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.

Blowing grammar

Each day brings more suprises. We had a very productive day yesterday, inventory-ing and relabeling the samples. The process was slow and mildly painful, but we persevered and managed to finish. Upon nearly finishing, however, we realized we were nearly out of liquid nitrogen, which is essential for storing our samples, especially since there is electricity for maybe an hour or two a day. So one of the lab members is making an emergency trip to Lagos for more, hopefully saving the day.

Seeing the situation in this country has made me think a lot about the priviledge and opportunities we have had growing up in America. Christian says that only about 5% of the population here graduates from any kind of school, and maybe 25% attends school at all. I asked why he though that was - would more schools help? Maybe, he said, but the real problem was the lack of jobs when you finish. Why go to school if there is nothing to do when you're done? You might as well just start working immediately. Because of the corruption, the jobs rarely go to those who deserve them, so there is very little incentive to get an education.

This lead to a discussion of the corruption in the government. He told us how the politicians do not even try to campaign with educated people, instead going straight to villages and buying votes with bags of rice or similar things. Many people distrust the educated, and when someone with too much education runs for office, people say he is just "blowing grammar." It's a shame, though we can't really judge, since America has anti-intellectual elements of its own.

Anyways, we are off to lab again now, to continue organizing the collections and working with the members of Christian's lab to get everyone on the same page with our data collection system. Kristian will also give a talk to the department today. And everyone cross your fingers our liquid nitrogen arrives!

Days 1-3

After spending the weekend in the air or in the car, we have finally arrived at our first destination of interest, Christian Happi’s lab at the College of Medicine, Irrua University. We have been staying at guesthouses operated by the International Institute of Tropical Agriculture, which on the whole has treated us very well.

On our way to Ibadan we experienced one of the many pleasures of domestic road travel. At an instant, our north-bound highway lane turned southbound. We joined in the mass reversal, turning around in the middle of the highway to find ourselves sandwiched between traffic going in every possible direction. In the end we took smaller dirt village roads. The detour ended up carving a 4-car wide swatch of belching automobiles where an hour earlier kids had been playing and goats resting.

Christian was kind enough to welcome us into his home, where we spent a good deal of time playing with his adorable daughter, dining on Nigerian delicacies, and planning the week.

Our current home at the IITA campus is at odds with the local environment. Outside of the gates are poverty, congestion and environmental wreckage, while just inside is a campus that feels plucked out of Florida or California. Some of us are having trouble reconciling the contrast.

This morning I had the unfortunate pleasure of becoming sick, and introducing myself to a Nigerian street market as I hurled myself out of Christian’s car just in time to avoid ‘being sick’ in his back seat. I can say now that I have partaken in the Nigerian Health care system; my doctor said it was the food, gave me a handful of medicines, and instructions to rest. He used a really nifty little thermometer strip made by 3M which turns dots colors to identify body temperature.

On our way to bring me home to rest we took a detour and were summarily harassed by the police carrying multicolored rifles who kept us roadside for 30 minutes, coming up with every reason Christian should hand him a ‘dash’ (bribe). The situation finally ended when the big boss came and a larger financial opportunity presented itself!

I have recovered now and look forward to getting into the lab where Kristian and Shari have been learning about our samples. I’d like to get started with an inventory tonight so that no time has been wasted, and tomorrow we can start processing some specimens.

All in all a good time so far, many lessons learned, and only anticipation for tomorrow.

Many, many flights!

The booking and planning is done, and we are almost ready to go. As I walked down the hall here at the Northwest Lab, I saw a world map, and thought would our trip might look like plotted out. It's not totally ridiculous, but still A LOT of travel in 3-5 weeks!

It's 19,906 miles for me! That's only 5K less than the circumference of the earth... and no frequent flier miles!

Hello World!

We are about to embark on our first lab voyage to our field site in Irrua, Nigeria, where we have been quickly building a Lassa diagnostic, treatment and research center.

Our collaborator, and main man in Nigeria, Christian Happi will open is lab and his home to Kristian Andersen, or first bio-lab experienced post-doc, and Shari Grossman, research assistant, and mathematician extraordinaire and me, the project manager. We will be joined later by geneticist post-doc Elinor Karlsson.

This is where we will share our adventure with the world (mostly our parents) so please check in every once in a while for videos, pictures and , hopefully, exciting stories.