While waiting for the next variant (are we expecting π ?) and because I have to prepare a lecture for masters, it is perhaps a good time to reiterate, deepen a few topics and make some critical notes.
- About the origin of SARS-CoV-2
Ep 237-1: Holmes Cell Sept 2021: clearly defends the “natural” zoonotic origin
The phylogenetic tree and the early epidemiological investigations clearly show a link to the Huanan market and not to the Wuhan Institute of Virology (WIV)
This phylogenetic pattern is consistent with the emergence of SARS-CoV-2 involving one or more contacts with infected animals and/or traders, including multiple spill-over events (leading to sublineages from the beginning?), as potentially infected or susceptible animals were moved into or between Wuhan markets via shared supply chains and sold for human consumption.
There is a significant evolutionary gap between SARS-CoV-2 and the closest related animal viruses:
for example, the bat virus RaTG13 collected by the WIV has a genetic distance of 4% (1,150 mutations) to the Wuhan-Hu-1 reference sequence of SARS-CoV-2, reflecting decades of evolutionary divergence
RmYN02, RpYN06, and PrC31—are closer in most of the virus genome than RaTG13 (particularly ORF1ab) and thus share a more recent common ancestor with SARS-CoV-2
The animal origins of many well-known human pathogens, including Ebola virus, hepatitis C virus, poliovirus, and the coronaviruses HCoV-HKU1 and HCoV-NL63, are yet to be identified, while it took over a decade
to discover bat viruses with >95% similarity to SARS-CoV and able to use human ACE-2 as a receptor
- No data to suggest that the WIV—or any other laboratory—was working on SARS-CoV-2, or any virus close enough to be the progenitor, prior to the COVID-19 pandemic.
- There have been no reported cases related to any laboratory staff at the WIV, and all staff in the laboratory of Dr. Shi Zhengli were said to be seronegative SARS-CoV-2 when tested in March 2020.
- Bat virus RaTG13 from the WIV has reportedly never been isolated or cultured and only exists as a nucleotide sequence assembled from short sequencing reads.
- Amplification in Vero E6 cells, a process that consistently results in the loss of the SARS-CoV-2 furin cleavage site
And what about omicron?
Ep 237-2: Mallapaty Nature 3 Feb 2022: three hypotheses
- Long unnoticed evolution in a human population: closest known ancestor dates back to mid 2020.
- Evolution via rodent (rat, mouse).
- Evolution in chronically infected immune-compromised person.
Ad 1) Long unnoticed evolution
Conclusion: It cannot be excluded, since coverage of genomic evolution is strong in only some countries (including South-Africa, where omicron has first been detected), but weak in most of its neighbors
Ad 2: Evolution via rodent?
Ep 237-3: Peacock bioRxiv 3 Jan 2022: Affinity change of omicron for animal ACE2
Omicron binds much better to ACE2 from mice, rats, horseshoe bats
(Receptor usage was screened using pseudoviruses expressing the indicated Spike proteins into BHK-21 cells expressing the indicated ACE2 protein. Viral entry was measured by assaying luciferase activity (RLU)
Ep 237-4: Changshuo Wei Journal of Genetics and Genomics Dec 2021: Omicron mutation pattern suggestive of adaptation to mouse.
Conclusion: there is clear change of receptor tropism towards rodents (but also other species). Previously, such evolution has been seen in mink farms: humans infecting minks and minks back-infecting humans with new “mink adapted” mutations. The question remains whether there is enough close contacts between humans and rodents (mice rats) for such a cycle of reverse zoonosis en back-zoonosis.
Ad 3: “Silent” evolution in immunocompromised host?
Ep 237-5: Cele Cell Host & Microbe 2022
“Ancestral” SARS-CoV-2 (= before Beta and Delta variants) in a person with advanced HIV in South Africa.
Evolution over 6 months
- a multitude of mutations found in Omicron and other variants
- weak neutralization by self-plasma
- substantial but incomplete escape from sera of people vaccinated with Pfizer BNT162b2
- extensive escape from sera of Delta infection-elicited neutralizing activity
Conclusion: Even pre-beta and delta SARS-CoV-2 in immune-compromised hosts may evolve into “Omicron-like” virus with immune escape of vaccines and enhanced escape of Delta immunity.
