Smut?  Australia?  Yes, they have smut in their sugarcane.  Particularly in the Bundaberg/Isis, Mackay, and Ingham districts in Queensland.

And no, it has nothing to do with sheep.

Pictures of this smut can be seen here and here.

The full report is on ProMED-mail.

As you know, I am a medical virologist.  Which means I deal with the biological type of virus, and their consequences.  But sometimes computer viruses can be interesting too, and I amuse myself at times with technovirology - computer viruses.

Jeevs' son, Reshlan, had a project for medical school on a flashdisk, and every time it was plugged into a PC with antivirus software, that file got deleted.  The file was a Word document.  The virus had inserted executable code in the beginning of the file, and renamed it with the extension SCR.  SCR files are usually screensavers.

The logical person to ask for help is ... the virologist.

The virus was W32.Rungbu, as named by Norton.

Here I describe how I chopped the virus out of the file, and got back the original Word document.

PLEASE NOTE: this is not for the faint hearted, or for anyone who, like me, doesn't really know what he's doing.  You risk your computer becoming infected, and losing data.  What I describe below is not something you should try at home.

First, I backed up my registry, and turned off System Restore, and then inactivated my antivirus software.

I copied the infected file.scr onto my hard drive.  Then I renamed the infected file so it had a TXT extension, and opened it in Notepad.  It looked like this:


Lower down, some of the text contained in the Word document was visible.  I didn't know what to do ... so I tried various things, none of which worked.  Forcing the file.scr to open in Word or Wordpad didn't work - it had non-Word header information that Word couldn't interpret.  I tried chopping off the top part of the document, including everything between the start of the document and the end of the code inserted by the virus.  I tried chopping out the part of the document that was clearly Word, and placing it into a document from which I removed that document's section from that position onwards.  For this I was using Notepad, and was probably saving it in some way I shouldn't have saved it - or maybe I shouldn't have been saving it at all in Notepad.  None of the final products opened in Word.

In the process I followed above, I discovered that all the Word documents I checked began the same way.  I already knew that this was the case with GIF, JPEG, PDF, RAR, and ZIP files, so I was expecting that.  The following three images show how three different Word files began:




I've highlighted the sequence common to all the files.

But, as I said above, deleting everything before that sequence and saving the result using Notepad produced a file that Word couldn't open.

Then I thought of using a hex editor to delete the infected section.  I used a fairly simple programme called 1Fh Binary+Hex Editor 1.07.

By searching for the specific sequence that the other Word documents began with, I found out that the first 46592 bytes of the file were something else.  This is what it looked like:


The B600 is the hexadecimal version of 46592, which I could have calculated by hand, but was too lazy, so I used HexDecBin 1.0 to do it for me:


I decided that using 1Fh to space over the extra 46592 bytes would simply take too long.  So I thought that maybe splitting the file into pieces, in such a way that the extra piece would be separated from the rest, might allow me to piece the file back together without that extra piece.

For this I used GSplit 2.0.  I simply split the file into pieces 46592 bytes in size - so that the first piece would be the the entirety of the extra piece, presumably the virus, and not contain any authentic piece of the original Word document.  I also set GSplit to omit headers to the pieces that it split the file into, to not create an executable file that would piece them back together again, and, in case it affected anything, deleted the code set to give the pieces a unique ID.


Then I split the file - 35 files resulted, namely disk1.gsd, disk2.gsd, ... disk35.gsd.

I checked disk2.gsd, and, not surprisingly, it began with the sequence that started all the other Word files.


I then ran a batch file to unite all the pieces except the first.  It looked like this:

copy /b disk2.gsd+disk3.gsd cow.gsd
copy /b cow.gsd+disk4.gsd cow.gsd
copy /b cow.gsd+disk5.gsd cow.gsd
...
copy /b cow.gsd+disk35.gsd cow.gsd

The /b was simply because I expected it to be a binary file and not an ASCII file like a text document.  (Probably something to do with Notepad saving it in a way that Word couldn't interpret as a Word file.)

I then renamed cow.gsd to cow.doc ... and tried to open it in Word.  And there was the original, opening fine as a normal Word document.  (It had another error in it, and wouldn't show page 48, but that I converted to a PDF and the PDF back into Word, and recovered the text that way.)

And that is amateur technovirology in action, as performed by a clinical virologist.  Viruses are indeed fun!

Three (3) weeks ago (10 April) I contacted S & K Unicom in Umtata to ask them to check my dish installation, which was not picking up DSTV.  They took my details, and said they might be able to help me the following week.  I have not yet heard back from them.

On the page listing them, it says "Services : n/a".

Last week I contacted Video Effex and they were extremely helpful, polite, and professional.  I was expecting another week's wait, but they solved my problem the same day.

On the page listing them, it says "Services : installations".

