Viral dynamics & duration of PCR positivity of the #Omicron variant

In this study, longitudinal RT-qPCR tests collected between July 5th 2021 & January 10th 2022. This included 97 Omicron infections and 107 confirmed Delta infections 1/
Here are trajectories from individuals detected ≤1 day or ≥2 days since a previous negative or inconclusive test. 2/
Omicron infection duration was similar to Delta (both ~10 days), but Omicron infections had lower peak viral loads (higher peak Ct values). 3/
There is more variability in estimated ‘proliferation times’ – that is the delay from infection to reaching peak Ct. Plot shows individual-level posterior mean estimates (Red:Omicron, Blue: Delta). 4/
This reflects that some Omicron infections with low viral load for a few days prior to growth, possibly reflecting suppression via immunity or different compartmentalization in the respiratory tract, while others grow rapidly. 5/
Was there some impact of ore-existing immunity on Omicron’s growth?

Yes, may be. As most of these individuals are vaccinated and many were boosted before the rise of Omicron. 6/
Key takeaways:

1- ~50% of individuals have low Cts ≥5 days post detection, even in this highly-boosted population

2-Peak viral load, proxied by Ct values, is lower, and peaks no sooner, than for Omicron than Delta. 7/
3-So Omicron’s increased infectiousness doesn’t seem to be through higher viral load 8/
Conclusions: While Omicron infections feature lower peak viral RNA & a shorter clearance than Delta infections, it is unclear to what extent these diff are attributable to more immunity in largely vaxxed population or intrinsic features of Omicron 8/…
@PeacockFlu has some interesting explanation on the lower viral load for tje Omicron to efficiently infect a greater number of cells in the upper respiratory tract at even a lower infectious dose

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More from @vipintukur

15 Jan
Comparison of Antibody Response Durability of mRNA-1273, BNT162b2, and Ad26.COV2.S SARS-CoV-2 Vaccines in Healthcare Workers

🟠 COVID-19 vaccination with mRNA-1273 (n=387); BNT162b2 (n=212); or Ad26.COV2.S (n=10); unvaccinated (n=10); or boosted (n=28). 1/
🟠 IgG anti-spike titers (AU/mL):

-mRNA-1273: 1539.5 (876.7-2626.7)
-BNT162b2: 751.2 (422.0-1381.5)
-Ad26.COV2.S: 451.6 (103.0-2396.7)

-Unvaccinated: 113.4 (3.7-194.0)
-Boosted: 31898.8 (21347.1-45820.1) 2/
🟠 Pseudo-neutralization percentages:

-mRNA-1273: 90.9% (80.1-95.0)
-BNT162b2: 77.2% (59.1-89.9)
-Ad26.COV2.S: 57.9% (36.6-95.8)

-Unvaccinated: 40.1% (21.7-60.6)
-Boosted: 96.4% (96.1-96.6) 3/
Read 5 tweets
1 Jan
How can you deal with a virus that has the capability of even switching its entry route?

Laboratory experiments demonstrate that #Omicron has switched its route of entry in to human cells. 1/
This is likely to influence #Omicron spread and the types of cells it can hijack. 2/
#SARS2 can enter cells via two routes, both routes require spike activation by proteases.

Route 1: Cell surface fusion, triggered by #TMPRRS2.

Route 2: endosomal fusion, triggered by cathepsins.

So far SARS2 has favoured Route 1.
Read 15 tweets
13 Nov 21
What happens if we allow #SARS2 to become endemic? What’s going to happen to us & what’s going to happen to the virus?

If we allow it to become endemic—and some would argue that it is already endemic—this does not mean that it is going to attenuate, not whatsoever. 1/
It is not true that more transmissible versions of #SARS2 will be more benign. What we are seeing is more aggressive, more transmissible versions which are creating more severe illness. And the virus is still adapting to our physiology. It’s doing it at a fantastic rate 2/
What we’re going to see is that it will continue to work against our immune systems, meaning become more immune evasive. It’s going to become more chronic as an infection. 3/
Read 14 tweets
12 Nov 21
Natural immunity post-#SARS2 infection may not be perfect agains #Delta variant!!

A new study from #Australia:

“The duration & magnitude of #SARS2 immunity after infection, especially wrt the emergence of new VOCs”

At 12 months after mild-COVID19:

1->90% of convalescents remained seropositive for RBD-IgG & 88.9% had circulating RBD-specific memory B cells.

2-Despite this, only 51.2% convalescents had serum neutralising activity against homologous live-SARS2 virus

3-The neutralising activity decreased to 44.2% against live Alpha, 4.6% against Beta, 11.6% against Gamma & 16.2%, against Delta

4-Spike & non-Spike-specific T cells were detected in >50% of convalescents

Read 7 tweets
15 Oct 21
Iranian #COVID19 epidemic: Salient features

Continued circulation of #SARS2 from late jan 2020 to Sep 2021 in iran despite >100% attack rates in 11 provinces. 1/ Image
As of Sep 21, only 48% (95% CI: 43-55%) of COVID deaths in Iran have been reported. Approx 0.4% of the population have died of COVID so far
Estimated #IFR increased by a factor of ~2 over the course of the epidemic (from wave 1 to 5).

Across different ages, the 3rd wave in Oct 2020 & the current wave with #Delta had the largest impact on younger age-groups. 3/
Read 5 tweets
14 Oct 21
Are the #boosters already waning?

Booster effectiveness against breakthrough coronavirus infection is already waning.

The protection against infection among Pfizer booster recipients ages 60+ topped out by day 30 then fell steadily. 1/ Image
By day 58, the #booster appeared to be providing around 40% of the maximum increased level of protection above the initial 2-dose series.

New data finds boosters are helping more than just 50+, but that the effects already appear to be decreasing. 2/ Image
Bottom line: The case for boosters to prevent infection for all adults is now far stronger, if that is our goal. But how long that protection lasts remains unclear at best and boosters may turn out to lower the #Ro of #SARS2 only briefly. 3/
Read 5 tweets

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