Covid-19 vaccines and treatments: we must have raw data, now • Hacker News Board

Re: Covid-19 vaccines and treatments: we must have raw data, now

#241

Post by rsfern » Fri, Jan 21, 2022, 11:58 AM UTC

guywhocodes wrote: post #221

rsfern wrote: post #208

Earlier quoted context omitted.

You shouldn’t distrust VAERS per se, but it’s purpose is not risk assessment. It’s purpose is surfacing rare side effects for further study. You don’t have to trust the drug co’s for that, we also have vaccine safety datalink system; so far the only notable side effect of the mRNA vaccines has been the myocarditis in younger people. https://pubmed.ncbi.nlm.nih.gov/34477809/ Also your point about PCR testing is not ac…

> Also your point about PCR testing is not accurate. Source on that? Because all graphs I've seen show impossible to miss fluorescence around 35 cycles and up. AFAICT VSD only does specific research at their own behest and currently don't have a section on COVID-19 vaccines. Btw your link is dead. I had pericarditis and some immediate reaction, my cardiologist thinks it was partially intravenously applied. Looking at…

The link isn’t dead for me, but I guess there’s no abstract on pubmed, sorry. This is the DOI link: https://DOI.org/10.1001/jama.2021.14808

It’s an editorial summarizing the first VSD report on Covid vaccine side effect research that I was describing (https://DOI.org/10.1001/jama.2021.15072)

I’m not going to argue that the US seemed to take longer and have worse communication about the myo/pericarditis issue than some other countries, but these things are being followed up on. The absolute timing I think is hard to discuss with a definite time frame

Here are some resources on PCR amplification:

- https://www.mcgill.ca/oss/article/covid-19-critical-thinking...

- https://www.thermofisher.com/us/en/home/life-science/cloning...

Re: Covid-19 vaccines and treatments: we must have raw data, now

#242

Post by Fogest » Fri, Jan 21, 2022, 12:34 PM UTC

diroussel wrote: post #233

Fogest wrote: post #80

Earlier quoted context omitted.

This is my thing as well. I work at vaccine clinics and obviously am onboard with the vaccines, however I still feel bad helping administer these vaccines to people who are hesitant. Because of government vaccine mandates or employer vaccine mandates it has made some people who come in feeling "forced" to get a vaccine. And it honestly does not feel like this is the proper scientific or medical way. It sucks to give…

As far as I can see, in the UK, these adverse effects are not being logged or recorded in such a way that any analysis could be done to determine the scale, or even existence of any problem. I heard that there was a public database in US for this sort of thing. But it has it’s own problems about data quality.

I'm in Canada and we do have an official way primary care doctors and public health officials and report and have adverse conditions investigated. The problem is that when a patient presents with symptoms that started shortly after the vaccine administration they are often dismissed by their primary physician. Often the doctors even do scans or blood work and they find "nothing" and deem the person being okay. Rather then doing further investigation the patient is often treated like they are making up symptoms or exaggerating. Basically they treat them like an anti-vaxxer instead of properly investigating their condition. They just tell them not to worry "it'll go away".

We have people who come in to get additional doses and they'll mention having some pretty serious symptoms after their last vaccine and we will be so surprised with how often we are told they went to both the hospital and their family doctor and got zero resolution and the doctor did not report it to public health.

In many cases we just seem them medically inelligble in these cases and tell them they need to go to their doctor and followup more to ensure they will be safe to get another dose.

And this is where I think a lot of the problems with vaccine mandates and pressure from employers can lie. You end up with people who feel like they have no choice to get the vaccine, they have a bad reaction to it, and then doctors treat them like they are lying or that it's no big deal. Then they go for their next dose feeling even more untrusting of science and get another vaccine.

We are ruining a lot of people's trust in science and medicine by how hard these things are pushed. Because of how much push back there is against anything negative with vaccines, it means doctors also often end up with this same bias. They are afraid to attribute any problem a patient has to the vaccine.

