Powerful talks

We spent yesterday in Ibadan, at the university. Kristian and Eric worked with Nike, Christian's postdoc, to sort out the last details on running the ELISAs and using the sample database. Thanks to Eric and Shari's hard work we now have a wonderful , barcode based pipeline for sample processing and storage that starts right at the point of collection in Irrua. Kristian and Nike have sorted out the details of the ELISA protocol and the output is looking good, so now we can get serological data from our well-tracked samples.

Kristian and I (Elinor) each gave 30 minute talks at midday at the university. Kristian's was called "Fighting immune disorders with undercover agents" and mine was on "Finding disease genes using genome sequences". The talks went well, with one little hitch. Right near the end of Kristian's talk (he went first) the power cut out, a very common occurrence here. We took a twenty minute hiatus while Christian went and found a portable generator, set it up in an office down the hall, ran power cords through the hallways, and hooked up the projector again. And closed the door to the office with the generator so we could actually be heard. Then we continued, without lights, or fans, or microphone. Or A.C. - which the Nigerians dealt with much better than Kristian and I, who were pretty much drenched in sweat by the time we finished! (it was over 95F / 35C and 80% humidity outside.) The power came back on about 15 minutes before I finished. We were very well received and the Nigerians had lots of great questions.

We're heading to Lagos later today after saying our goodbyes, and flying home tonight - all except Eric, who is off to London, and then Sierra Leone.

Goodbye Irrua

We left Irrua yesterday for the five hour drive back to Ibadan - the west bound road is much better paved than the east bound road, so the trip is a bit quicker. Of course, this also means there aren't so many street vendors and fruit stands. On the east bound road, dozens cluster around every big crater in the road and hawk their wares to the drivers slowing down to gingerly navigate past. Kristian and I still wonder - which comes first, the pothole or the market stands?

We went for dinner the night before with the adminstrative staff from the hospital at a beautiful outdoor restaurant. Eric, Kristian and I took it upon ourselves to entertain the crowds, by diligently spraying ourselves with bug repellant - apparently, this is a novel concept! We tasted palm wine - a low alcohol, fermented beverage which must be an aquired taste. We didn't aquire it. The food - fresh cooked fish - was absolutely delicious and quite spicy - except that a mysterious mixup resulted in two fish being cooked for a crowd of about thirty, so we all left a bit hungry. We went back to the hotel afterward and feasted on pineapple and powerbars.

We said our goodbyes to the lab staff yesterday morning and got all the samples and equipment packed into our jeep. After a final, farewell photograph (see below) we hit the road!

Chasing patience

Chasing patients, actually. Shari and I went out with the clinic staff today to collect follow-up samples from Lassa fever patients and their household members. We discover that, like most things in Nigeria, that is much more complicated then it sounds! People just choose their own house numbers, so they often aren't even remotely consecutive. On one road, we found two different No. 10 houses. At another place, we found not the patient, but her daughter, who helpfully hopped in our car and directed us to her mother's house. At the next house, we discovered the patient actually lived out of town, and just stayed with his brother while he was sick.

Getting to each new place took a while, since the roads are unpaved and very bumpy, and there are no maps. We had to rely on asking passerbys for help, which usually led to lots of very animated discussions and more and more people coming over to offer assistance. And have I mentioned it is really HOT here?

At the end of the day, though, our very diligent collaborators here had managed to find two patients and sample them and their families. A very successful day here in Nigeria, given all of the roadblocks, both literal and figurative!

We're heading back to Ibadan tomorrow, having finished everything we wanted to do in Irrua - thanks to Eric's and Christian's planning, and everyone's hard work.

