Part of the government fear-mongering[7] to keep you unbalanced and under its control is the fear that “the variants are coming”. We have already seen that from politicians as the first variants arose. Indeed, the latest variant called the “India” variant or “Delta” to avoid racist implication that might offend our woke culture, is about to be hyped as the reason to keep authoritarian practices such as lock-downs in place. After all, your friendly autocrats are doing all this for the common good.

Discussion of Variants

The COVID-19 Genomics UK Consortium (COG-UK) provides an excellent body of work on identifying variants by genome sequencing, having sequenced 567,371 samples as of this writing. Figure 1 below shows how variants progressively evolve and replace earlier variants.

Figure 1. Variant genome sequences performed per week, COG-UK.

Note how the Delta (Indian) variant (blue bars) is rapidly replacing the dominant earlier UK variant labelled Alpha or B.1.1.7 (green bars). This in turn had out-competed the original virus (pink bars). This genetic drift in the virus genome is due to mutations that confer some improved property of the virus that increases its fitness or survivability.

One such property is known as immune escape[1][2][4]. A corona virus mutation may change the shape of the protein structure (the spike protein) of the virus such that natural or vaccine-induced immunity, called antigenicity[3], is less or not at all effective. This gives the variant a selective advantage over an older variant for which greater immunity exists in the population.

Another property which was observed[3] in the early D614G variant is increase infectiousness or transmissibility due to improved human cellular (ACE-2) binding. This variant rapidly replaced the original virus in the Southern US. It’s lethality, however was unchanged.

One might have by now realized that mutations compound over time. Indeed, scientists create a family tree of the tens of thousands of variants that they sequence. A current variant that has mutated from an earlier variant must retain genetic changes acquired by the earlier variant. While infectiousness is a property that is naturally selected for, lethality is not. Indeed, a virus that through a mutation becomes highly lethal, might kill its host before it could be passed to another host.

Kantor et al[6] note, ‘it would be expected that SARS-CoV-2 will evolve into more infectious and less virulent [lethal] variants” and therefore less lethal. The exception to this is “gain-of-function” research in the laboratory which intentionally tries to increase viral lethality. This is a central theme in the current SARS-CoV-2 virus origin controversy.

Transmissibility and Lethality of the Delta Variant

A search of the PubMed data base using search terms including”{India, Delta} SARS-CoV-2 variant {lethality, mortality}” produced no results for mortality or lethality studies associated with the Delta variant.

One UK study by Davies et al[10] found that for the Alpha variant, “the absolute risk of death for a 55–69-year-old man increasing from 0.6% to 0.9% (95% confidence interval, 0.8–1.0%)“, but this variant has been supplanted by the Delta variant in the UK.

A paper by SeyedAlinaghi et al[8] performed a survey of the existing literature on variants with respect to their morbidity and mortality. After a review of all papers cited in Table 1 of their report, I found no information about increased mortality associated with any of the dozens of variants reviewed. A couple of their references such as [56] indicated a reduced severity and therefor mortality. This is consistent with what Ravikanth et al[9] found with one variant that they studied.

A Public Health England report[11] found “an increased risk of hospitalisation with Delta compared to Alpha” but that for the Delta variant “the crude case fatality rate remains lower for Delta than other variants[12] but cautioned that this could change as more data accumulates.

Comments from officials at the World Health Organization note the increased fitness and transmissibility of Delta, and infer increased mortality. Their argument is that the increase in transmissibility means a faster spread and the possibility of overwhelming a country’s health care system. While a concern, this is not a comment on the lethality of the virus for which they provide no data. Further, present prevention controls available or in place reduce the liklihood of this.

Summary

The Delta variant is the dominant variant today due to its higher infectiousness. There is some indication that the severity, meaning number of required hospitalizations, is greater than earlier variants but there is no indication at this time that it is more lethal and may in fact be more benign. It is not clear yet to what degree natural and vaccine-induced immunity will affect Delta. Countries that have maintained a COVID-19 response leading to herd immunity may have little to fear.

References

  1. Carabelli AM, Robertson DL, and Peacock SJ. SARS-CoV-2 variants, spike mutations and immune escape – an update. COG-UK. June 01, 2021.
  2. Chao C. Fitness of RNA virus decreased by Muller’s ratchet. Nature 348, 454–455 (1990). November 29, 1990. https://doi.org/10.1038/348454a0.
  3. Yurkovetskiy L, Wang X, Pascal KE, et al. Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Cell. 2020 Oct 29;183(3):739-751.e8. doi: 10.1016/j.cell.2020.09.032. Epub 2020 Sep 15. PMID: 32991842; PMCID: PMC7492024.
  4. Harvey WT, Carabelli AM, Jackson B et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol 19, 409–424 (2021). June 01 2021. https://doi.org/10 1038/s41579-021-00573-0. PDF.
  5. Mull NK, Mitchell MD, and Brennan PJ. An Evidence Review from the Penn Medicine Center for Evidence-based Practice. December 2020. PDF.
  6. Kantor IN, Lüthy IA, Ritacco V. SARS-CoV-2 variants and the so-called resistance to vaccines. Medicina (B Aires). 2021;81(3):421-426. English. PMID: 34137703. PDF.
  7. Mercola J. COVID Delta Variant Reignites Fear — How Real Is the Threat? Defender. June 23, 2021.
  8. SeyedAlinaghi S, Mirzapour P, Dadras O, et al. Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. Eur J Med Res. 2021 Jun 8;26(1):51. doi: 10.1186/s40001-021-00524-8. PMID: 34103090; PMCID: PMC8185313.
  9. Ravikanth V, Sasikala M, Naveen V, et al. A variant in TMPRSS2 is associated with decreased disease severity in COVID-19. Meta Gene. 2021 Sep;29:100930. doi: 10.1016/j.mgene.2021.100930. Epub 2021 May 28. PMID: 34075330; PMCID: PMC8161869.
  10. Davies NG, Jarvis CI, Edmunds WJ, et al. Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7. Nature 593, 270–274 (2021). May 13 2021. https://doi.org/10.1038/s41586-021-03426-1.
  11. SARS-CoV-2 variants of concern and variants under investigation in England – Technical briefing 15. PHE. June 11, 2021. PDF.
  12. SARS-CoV-2 variants of concern and variants under investigation in England – Technical briefing 16. PHE. June 18, 2021. PDF.
Categories: COVID-19

The POOG

I started a blog in 2011 called The POOG, an acronym for "pissed off old guy". This is the current incarnation.

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