I have no problem with vaccines and have 3 doses currently. But I can empathize with these people who feel hesitant and I myself definitely have lost some faith over the last year of doing this work.

It really seems like a lot of scientific and medical standards have been tossed out the window because of politics.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#243

Post by rsfern » Fri, Jan 21, 2022, 12:38 PM UTC

diroussel wrote: post #233

Fogest wrote: post #80

Earlier quoted context omitted.

This is my thing as well. I work at vaccine clinics and obviously am onboard with the vaccines, however I still feel bad helping administer these vaccines to people who are hesitant. Because of government vaccine mandates or employer vaccine mandates it has made some people who come in feeling "forced" to get a vaccine. And it honestly does not feel like this is the proper scientific or medical way. It sucks to give…

As far as I can see, in the UK, these adverse effects are not being logged or recorded in such a way that any analysis could be done to determine the scale, or even existence of any problem. I heard that there was a public database in US for this sort of thing. But it has it’s own problems about data quality.

The US has multiple such systems that serve different purposes. We have a passive monitoring system (VAERS) that you might be referring to in data quality issue. It’s for identifying side effects for further study, and it’s explicitly but for estimating risk. That doesn’t stop people from publishing studies based on data they try to filter and verify validate from VAERS.

We also have the vaccine safety datalink, which is intended for causal and quantitative studies of the things surfaced in VAERS, etc. it’s based on electronic health record integration across a network of hospitals covering I think about 3% of the US population. It is public as in publicly funded I guess, but not as in public access. You can read the first report here: https://doi.org/10.1001/jama.2021.15072

I am reasonably sure the UK has a similar setup, with some passive monitoring system and a much better health record integration story through NHS.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#244

Post by ashtonkem » Fri, Jan 21, 2022, 3:22 PM UTC

diroussel wrote: post #235

ashtonkem wrote: post #218

Earlier quoted context omitted.

> and it can be hard to argue with them that vaccines are totally safe and effective for them (not talking about the population as a whole). Right, and do you believe that a full release of the phase 3 trial data would convince them? I sure don't. Anti-vaxx is a fundamentally anti-expert stance, and most people have not logically convinced themselves into that position. Give them the full data set and I bet 9 out of…

I don’t believe it will convince those that don’t want to be convinced. But I want to be convinced, and I want transparency in the science that my taxes are funding and in the enlightened society in which I wish to live. Transparency in science should include publishing raw data, as apart from re-creating the statistics in the report there is no other way the trial is repeatable.

That’s moving the goal posts though. Now we’re balancing the privacy of those on the trial against your interest in seeing the data even though you’re already vaccinated. And you yourself don’t think that it would convince anyone that’s antivaxx. I don’t see the social benefit here, other than you’ll feel better.

Furthermore, it’s not obvious full transparency will help. You’re almost certainly not a medical researcher, so it's not clear if you could do anything useful with the full data set. And our experience with VAERS shows that bad faith actors absolutely can and will lie about it. I see absolutely no upside to releasing the full data set, and a lot of downside for those who volunteered for the trials.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#245

Post by eminence32 » Fri, Jan 21, 2022, 3:25 PM UTC

noogle wrote: post #220

eminence32 wrote: post #168

Earlier quoted context omitted.

Focusing on the date aspect for a minute: is it possible to adjust the data (before the deidentification process) and convert relevant absolute dates into durations? For example, is it possible (and is it useful) to adjust the data so that it says something like "patient abc123 entered the study in 2021 and 83 days after receiving a vaccine they showed started to show symptoms. Symptoms ended 3 days later"

COVID has a strong absolute-calendar trends (variants, waves), so removing the absolute dates might harm the analysis.

