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Category: Omicron

Kort om immuniteten post COVID-19 och efter vaccination

Ett kortare inlägg om hur immuniteten jämför sig efter infektion med SARS-CoV-2 (COVID-19), kontra efter vaccinering mot COVID-19. Vi har nu data som tyder på att Omicron sänker skyddet från vaccinen, och även vid tidigare COVID-19. Därav är det enligt många (t.ex. FHM, ECDC och CDC) viktigt att vaccinera med en 3:e vaccindos (hos fullvaccinerade), och åtminstone med 1 (men helst med 2) doser hos de med genomgången COVID-19. Anledningar redovisas i en längre utläggning nedan, liksom i min tidigare bloggpost här. Se även längre ner Folkhälsomyndighetens rekommendationer, som är de som gäller.
 
Dels finns det en variabilitet i immunsvaret efter genomgången infektion – en betydande andel serokonverterar inte enligt flera studier (se återigen mitt tidigare blogginlägg, samt denna tråd). Nivåerna av neutraliserande antikroppar är därtill mycket variabla över tid efter COVID-19. Antikroppsnivåerna (mot spike-proteinet som man vaccinerar mot) är därtill t.ex. över lång tid betydligt högre efter vaccinering jämfört med efter COVID-19, och 99% av alla som vaccineras serokonverterar (dvs. i princip alla med ett normalt fungerande immunförsvar).
 
Att antikroppsnivåerna åtminstone initialt är högre efter vaccinering, är ett fynd som ses genomgående i många studier, åtminstone för mRNA-vaccinen. Nivåerna tycks emellertid (av naturliga skäl) gå ner fortare från den initialt mycket höga nivån, efter vaccinering (se även mitt tidigare Facebook-inlägg här – den i inlägget beskrivna studien har nu publicerats i tidskriften Vaccines). Till detta kan man tillägga preliminär data som tyder på att de som har fått 3 vaccindoser, uppvisar högre antikroppsnivåer än de som bara har haft COVID-19 och hade vaccinerats med 2 doser, samt givetvis betydligt fler än de som bara hade haft COVID-19 (det kan givetvis finnas variation eller selektionsbias i denna studie; se även punkt 3 i mitt tidigare blogginlägg om Omicron här).
 
Samtidigt tycks just tre vaccindoser – utifrån antikroppsbaserad immunitet – också på många sätt överträffa eller vara likvärdigt med den som fås av tidigare COVID-19 och efterföljande vaccinering, eller genom genombrottsinfektion efter tidigare tvådosvaccinering (se tråd här).
 
De olika typerna av immunitet tycks därmed hålla olika väl över tid utifrån olika aspekter och analyser, och denna bild kan givetvis ändra sig ytterligare med tiden och nya varianter (många argumenterar vidare för att det vore konstigt om det inte i de flesta fall – men med ovan nämnda variabilitet – sågs en hyfsat god och lång immunitet mot svår COVID-19, efter en sådan genomgången infektion, eftersom man exponeras för så mycket av viruset, och så många olika virusproteiner).
 
Men exponering för virusets proteiner på ett av sätten – genom en SARS-CoV-2-infektion – är givetvis betydligt mer riskabelt.
 
Om något tycks det immunologiska T-cellssvaret ur flera aspekter kunna vara något sämre mot Omicrons Spikeprotein, hos de med tidigare COVID-19, jämfört med efter vaccinering, enligt en ny studie i Nature Medicine av forskare från Karolinska Institutet. Detta fynd gäller både på CD4+ och CD8+ T-cellssidan. T.ex. sågs 8% lägre CD8+ T-cellssvar mot Omicrons Spike-protein hos de som hade vacccinerats med två doser Pfizers mRNA-vaccin (BNT162b2), medan reduktionen var 30% hos de som tidigare hade haft COVID-19 (maximal reduktion var 55% respektive 63%). För CD4+ T-cellssvaret var reduktion icke-signifikant på 9% hos de vaccinerade individerna, kontra signifikanta 16% hos de med tidigare COVID-19 (se skärmdumpen nedan, från Gao et al.).

När de slog samman CD4+ och CD8+ T-cellssvaret mot Omicron, sågs ett försämrat svar hos de som tidigare hade haft COVID-19, men ingen reduktion i svaret hos de som hade vaccinerats. Notera att de med tidigare COVID-19 i denna studie hade smittats under våren 2020, så de var inte smittade med de senare varianterna (såsom Alpha, Beta eller Delta). Resultaten kan därmed eventuellt skilja sig för de som smittats av andra varianter av SARS-CoV-2.
 
Annan data tyder på ett likvärdigt T-cellssvar mot Omicron hos de med tidigare COVID-19, jämfört med de som har vaccinerats. Givetvis får man dock efter vaccinering inte ett T-cellssvar mot lika många proteiner – vaccinen immuniserar mot Spike-proteinet.
 
Så man kan inte heller påstå att genomgången COVID-19 i sig skyddar bättre rakt av, det blir missvisande – även om många analyser finner att i snitt så har de med tidigare COVID-19 ett bra eller rentav bättre skydd i jämförelse med vaccinen över tid – åtminstone under Delta-perioden (se preprintsstudien av Gazit et al., samt ny publicerad CDC-data).
 