If you want a DSTV installation or repairs done in Umtata, get hold of Video Effex.

I am a fan of George Romero's Dead movies:

Night of the Living Dead [1968]
Dawn of the Dead [1978]
Day of the Dead [1985]
Land of the Dead [2005]

Diary of the Dead, for release in 2007, is a 5th, but not a sequel to Land of the Dead, as it takes place at the during the initial outbreak of the zombies that occurred in Night of the Living Dead.

Remakes of these movies by other directors:

Night of the Living Dead [1990]
Dawn of the Dead [2004]
Night of the Living Dead 3D [2006]
Day of the Dead [2007]

And then of course there's Shaun of the Dead [2004], a spoof of the above, not by George Romero.  See also Night of the Living Bread [1990].

Wikipedia has a good explanation of which are Romero movies, which are Russo movies, and which are non-Romero "sequels" and related and unrelated movies, such as unofficial non-Romero non-Russo sequels Day of the Dead 2: Contagium and Zombi 2.

The original Night of the Living Dead was co-written by George Romero and John Russo.  Romero sequels are "Dead" movies and Russo sequels are "Living Dead" movies.

I haven't a clue what this means:


Probably something to do with Άννα Βισση coming to Sun City in May.

They linked to me ... so here's the Anna Vissi blogspot.

My deltoid muscle hurts tonight.  I had my flu vaccine today ... and that's a fairly common minor side effect, but a sign that something's going on there.

The flu vaccine recommendations for the last few years are as follows:

2004/5 Northern hemisphere winter:
an A/New Caledonia/20/99(H1N1)-like virus
an A/Fujian/411/2002(H3N2)-like virus
a B/Shanghai/361/2002-like virus

2005 Southern hemisphere winter:
an A/New Caledonia/20/99(H1N1)-like virus
an A/Wellington/1/2004(H3N2)-like virus
a B/Shanghai/361/2002-like virus

2005/6 Northern hemisphere winter:
an A/New Caledonia/20/99(H1N1)-like virus
an A/California/7/2004(H3N2)-like virus
a B/Shanghai/361/2002-like virus

2006 Southern hemisphere winter:
an A/New Caledonia/20/99(H1N1)-like virus
an A/California/7/2004(H3N2)-like virus
a B/Malaysia/2506/2004-like virus

2006/7 Northern hemisphere winter:
A/New Caledonia/20/99(H1N1)-like
A/California/7/2004(H3N2)-like
B/Malaysia/2506/2004-like

2007 Southern hemisphere winter:
A/New Caledonia/20/99(H1N1)-like
A/Wisconsin/67/2005(H3N2)-like
B/Malaysia/2506/2004-like

Changes from season to season are in italics.

Note that the H1N1 part of the vaccine has remained the same.  It's H2N3 that changes regularly.

As I pointed out before, South African virologists like Anna Vissi music.

She'll be here in South Africa soon, and will have a concert at Sun City.

Tickets can be booked on the Kalahari.net website.

I have a reputation, and am living up to it.  I think this is quite a good way to use a box, but it needs a table cloth - when I get round to getting one.


This is some sort of crate packing support device that I have turned into a shelf for my DVDs and CDs, and maybe a few books when I get more of those unpacked.


Very fashionable.

Here in Umtata we don't always have good access to our e-mail.

Google has the answer - Gmail paper.

I trained as a medical virologist at Stellenbosch University, Tygerberg Medical Campus, and, prior to the current head of department, Prof Estrelita Janse van Rensburg was the head there, so I spent the first few years of my training under her.  Now she's head of the virology department at Pretoria University, where I did my undergraduate medical training.

On 28 March, she was awarded an Exceptional Achievers Award.

The Pretoria News (which we don't get in Umtata - my mom e-mailed me the article) said:


The article can be read here.

I also know Prof Louis Nel, Prof Brenda Wingfield, and Prof Mike Wingfield.

Congratulations!

Mycobacterium tuberculosis and related bacteria are bacteria, NOT viruses.

The following are also not viruses:

• malaria
• typhoid
• tick bite fever
• syphilis
• gonorrhoea
• cats and dogs

"More hospitals to treat TB virus" published on 14 March 2007 in The Mercury (a newspaper) should have a better headline.

Some snippets:


I am sure they are ... it's quite a problem.  The local stats sound quite scary.


Hmmm ... do they mean that MDR and XDR TB in a patient result from that patient's treatment failure?  MDR often yes, and I'm not an expert on the genetics (I'm a virologist, and TB is NOT a virus) but I think the jury is still out on XDR TB, and there is some evidence that XDR infections are usually caused by an XDR strain infecting the person.


We definitely need more money to fight HIV and TB in this country.

We've all seen the photos of power cuts in Johannesburg and Cape Town.  Now I am providing some from Umtata.

