14 February Episode 238 Differences between delta and omicron diagnostics virology clinic and serotype

Mon, 02/14/2022 - 18:08

Dear colleagues,

Based on a special request, I tried to find some papers that focus on omicron versus delta in various fields.



Ep 238-1: Metzger Swiss Weekly Dec 2021

  • Early reports suggested that Omicron, just like Alpha, would show a “S-gene dropout” or “S-Gene Target Failure” (SGTF) due to the 69-70 deletion, common to both VOC, but this phenomenon was based on TaqPath Combo test by Thermo-Fisher.  
  • Metzger investigated the performance of 40 commercially available COVID PCR tests and found that, besides  TaqPath, only 1 other test showed this dropout (see Fig 1 p. 3).  
  • An additional problem is that the BA.2 Omicron sublineage does  not contain the 69-70 deletion and therefore doesn’t show SGTF, hence the nick name “stealth omicron”.

Ep 238-2: Harankhedkar medRxiv 1 Feb proposes “N-gene target failure” (NGT) as a way out. It is based on the Huwei Life Sciences PCR test, which has 3 targets in RNAseP, Envelope and Nucleoprotein.  The reason for the selective N dropout in omicron is the ERS31-33 deletion (nucleotide 28362-28370del).  It is not seen in any other VOC.  An example of a regular result for delta is shown in a), while the NGTF in omicron is illustrated in b)


Ep 238-3:  Fasching medRxiv 3 Feb presents a rapid COVID-19 variant DETECTR® assay incorporating loop-mediated isothermal amplification (LAMP) followed by CRISPR-Cas12 based identification of single nucleotide polymorphism (SNP) mutations in the SARS-CoV-2 spike (S) gene.  Based on 3 S amino acid positions (452, 484 and 501) a broad distinction between VOC can be made, but some VOC still need more precise genotyping e.g. Beta-Gamma-Mu, Delta-Epsilon and Eta-Iota-Zeta


Ep 238-4: Var-LOCK is a further development of the SARS-CoV-2 CRISPR-Cas detection technology (SHERLOCK).  The principle is to determine either single or combined mutations that are specific for each variant, as shown in the Figure.


SARS-CoV-2 Variant of Concern identification by VarLOCK assay. A) illustration of the VarLOCK assay. The region with wildtype (green) or mutant (pink) sequence of SARS-CoV-2 RNA is amplified by either RPA, LAMP or PCR. Amplified DNA fragments are subjected to SHERLOCK assay with a pair of guide RNAs matching the wildtype sequence (wt gRNA, green) or the mutant sequence (VOC gRNA, pink). We aimed to find conditions in which only a perfect match between the gRNA and the amplified DNA can trigger a collateral nuclease activation of the Cas12b protein to cleave a quenched fluorescent reporter. This allows nuclease activity to be monitored by the increase in fluorescence. The ratiometric response of an unknown SARS-CoV-2 variant sample indicates the presence, or absence, of the targeted mutation and thus enables identification of the VOC. B) Schematic of the genome of SARS-CoV-2 (left) with blow-up of the Spike protein encoding region showing the location of RBD, S1 and S2. Nineteen mutation sites were chosen for VarLOCK assay for which gRNA pairs were designed and optimised. Nucleotide sequences encoding the relevant amino acids are shown in the table and the nucleotide substitutions/deletions are marked in red. The association of the mutations with various variants of concern is indicated in the table, creating a barcode-like identification matrix


Ep 238-5: Salcedo medRxiv 28 Jan on the analytical performance of E25Bio rapid antigen test, compared to culture (plaque forming units or PFU). According to the authors it is very sensitive for alpha and gamma (10 PFU), less to omicron (100 PFU) and even less to Delta (1000 PFU)


In all honesty, I fail to see the positive lines for omicron at 100 PFU and for alpha/gamma at 10 PFU….

Conclusion on diagnostics

Sensitive and specific tests are available based on LAMP and CRISP-Cas technology.

Sensitivity of rapid antigen tests remains problematic



Ep 238-6: Puhach medRxiv 28 Jan 2022:  Infectious viral load in unvaccinated and vaccinated patients infected with SARS-CoV-2 WT, Delta and Omicron


  1. Significant, but rather poor correlation between PCR and culture results.
  1. RNA load and infectious titers over time (days after positivity) rather similar in WT and unvaccinated delta infection
  1. Infectious titers lower in delta breakthrough infections than unvaccinated delta
  1. RNA copy number and infectious titers similar in delta and omicron breakthrough infection


  • Delta vaccine-breakthrough  associated with lower infectious titres and faster clearance for Delta, showing that vaccination would also lower transmission risk.
  • Omicron vaccine-breakthrough infections did not show elevated infectious titres compared to Delta, suggesting other mechanisms than increase VL for  high infectiousness of Omicron.