Detta skydd (både efter tidigare COVID-19 och medierat av vaccinen) har dock försämrats betydligt i och med Omicron, åtminstone vad avser skyddet mot infektion/symptomatisk COVID-19. Därutöver, om man tittar under den tidigare Alpha-perioden (visserligen närmare inpå när vaccinen hade getts och antikroppsnivåerna är så höga), så hade i stället de med COVID-19 sämre skydd mot infektion, än fullvaccinerade individer (och som teknikalitet är detta därtill ingen preprintstudie, utan redan publicerad i Nature Medicine). Denna fördel för vaccinen sågs även i den ovan nämnda CDC-artikeln.
 
Allt detta är då återigen med den brasklappen, att det innebär en mängd risker att smittas med SARS-CoV-2 och riskera olika former av COVID-19 och dess följdeffekter – inte minst död i sjukdomen (risker som i snitt är betydligt lägre vid en reinfektion, efter tidigare immunitet). Mer om det kan ni läsa i mitt tidigare blogginlägg här, samt i denna studie av Barda et al. i NEJM.
 
I stället anses vaccinen vara oerhört säkra, något som är redovisat i många analyser i peer-review-granskade tidskrifter från flera olika länder, och av varandra oberoende forskare, samt utifrån miljontals givna doser – även avseende riskerna för hjärtat (även om det finns en låg risk, liksom det finns med de flesta vaccin). Det finns därtill nu data för skyddet som fås av 2 och 3 doser vaccin, upp till 3-4 månader mot Omicron-varianten.

Att 3 doser kan ge ett gott skydd mot svår COVID-19, har observerats i analyser av stora delar av den allmänna befolkningen (ålder 18+) samt för äldre individer (65+), som utgör en riskgrupp för svårare COVID-19. Datan visar att överlag, med 3 vaccindoser, erhåller man i snitt runt 90% skydd mot svår COVID-19 orsakad av Omicron-varianten, och detta i åtminstone 3 månaders tid (se gärna här, samt mitt uppdaterade blogginlägg här). En full vaccinationsserie har samtidigt tidigare visat sig ge lägre risk för en reinfektion för de som tidigare har haft COVID-19.
 
Antikropparna håller sig därtill enligt ny preliminär data på relativt hög nivå – mot just Omicron – upp till 4 månader efter den 3:e dosen. Men oavsett det är alltså risken för reinfektion (efter tidigare COVID-19) eller genombrottsinfektion (vid vaccinering) alltså betydligt förhöjd med den nu dominerande Omicron-varianten (B.1.1.529).

Därav har t.ex. ECDC tidigt under Omicrons spridning – liksom nu WHO, för vuxna – påpekat vikten av att vaccinera med en 3:e dos. Vid tidigare COVID-19 anser många experter att man åtminstone borde ta någon vaccindos (i det senare fallet anser en del att det är bättre med två vaccindoser, se även punkt 2 här i mitt tidigare blogginlägg). En del argumenterar därför för att man ska erkänna tidigare COVID-19 som att motsvara skyddseffekten av en vaccindos.
 
Här är det viktigt att påpeka att t.ex. Folkhälsomyndigheten och CDC alltså anger att man ska vaccinera sig även efter genomgången COVID-19. Liksom jag redovisar ovan nämner de som anledning att man inte vet hur varaktigt skyddet efter COVID-19 är, att skyddet efter COVID-19 är variabelt, samt att vaccinationen då [ytterligare] minskar risken att man smittar andra (Detta tycks även i viss mån gälla under Omicron-smittspridningen, i alla fall ifall om man tittar på de som har fått åtminstone två, men särskilt tre vaccindoser – noter att detta också är en preprintstudie som därmed behöver granskas externt). Folkhälsomyndigheten anger även att man ska ta en boosterdos (vid det angivna dosintervallet), även om man tidigare har haft COVID-19.
 
Sen är det även missvisande att som vissa gör påstå att vaccinskyddet alltid är mer kortvarigt och “begränsat”. T-cellssvaret efter vaccination består liksom efter COVID-19 också väl över tid, även vid en given dos som är lägre än de nuvarande använda vaccinen (25 µg här, kontra 30 µg i Pfizers, och 50-100 µg i Modernas vaccindoser, se Mateus et al., Science 2021). Ni får vidare gärna läsa punkt 3 i mitt tidigare blogginlägg, där jag går igenom hur vaccinskyddet har hållit väl över tid, inklusive under Deltaperioden, dvs. en period som inträffade flera månader efter många hade vaccinerats i t.ex. USA (som de flesta av studierna i inlägget berör).

 

Ovanstående berör bara ett urval av alla studier, och det kommer givetvis komma fler jämförelser över tid, t.ex. fler långtidsstudier avseende skyddseffekten av olika typer av tidigare immunitet mot Omicron-varianten.

Med vänliga hälsningar,

Jonathan Cedernaes

Leg. läkare, PhD, docent i medicinsk cellbiologi

Screenshot below from Figure 1b. Gao et al. Nature Medicine 2022, showing the T-cell response against WT and the Omicron variant (B.1.1.529) of SARS-CoV-2.

Screenshot. Figure 1b. Gao et al. Nature Medicine 2022. 0.1038-s41591-022-01700-x
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Preliminary vaccine effectiveness data against the Omicron variant of SARS-CoV-2

After an initial summary in Swedish, please see individual English summaries below.
 
