Reinfections in Israel

Are on the rise. But is it Omicron, or "Omicron"?

I mentioned that the Israel dashboard features two new segments on “recurrent morbidity,” i.e. reinfections. The “guide” page confirms that these are PCR positives that are more than 90 days separated from a previous PCR positive.

Reinfections, of course, should be in scare-quotes as well: Because these are rarer, they may be more prone to false positives; because they are believed to be rarer, they may go under-tested.

Either way, rates have been low in Israel and throughout every study setting in the era before Omicron, indicating that previously testing PCR positive confers a lower likelihood of testing positive again, regardless of whether the first or second positive is “false.”

This is no longer the case:

source: https://datadashboard.health.gov.il/COVID-19/general

How does this translate to reinfection rate vs naive infection rate? Let’s wade into the numbers.

First, the Google-translated guide text for the definitions on these graphs:

“Repeat-verified” are those who have been tested and found positive once again for the COVID-19 virus in a PCR test, starting 90 days after the previous discovery, whether or not they have had symptoms, whether they are sick, recovered or have died¹ […] The data are presented as a division between repeat verifiers who were vaccinated at least once on the day of the additional verification and repeat verifiers who were not vaccinated at all.

Absolute values are reported on the related graph. The combined view:

Absolute (by age) values can also be displayed for last-30 days alone (to be displayed below). The results are stunning. Crudely adding all ages together:

All-time reinfections: 24,700

Last 30 days: 12,900

That’s more reinfections in the last 30 days than there had been before (11,800).

Onto the per-100k rates. “Reinfections,” again, are PCR positives among Israelis in the “PCR positive over 90 days ago pool.” “90 days ago” changes each day, so I used the October 21 value as the halfway point for the previous 30 days. This gives us our two populations of “Omicron susceptibles” in Israel:

“Omicron Susceptibles” (in millions)

“90 Days+ Previously PCR positive,” crude: 1.3239*-.0118-.0082* = 1.304²

December 8 Naive, crude: 9.217**-1.348* = 7.869

“Omicron infections” (in millions)

All infections, last 30 days: 1.4632*-1.3483* = .1149

Reinfections, last 30 days: .0129

Naive infections, last 30 days: .1149-.0129 = .102

(*=Worldometers.³ **=Israel Population. Other values from MOH Dashboard)

30-day Reinfection rate, last 30 days:

(.0129 / 1.304) x 100k = 989 per 100k

30-day Naive infection rate, last 30 days:

(.102 / 7.869) x 100k = 1,296 per 100k

Hazard Ratio:

Pretty Similar!

The result appears to confirm the reports from the UK and (it must begrudgingly be acknowledged) the very shoddy South Africa study update.⁴ Omicron substantially circumvents natural immunity from previous infection.

While an increased number of reinfections in general can be expected as there are more previously infected, the relative per capita rate should not jump in kind. Obviously some of the “naive” will in fact have immunity from prior encounter with SARS-CoV-2 - but this was also true in the summer, and yet “Delta (and prior) reinfection” rates were only ~.1-.2 of naive infection rates.⁵

Of course, all of this could be an artifact of a change in false-positivity rates associated with Omicron; if all of these positives are “false,” then there are no true reinfections, to take the extreme case.

Since Omicron is mild, defining the corresponding, new meaning of a “false positive” is philosophically tricky. But as PCR positives were never a good proxy for “Severe Covid 19” to begin with, we must deal with them as nothing more than what they are. In that sense, Omicron has clearly increased “reoccurrence of PCR positive.” The meaning of that fact will only become clear later: Either the virus is evading prior immunity, or the test no longer tells us anything.

Or, it could be a bit of both.

Omicron has changed niche: It appears to replicate with more affinity in nasal airway cells,⁶ whereas prior iterations of SARS-CoV-2 seemed only to be detectable in nasal swabs after a certain threshold of replication had taken place.⁷ This could be due to a shift in dynamics in which Omicron no longer requires TMPRSS2 for binding with ACE2. As found by Peacock, et al. (emphasis added):

In [human nasal epithelial cultures] Omicron showed a large early replication advantage, yielding viral titres ~100-fold higher than Delta by 24 hours post- infection. […]

We propose that Omicron achieved this rapid replication rate by becoming less specialised in terms of its cellular tropism. Earlier SARS-CoV-2 isolates were limited in their tropism by their requirement for cell surface entry using the TMPRSS2 protease, and it appears subsequent variants, such as Alpha and Delta, became even more heavily reliant. However only a low proportion of cells in the upper respiratory tract express both ACE2 and TMPRSS2.⁸

This could represent a break in prior associations between PCR positivity, seroconversion (the appearance of new antibodies in the blood), and transmission - as well as natural immunity as defined in respect to all three of those.

