I know the technical PCR nerdery is hard for the general public. I feel this whenever I read a hardcore immunology paper!
A few thoughts on the concerns about PCR...
PCR threshold cycles are test-/machine-/reagent-/kit-/lab-/handler-/sample site-/sample storage/sample handling/..
..cold chain-/extraction method-/primer pair-/probe-/disease stage-specific.
To compare one lab's results to another lab's results (or even another run within the same lab), needs both labs to be using the same PCR setup & to have the same controls or calibrators.
This is easier when using commercial kits because they all use the same reagents and they've been optimised and (hopefully) well validated. But that doesn't mean they've done the work to correlate result with infectiousness, disease severity etc-it would be helpful if they did.
PCR doesn't make RNA, it makes DNA (it even says so in the figure!). PCR isn't making "copies of a specific DNA/RNA sample", but of a sequence region (if present) in a sample. "Covid" isn't a virus.
Here's a warts-n-all example of the sort of "drift" you can get. The 2 sigmoidal (S-shaped) curves are a POS control & a clinical positive for HCoV-NL63 (this is data from 2010). The rest are negative samples-but there's some drift above the threshold as the test goes on.
@satchitanand21@ColleenHuberNMD So yeah, the thing is the human genome is big & has bits & pieces that sometimes match up with bits & pieces in other [parts of the tree of life. But that doesn't really mean anything by itself. Unless you're doing a PhD on the topic I guess.
So I took that primer sequence...
@satchitanand21@ColleenHuberNMD ..it's a reverse primer (so actually hybridises to the reverse complement of that sequence; long story I won't cover here if you didn't get what I just said).
If we take that sequence and compare it against a tree-of-life sequence database (called BLAST-blast.ncbi.nlm.nih.gov/Blast.cgi)..
@satchitanand21@ColleenHuberNMD ...as Capt Conspiracy did...we get some results.
First up I've excluded any matches to SARS-CoV-2, there is indeed 100% match to human DNA but also dog, chimp, malaria parasites, some bacteria, fish & bird. Guess what?
"can you link to evidence that the virus was isolated" is becoming fake moon landing level stupid
Study1: 23JAN2020 biorxiv.org/content/10.110…
🧫bronchoalveolar lavage fluid from RT-PCR-positive patient (ICU-06 in Spike tree=WIV04/2019 virus)
🧫successfully isolated nCoV-2019
124 BetaCoV/Wuhan/WIV04/2019 in Vero and Huh7 cells
🦠cytopathic effects (CPE) seen
🦠culture supernatant (s/n) tested (+) by RT-PCR
🦠rabbit antisera against a bat SARS-related coronavirus (SARSr-CoV) reacted with infected cells
🦠electron microscopy (EM) images of virus particles from infected VeroE6 cells
@noname_2112 Keep in mind that these postulates were never meant to be taken as some sort of commandment
"The limitations of Koch’s postulates, evident in the 1800s,
are even more pronounced today." cmr.asm.org/content/9/1/18
@noname_2112 These were formulated in a time before viruses were defined and well before sensitive detection methods existed!
"is unfortunate that so many workers blindly followed the rules, because Koch himself quickly realized that in certain instances all the conditions could not be met"
Yes, lab studies use amounts of virus that may not reflect "real-life situations". Some of the reality beneath this is that cell culture struggles to detect infectious virus at what might be *truly* real-life levels. Yes, lab studies have always been perfect world experiments
But without these expts, we may get a false sense of the role of surfaces (and airborne transmission in which we can also find an infectious virus in aged aerosols for 3h during which the viral load drops from 10^3.5 to 10^2.7 TCID50) nejm.org/doi/full/10.10…
Australia now 1-month into easing of restrictions. Chief Medical Officer (CMO) notes...
-more than half of the past week's #COVID19 cases via travel
-only community transmission in 1 State in past week
-Aus well prepared for more via returning travel, pockets of local cases, small outbreaks
-everyone needs 2b tested
-protests create risk and make contact tracing very difficult ("these sort of events really are dangerous")
-please don't attend further events - "you cannot make them safe"
-"Please express your genuine concerns about issues in other ways"
This is crap. Don't listen to me over the @who (alongside... maybe)
These guys do their job FOR A LIVING. All the time. No one gets everything 100% right 100% of the time.
Dial this anti-WHO BS down. You're playing into the hands of dusruptors and morons.
When I whinge about the @WHO, it’s about a specific issue. Something that could be done differently – or IMHO - better. I’m never saying the Organization has failed. To say that is to fail to understand the sheer scope of what they try to do..
.., how much dancing on eggshells around fragile, despotic and disparate egos they have to excel at to get things done and to be funded on any given day, how many lives they have/do save with that funding (despite often the wrong-headed & petulant reasons for..