En 3:e dos tycks ge ett gott (89-94%) & långvarigt (≥3 månader) skydd mot svår COVID-19 orsakad av Omicron-varianten både i den breda befolkningen, samt specifikt hos äldre (65+). Därtill ger vaccinen åtminstone i någon månad ett visst skydd mot att testa positivt för Omicron, i gruppen 18+ (59-71% skydd).
  • De med tidigare COVID-19 hade enligt en av analyserna ett hyfsat skydd mot infektion med Omicron (som dock var betydligt lägre enligt en annan analys, se nedan samt punkt 2), men skyddet var i den nya analysen deskriptivt lägre än för de som hade fått tre doser vaccin.

  • Som redogörs här i inlägget är emellertid det viktiga skyddet mot svår COVID-19 orsakad av Omikron mycket robustare över tid, jämfört med skyddet mot infektion i sig. Detta har man i senare data visat sig håller väl över tid (≥3 månader) på en hög nivå efter tre doser (~90% riskreduktion), jämfört med en lägre skyddseffekt efter enbart två doser (~50-70% skydd)..
  • Enligt ny brittisk preliminär data redovisad nedan så ses sådant gott skydd mot svår COVID-19 orsakad av Omicron-varianten även för den äldre gruppen (65+), för de som har fått 3 doser vaccin. Att skyddet är avsevärt högre för gruppen som fått tre kontra två vaccindoser, stöds även av en sydafrikansk studie i New England Journal of Medicine (två doser gav ~70% skydd), samt ytterligare preliminär brittisk data: I en bredare åldersgrupp ökade skyddet från 44-68% med två doser, till 83-92% efter tre doser (i annan data från ~70% till ~90%).
  • För gruppen 65+, var emellertid skyddet som 3 doser gav mot symptomatisk COVID-19 orsakad av Omicron, betydligt lägre än skyddet mot svår COVID-19: Runt 50% skydd sågs vecka 5-9 efter 3:e dosen (därefter ev. ner mot 30% vid perioden ≥10 veckor). Därtill ses kanske åtminstone en indikation, liksom i viss tidigare data, för att skyddet kan vara något högre på sikt för de som fått Moderna som booster (tidigare tvådosdata som indikerar detta har observerats i jämförelser av Moderna kontra Pfizer; se även denna meta-analys).

I en annan analys från Skottland (se skärmdump här nedanför, samt punkt 2) undersöktes alltså vaccinskyddet mot infektion i sig med Omicron-varianten, för gruppen 18 år och uppåt. Här ser vi att efter enbart 2 doser tycks skyddet mot infektion i sig med Omicron-varianten vara helt borta på sikt, hos gruppen 18+. Observera att detta alltså ej är detsamma som skyddet mot svår COVID-19 – det är generellt sett betydligt svårare att erhålla skydd mot infektion än mot symptomatisk eller svår COVID-19 (för detta tycks i fallet SARS-CoV-2 krävas höga nivåer av neutraliserande antikroppar, och det är naturligt att nivån av dessa avtar över tid).

  • Efter en (3:e) boosterdos, återställdes dock – åtminstone tillfälligt – i hög grad skyddet mot infektion i sig med Omicron (~68-71% skydd; ~59-65% efter justering för tidseffekt, så kallad “waning”). Individerna tycks ha fått den 3:e dosen runt 7 veckor tidigare (detta avser vuxna i åldern 18+, och utgör också preliminär brittisk data). Utifrån den tidsdynamik som ses i många av dessa analyser kan man dock anta att detta skydd också avtar mer över tid (liksom meta-analysen tyder på, utifrån data som inkluderade skyddet mot Delta-varianten).
  • Efter 3 doser finns det nu även preliminär data som tyder på att nivåerna av antikroppar (specifika mot
    Omicron-varianten) ligger kvar på en skyddande nivå i åtminstone upp till 3 månader (antikroppar utgör en del av immunförsvaret, höga nivåer kan hjälpa ytterligare för skyddet mot infektion och symptomatisk COVID-19).
  • Notera också att dessa analyser finner att skyddet mot infektion med Delta-varianten var ganska välbevarat över tid efter “enbart” 2 doser vaccin: runt 70% skydd efter två doser (med en andrados given runt 5 månader tidigare). Dock var detta ej någon slumpmässig provtagning, så sannolikt föreligger bias mot symptomatiska infektioner. Annan data finner samtidigt att skyddet mot svår sjukdom med Deltavarianten har varit extremt välbevarat över tid, särskilt hos yngre, även efter två vaccindoser. Men observera att vaccinen alltså skyddar sämre mot Omicron, särskilt efter enbart två vaccindoser, och särskilt mot infektion i sig – skyddet mot svår sjukdom är alltså enligt ovan betydligt mer välbevarat efter tre doser.
  • Medan skyddet mot infektion i sig med Omicron-varianten därmed är mycket lågt, har tidigare data har samtidigt visat på ett hyfsat skydd mot symptomatisk COVID-19 orsakad av Omicron-varianten, i åtminstone någon månad efter 2 doser av mRNA-vaccin (men ej efter enbart 2 doser av AstraZenecas vaccin, se preprint-studien av Andrews et al.; Twitter-tråd här, samt en längre Facebook-sammanfattning här). Detta skydd tycktes dock i enlighet med ovanstående analyser vara betydligt bättre efter tre vaccindoser.
  • Den nya Skotska preprint-analysen fann också att skyddet mot infektion i sig (att testa positivt) med Omicron-varianten var ganska bevarat efter tidigare COVID-19 (enbart tidigare infektion, dvs. ej vaccinerade individer). Skyddet var runt 53%, men det var ändå betydligt lägre än vad tidigare COVID-19 gav mot Delta (runt 89% skydd). Detta skiljer sig från Imperials beräkning på skydd mot Omicron-infektion i sig på ~19% efter tidigare COVID-19, så här kan det ännu finnas en osäkerhet eller variation utifrån exempelvis studerad population eller tid efter en föregående infektion.