- Clinical characteristics
Ep 237-6: Paul Drain NEJM a didactic overview of course, symptoms and use of rapid antigen tests.
Critical note: this review does NOT contain a really critical evaluation of the performance of rapid antigen tests (RAT), but refers to CDC (ref 31) and European Commission (ref 33). Unfortunately, I could not reach the CDC site, but the very long EC document, updated on 21st Jan 2022, is included (Ep 237-6 B). It contains detailed instructions on how evaluation should be done and an exhaustive Annex 1 (from p. 10 on), with all the tests approved in the EU and their reported performance. Two remarks:
- Whenever sensitivity has been evaluated by an independent validation study: usually by Paul Ehrlich Institute, only the value for Ct < 25 (the highest possible viral load) is considered, while at lower viral loads sensitivity is often much lower (see Ep 237-6 C).
- The column “Detection of Omicron” is empty in > 90 %
Clearly, we remain VERY UNSURE about the diagnostic value for omicron of the large majority of the RAT on sale everywhere, while the uncontrolled use of these tests has been one of the main the “cornerstones” to tackle the omicron wave. It is like sailing without a compass in the dark!
Ep 237-7: Max Kozlov Nature Briefings 4 Feb ’22: Does Omicron hit kids harder?
There have been alarmin figures from UK and US about children making up about 5% of all COVID-19 hospitalizations — a proportion up to four times higher than that of previous coronavirus waves.
Why? Much higher transmission and lack of build-up immunity
- The individual risk of a child with Omicron being hospitalized is, in fact, lower — by one-third to one-half — than it was when the Delta variant was dominant.
- Kids are not presenting with any more severe illness than they were with other variants, in fact: fewer medical interventions such as supplemental oxygen or ventilators
There is an increase in the number of children with ‘COVID croup’, which is an inflammation of the upper airway that produces a characteristic ‘barking’ cough.
The occurrence of MISC after omicron is still unclear (but, from the delta wave in adolescents, we do know that it can be prevented by vaccination).
Ep 237-8: Maryam Ayad Res Square 2022: Neurodevelopmental delay in infants born to mothers with SARS-CoV-2 during pregnancy. Study using the ASQ-3 questionnaire in Kuwait on 298 pregnancies, but without a control group.
- Only 2 positive for SARS-CoV-2 and normal development
- 10 % of infants showed developmental delays after 10-12 months
- Main risk factors were SARS-CoV-2 infection early (1st or 2nd trimester) and born before 31st week.
Note: Interesting warning, but limited value by the lack of a control group.
Ep 237-9: Brit Long Am J Emerg Med Jan 22 Clinical update on COVID-19 for the emergency clinician provides an overview of organ involvement during severe COVID and several clinical scoring systems to predict clinical deterioration.
Ep 237-10: Amary Fall medRxiv 28 Jan ’22: Comparison of delta and omicron in US
- CLINIC: Omicron associated with a significant increase in infections in fully and booster vaccinated individuals but with less admissions and ICU level care
BUT: Omicon- admitted patients showed similar requirements for supplemental oxygen and ICU level care when compared to Delta admitted patients
- VIRUS: Viral loads were similar in samples from Omicron and Delta infected patients regardless of the vaccination status.
However: Recovery of infectious virus (CPE)
- Delta: reduced from patients infected with Delta who received a booster dose,
- Omicron: equivalent in Omicron infected unvaccinated, fully vaccinated, and boosted patients, suggesting that infectiousness of omicron is not reduced by vaccination
- Prevention and therapy
Ep 237-11: Andrejko MMWR 4 Feb 2022 : Effectiveness of Face Mask or Respirator Use in Indoor Public Settings
- Consistent use of a face mask or respirator in indoor public settings was associated with lower odds of a positive SARS-CoV-2 test result (adjusted odds ratio = 0.44).
- Use of respirators with higher filtration capacity was associated with the most protection, compared with no mask use.
Critical Note: The study is based on telephone interview of matched positive and negative cases. The interviewer was not blinded, there are several (8!) other limitations listed and the complicated statistics is non-intuitive. Nevertheless, these “real world” data add to a long list of arguments in favor of systematically using high quality face masks to protect against respiratory infections.