If Omicron is more “teens egging the coach’s house” than “methed-out home invader,” we should make less of the similar attack rates between those who have or have not installed a security system.

What higher PRC re-positive rates in Omicron do not appear to represent, is any evidence that the Covid vaccines diminish post-infection immunity. Regardless of whether the original PCR positive was before or after receipt of the Covid vaccines, the “at least 1 dose” group seems to be outperforming the unvaccinated in the Omicron era:

The Covid-vaccinated + previously infected are apparently outperforming the unvaccinated + previously infected in every age group, even though naive per-100k rates are similar.

This could reflect a million different things - particularly a higher percentage of “previously PCR positive” in the unvaccinated pool; or perhaps a higher percentage of “previously PCR positive before the summer,” either of which would indicate that non-vaccination is not a proxy for “reinfection risk,” but merely for higher rate of prior infection or longer time since prior infection.

I think it also represents some flaws in the data collection - otherwise, at a glance, these results suggest that a re-calculation of PCR positive rates for just the unvaccinated + previously infected would reveal “negative natural immunity efficacy.” Additionally, the correlation between risk ratio and age seems explained by the secondary trend in “unvaccinated cohort size.” This could mean that the percentages for “overall unvaccinated” are inaccurately low in older groups (due to an exaggeration of the percent vaccinated).

These results, overall, are confusing and challenging; but they at least help clarify some of the apparent data over “negative efficacy” for the Covid vaccinated,⁹ and for Omicron’s apparent evasion of prior immunity: Neither is easily explained by “rampant reinfections” among the Covid-vaccinated. We can rule that out as a distortion to the signal.

The Covid vaccinated + previously infected do not seem to be driving Omicron infections to a particularly meaningful extent.

1. If you believe a deceased family member or coworker has been re-exposed to the virus, please have them tested immediately.

2. Pre-December 8 reinfections (.0118m, via MOH dashboard) and deaths (.0082m, Worldometers) are subtracted from the October 21 total case value (Worldometers), as they do not add new individuals to the “reinfection susceptible” pool.

3. See https://www.worldometers.info/coronavirus/country/israel/, total cases by date, 2021 October 21 (1.3239), December 8 (1.3483), and 2022 January 7 (1.4632); total deaths, 2021 December 8 (.0082)

4. Dissected in “Oh Nomicron!”

5. See NIII Pt. 2.

6. A highly-recommended report on two recent studies exploring Omicron’s changes in tropism and severity is at:

Omicron's generally less harmful mechanisms emerge

which reviews

Peacock, T. et al. “The SARS-CoV-2 variant, Omicron, shows rapid replication in human primary nasal epithelial cultures and efficiently uses the endosomal route of entry.” biorxiv.org.

Willet, B. et al. “The hyper-transmissible SARS-CoV-2 Omicron variant exhibits significant antigenic change, vaccine escape and a switch in cell entry mechanism.” medrxiv.org.

7. As discussed in “Travels to Maskladesh”:

This study is nonetheless interesting in another respect, which is the use of oral swabs (represented by the light blue squares) as one of the markers of “infection.” In fact, one of the subjects - who was 52 days post- second dose - never would have been detected on a normal (nasal) PCR test to begin with. An earlier paper by the same authors includes additional interesting findings, along similar lines, but for natural infection: The virus is detectable in the mouth before the nose (I haven’t yet reviewed the earlier paper itself). There appears to be a second realm of transitional, asymptomatic “infection” with this and probably other respiratory viruses, yet to be well-explored.

Similarly, Omicron likely “breaks” the association between (nasal PCR swab) cycle counts and “transmissibility,” if indeed there ever was one (the association was never more than an assumption to begin with).

Omicron transmission, after all, may have less to do with replication in humans than in mice, or some combination of the two. See “Mouse Party.”

8. See footnote 6

9. The immortal controversy. For previous comments on “negative efficacy” and innate immune suppression, see “Neg.”