På slutet redogör jag i en separat punkt just för studier som visar att vaccinen har fungerat väl även över tid mot tidigare varianter, dvs. inklusive för Delta-varianten (punkt 3). Detta avser framförallt skyddet mot svår och dödlig COVID-19, och stöds av meta-analysdata som finner att vaccineffekten för detta skydd avtog sparsamt över sex månaders tid (men detta gäller återigen Delta-varianten; vi saknar ännu motsvarande data för hur vaccinskyddet på sikt ter sig mot Omicron-varianten).

Screenshot Willett et al. medRxiv DOI 10.1101/2022.01.03.21268111

1. Very good protection against severe COVID-19 caused by Omicron, even among those aged 65+, who have received 3 vaccine doses

In an updated report (briefing #34) from the UK Health Security Agency (UKHSA), they find that those who have received three vaccine doses, confers ~90% protection against hospitalization with COVID-19 due to the omicron variant, dropping slightly to ~83% at 10+ weeks. In contrast, the effectiveness after only two vaccine doses was initially at 58-64%, but dropped to ~44% after about 6 months time.
 
At the same time, a U.S. preprint study from Tartof et al. (Table shown here), found that even after three months after the last vaccine dose, those who had received three mRNA (Pfizer) vaccine doses had ~90% protection against hospitalization with COVID-19 due to the omicron variant. In contrast, those who had only received two vaccine doses had ~70% protection against such hospitalization, both at 3-6 months, but also after 6 months time, after vaccination.
 
In another British report that covers adults age 65+ and who had gotten 3 vaccine doses, protection against severe COVID-19 with the omicron variant was found to be:
  • 89% at 10 weeks and onward (may drop somewhat later).

  • The protection was 94% up until and including week 9 (please see the screenshot below).
  • In analyses of the symptomatic cases (meaning, how likely is a symptomatic case to get hospitalized) protection was around this range (85-89%) in this older, more vulnerable age group.
 (second link if the above one doesn’t work)
  • The above data can also be complemented data from South Africa, where a study at NEJM, by Collie et al., found ~70% protection against hospitalization due to COVID-19 after just two doses. Remember that South Africa has a relatively young population – here, most (24.2%) admissions were in the 30-39 age group – so this may not be representative for a broader population.
  • Related to the broader age group in the U.K., a preliminary report (the Jan 14 Technical briefing #34), found that vaccine-mediated protection against the risk of hospitalization (from COVID-19 with Omicron), was initially over 90% from three doses, and declined somewhat to ~83% after 10+ weeks. However, the corresponding protection after only 2 doses was considerably lower (initially 58-64%, but at 44% at the 6-month time point)
This shows that very strong protection can be achieved in the older population, even against severe COVID-19 caused by the omicron variant. This also fits with the present data for hospitalization: even during Omicron, most of the hospitalized cases in New York are unvaccinated. However, currently it’s not known for how long this protection may be maintained at this level (we lack data at this point), but long-term protection against severe COVID-19 is typically maintained far better than that against infections (see here for a meta analysis).

 
However, the drop detailed below for protection against mild (symptomatic) COVID-19 due to Omicron shows that our present vaccines were not designed against this variant – but again, protection against severe outcomes is maintained very well in 3-dose recipients for over 2 months.
 
As detailed in the later summaries further down, protection has still been very good over time against the Delta variant.
 And remember, our flu vaccines require updates every year because we encounter a new version of the influenza virus, every year. Updated (targeted) versions of the COVID-19 vaccines (of the ones approved) are supposedly underway.


The same analysis also examined vaccine-mediated protection against (mild) symptomatic COVID-19 caused by the omicron variant, in the 65+ age group (for protection the broader adult population, see the next summary further down):
  • In the 65+ age group, protection was minimal or absent against mild symptomatic omicron COVID-19 when examining the period 20 weeks after receipt of only 2 vaccine doses (Pfizer or Astrazeneca vaccine recipients).
  • However, after a third (booster) dose, effectiveness rose to 62-65% at week 2-4 in those who had initially received AstraZeneca‘s vaccine, but was down to 48-56% at week 5-9
.
  • Those aged 65+ who had been vaccinated with 3 doses of Pfizer’s vaccine had 65% protection from mild omicron COVID-19 at week 2-4, but this was down to 49% at week 5-9, and only at 31% starting at week 10.
  • Those vaccinated with 2 doses of Pfizer’s vaccine followed by a Moderna booster, had 70% protection from mild omicron COVID-19 at 2-4 weeks after the booster; down to to 57% at 5-9 weeks.
A potential limitation with the above analysis is partly that it was based on a rather low number (98) of hospitalizations, so the findings may have some biases: “These results should be interpreted with caution due to the low numbers and the possible biases related to differences in vaccine coverage and exposure to Omicron in different population groups“
 
 

Below is a screenshot of Table 1 from the Jan 7 (2022) analysis from the UK Health Security Agency – this applies to the age group 65+, but as detailed above, the data seems similar for based on a broader age group.