Our visit Mr. Adomeh's village

I'm just going to put up a short post here now, because things are crazy busy as we try to get everything done before leaving Irrua for Ibadan on Wednesday - and somehow it is already 5pm!
Yesterday was Sunday and we had big social plans. In the morning, Shari and Eric went to church with Filomena for about two hours (started at 6am!) while Kristian and I chose to sleep in and louge around and enjoy a luxurious hotel breakfast of toast. Just toast. No butter, no jam, no coffee. But we did have to wait 45 minutes for it. This morning we just ate powerbars instead.


In the afternoon we went off on a two hour drive to Mr. Adomeh's home village, where he grew up until he was 13 years old and left for secondary school. The road was unpaved, and apparently graded about 10 years ago, but since it floods every year it was hard to tell. The jeep stayed upright, though, and just a few of the bridges actually had gaping holes.

We spent several hours up in Mr. Adomeh's village. Kristian just put in his two cents - "it was awesome!" Everyone was extremely friendly, like everywhere we've been - although I think the children (the many, many children) weren't quite sure whether we were incredibly exciting or a bit scary. We had a very impressive entourage following about 30 feet behind us all the way through the village. We met the chief and ate lunch with Mr. Adomeh's brother. In the evening, we had dinner Ekpoma with Mr Adomeh, his wife and their three children. Thank you to all the Adomehs, and Filomena, for a wonderful day!

I better sign off now- I need to go and help Kristian aliquot, so I'll leave you with a photo of our new friends, all trying to look very cool for the camera ...

Elinor

Oyibos on Parade

We had a bit of time on Sunday for a walk around our neighborhood. What started as a stroll became quite a trek into the woods in search of an elusive village we were hoping to find in the distance.

Where we are staying is apparently the city with a population of around 100,000. I would have guessed we were in a tiny village. Our hotel is on a paved road, and while we were walking Shari and I took advantage of the fact that Christian was distracted on the phone to redirect our meandering onto the far more interesting mud roads. My brain is too tired to write full sentences now, so I will instead list the interesting sights:

I. Beautifully colored, if extremely worn facades
II. Goats, goats and more goats
III. A construction man roasting the rat he killed that morning ( He was happy I photographed it, so that ‘the world could see his rat’)
IV. Shari, desperate for vegetables, chewing on monkey cane
V. Eric, not wanting to dirty his trousers, exposing his ridiculous socks and shoes
VI. Beautiful wooden church, built with rough-hewn wood
VII. A public school, aged as a ruin, only 30 years old
VIII. Shari doing math in said public school
IX. Wonderful Sunset

Irrua

Since Saturday evening, Eric, Christian and I have been in Irrua. We are staying at a nice hotel, though electricity is rare and hot water, as Eric put it, is never. They make good food though, and so far no one has been sick. Eric discovered his true Nigerian roots last night when he ordered bushmeat (grasscutter), and to my amazement thought it was delicious!

We have begun our work at the Irrua Specialist Teaching Hospital, where our Lassa ward and sample collection is located. Soon after we arrived on Saturday, we began to hear of the many headaches that had sprung up since Christian’s last visit here several months ago. The printer had disappeared from the office, some people were not doing their jobs, we needed a new freezer, none of the forms had been entered, and the list went on. Christian tackled each with his characteristic mix of exasperation and energy, and things began to get done.

Yesterday we made the frustrating discovery that none of the patient data had been entered, and the samples were not in the labeled kits we had sent. Eric and I spent the day entering hundreds of forms, while the lab technicians, admonished by Christian, relabeled the samples.

Even from just the sparse information on the records, personalities shined through. These brief glimpses into patients’ lives began to put a face to the horrible symptoms I had read about back in the US - fever, deafness, edema, conjunctival hemorrhage, spontaneous abortion.

We met with one of the directors of the hospital, and had a very interesting discussion about our project and his experience here in the field with Lassa. He said he was very interested and reassured to hear our preliminary estimates that the diagnostic was only 50% sensitive, because he sees many cases he is sure is Lassa which came up PCR-negative. He also told us about a very interesting case of a woman who had Lassa in pregnancy, refused treatment, and survived with her baby. Since current wisdom says fatality is 100% for fetuses during pregnancy, we were happy to hear this and excited to follow the case up.

