" The reference genome was originally derived from a single patient and constructed without additional scientific controls, such as sequencing PCR negative patients with similar etiology from the same hospital."
How could anyone sequence "PCR negative patients"? If they "negative" then nothing to sequence.
Would it be better to write: take equivalent samples from the "PCR negative" patents and subject these samples to sequencing in parallel with samples from "PCR positive" patients?
By “PCR negative patients,” I specifically refer to individuals tested for SARS-CoV-2. A study noted that in 62% of pneumonia cases, no pathogen could be identified (https://pubmed.ncbi.nlm.nih.gov/26172429/). Since bronchoalveolar lavage fluid (BLF) is typically present in these patients, it could have been sequenced in these cases as well. Note that this fluid contains a whole mix of human (host) & other organisms genetic material. That is the essential problem.
They saying that the lung fluid is teeming with baby virus particles why don't they just purify the virus particles directly from the lung fluid and then purify the intact 30,000 nucleotide-long virus RNA and only then do the sequencing?
If they never find and purify the virus, how can anyone know if the RNA sequences of interest actually belong to "a virus"?
Maybe the RNA they studying comes from the person due to such a person being sick or just being very nervous.
Yeah. they could just purify the 'virus' directly from lung fluid and then do electrophoresis to get the intact virus RNA. Instead of all the bizarre alchemy with chicken eggs or cultures of crazy cancer cells.
" The reference genome was originally derived from a single patient and constructed without additional scientific controls, such as sequencing PCR negative patients with similar etiology from the same hospital."
How could anyone sequence "PCR negative patients"? If they "negative" then nothing to sequence.
Would it be better to write: take equivalent samples from the "PCR negative" patents and subject these samples to sequencing in parallel with samples from "PCR positive" patients?
I don't understand.
By “PCR negative patients,” I specifically refer to individuals tested for SARS-CoV-2. A study noted that in 62% of pneumonia cases, no pathogen could be identified (https://pubmed.ncbi.nlm.nih.gov/26172429/). Since bronchoalveolar lavage fluid (BLF) is typically present in these patients, it could have been sequenced in these cases as well. Note that this fluid contains a whole mix of human (host) & other organisms genetic material. That is the essential problem.
But they use the same PCR primers for the test as in the sequencing, no?
Yes, but how do we know these are specific to the said sequence - also they might have found other sequences as well..
They saying that the lung fluid is teeming with baby virus particles why don't they just purify the virus particles directly from the lung fluid and then purify the intact 30,000 nucleotide-long virus RNA and only then do the sequencing?
If they never find and purify the virus, how can anyone know if the RNA sequences of interest actually belong to "a virus"?
Maybe the RNA they studying comes from the person due to such a person being sick or just being very nervous.
This is exactly the problem!
Yeah. they could just purify the 'virus' directly from lung fluid and then do electrophoresis to get the intact virus RNA. Instead of all the bizarre alchemy with chicken eggs or cultures of crazy cancer cells.
How can so many people be fooled?