Here the power doesn't go out because too much is being used.  It goes out because it rains.  And sometimes just for fun.  It's very frustrating, because I take a lot of work home with me, and I'd like to be able to use my computer to do that work.  I've thought about a generator with a UPS to stabilise the current, but maybe I should go to bed early sometimes.  Power failures are usually at night, the most impractical time.

Here's the photo of Umtata at night with no electricity.


If you click on the picture, a larger version will load.

More on rabies vaccination ar the Journal of Travel Medicine, March/April 2007.

Gautret P, Parola P, Shaw M, Torresi J. Rabies preexposure vaccination in travelers. J Travel Med 2007; 14: 136. PubMed abstract

Probably worth reading ... I can't get at it, though.  I'll try other ways.  All my usual ones are exhausted.

In the February Weekly Epidemiological Record, put out by the World Health Organisation, there is an update on rabies vaccination.

I've previously commented on rabies and post-exposure prophylaxis on one of my other blogs.  I've had my pre-exposure prophylaxis.

Virologists have good taste in music.  Άννα Βίσση, or Anna Vissi, is one of the most popular modern music artists amongst virologists in South Africa, and probably worldwide.  Those virologists who haven't heard her music should listen ASAP.  They'll be hooked.

Anna is a Cypriot Greek with an incredible voice.  She was born in 1957, so she turns 50 this year ... but she looks like she's in her 20's or 30's, at least in concert and on her CD covers and in her music videos.  Her husband, Nikos Karvelas, is 6 years older than she is, and he looks his age.

She took part in the Eurovision contest for the first time in 1980, and most recently in 2006 - her 2006 song was Everything, which was played a fair bit on the radio here in South Africa around the time of the contest.  The last time I looked it could be heard on her official site.  There are apparently music videos available on YouTube and MetaCafe.

Another Anna Vissi site worth visiting.  It has downloadable music and tour info.

Wikipedia has a detailed discography.

Dodeka (Δωδεκα) is one of her very popular songs ... it seems to be part of many of her concerts.  Listening to it explains why.  It means Midnight in English (dodeka = do + deka = 2+10).

Anna Vissi lyrics

Dodeka is one of the first Anna Vissi songs I heard back in high school.  You can scroll up and down with the various buttons on the flash thingie - the pause is on the right of the scrolling lyrics (from lyricsdownload.com - move your mouse out of the scrolling lyrics to pause.

I still need to get used to the new camera - it has nearly as many settings as my PC.  But here are some photos.

This is Walter Sisulu University, previously University of the Transkei (Unitra), by day and by night:

The hills seen from the townhouse I stay in:

Umtata Dam after the rain, seen from where I stay:

The driveway and garages in the place where my townhouse is:

From my balcony looking onto the nearby nature reserve in a misty day:

The Anglican Cathedral, which looks very much like a Catholic one from the outside.  I must still find the Catholic Cathedral here.

Welcome to Umtata!

That is Skillie's other name.  She's now eating well, and her health has improved a lot.

You can read all about Skillie and her relatives here:

Angulate tortoise
Angulate tortoise care

Okay ... this blog isn't only about Skillie and elevators lifts ... so I'll put a post on with some photos of the Eastern Cape and Umtata.

This is a photo of Jeevamoney Govender (Jeevs), the currently acting business manager of the Umtata NHLS laboratory - NMTL, or Nelson Mandela Tertiary Laboratory.  There's always a cup of coffee waiting in her office for you ... except during power failures.

This is Jeevs with her secretary, Mardi Nolands.

They're in Jeevs' office.

The laboratory is connected to the academic hospital, and is partly on the 2nd floor (level with the ground) and partly on the 3rd floor (one up from the 2nd floor.)  The lift has buttons for floors 2, 3, and 4.  The first thing I thought odd was that there were no stairs near the lifts.  If you want to go up or down, the lifts are the only option.  If you really need to take the stairs, you can go to the other side of the building, which isn't far, and on that side there are no lifts.

I feel quite silly going up one floor in a lift instead of taking the stairs, and even worse going down one floor, but everyone does it.  Eventually I'll have my bearings better and know instinctively which way the stairs are - most things I need downstairs are on the side of the building with the stairs.

The highly unusual thing about these lifts is that, due to their distance from the stairs, they remain functional.  I've only been here for two weeks now, but they have always worked, they stop on all floors, and their buttons don't turn on and off by themselves.

At the Tygerberg Medical Campus of Stellenbosch University one of the places I worked before, the lifts are controlled very ingeniously by a team of experts whose job it is to provide a new puzzle every day for lift users.  On some days, certain buttons remain on all day (that had nothing to do with infection control during the Namibian polio outbreak, which was first identified by my old lab at the top of these lifts); sometimes you cannot call the lift from certain floors; sometimes the experts want people to guess which floor they need to run to in order to catch the lift ... and they are sneaky!  When you reach that floor, sensors detect that you're approaching, and the lift closes and goes up to another floor (usually the 4th), waits there a while, and then comes down slowly, opening on each level for the invisible person who didn't press any buttons.

