I’ll have to do a full genome sequence of both samples to confirm there are more mutations.

Got a new sticker for my laptop today (along with a super cool lab tour) 😁

What are the chances that in 20 years we all use nasal sprays to prevent respiratory infection they way we (sometimes) use sunblock to prevent sunburn?

I’m attending a conference this week and decided to use Vicks Early Defense 2-3 times daily. See eg.
https://pubmed.ncbi.nlm.nih.gov/39004091/

Of course if I was really concerned, I’d wear a good respirator too, which I do on planes and other high-CO2 environments. So I’m definitely not arguing for a reduction in masking. But if I’m not going to mask in a moderate-risk setting anyway, spray seems worth doing to me.

Just got a KP.2 vaccine. Knowing I had XBB.1.9.2 in Feb (even though XBB was rare at the time), I’m extra glad to be getting updated immunity!

Wow, new study shows that having a COVID shot within 5 months of infection cuts major long COVID risk (eg. heart or lung failure) in half!

I imagine a device like PlusLife that has hundreds of tiny channels instead of just 7. Every common pathogen, many replicates and multiple targets for more reliability. A cheap and quick answer to “what do I have”. Doesn’t need to be perfect to be transformative!
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