COVID-19 Paper Results: Genetic Characterization of the "Virus"

In this video I go over the results section on the main COVID-19 "virus" isolation paper and look at the section that supposedly provides the genome and phylogenetic tree of this "new virus". De novo sequencing was performed on airway fluid samples and cell culture supernatants from the three Wuhan patients, and supposedly a "novel coronavirus" was identified in all three patients. These sequences were sent to the GISAID global flu "virus" database and compared with previous "virus" genomes. The 3 "virus" genomes had 86.9% similarity with previous "bat coronaviruses", but had less than 90% similarity of supposed specific genes involved in "viral" replication. Since they were less than 90% similar, this "new virus" was given its own clade on the phylogenetic tree.

Interestingly, the paper refers to the cell culture supernatants as "virus isolates", even though no common sense isolation was performed. It is clear that no actual "virus" is being observed, but it still raises the question of what these "genomes" refer to, how they are obtained, and what is the reasoning for grouping them in their respective clades.

The paper is listed below:

A Novel Coronavirus from Patients with Pneumonia in China, 2019
Authors: Na Zhu et al
Published on January 24, 2020 in The New England Journal of Medicine (NEJM)
https://www.nejm.org/doi/full/10.1056/NEJMoa2001017

The timestamps of key parts of the video are listed below:

Genetic Characterization of the "Virus": 0:00
De Novo Sequencing: 0:48
Complete Genome Sequences Somehow Obtained: 1:19
Global Initiative on Sharing All Influenza Data (GISAID), Influenza: 4:34
2019-nCoV Supposedly forms a Distinct Clade: 5:24
Replicase Domains (ORF 1ab): 7:00
New BetaCoV Alleged Genome and Phylogenetic Tree: 7:12
Summary of the Genetic Characterization of the "Virus": 9:16

This video is taken from my earlier video listed below:

🔥#MESScience 4: Review of COVID-19 "Virus" Isolation Paper: https://youtu.be/cvDO85Rw4d8
Video notes: https://peakd.com/hive-128780/@mes/messcience-4-review-of-covid-19-virus-isolation-paper
Playlist: https://www.youtube.com/playlist?list=PLai3U8-WIK0E4aQ_cq4ZDD2WGiDU5vVgx