Physical distancing, face masks, and eye protection to prevent person-to-person transmission of SARS-CoV-2 and COVID-19: a systematic review and meta-analysis thelancet.com/journals/lance…
"The findings of this systematic review and meta-analysis support physical distancing of 1 m or more "
"From a policy and public health perspective, current policies of at least 1 m physical distancing seem to be strongly associated with a large protective effect, and distances of 2 m could be more effective"
What is a false positive coronavirus test? How is it possible? abc.net.au/news/2020-06-0…
"Usually due to a lab being contaminated with the virus or with product from a previous test"
-also sometimes due to quirks of the test; which is why we try to validate well
And to clarify
"Certainly at the moment there was no active infection present, but what may have happened is that it was the end of a previous infection — the test may have detected a little bit of that going on,"
- certainly is too strong a sentence starter.
Just to be clear, I don't have any inside info on the autopsy. It was reported that the deceased "did not have the disease after all" (news.com.au/lifestyle/heal…)
😷#Flu (is not) in Queensland to 31MAY2020.
Record lowest baseline in 6 years thanks to physical distancing and perhaps related to decreased testing levels as well
😷Nationally, Australia has also seen its lowest #flu case numbers (& rates, not shown) in April and May since 2010/2007 respectively (also much less testing was done back then).
In Queensland, private lab Sullivan Nicolaides virus testing data shows the same #flu pattern, but adds info about the non-enveloped rhinoviruses (RVs) and adenoviruses. RVs are on the surge (⬆colds and asthma attacks) snp.com.au/clinicians/res…
@diviacaroline No. That's what that person says to be the case.
If you use kit-based tests, that can be the issue. If you use in-house test there can be PCR product contamination from previous runs that could affect your clean mastermix area, extraction area or template loading area.
@diviacaroline There are also some designs that can give "noise" which can look like late low positive when conditions favour that. There can be weird results when using duplex or triplex or multiplex test that don't show up when using uniplex formats.
@diviacaroline So it can be complex. When using kits rather than in-house tests, you hope that's all been sorted. But I'm seeing some examples where kits have come out with little validation (testing same sample types, samples from same sort of disease, (+) for other viruses) has yet to be done
Qld Health Minister...
-we have to treat ever POS test as though it is a positive case-however, personally apologises to partner and family for distress caused, scrutiny sufered
-1 *new* case, traveller from Africa, infectious while on plane (contact tracing underway)
-Blackwater case repeatedly negative
--1st postmortem test due to 4wks flu-like symptoms
--2nd test urgent, that night sent to Rockhampton-result invalid (contaminated with blood)
--further tests were done, no other pathogen found
--605 were tested in Blackwater, all NEG (great response)
--close contacts can end quarantine (63k Qld'ers have gone through quarantine thus far)
@Billy__Grove@horrdorr@statnews That we could have a pandemic at any ti..oh you mean 5 months
-doesn't just cause pneumonia, asympto spread, PCR is *not* too sensitive, SARS-CoV-2 doesn't make kids regularly very sick, we can close down nations & stops importation,
@Billy__Grove@horrdorr@statnews -virus naming takes too long and isn't inclusive
-conspiracy theorists love a pandemic
-we still don't have good data on mask use
-finding a treatment fo COVId-19 takes a lot of time despite all the promise of the lit
-very few seem to know much about how viruses can emerge
@Billy__Grove@horrdorr@statnews -SARS-CoV-2 receptor is located all over the body; disease at each of those sites has been identified
-virus sheds for 3wk+ in ill people
-SARS-CoV-2 kills more people than flu
-pandemics aren't just about death but also jobs, people, illness, resources, leadership & POLITICS
@horrdorr@statnews 1. Droplets, close and prolonged contact 2. Physical distance, testing, tracing, isolation of the ill 3. <25% seem to remain asympto 4. Can have same viral loads as sympto, so yes. No idea about % 5. Remdesivir maybe, but nothing great yet
@horrdorr@statnews 6. 3 hours (aerosol) to 3 days (shiny hard surfaces) 7. steel, glass, plastic, copper, cardboard, paper, wood, cloth, banknotes, surgical masks - all under *unrealistic* lab conditions. Less IRL 8. Keeping humans 1.5-2m apart is good
@horrdorr@statnews 9. That alone has no $ number to it that I know of, but means a change to indoor spaces where people were traditionally closer than that, if the virus in popn 10. Contact tracing - phone calls/shoe leather, and Apps but privacy & functional issues remain around the latter
I really do wonder if "fever clinic" terminology is keeping people away from seeking a SARS-CoV-2 test - if they don't feel they have a fever.
In Australia - under half of #COVID19 cases have had any fever recorded (from those with info available).
This is why it's essential that "anyone who has any symptoms no matter how mild they are" (Qld's Chief Health Officer, 28MAY2020) present for testing.
Don't limit your actions to whether you feel like you have a fever or not.
You can see from the image I've marked up below that there is a full spectrum of symptom combinations that do *not* (circled in red) necessarily include a fever (yellow) among Australian cases of #COVID19.
Source: Report 16. www1.health.gov.au/internet/main/…