Alina Chan Profile picture
30 Sep, 17 tweets, 4 min read
Been hearing a lot about using Vitamin D to fight COVID. Finally got around to reading the paper that is at the root of all this.

tldr the science is far from settled, but, yes, it should be considered for -elderly- patients with Vitamin D deficiency.

sciencedirect.com/science/articl…
First things first, the form of vitamin D used in this study is not the nutritional vitamin D you can buy off the shelf. The authors say as much in the paper: "Our study does not include a comparison with cholecalciferol, the native vitamin D3 form"
2nd, although patients were selected at random, the authors clarify this study was NOT double-blind placebo controlled. What this means: the doctors/organizers (and the patients) knew who was or was not receiving calcifediol (prehormone produced by hydroxylation of vitamin D).
3rd, and possibly most importantly, this study did NOT check for vitamin D deficiency in the patients before or after treatment: "Serum 25OHD (calcifediol) concentrations at baseline or during treatment are not available".

That means we don't know which patients were deficient!
4th, looking at the patient traits, the group that did not receive the calcifediol treatment was very significantly more likely to have/have had high blood pressure; 15 of the 26 patients had previous high blood pressure, which is a risk factor for severe COVID.
Plus, ~1 in 5 (=10/50) of the no-calcifediol group suffered from diabetes compared to 3/50 in the calcifediol-treated group. Another risk factor for severe COVID.
5th, the authors said "we did not collect the BMI, which would have allowed us to add obesity as a risk factor for severe evolution of COVID-19" --- we now know that obesity is a major risk factor, multiplying the risk of severe COVID.
6th, these patients had an average age of ~53 years in both treated and untreated groups. Meaning that if you're a young-ish healthy person without a vitamin D deficiency, this strategy probably does not apply to you.
In summary, due to how the study was designed, not controlling for major risk factors across the treated and untreated groups, the conclusions are far from solid. It would be dangerous for people to think that taking vitamin D will prevent development of severe covid.
So, is there a paper that actually looks at vitamin D deficiency and its effect on severe COVID?

Yes, there is, but it also suffers from caveats: journals.plos.org/plosone/articl…
Sorry, wrong paper, by the same group in the same journal, published in the same month; this is the one that looks at vitamin D deficiency and its effect on severe COVID: journals.plos.org/plosone/articl…
Keep in mind, this paper did not treat the patients with vitamin D, their objective was to compare how patients with or without vitamin D deficiency fared after catching COVID.
Important numbers from this study performed in Iran:

Patient mean age of 58.7 years; more than a third were >65 years old.

1 in 3 of their patients were vitamin D sufficient; two-thirds were vitamin D deficient.

3 in 4 of their patients had severe COVID.
This is the finding regarding vitamin D sufficiency and COVID severity: "The data analyses revealed that the severe disease infection was less prevalent in patients with vitamin D sufficiency (63.6% vs. 77.2% p = 0.02)."

63.6% vs 77.2% -- patient mean age of 58.7 years.
My interpretation of these papers is that it's probably not bad to make sure your vitamin D levels are adequate, BUT a cause-and-effect relationship between vitamin D levels and severe COVID has NOT been demonstrated.

Vitamin D cannot be used to sanction risky pandemic behavior.
I know everyone is desperate for a cure or prophylactic against COVID. It would be great if there was a magic pill that we can take and immediately not be vulnerable to (severe) COVID. But this is not it... maybe it helps a bit in elderly patients, but the data is inconclusive.
Although it probably won't harm people to eat Vitamin D supplements, these supplements are not a replacement for proper anti-pandemic measures.

For instance, infusing all nursing home members with Vitamin D is probably not going to save the majority from severe covid.

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More from @Ayjchan

14 Oct
"The Guangdong (pangolin CoV) strains, which were isolated or sequenced by different research groups from smuggled pangolins, have 99.8% sequence identity with each other."