Interesting point, that makes sense. Thanks.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#246

Post by ashtonkem » Fri, Jan 21, 2022, 3:27 PM UTC

tpoacher wrote: post #180

invokestatic wrote: post #59

I’m a software consultant for Pharma companies and have worked on projects that used the same kind of study design as the Pfizer COVID vaccine (Kaplan-Meier). “Raw data” is submitted to the FDA in the CDISC format. This format contains a lot of pretty sensitive medical information, including which diseases a patient has, their medical history, what drugs they take, etc. This is supposed to be anonymized, but if the p…

I hear the concern, but no. There are ways to inject randomness into a dataset, giving subjects plausible deniability without compromising the integrity of the outputs. See https://pair.withgoogle.com/explorables/anonymization/ for a nice example. Bottom line is, there are ways to share such data safely. Whether the data owner cares enough to do the extra work, especially if doing so removes a competitive advantage,…

If the point is to improve public trust “don’t worry, we manipulated the data to make it more anonymous, but we pinky swear that we didn’t manipulate it in a way that changes the results” is not a good approach.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#247

Post by nradov » Fri, Jan 21, 2022, 3:48 PM UTC

throwawaygh wrote: post #154

rvnx wrote: post #149

Earlier quoted context omitted.

The thing is; in practice, how can you re-id someone that has a very rare medical condition if you don't already know that the person has this very rare medical condition ?

"this person is certainly my biology teacher, who shared the fact that she had a rare genetic disorder during our Genetics unit as well as . She has herpes. Or also she has an alcohol problem and used to do acid." Teacher is now fired. You also keep ignoring the issue of consent. Step one is to ask patients. Or the person shared their story on the public website of a "Run For The Cure" style website about that geneti…

You can construct all sorts of artificial theoretical risks. There's no evidence of that being a real risk with this particular data set.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#248

Post by srcreigh » Fri, Jan 21, 2022, 5:59 PM UTC

epgui wrote: post #227

srcreigh wrote: post #196

Earlier quoted context omitted.

Would it be so hard to state the limitations of their investigation, and clearly explain that a few key misconceptions are incorrect? Based on their original censored article, it seems like they're heavily invested to make things seem problematic, and carefully avoid any indication that the status quo is acceptable. I don't think it's purely misinterpretation when anti vax people become generally skeptical of govt an…

They were not putting into question the safety of vaccines, that issue was tangential. I know the article has the literal words "patient safety" and raises potential safety concerns, but that all has to be read in full context: advocating for better data controls and better rigour in research. It might seem obvious to you that the article would be misinterpreted or parts of it taken out of context by a lay public, bu…

Considering that BMJ made an entire article objecting to FB fact checking BMJ for public audiences [0], I really have to disagree that the article was only meant for expert eyes.

Given that, a few disclaimers and limitations to help quell public misinterpretation is required. Not to do so is irresponsible.

[0]: https://www.bmj.com/content/376/bmj.o95

Re: Covid-19 vaccines and treatments: we must have raw data, now

#249

Post by a45a33s » Fri, Jan 21, 2022, 9:31 PM UTC

rsfern wrote: post #211

a45a33s wrote: post #119

Earlier quoted context omitted.

the covid vaccine trials had no control groups either

They were all doubly blinded placebo controlled trials… Are you talking about how they unblinded the study after efficacy results started coming in?

yes i am talking about how they got rid of the control groups once it appeared to be working

Re: Covid-19 vaccines and treatments: we must have raw data, now

#250

Post by epgui » Fri, Jan 21, 2022, 10:33 PM UTC

srcreigh wrote: post #248

epgui wrote: post #227

Earlier quoted context omitted.

They were not putting into question the safety of vaccines, that issue was tangential. I know the article has the literal words "patient safety" and raises potential safety concerns, but that all has to be read in full context: advocating for better data controls and better rigour in research. It might seem obvious to you that the article would be misinterpreted or parts of it taken out of context by a lay public, bu…

Considering that BMJ made an entire article objecting to FB fact checking BMJ for public audiences [0], I really have to disagree that the article was only meant for expert eyes. Given that, a few disclaimers and limitations to help quell public misinterpretation is required. Not to do so is irresponsible. [0]: https://www.bmj.com/content/376/bmj.o95

I really don't think the objection (and reasons for the objection) to the fact check (1) and the intended audience being largely composed of experts (2) are mutually exclusive.