At that place still fresh in my memory, the same experts are training people for the special olympics - they have a special electric door for people in wheelchairs, and the door is specially fitted with a device that senses when someone is in the doorway, and then it closes on them.  Only the fastest get through in time.  My advice: if you're already injured, in a wheelchair, blind, or use a walking stick, climb over the turnstiles and go up the stairs - it's safer!

None of that excitement at my new lab.  Here there are only 2 relevant floors for the lab staff - they wouldn't get away with it even if they wanted to.

These are the lifts from the outside:

And from the inside:

These are the stairs, looking up from the ground (i.e. 2nd) floor:

These are the stairs from the outside of the building:

I suppose not many blogs have an entire post dedicated to a discussion of the lifts the blog writers use.  I promise to have more virology in future posts, but this is also about my new life, and therefore functioning rural elevators are topical.  In the places I've worked in, functioning elevators are topical, rural or not.

Maybe in a future post I'll go into the fascinating aspects of the buttons in these lifts ...

Key word for the day:

English: lift; plural lifts
Americanese translation: elevator; plural elevators

I arrived in Umtata on the evening of 27 January, and my belongings arrived the following day.

This is a photo of Umtata at night, taken from the Garden Court hotel along the N2 highway as it passes through Umtata, where it is known as Nelson Mandela Drive.  A larger picture will load if you click on it.

Some scenic photos of the area later ... but after doing some of my unpacking, I started work on 1 February.  At first I felt a bit lost, and although the lab is in somewhat of a rectangle with passages going right around, it was a bit confusing in the beginning.  I still have to think about which way the lifts are, and which way the stairs are - they're on opposite ends of the lab.

I am the new pathologist for the diagnostic virology laboratory.  At the moment they do HIV DNA PCRs on blood and dried blood spots, and HIV viral loads.  Serology for HIV, Hepatitides A, B, and C, Rubella, and Cytomegalovirus get done in the Chemical Pathology laboratory, and don't fall under the Virology section, which is dedicated to supporting the antiretroviral rollout in the Eastern Cape.  We have place to expand, and the section will eventually do a lot of other viral diagnostics, and incorporate the serology as well.

These are the people working in the Virology laboratory:

Tobeka Gibson (Toto) is the laboratory manager.  Here you can see her preparing samples for HIV PCRs.

Nandipha Tinzi (Nandi) is sorting specimens that will get viral load testing later.

Nokwanda Busakwe (Skwash) is preparing plasma samples for RNA extraction prior to viral load testing.

Masixole Nkanyuza (Masi) is the youngest; he's preparing the reagents for the detection step of the viral load assay.

More soon.

There are wedding plans for Skillie, for when she's better.

This is her future stepdaughter.

Her future stepdaughter likes apples, and prefers to eat them out of her adoptive mother's hand.

She thinks she can climb stairs.  Not very well, it seems.

Skillie's babies will fortunately have four legs.

My current head of department, Wolfgang, and his fiancée were recently in the Eastern Cape, and came across a tortoise that had been hit by a car.  They rescued her, and she has been to hospital.  Unfortunately she had to have her foot amputated, and gets daily antibiotic injections, which she doesn't like at all.

It's unlikely that she will be able to be released back into the wild, so she's getting a new home, all legal with the right permits.

Her name is Skillie.

This is her being told she's going to get her medicine.  When she realises this, she goes into her shell fast.  The vet taught Wolfgang how to give her her injections.

She wouldn't come out, so I took her, and I was new to her, so she came out to look.  That gave us a chance to get hold of her leg.  Here she is getting her injection.

This is Wolfgang with Skillie after her injection.

This is me with Skillie.  Her shell had cracked underneath, and her one back leg broken.  The foot has been amputated and bandaged.

Skillie doesn't bite.

A close up of Skillie.

Skillie had been to the toilet before the injection.

Hopefully she'll recover well.

Welcome to my new blog, about medical virology, rural medicine, and the Eastern Cape in South Africa.

In 2005, I qualified as a medical virologist, FCPathSA(Virol), and in 2006 I finished my MMed in virology at Stellenbosch University.

As from February 2007, I will be working in Umtata, as the only medical virologist in the Eastern Cape province, with plans to build up the virology service there, and to consult on laboratory, diagnostic, and clinical virology in the Eastern Cape.

On this blog, I plan to document my journey in rural medicine, and let people know more about the life of a virologist, and about the Eastern Cape.

Please join me on this journey.