Results of ZIFIVAX (ZF2001) a Chinese protein trimeric receptor binding domain subunit vaccine
Ep 237-12 A: Preclinical studies in mice and non-human primates (NPH)
- ZF2001 induced high levels of RBD-binding and SARS-CoV-2 neutralizing antibody in both mice and NHPs, and also 56 elicited balanced TH1/TH2 cellular responses in NHPs.
- NHPs, vaccination of either 25 μg or 50 μg ZF2001 prevented infection with SARS-CoV-2 in lung, trachea and bronchi, with milder lung lesions.
Ep 237-12 B: Yang Lancet Infect Dis March 2021 Phase 1+2 of a “ tandem-repeat dimeric RBD-based protein subunit vaccine (ZF2001)”
- Three immunisations with 25 or 50 µg at day 0, 30, and 60 achieved 93–100% seroconversion of neutralising antibodies, with the geometric mean titres exceeding the magnitude of convalescent serum.
- Moderate cellular immune responses, as demonstrated by the balanced production of cytokines associated with T-helper 1 and T-helper 2 cells.
HCS = human convalesecent serum
Ep 237-12 C: Xin Zhao NEJM 26 Jan 2022 Beneficial effect of prolonging interval for booster of subunit vaccine (from 1 to 4 months
- G The persons in the inactivated-vaccine group received the second priming dose 1 month after the first dose and then the third dose more than 6 months after the second dose.
- H The persons in the short-interval ZF2001 group received the second priming dose 1 month after the first dose and then the third dose 1 month after the second dose.
- I The persons in the prolonged-interval ZF2001 group received the second priming dose 1 month after the first dose and then the third dose 4 months after the second dose.
- J Same as I, but collected 4-6 months after third dose.
(Sorry, I could not find when the samples were taken in E-I, but presumably a few weeks after the third dose).
- Using 3 doses of the RBD subunit vaccine in a short interval (H) is not much better than using an inactivated vaccine (G)
- Prolonging the interval (I) boosts the neutralizing titers a lot, including good neutralization of omicron.
- As could be expected, the titers wane after 4-6 months
Ep 237-12 D: Update on 15 Jan summarized the above data, but also indicates that the phase 3 trial is still underway….
Critical note: all the evidence remains “circumstantial” as long as we have no solid data from a phase 3 study. Nevertheless, it is remarkable that repeated immunization with the most variable RBD part of Spike (where many of the variant-specific “escape” mutations occur) also results in broadening of the antibody responses, including very significant neutralization of omicron.
ACTIVITY OF NEUTRALZING ANTIBODIES AND ANTIVIRAL DRUGS AGAINST OMICRON
Ep 237-13: Takashita 26 Jan 2022: in vitro studies with most important VOC
- Neutralizing monoclonal antibodies
- The antibody cocktails REGN 10,087 + 10,033 from Regeneron and LY-CoV 016 + 55 from Eli Lilly completely lose activity
- Sotrovimab (VIR-GSK) and the Evusheld cocktail COV2 2196 + 2130 cocktail (Astra-Zeneca) remain active at similar sub-µg/ml (EC50 of 373 and 255 ng/ml resp.), but with differential reduced potency:
- Sotrovimab against omicron only 3 X less potent than against delta
- Evusheld against omicron 50 X less potent than against delta
- The antiviral drugs : (Remdesivir, Molnupiravir and Paxlovid): keep activity against omicron 100 %
Critical Note: While the antiviral drugs can be used against omicron, the use of the presently available neutralizing Ab can be questioned. Can high enough concentrations be obtained with regular dosing and for how long? The risk is clear: if these mAb are used in immunocompromised subjects, exposing the omicron to suboptimal concentrations in subjects with a risk on chronic infection could select for new mutations that might give rise to new variants of concern….
As we have explained in Episode 227 7-11 new very broad (“pansarbeco”) neutralizing Ab are on the horizon, but, of course, they should first go through clinical evaluation….
I will have to focus on my presentation for a few days. Episode 238 probably for after the WE?
Best wishes !!!
5 Oct 2022 Episode 289: Omicron BA.2.75 revisited and the outlook for new variants, including BQ.1.1
> More info