We finally finished entering the forms in the evening, and headed back to the hotel for our late dinner. The unbelievably good pineapple and papaya we had for dessert nearly made up for the long day – I don’t think I’ll ever be able to eat American pineapple again. Today we plan to go through the hospital records for all of our suspected and confirmed cases.

It’s like walking upstream (distinctly different than swimming)

That’s how Shari describes it here, like walking upstream: walking because, if you tried to swim, you’d just get washed away. I left off with my last entry, days 1-3, on Monday, the day I was sick.

Tuesday turned out to be one of our two most productive days. Shari and Nike (who works with Christian Happi, our main collaborator in Nigeria) re-labeled all of the handwritten tubes with pre-printed barcodes provided by the Broad. Kristian and I recorded the volume and locations of every single one of our 1257 cryovials - I have developed a data and sample management system that takes advantage of the 2D barcoded kits of cryovials we get from the Broad, and integrates handheld collection technology, and other bells and whistles to bring data straight from collection to analysis. In order for the system to be effective, however, all of the old specimens first needed to be conformed to a single standard. - By 7 or 8 PM Tuesday we were successful on that front.

Then came Wednesday.

Late Tuesday, as we were finishing up, we realized that we were low on liquid nitrogen, so Christian and Kristian decided we should keep the tank closed until we got more from Lagos the next day. Lagos had other plans. The liquid nitrogen plant was ‘broken’, and dry ice wouldn’t be available until Wednesday around noon.

On Wednesday, Kristian Andersen woke up feeling very sick, so we had to cancel his talk, the car broke down on the way to Lagos to pick up the dry ice, and there was no electricity in the lab [electricity is inconsistent, running water is never]. Shari and I did persuade Christian to bring us to a local art shop where we are certain the guy has not sold anything all year. I picked up a neat tribal Yam Harvest Mask, bronze and some wall decoration. Shari got a pair of twins and a bronze statuette that apparently doubles as a weapon! As far as science goes however, not much could be done.

Thursday morning Kristian was still sick, and his condition was getting worse. As he continued to rehydrate himself, he seemed to only become more sick…then the eureka moment. I first became violently sick after drinking a whole bottle of La Voltic water, this was from the same case from which Kristian had been rehydrating himself. He turned over one of his bottles, and there it was, lots of visible white sediment floating around. Shari and I went over the data files with Nike, and I had a good sense of the HUGE amount of work that would need to be done that night.

After an all night data crunching session (and another bout of illness), trying to get many many different files of patient and sample information to fit nicely together, we were poised for a more successful day today, Friday. Shari and I prepared all of the new, barcoded (with my system) tubes and cryoboxes for the aliquots we are sending to collaborators in Sierra Leone, aliquots for viral sequencing, and additional controls for Kristian to fiddle around with the ELISA over the next week.

For a number of reasons, major changes have been made to my workflow plan. Kristian Andersen will now remain behind in Ibadan to work on the ELISA with Nike, as we will now keep the equipment for the ELISA in Ibadan rather than Irrua. Shari, Christian and I will head to Irrua where we will gather the rest of the information and samples there, clinical records, and begin thinking about how to optimize the collection procedures. Christian will pick up Elinor on the 26th, swing by Ibadan to pick up Kristian, and they will all join us in Irrua for the rest of the time here.

With regards to the database system, we decided that in order to have a seamless and gradual introduction of the technology, we will keep the database in Ibadan, and Nike (and hopefully a helper) will process, curate and test all specimens in Ibadan rather than in the field (Irrua), where infrastructure and staff are less reliable. Nike and Christian are our saviors in this project, without whom we would be absolutely unable to function here.

Tomorrow we head out for Irrua; the trip should take around 6 hours (optimistic), and if history informs us at all, it is sure to be eventful.