Table 1 Jan 7 2022 updated analysis from UK Health Security Agency

2. A third (booster) dose with the mRNA vaccines significantly increased protection against infection & symptomatic COVID-19 caused by Omicron

 
This new preprint by Willett et al. is based on 1.2 million inhabitants tested during early December when Omicron became dominant. On average, boosters were received around mid October (so ~7 weeks prior to (on average) testing positive in early December).

  • After a period about 5 months after just 2 doses, protection against infection with the Omicron variant was basically gone (see figure). But note, this refers to protection against infection itself – vaccine-mediated protection against severe COVID-19 is much higher (as detailed in summary 1 above).

  • Protection was however maintained at ~52% in those with prior COVID-19. This is far higher than the 19% protection against infection with Omicron from prior COVID-19, that was calculated by Imperial College London researchers, so there may still be some uncertainties in the exact protection afforded from just prior COVID-19, against infection with the Omicron variant. At the same time, preprint data based on in vitro studies (see also this preprint data) suggest that those with prior COVID-19 who get vaccinated, will achieve similar protection against Omicron, as those who have received three vaccine doses.
  • However, after a third (booster) dose, with Pfizer or Moderna’s vaccine, protection rose to ~68% and 71% against Omicron, respectively, and was thus at a higher level than after prior COVID-19 (likely, those with prior COVID-19 would achieve similar or higher protection if they got vaccinated).
    • When waning was taken into account, these figures were slightly lower, at ~59% and 65%, respectively, after booster doses with Pfizer’s and Moderna’s mRNA vaccines.
    • Overall, this data is thus consistent with prior preprint data by Andrews et al., which I have described previously on Twitter, and Facebook. The data is also somewhat consistent with a new preprint by Buchan et al. and by Tseng et al., who examined the effectiveness from a Moderna booster (3rd dose) against Omicron (these latter studies are described in the next section).
    • This data is also consistent with the preliminary Jan 14 Technical briefing (#34) from the UKHSA, which however found that protection, after 3 vaccine doses, against symptomatic COVID-19 due to Omicron dropped to 45-50% at week 10 and onwards. While there wasn’t enough data for the Moderna booster, protection may have held better over time (i.e., at 10+ weeks) – this may be revealed by later data.
What’s also notable in the preprint data from Willett et al. is that two vaccine doses did however provide good protection against the previously dominant Delta variant (green bars in the screenshot below). However, clearly 3 doses are needed to enable protection against infection itself with the Omicron variant (at least for a certain time period).
Screenshot from Willett et al. medRxiv 2022, medRxiv DOI 10.1101/2022.01.03.21268111
Here are some other studies that detail the protection against infection or symptomatic COVID-19 caused by the Omicron variant (please note that I also list Delta variant-specific protection for some studies):


Buchan et al.: Around 37% protection against infection with the Omicron variant ≥7 days after receiving a mRNA vaccine as the 3rd dose – but no protection against infection itself, after only 2 doses. This was based on 3,442 Omicron-positive cases, 9,201 Delta-positive cases, and 471,545 test-negative controls.

Tseng et al.: Recipients of 3 doses of Moderna’s mRNA vaccine had an initial vaccine effectiveness around 95% (93%-96%) against infection with the delta variant, but a lower 62.5% (56%-68%) against infection with the Omicron variant, in those who were recently (~5 weeks earlier) vaccinated. In those who received their third dose around 15 weeks earlier, effectiveness was ~49%.

  • This analysis was based on 6657 cases that tested positive (56% omicron; 44% delta), and the numbers above apply to the immunocompetent individuals (meaning they had intact immune systems).
  • They also saw that 2-dose recipients of Moderna’s vaccine, initially had some protection against infection with the Omicron variant (~30% day 14-90), but this was gone at later time points.
  • Here they also studied the 3-dose vaccine effectiveness against infection with the Omicron variant in immunocompromised individuals, and found quite low protection (11.5%; 95% CI 0%-67%).

Andrews et al.: Here 3 vaccine doses provided around 70-75% protection against symptomatic COVID-19 caused by the Omicron variant, in an analysis based on 56,439 Delta and 581 Omicron cases, and 130,867 test-negative controls.

  • This was calculated at the point of 2 weeks or longer after a third (booster) dose with Pfizer’s mRNA vaccine, with:
    • ~71% protection among those who received AstraZeneca as the primary vaccine course (2 doses), followed by a Pfizer dose (a total of 3 doses).
    • ~76% protection among those who received 3 doses of Pfizer’s vaccine (see screenshot below).
  • Here they also noted that 2 doses of Pfizer’s mRNA vaccine may at least initially offer some protection against symptomatic COVID-19 caused by the Omicron variant (at 88% at week 2-9 after the second dose; ~48.5% at week 10-14, and ~34-37% at 15+ weeks).
  • This effect was thus overall a) at an overall lower level than after a booster, and b) this effect seems to be very low (wide interval) starting already at week 15, being gone after around 5 months. But again, please note that this specific analysis only applies to protection against symptomatic, not severe, COVID-19, and specifically that caused by the Omicron variant.
  • Note that this analysis was based on quite early data and did not include that many Omicron cases. Furthermore, the observation that the estimates are negative at earlier weeks post dose 2 for AstraZeneca, is likely explained by this group including older individuals with more co-morbidities.
  • Against the Delta variant: This analysis also indicates that even after 6 months (see Figure 1), protection was still >60% against symptomatic COVID-19 caused by the Delta variant, in those who had received just 2 Pfizer mRNA vaccine doses (so as expected based on the other data presented above, higher than against the Omicron variant). Similar findings were seen above in the Tseng et al. preprint (see also the next summary regarding vaccine-mediated protection against the Delta variant)