Ep 238-7: Backer medRxiv 28 Jan 2022 : A shorter serial interval was observed for omicron (S-Gene Target Failure) as compared to delta (non-SGTF) for within household transmission in the Netherlands: 3.45 versus 4.05 days.


This shorter serial interval, together with higher transmissibility and immune escape may explain the rapid spread of omicron in the Netherlands




Ep 238-8: Yan Xie Nat Med Feb 2022 Increased cardiovascular risk post-COVID in veterans US


Individuals with COVID-19 are at increased risk of incident cardiovascular disease spanning several categories, including cerebrovascular disorders, dysrhythmias, ischemic and non-ischemic heart disease, pericarditis, myocarditis, heart failure and thromboembolic disease during 1 year post


  • Cardiovascular incidents increases depending on severity of acute phase
  • Remarkably, CV incidents also present in those with less pre-existing cardiovascular risk factors (age, smoking, obesity etc)


= clear argument pro vaccination


Ep 238-9: Lauring medRxiv 7 Feb 2022 Clinical Severity and mRNA Vaccine Effectiveness for Omicron, Delta, and Alpha VOC in US


Vaccine effectiveness against hospitalization

  • 2 doses: 85 % for Alpha, 85 % for Delta and 65 % for Omicron
  • 3 doses: 94 % for Delta and 86 % against omicron


WHO clinical severity for hospitalized patients

  • Unvaccinated: Delta (1.28) > Alpha (1.0) > Omicron (0.61)
  • Vaccination protected against severity within each VOC:  adjusted risk 0.33 (Alpha-Delta) -0.61 (Omicron).


Conclusions clinical aspects


  • Confirmation that delta has higher severity than alpha and omicron least
  • 3 doses of vaccine needed for optimal protection against severity in delta and omicron
  • Important observations on various cardiovascular complications after the acute phase further support vaccination as prevention for post-acute prevention.



OMICRON can be considered as a SEPARATE SEROTYPE


Ep 238-10 = Ep 225-5:   Rössler NEJM Jan 2022



Ep 238-11: Rossler medRxiv Feb 2022 Neutralization profile of Omicron variant convalescent individuals


Ep 238-12: K van der Straten medRxiv Jan 2022

SARS-CoV-2 antigenic cartography.

  1. Antigenic map of SARS-CoV-2 VOCs based on post-SARS-CoV-2 infection sera. SARS-CoV-2 VOCs are shown as circles and sera are indicated as squares. Each square corresponds to sera of one individual and is coloured by the infecting SARS-CoV-2 variant.

Both axes of the map are antigenic distance and each grid square (1 antigenic unit) represents a two-fold change in neutralization titre. The distance between points in the map can be interpreted as a measure of antigenic similarity or similarity in reactivity where closer together points are more similar.


  1. Antigenic map of SARS-CoV-2 VOCs based on post-vaccination sera from individuals without prior SARS-CoV-2 infections. Each serum is coloured by the vaccine that individual received.

The ancestral and Alpha viruses cluster tightly together in the centre of the map, while the Beta, Gamma, and Delta variants all lie within 2 antigenic units (1 unit = 2-fold change in neutralization titre) of the ancestral virus suggesting a high degree of antigenic similarity = one antigenic cluster

The distance between this antigenic cluster and Omicron is more than 5 antigenic units = separate antigenic cluster.


Conclusion: omicron has clearly distinct immuno-type: development of omicron specific booster important for non-infected wild-type vaccinated people.   





Ep 238-13: Sokol BMJ 24 Jan 2022 argues pro mandatory vaccination in HCW

Healthcare workers… are free to refuse the covid vaccine. If they exercise this right, however, they cannot work with vulnerable patients. To do so would be contrary to the ethics of their profession, as set out in their professional codes, and is likely to damage public trust and confidence in the medical profession


Ep 238-14: Barbara Michiels: The scientific arguments in favour of mandatory Covid-19 vaccination in healthcare workers are ‘waning’

… The efficacy of current Covid vaccines, including booster shots, against transmission in HCWs is declining and is uncertain in the long term. The cost of an implementation is likely to outweigh the profit. The WHO criteria for a mandatory vaccination policy are insufficiently met.


Ep 238-15: FDA has decided to wait for results of 3 dose Pfizer regimen in children under 5 before considering early approval, which will delay decision till April. This looks like a reversal of an earlier decision see Ep 234-11.


Best wishes,