White House touts Covid-19 'lab leak' theory on new website

[xocetaceans]

23. Yes, that alteration in your post from DNA to RNA is now acknowledged. Other questions that need to be addressed...

...are what "close enough" means in your statement and why it seems (based on what was in your statement) that some sort of linear progression from SARS-CoV to SARS-CoV-2 might be being imagined and that any progression (i.e., more realistically, a divergence from that common ancestor) was not in the presence of other similar viruses from that subgenus which might also contribute to affecting changes to their respective viral genomes. In looking at the "genealogy" (Do you mean "phylogeny" by chance? See the second referenced paper below for a phylogeny.) it IS clear that SARS-CoV and SARS-CoV-2 have a common ancestor in the subgenus Sarbecovirus. Is it your contention that they are the only inhabitants of that subgenus or that they are have some sort of linear progression from one to the other? From the way that you've stated your claims, that seems to be what you're implying.

Also, your other comment about "What they do look for in (DNA) extractions are the markers of the virus in human (DNA)." is wholly unrelated to anything relevant to the origin of SARS-CoV-2, and it really seems to be quite a random remark.

All in all, it seems that you have not followed the pandemic very closely, and that is ok, but amplifying evidence-free conspiracy-adjacent ideas (Russia did it?) is not useful to fostering public health or science in the USA. In fact, your cited genomic similarities are more indicative of the position that the virus did not originate in a lab leak than of anything else: it makes both design (too complicated) and passaging (too lengthy a process) unlikely sources.

So, given the present state of the ACTUAL EVIDENCE, a zoonotic origin for SARS-CoV-2 is the only currently tenable hypothesis.

Published: 16 February 2022
Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Sarah Temmam, ..., & Marc Eloit
Nature 604, pages 330–336 (2022)

Abstract

...

Main

The origin of SARS-CoV-2, as well as its mode of introduction into the human population, are unknown at present. Since its emergence, numerous animal species have been studied to identify possible reservoirs and/or intermediate hosts of the virus, including a large diversity of insectivorous bats of the genus Rhinolophus. Despite the recent report of various SARS-CoV-2-related viruses in R. shameli (isolated in Cambodia in 2010 (13)), R. pusillus and R. malayanus (China, 2020 and 2019, respectively(2)), R. acuminatus (Thailand, 2020(3)) and R. cornutus (Japan, 2013(4)), the closest SARS-CoV-2 bat-borne genome still remains the one from R. affinis, RaTG13 (China, 2013(5,6)), with 96.1% identity at the whole-genome level. Several studies also suggested the involvement of pangolin coronaviruses in the emergence of SARS-CoV-2 (refs. 7,8,9). Since its appearance in humans, SARS-CoV-2 has evolved through sporadic mutations and recombination events(14), some of which correspond to gains in fitness allowing the virus to spread more widely, or to escape neutralizing antibodies(15).

To decipher the origin of SARS-CoV-2, it is therefore essential to ascertain the diversity of animal coronaviruses, and more specifically, that of bat coronaviruses. Although the identification of SARS-CoV-2 in bats is a main goal, a more realistic objective is to identify the sequences that contribute to its mosaicism. The spike sequence seems essential, as it determines the binding affinity and accessibility of the receptor-binding domain (RBD) to the cellular ACE2 receptor and is therefore responsible for host range(10,11,12). The closest related bat strain identified so far (RaTG13) has a low RBD sequence similarity to SARS-CoV-2, and with only 11/17 hACE2 contact amino acid residues conserved with SARS-CoV-2, its affinity for hACE2 is very limited16. Moreover, SARS-CoV-2 poorly infects bats and bat cells tested so far(17). In addition, no bat SARS-CoV-2-like virus has been shown to use hACE2 to efficiently enter human cells, and none has the furin cleavage site that is associated with an increased pathogenicity in humans(18). The SARS-CoV-2 RBD binds to R. macrotis ACE2 with a lower affinity than to hACE2 (ref. 19). An essential piece of information—finding bat viruses with an RBD motif genetically close to that of SARS-CoV-2 and capable of binding to hACE2 with high affinity—is therefore missing.

We speculated that this type of virus could be identified in bats living in the limestone karstic terrain common to China, Laos and Vietnam in the Indochinese peninsula. Here we report the presence of sarbecoviruses close to SARS-CoV-2 whose RBDs differ from that of SARS-CoV-2 by only one or two contact residues, strongly bind to the hACE2 protein and mediate hACE2-dependent entry and replication into human cells. Despite the absence of the furin cleavage site, these viruses may have contributed to the origin of SARS-CoV-2 and may intrinsically pose a future risk of direct transmission to humans.

...

https://www.nature.com/articles/s41586-022-04532-4

J Virol Methods. 2020 Dec 5;289:114032.
Genomic and evolutionary comparison between SARS-CoV-2 and other human coronaviruses
Zigui Chen, ..., Paul KS Chan

...

1. Introduction

...

Phylogenetically, SARS-CoV and SARS-CoV-2 share a most recent common ancestor within the subgenus Sarbecovirus, and are relatively distant to MERS-CoV (belonging to the subgenus Merbecovirus) in the genus Betacoronavirus (Fig. 1 ).

...

https://pmc.ncbi.nlm.nih.gov/articles/PMC7718587/

Encyclopedia of Virology. 2008 Jul 30:125–129
Phylogeny of Viruses
AE Gorbalenya

...

Phylogenetic analysis is used in a wide range of studies to address both applied and fundamental issues of virus research, including epidemiology, diagnostics, forensic studies, phylogeography, origin, evolution, and taxonomy of viruses. First question to be answered during an outbreak of a virus epidemic concern the virus identity and origin. Answers to these questions form the basis for implementing immediate practical measures and prospective planning enabling specific and rapid virus detection and epidemic containment, which may include the use and development of antiviral drugs and vaccines. Among different analyses performed for virus identification at the early stage of a virus epidemic, the phylogenetic characterization is used for determining the relationship of a newly identified virus with all other previously characterized and sequenced viruses.

...

https://pmc.ncbi.nlm.nih.gov/articles/PMC7150205/