Similar data was more recently reported in the 34th technical briefing from UKHSA:

  • For those who had received 2 doses of either the Pfizer or Moderna mRNA vaccines, around 20 weeks after the 2nd dose, effectiveness had dropped (from ~65-70%) to ~10%.
  • At ~2-4 weeks after the 3rd dose (a booster), protection against symptomatic COVID-19 caused by Omicon was ~65-75%. However, this dropped to ~55-65% at the 5-9-week period, and to ~45-50% at and beyond 10 weeks after receiving this 3rd vaccine dose.
  • At 3 months time after receiving the 3rd vaccine dose, there is now also preliminary data showing that antibody levels remain at a level that can neutralize the Omicron variant to some extent.

Below is a screenshot from Figure 1 from Andrews et al. (described above)

Figure 1 screenshot from Andrews et al. medRxiv 2021. DOI 10.1101/2021.12.14.21267615

3. During the Delta period vaccines continued to provide good protection against infections and hospitalization – especially with an added third vaccine dose

This is from a preprint by Drawz et al., with data from Minnesota that included 4.5 million patients (and a test-negative design), and included data from August 29 to November 27 2021 – that is, a period when booster doses were recommended in the U.S.

After six months, a second mRNA vaccine dose offered ~45% protection for Pfizer recipients, and ~65% for Moderna vaccine recipients, against infection with SARS-CoV-2, during a period when the Delta variant dominated.
 With a third (booster) mRNA vaccine dose, these figures rose to ~88% and 91%, respectively.


Against hospitalization, six months after a second dose, vaccine effectiveness against COVID-19 hospitalizations, was ~67% for Pfizer recipients and ~73% for Moderna vaccine recipients. These figures rose to 88% and 86%, respectively, in participants who had received a third (booster) dose.


What this data also shows, is that in the 19-64 age groups, even at the 6-month time point and from just two mRNA vaccine doses, protection was very good against severe COVID-19 caused by the Delta variant.


However, at the same time, the data shows that in individuals who had a range of co-morbidities (that are known to increase the risk of severe COVID-19), protection was quite low against hospitalization with the Delta variant, from just two mRNA vaccine doses. However, almost across the board, that protection increased significantly in those who had received a third (booster) dose of the mRNA vaccines.

That protection against hospitalization is maintained well over time, even against the Delta variant of SARS-CoV-2, is also supported by a November 2021 preprint meta analysis, by Feikin et al..

  • In that preprint, they found a decline in vaccine effectiveness over time (they used or inferred six-month data). However, this decline was most notable for vaccine-mediated protection against infection & symptomatic disease, in the ~20-32% range.
    • Against any type of SARS-CoV-2 infection (i.e. including asymptomatic infection), vaccine effectiveness dropped ~19-20%. This was consistent across all ages, when examining a mix of variants (but of course this did not include assessments for protection against Omicron, as this analysis was posted in November, 2021).
  • The decline over time was far less pronounced against severe COVID-19, as vaccine effectiveness was maintained at >70% in all the included studies. Against severe COVID-19, no study showed a ≥25% drop in vaccine effectiveness over the 6-month analysis period. Overall, for this outcome over time, the drop in vaccine effectiveness was ~8% for all ages; and ~9.7% for older individuals.

An example of a (preprint) study that was included in the above meta analysis, and which showed high vaccine-mediated protection over time against hospitalization and death, is the 2021 preprint by Lin et al., which has since been published in the New England Journal of Medicine. This is based on data from ~10.6 million North Carolina residents. That study found that at 7 months after the second dose, vaccine-mediated protection was >80% against symptomatic infection for Moderna mRNA vaccine recipients, and ~67% for Pfizer vaccine recipients (again, this does not cover Omicron). At this 7-month time point, protection was at an even higher 89-94% against severe COVID-19, and 90.5-95.5% protective against death due to COVID-19, among recipients of the Moderna and Pfizer mRNA vaccines.

Below: a screenshot from the preprint by Drawz et al., showing vaccine-mediated protection from Pfizer’s vaccine (PFR) and Moderna’s vaccine (MOD), at a period when the Delta variant was dominant. Protection estimated for the period >6 months (“>26wks”) after 2 doses, and with a third (“booster”) dose.

Figure 1 screenshot Drawz et al. medRxiv 2021 DOI 10.1101-2021.12.23.21267853v1
Best regards, Med vänliga hälsningar,
 
Jonathan Cedernaes
 
Leg. Läkare, PhD, docent i medicinsk cellbiologi
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Preliminary observations & uncertainties regarding Omicron (variant B.1.1.529)

Note that many aspects regarding this variant are *very* preliminary, as is hopefully highlighted throughout the text.

1. The spread of omicron at this point

Omicron has already been detected in several places including in numerous spots in across Europe. Its further spread across Europe is therefore likely very hard to fully prevent, if it is a more transmissible variant than the Delta variant. Slowing its spread is a different aspect (more on that below).

