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When I was in college, I remember IBM representatives trying to sell OS/2 Warp to students and teachers by saying that there were no (known) viruses for OS/2. (Of course, that didn't stop the makers of IBM AntiVirus for OS/2 and Norton AntiVirus for OS/2.)

The paper "The effect of computer viruses on OS/2 and Warp" (presented in September 1995 by John F. Morar and David M. Chess of the IBM Thomas J. Watson Research Center) mentions that there "are currently only two OS/2 viruses known to us."

Is there any reference that states how many native OS/2 viruses there were by the time IBM discontinued its support for OS/2 (on December 31, 2006)?

The cited source from the question is the source for the English Wikipedia page as well, that claims that there are only very few known viruses for that system.

But the low amount of viruses seems to be much bigger.

Not two, but at least five viruses are well known. That's more than double.

Arelocs also known as Aep is one of a few viruses for IBM's OS/2 operating system. It is considered "the first known virus that affects OS/2 files in the 'right way'" as it writes itself to the file and modifies the NewEXE header and other system areas.

Type  File virus

Creator Mark Ludwig

Date Discovered 1995

Place of Origin Show Low, Arizona, USA

Source Language 

Platform    OS/2

File Type(s)    .dll, .exe

Jiskefet
Jiskefet is a rare example of an OS/2 virus. It was coded by Masud Khafir, who named it after a Dutch comedy troupe.

Type    File virus

Creator Masud Khafir

Date Discovered 1994

Place of Origin The Netherlands

Source Language Assembly

Platform    OS/2

File Type(s)    .exe

Infection Length    2,048 bytes

Myname is an OS/2 virus. When executed, the virus infects OS/2 NewEXE files, overwriting them. While the virus has no malicious payload, the overwriting of the files damages them irreparably.

Type  File virus

Creator 

Date Discovered 1993.12

Place of Origin United States

Source Language 

Platform    OS/2

File Type(s)    .exe

Infection Length    2,048 bytes

Rexx is a virus for OS/2. Very little information is available about the virus. Our tests seem to show it overwrites files it infects.

Rexx is also the name of a scripting language. It predates OS/2 appearing in 1979 and it was the primary scripting language for that OS, along with Amiga and a few others.

Type  File virus

Creator 

Date Discovered 

Place of Origin 

Source Language 

Platform    OS/2

File Type(s)    .exe

Infection Length    38,620 bytes

Reported Costs  

Uxia is an OS/2 virus. All that seems to be known about it any more is that it is 7,200 bytes long and for IBM's OS/2.

Type  File virus

Creator 

Date Discovered 

Place of Origin 

Source Language 

Platform    OS/2

Infection Length    7,200 bytes

Reported Costs  

As we know there is something like
IBM AntiVirus Version 2.5 running on OS/2. Advertised as:

So, tell me how does it work really?

In a nutshell, pretty darn well. Over the years as a network administrator, I have taken a few viruses prisoner. Since I found these in "the wild" I used them for my "live" testing. The FORM virus is probably the most common boot sector virus in the wild.

But what is FORM? A DOS virus:

Form is a boot sector virus from the 1990's. It often topped charts for the most common virus. Form was extremely long-lived, on the list of viruses in the wild up until 2006, 16 years after its initial release.

Type  Boot sector virus

Creator 

Date Discovered 1990.02

Place of Origin Zurich, Switzerland

Source Language Assembly

Platform    DOS

Infection Length    3 disk sectors

Reported Costs  

That seems to narrow down the viruses truly and specifically targeting OS/2 only to be quite small. But:

Dr. Solomon's Anti-Virus Toolkit for OS/2 - by Noah Sumner (1997)
If you are like the vast majority of OS/2 users you think you don't need an anti-virus program. We all know that DOS viruses can't affect OS/2, right? Wrong. The experts tell me that there are probably somewhere around 200 viruses that can and will affect you even if you are running OS/2 under HPFS. If you are running under FAT that number is much higher.

Well, at least none of them will really attack OS/2, right? Wrong again. There are currently three known viruses that are designed to attack OS/2 users only, and if Warp 4 is a success that number will start to rise.

Now you are probably saying, "Well, maybe I should protect myself from viruses." That is where our good friend from Dr. Solomon comes in to play. Why should you use Dr. Solomon's Anti-Virus for OS/2? Here are three good reasons:

it detects the OS/2 viruses (IBM's Anti-Virus doesn't)
it has a nice PM interface
it is truly 32 bit.

I have not found a reference, but here's a search for OS/2 on Trend Micro's virus encyclopedia. That finds 30 entries, some of which are actual OS/2 viruses, and some of which are interesting OS/2 security vulnerabilities.

It looks as if there are five OS/2 viruses in that list, but it's unknown if any of them are multiple names for the same virus, or virus variants. The number five also came up in the other answer: that may well be the total.