Tuesday, March 1, 2016

Does HPV have more VAERS events than any other vaccine?

tl;dr - No it doesn't, but here's why this fact is important.

It began with a post someone linked to on vaccineimpact.com it reads:
There are over 80 vaccines approved for use in the United States. HPV vaccines account for nearly 25% of the entire Vaccine Adverse Event Reporting System (VAERS) database. This is particularly disturbing because the VAERS system was established in 1990 and HPV vaccines were not introduced until mid-2006.

Now this isn't a very widely spread meme - Google only displays about eight sites which carry close to verbatim copies of it (some of those might just be mirrors of other anti-vaccination sites).  One of them is rather entertainingly a record from the UK House of Lords.  Where Margaret of Mar uses this completely incorrect factoid.
The Countess of Mar (CB): My Lords, I am grateful to the noble Lord, Lord Patel of Bradford, for bringing this question to our attention this evening. I am afraid that I do not share his enthusiasm or that of my noble friend Lady Gould for HPV vaccines.... In the USA, HPV vaccines account for nearly 25% of the entire Vaccine Adverse Event Reporting System, or VAERS, a system that was established in 1990—and HPV vaccines were not introduced before mid-2006. 
 ...and about another six which reference a similar meme apparently started by sanevax which says that HPV vaccines are responsible for "60% of the entire VAERS database of adverse events".

So what does the data really say?  

See for yourself...

Do we see HPV leading the pack?  Nope! FLU3 - The trivalent influenza vaccine is far and away the leader in VAERS reported adverse events but even holding that title it only covers 11.8% of the events.  HPV4 (Quadrivalent vaccines like Gardasil) are responsible for a mere 4.2% and HPV9 (Nonavalent vaccines like Gardasil9) sits at at a puny 1%.  There is also an HPVX vaccine in VAERS when the type of HPV vaccine was unknown. This is just under 1%.  Even adding all those together puts us at a mere 6%.

But wait! We don't exactly know when that report was written.  Isn't it possible that for some interval between 1990 and 2016 it WAS true.  Well here's a plot of HPV (HPV4, HPV9 and HPVX) and FLU3 and their percentage of the total number of VAERS events up to that point over time.  

As you can see the answer is a big, fat NOPE there too!  So not only is this not true now but it has NEVER been true at any point EVER!

So why is this important?

Personally I'd break down talking with people who are critical of vaccination into a number of different categories but two big ones are:

Knowledge gap - Sometimes you simply can't get them to understand something.  Like how you can have a large number of people have a serious problem shortly after vaccination and have it not be related.  People make these kind of statistical errors all the time.  People seem almost designed to take coincidence as a sign.  So to me, it's not unreasonable that some people would make that same kind of mistake with events that happen close to vaccination.

Trust gap - Some people simply can't bring themselves to trust some information.  Sometimes it's information from pharmaceutical companies, or the government.  Sometimes the position is very contrived and they simply don't trust any information that doesn't support their position but at least the pretense there is about trust.

Here we have an example of something that not only anyone can understand - literally everyone who has a computer has access to the VAERS data and could do a similar (but much less fancy) analysis to what I did above.  Not only that but it requires absolutely zero trust (assuming you already trust VAERS data which I assume these people would).   You can download the data, put it into a spreadsheet and figure out these things on your own.  IMHO anyone could have fact checked this in a mater of minutes.

Yet it's still there and I would defy anyone to try and get them taken down.  I've already made a request to at least one site which has gone unanswered and unfulfilled.

I'm not sure if this is just a "what we post online is forever" effect or if there's just a culture of expediency around those who are critical of vaccine.

Sources, Reference and Data:

You can get all the VAERS data in easy to process CSV files right here.  Annoyingly separated by year so if you have to work on the entire dataset you're stuck downloading 26 files.

My R code for generating the above charts can be found here.  If you want to use this code yourself please link back to my blog.  If you have any trouble with it or want to adapt it.  Feel free to leave a comment.

# Make sure your working directory is set to wherever you put the VAERSVAX csv files.
# You can set this with setwd("c:/where/you/put/them")
allData <- data.frame()
for (year in 1990:2016) {
temp<-read.csv( paste(year,"VAERSVAX.csv",sep=""))
temp <-cbind(temp[,1:2],year)
allData <- rbind(temp,allData)
newData <- data.frame(table(allData$VAX_TYPE))
newData <- cbind(newData,newData$Freq/sum(newData$Freq))
names(newData) <- c("Vaccine","Count","Frequency")
newData$Vaccine <-factor(newData$Vaccine, levels=newData[order(newData$Frequency,decreasing = TRUE),"Vaccine"])
allvac <- ggplot(newData,aes(x=Vaccine,y=Frequency,fill=Vaccine))+geom_bar(sta="identity")+theme(axis.text.x=element_text(angle=90,hjust=1,vjust=0.5,size=11))+scale_fill_hue(guide=FALSE)+labs(x="Vaccine",y="Percent of Adverse Events")
hpv <- data.frame()
for (testyear in 1990:2016) {
temp <- allData[allData$year %in% 1990:testyear,]
temprow <- data.frame(vaccine='HPV',year=testyear,frequency=length(temp[temp$VAX_TYPE %in% c('HPV9','HPV4','HPVX','HPV'),1])/length(unique(allData[,1])))
hpv <- rbind(temprow,hpv)
temprow <- data.frame(vaccine='FLU',year=testyear,frequency=length(temp[temp$VAX_TYPE %in% c('FLU3','FLU4'),1])/length(unique(allData[,1])))
hpv <- rbind(hpv,temprow)
hpvflu <- ggplot(data=hpv, aes(x=year, y=frequency, group = vaccine, colour = vaccine)) + geom_line(size=4) + geom_point( size=4, shape=21, fill="white")

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