COVID19 brief update, October 28, 2020: the devil is in the amplification cycle count; do flu shots also enhance COVID19 resilience?

(1) Twitter user ‘Black Swan Hunter’ [*] draws my attention to the following thread https://threadreaderapp.com/thread/1320536482298384390.html in which Kevin McKernan discusses the “The Live-Dead qRT-PCR problem”, citing this paper (really a Note to the Editor) by Jaafar et al https://doi.org/10.1093/cid/ciaa1491 which compares qRT-PCR test results with those of cell cultures—i.e., whether the sample can be used to grow a culture of the virus.

Basically, the said paper shows that beyond 3335 or so amplification cycles (each representing a doubling), positive results are unlikely to represent viable virus particles — yet testing centers in many countries routinely run out to 40 cycles (i.e., a factor of 128 32 more). It is probably more precise to speak of “meaningless positives” than of “false positives”, but that is a distinction without much of a difference in public health terms. I believe it would be best to report not “positive” or “negative”, but the lowest cycle count at which a positive result is obtained — the lower the count, the more likely the patient will not just be infected but infectious, and the higher the count, the more likely it is just some dead RNA fragments.

(2) (Hat tip: littleoldlady). Does a flu shot improve your immunity for COVID19?!

Netea and his team also conducted a laboratory experiment that suggested how flu shots could prevent coronavirus infections. First, they purified blood cells taken from healthy individuals. Then they exposed some of the cells to the Vaxigrip Tetra flu vaccine, made by Sanofi Pasteur, and let the cells grow for six days. After that, the researchers exposed the cells to SARS-CoV-2 and analyzed them one day later.

The cells that had first been primed with the flu vaccine produced more of several kinds of virus-fighting immune molecules, known as cytokines, than did those that had not been exposed to the vaccine. Though such molecules can be detrimental when they are produced late in a patient’s course of COVID-19—inciting a so-called cytokine storm, which can damage many body organs—cytokines produced early in the infection process are helpful, Divangahi explains. They “get rid of the pathogen,” he says, making the infection milder.

It might seem far-fetched that a vaccine designed to protect against one infection could protect against others, too. But a growing body of research suggests that this does, in fact, occur through a process called “trained innate immunity.”

Read the whole thing.

(3) Researchers at U. of Arizona, building on work from U. of British Columbia in Vancouver, created a new test based on a saltwater gargle (which pretty much everybody tolerates well) rather than the unpleasant nasopharyngeal swab. Moreover, the test generates results in as little as 18 minutes and appears to be at least competitive with RT-PCR in accuracy.

[*] I stopped spending time on Twitter some years ago — Insta rightly calls it “the crack cocaine of social media” — my whole presence there consists of WordPress auto-tweeting new posts there. I however saw saw the notification when I clicked through from a thread elsewhere.

One thought on “COVID19 brief update, October 28, 2020: the devil is in the amplification cycle count; do flu shots also enhance COVID19 resilience?

  1. Reblogged this on Head Noises and commented:
    In this episode:
    Article on the testing of how useful sample amplification is (basically, can you culture it– which is a good stand-in for “could anybody catch it from you”.
    Article on jump-starting the immune system via stimulating the cytokines with a flu shot (wow, when I say it that way it looks like clickbait or at least search engine fodder).
    Article on using salt-water gargle to get samples for testing, since most people don’t gag at the idea while the nasal swab stuck into your brain is a meme.

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