I wonder how that could happen!

nature.com/articles/s4157…
According to Google, Xiao et al. @nature has been cited 103 times; Liu et al. @PLOSPathogens has been cited 73x. Both were preprinted in Feb, accepted, and made available by the journals in May. Our preprint finally made available in July - cited 3 times. biorxiv.org/content/10.110…
Should I make public the emails and responses from these authors from May and July of this year before the journals have a good wake-up call as to what to do in situations where research integrity has been breached?
Read 7 tweets
13 Oct
COVID mink outbreaks: Netherlands (41+ farms), Denmark (63 farms), Spain, US (Utah, 9 farms; Wisconsin; Michigan)... we're going to have to add a host species feature to covidcg.org once sequences from mink SARS2 isolates are added to @GISAID. independent.co.uk/news/world/eur…
The only troubling part: "The (Danish) government says breeders with non-infected mink will be given 100 per cent compensation, while those with infected animals will receive less as an incentive for farmers to keep the infection out of their stock."
Wouldn't this incentivize farmers to hide mink outbreaks in their farms so that they can receive full compensation? Please reconsider this policy, Denmark!
Read 4 tweets
11 Oct
Read the 2nd Yan et al. report. It was frustrating... each statement requires fact-checking to the point where, instead of pointing out the errors, it may be better for someone to write an independent article discussing the circumstantial evidence pointing to lab origins.
The overarching message of Yan's 2nd report is that there has been unscientific behavior surrounding the reporting of SARS2-like CoVs. Based on this, they speculate that these genomes are coordinated fakes to make SARS2 look natural.
Again the report is littered with errors, but I do wonder why there hasn't been international impetus to investigate the source of these SARS2-like viruses. Why not go to the Yunnan mine to look for more RaTG13s? Why not investigate the miners - what actually happened in 2012?
Read 21 tweets
5 Oct
Beseeching employers in Canada to make work as remote as possible. If your employee is not, e.g., a healthcare worker, requiring in-person interaction, there is no reason why they should be out there at risk + increasing the risk for essential workers.
cbc.ca/news/canada/wo…
I wonder, often, at employers who think IT/admin people must be at the office. You can basically look South to see what happens when people treat this virus like it's not serious. Not everyone has access to (1) regular testing and (2) new therapeutics + a top class medical team.
The question at this point is how many deaths and disabilities your employer needs before they decide to make work remote. You already know cases are rising, that means many undetected cases. And you know people with pre-existing conditions have a fair chance of death/disability.
Read 8 tweets
25 Sep
I've been sitting on a major topic that I think the non-scientist public needs a primer on, with particular significance to COVID-19 research.

That topic: Research Misconduct
ori.hhs.gov/definition-mis…

And what to do about papers that are found to have engaged in misconduct.
One of the most notable instances of misconduct was the Surgisphere HCQ papers. @TheLancet eventually decided to retract the paper & commentary because they would be too misleading in their original form. They adopted a "retract and replace" approach... retractionwatch.com/2020/07/10/a-m…
... because the editorial had been written by innocent parties who were not aware of the data issues, @TheLancet published a new editorial to explain what had transpired - in order to rightfully preserve the reputations of scientists who had been misled. retractionwatch.com/2018/03/29/a-n…
Read 17 tweets
25 Sep
There's some confusion about how new the D614G mutation is. I'm going to use data on @GISAID visualized by @CovidCg to answer this question. The first time it appeared in China was Jan 23, 2020. So this mutation occurred pretty early on in the outbreak before travel restrictions.
When+where did D614G first get detected in Europe? It's not possible to tell using GISAID alone because many countries did not sequence virus isolates and deposit data till later in the pandemic. However, you can see that there are EU countries with D614G even in Jan.
It was only after January that travel restrictions started being sporadically imposed on China by other countries but it was too late because SARS2 (including D614G variants), as we now know, was already widespread. thinkglobalhealth.org/article/travel…
Read 17 tweets

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