Many argue that outright travel bans are just hurtful – like indicated above, a variant like this has already spread by the time it is detected (it likely originated/emerged around the start of October – so around 8 weeks ago).

If a country bans travel or trade with countries that reports a new variant, then it will de-incentivize countries from reporting new variants. Intense testing – and possibly [travel] quarantines – comprise a much more sensible approach, many argue. Here’s where more widespread use of face masks (high-grade filtration N95/FFP2-3 masks) and repeated or weekly rapid tests can help. Such rapid tests are excellent at detecting when someone is contagious.

South Africa did not have the first case of this variant, that was Botswana. But South Africa has done a tremendous job in analyzing data related to the emergence of this variant, and may soon deliver the first data – in vitro-based – on how the vaccine fares against it (in their recent briefing on Omicron, local scientists said they would also examine T cell responses).

Yet, South Africa has only fully vaccinated <24% of its population. Meaning this increases the risk that many people fall ill – especially if they get transmission of a highly transmissible variant. Data also indicates that low vaccination rate increases the risk of producing more new variants (see this preprint and this modeling data)

Researchers have from the start highlighted how unfair vaccine distribution is. So one important take home message from Omicron (even if it turns out not to be a serious variant that takes over Delta), should be that vaccine coverage has to increase rapidly on a global scale.

COVID-19 was just the other day detected in 61 (out of 600) passengers from South Africa to the Netherlands. It’s at this point uncertain how many who may have had the Omicron variant. If Omicron does spread as well as some think, then just in and around these few (now known/detected events), we should expect to also see many more cases (so this by itself will tell us how well Omicron may actually take over, and how well/poorly it may transmit). But while it does seem to keep spreading fast locally, we don’t yet know whether Omicron has higher transmisssibility per se. This was also highlighted in ECDC’s recent report, see quote below.

While there is some potentially reassuring data to indicate that at least some infected with the Omicron SARS-CoV-2 variant may primarily have mild symptoms, this may not tell the whole truth: if the cases one are observing are primarily in young individuals, this may bias the clinical presentation. Young individuals typically have milder COVID-19 symptoms, and are typically more often asymptomatic

Other data indicates it may impact young individuals with moderate to severe disease, but also that this is primarily occurring in unvaccinated individuals, or in partially vaccinated individuals. In this context, it’s important to note that Gauteng only has ~38% fully vaccinated individuals (see the photo below); they’ve primarily used the Pfizer, AstraZeneca and J&J vaccines.

South Africa vaccine statistics from https://sacoronavirus.co.za/latest-vaccine-statistics/

2. Potential impact of the Omicron variant on vaccine-mediated protection: many unknowns

Many researchers and epidemiologists think (of course they cannot know) that the vaccines will maintain either some or even high levels of protection (at least likely against severe disease – although with COVID-19, even mild disease is not to play around with, given the potential risk of long covid). That some level of protection should exist is more likely to be the case as many individuals (unfortunately not on a global scale) are able to get, or have already gotten, three vaccine doses.

This may be bit of a stretch, but that some protection should be maintained can potentially (note, not certain) be inferred from observations of how well the 3rd vaccine doses increase neutralization against other variants:

At first glance, the list of mutations in Omicron looks quite overwhelming, especially if you just “name drop” them:

  • A67V, Δ69-70, T95I, G142D, Δ143-145, Δ211, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493K, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F) (see the following figure (from this Twitter thread) for a list of what the most important changes may be). Note that it has the mutation E484*A* – i.e. not E484K which the beta variant has/had, and which has been tied to some of the properties of the beta variant.
  • 15 of these Spike protein mutations are located in the receptor binding domain (RBD) – to which at least some of the vaccine-induced antibodies bind; a domain that the virus uses to attach to cells (via the ACE2 receptor).
Screenshot from tweet https://twitter.com/miamalan/status/1463846528578109444

This list is long (32 spike mutations), but for context, we’ve had variants with almost as many mutations (25-29 mutations), and they didn’t spread well – even though they may have avoided the vaccines to a greater extent (but this didn’t become relevant, because of their poor spread). Nevertheless, the number of mutations are definitely a cause for concern and rapid in-lab assessment of the variant, according to many researchers.

There could very well be a founder effect with Omicron (that makes it seem that it spreads better than it actually does). Essentially at this point, there are many parameters that we don’t know yet, although multiple researchers do point out that this is perhaps the most challenging variant that we have seen so far (meaning *potentially* very challenging for our vaccines to neutralize, but this is again, still quite unknown at this point).

In terms of its transmissibility (which some prefer to refer to as the virus’ fitness), there are also many unknowns:

  • While the rate of “takeover” has been very fast with Omicron (look at the larger, top figure below), it started from a point where community transmission was very low.
  • This means that it would appear to spread well, but really be due to its spread in an overall, fairly low number of local COVID-19 cases (a founder effect). In such a setting, even “only” a slightly more transmissible variant could appear to “take over” (e.g. after a local superspreading event). See the lower left figure below.
  • Its detection in multiple countries and places at this point, and some anecdotal cases, could potentially also indicate increased transmissibility. But it could also be the case that the variant has circulated for some time in these places (we will likely know more within a week or so, given that there are simple PCR-based methods for detecting this variant). The latter case, many argue, is another reason why outright travel bans do not serve a real purpose.
Prevalence graphs from https://twitter.com/jburnmurdoch/status/1463956686075580421?s=20

