Metagenomic sequencing was conducted at Wuhan BGI. Nucleic acid was extracted using Qiagen’s viral RNA microextraction kit and human nucleic acid was removed using an enrichment kit to improve the sensitivity of viral RNA detection. Extracted RNA was reverse transcribed into cDNA and segmented into 150-200 bp by enzyme digestion. After repair, fitting, purification, PCR amplification and purification, sample concentration was assayed and SE50+10 sequencing performed by DNBSEQ-T7, and an average output of more than 200 million reads was obtained. Sequencing data were compared with those in a SARS-CoV-2 database to determine whether the samples contained coronavirus sequences.
Identification of the species abundances
The species abundances were obtained from the RNA-seq datasets of the environmental samples. The raw sequenced reads were mapped to the NCBI Nucleotide database using the kraken2 software (confidence 0.05) (32). The matrix of species was obtained by using the pavian algorithm (33). The correlation value between SARS-COV-2 and other species were examined by the Pearson’s and Spearman’s correlation coefficient method."
10^3-10^4 SARS-COV-2 reads out of more than 10^8 total reads. It would be nice to know how the authors controlled for contamination in the sequencing.
Also, the plot shows a bit more than 10^6 reads (max, for a couple of samples) of human sequences. 90-99% of the reads would seem to be unaccounted for. I wonder what they look like. (If anyone can dig up an SRA accession, let me know. My curiosity is piqued.)
One more thing - they say they scrubbed “human nucleic acid” before making libraries. Makes one wonder about the “human” reads, no? Maybe I am not reading the methods correctly, but this is all very confusing.
I’m with @evograd - this report may have some useful information, but I am not drawing strong conclusions based solely on these data.
I totally agree with that (last partial sentence quoted) (before I’m accused of taking it out of context, click the up arrow to see the context) It is the clipped part that I’m saying I totally agree with.
What is antithetical to science is the attempt to shut down legit debate. Not being willing to engage in debate and resorting to slander (if not outright lies) If Sunetra Gupta of the University of Oxford, Jay Bhattacharya of Stanford University, and Martin Kulldorff of Harvard University, are fringe epidemiologists, who isn’t a fringe epidemiologist?
Are you, 1) supportive of Collins referring to these scientists in this way, and 2) and supportive of him attempting to shut down the discussion of scientists wishing only to limit harm? Two of them seem anything but fringe in their testimony to Select Subcommittee Roundtable: Examining COVID Policy Decisions
You know that you can answer No to 1) and 2) or do you need the permission of the thought police?
To me, Collins owes Gupta, Bhattacharya and Kulldorff apologies for using his vaunted international position and reputation to slander these folk. To me, it smack of Peaceful Science modus operandi. To be fair, I’m not referring to official modus operandi but how it works out in practice.
Not a great deal like the piffle,
and
That you think my computer skills or lack thereof and that my need to be informed that you and yours are laughing at me make for worthwhile posts is, at least for me more telling of you than me. I actually find them amusing. Remember, you are a member of Peaceful Science which gives me that oh-so-warm Peaceful Science feeling.
But it is not fatal. Redemption is as close as an, “I miss spoke” away.
Maybe. And I did wonder about it. But, I’m still not sure. So, I’m kind of sorry.
But is it not bad form to challenge me on something in the public space as if I hadn’t engaged with it, when in fact, I actually did, attempting to engage you and you ignored it? That seems to at least border on deceit.
Oh, and I just noticed that my comment linked to the actual PM.
I am certainly sorry about that and have removed the required amount of material so that the link is removed and your, tl;dr remains. That is the part that I wanted to reveal with something else to show it as legitimately from you. It was that part that I see allowed the entire correspondence to be seen. So, once again certainly sorry that I allowed that to be opened publically.
And you understand that as me saying you did not engage with or respond to the video?
You really have a hard time understanding things you read and see, don’t you?
Tell you what: feel free to repeat the entire content of our exchange, or whatever you think is pertinent to your accusation. You have my consent. I only reserve the right to add any parts you omit and which by omission, in my opinion, alter the apparent meaning of anything that was written by either of us. Other than that, I won’t respond. People here have better things to read about, I am sure.
I attempted to engage with the video by asking, among other things,
Did you intend for the video to open at 49:57? Is there a specific part of that discussion you find particularly germane?
Does anything in what is said give you warrant to be suspicious that they are addressing the topic in a pertinent way?
I wanted to engage on it but apparently it was too long for you.
That’s cool, but let’s make it clear. It is not that you claimed I was confused. Your accusation was that I was not just confused, but greatly confused and specifically about the video,
You’ve already demonstrated my general confusion with your most rigorous of Peaceful Science techniques,as in the following,
I’ll be quite interested in Peaceful Science adjudication.
The quote from the email is “There needs to be a quick and devastating published take down of its premises.”
If you publish a statement that X is the best policy, and I want to publish a second statement saying “policy X is flawed for reasons A, B, and C”, in what universe am I “shutting down legit debate”?
If anything, the published response would BE the debate.
You seem to be imagining a world where the GBD said “we need to have a public debate about the most appropriate policies moving forward” and Collins was caught in an email saying “Nooo we can’t let anyone debate this, shut down their site!”
You see, this is exactly what I was talking about.
In our earlier discussion, Washburne’s claims were dissected and refuted, one by one and in painstaking detail. At the conclusion of this, you wrote:
However, I was skeptical regarding your response and highly suspected that, regardless of whether Washburne actually provided subtantive rebuttals to the objections that had been raised, in short order you would be back here bleating out the same talking points as if that entire discussion had never taken place.
And here we are.
Correct. Thanks for that very important clarification.