In their recent threat assessment brief for the Omicron variant, ECDC also highlighted these possibilities (including potential immune properties as a potential cause for increased spread):

  • “The rapid pace of replacement of the Delta variant by Omicron in South Africa raises concerns that this variant is significantly more transmissible than Delta, however the overall COVID-19 case numbers in South Africa are currently low which could increase the proportional effect of any superspreading events involving a specific variant.
  • In addition, the high observed growth rate could be due to immune escape. Further data are needed to be able to provide a reliable estimate of the transmissibility of the variant”

If vaccines do outright fail, we now have the technology and pipelines to update the vaccines within 100 days – because it’s still the same protein we would be targeting, just with some more changes

Moderna has already shown data one updated booster targeting a variant – the beta (B.1.351) variant – was safe and quite effective (at least in vitro; summary (Swedish summary)).

3. Omicron – another reason to get vaccinated, on a global scale

We don’t know how much, but variants like Omicron are, as also highlighted above, assessed as far likelier than any other prior variant to evade immune responses from prior COVID-19, or from vaccines.

  • In an in vitro-based study published in Nature, in the lab – under highly controlled conditions – they modified SARS-CoV-2 to generate a “polymutant” virus (a version that had 20 mutations that also occur naturally in SARS-CoV-2 variants across the globe; note that they used a pseudotypded virus, so not live SARS-CoV-2 virus, thus these results may not be totally applicable to real-life findings). 
  • What one of the researchers pointed out, is that Omicron has mutations in a lot of the regions of this modified SARS-CoV-2 in-lab version. This is noteworthy, as this modified in-lab virus version was able to evade neutralization by serum from all individuals who had *not* gotten vaccinated, but who had “only” recovered from COVID-19 (so-called convalescent individuals; i.e. they were using post-COVID-19 serum).
  • However, in individuals who after COVID-19 *also* got vaccinated (the “ITV” group in the figure below), they still observed some maintained neutralization (meaning they should be able to neutralize the virus if they encounter it, at least to some degree).
    • The COVID-19 with vaccine (ITV) group had a more sustained ability to neutralize this heavily mutated (in-lab) version of SARS-CoV-2 (this in-lab version was essentially tested to see how much a heavily mutated version of the virus would reduce our antibody-based immunity; once more an example of where science has been presciently helpful).
  • And now we also have data from Northwestern University to show that those who get 3 doses of vaccines (e.g. 3 doses of Pfizer or Moderna), have even better antibody-based immunity than those who had COVID-19 and then got vaccinated (previously, COVID-19 followed by vaccination – or vice versa – was repeatedly found to provide the greatest degree of protection). See panel C from the screenshot below (the individuals who got a booster are shown in the blue part of the graph)
  • Indeed, as indicated above, a 3rd dose of the vaccines boost antibody titers (as I’ve explained before) to complex variants, to a considerable degree (15–32x to the beta variant).
  • One observation – just a report, not statistical data – that we have regarding the protective role of vaccination against the variant Omicron, is that moderate-to-severe cases in South Africa (a region that seems to have a lot of Omicron transmission), seem to primarily occur in unvaccinated or (to a lesser degree) in partially vaccinated individual.

So in sum: There are now more than reasons than ever to get vaccinated. If Omicron does transmit more easily, then it could put unvaccinated individuals at even greater risk, especially in places (like the northern hemisphere), where winter conditions are certain to increase the likelihood of greater spread of SARS-CoV-2 (because of colder weather, lower humidity and less time spent outdoors vs. indoors).

Figure 1 from Figure 1 from https://www.medrxiv.org/content/10.1101/2021.11.19.21266555v1.full

4. Hur man detekterar Omicron

Slutligen (här blir det svenska) kan man detektera B.1.1.529 (omicron) med TaqPath Assay:

  • Liksom Alpha-varianten (B.1.1.7) så ger Omicron S gene target failure (SGTF), dvs. pga. en deletion i Spike-proteinet, som gör att man får negativ signal för en av proberna. Denna deletion hade även Alpha-varianten (B.1.1.7) av SARS-CoV-2-viruset.
  • I sin rapport beskriver ECDC att bland 77 selekterade SGTF-prover som sekvenserades (från Gauteng i Sydafrika), så var alla Omicron (dvs. belyser att den PCR-baserade metoden tycks finna samtliga fall av denna variant; eftersom Alpha inte längre sprids).

5. ECDC:s bedömning

Oavsett vad jag skrivit ovan finns det redan en helt färsk riskbedömning från ECDC, där de bedömer risken med denna variant B.1.1.529 / Omicron som hög till mycket hög (high to very high).

  • De påpekar bland annat osäkerheten gällande vaccinens verkan, liksom avseende risken för reinfektioner.
  • De bedömer att risken för spridning i en delta-rik miljö är hög
  • Därtill bedömer de att inverkan av omicron [på samhällsnivå] skulle kunna vara mycket hög, om den sprids när delta är på uppgång (t.ex. pga. säsongsberoende faktorer eller lättade samhällsåtgärder, som sammantaget påskyndar samhällsspridningen).

Finally, once more, please note that everything regarding this variant is still very preliminary. Many of the observations above may be old news or outdated within a few days to weeks from now.

Med vänliga hälsningar,
Jonathan Cedernaes
Leg. läkare, PhD och senior forskare

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