Les Roberts – “Day 53: What R0 is not.”

Les Roberts – Freetown, Sierra Leone – November 26th, 2014

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Day 53: What R₀ is not

If you believe all those old CDC guys, the first cohort of HIV cases in San Francisco in the 1980’s supposedly had sexual encounters with, on average, over 1000 people in the year before becoming ill. Certainly something close to HIV had been circulating around in the Congo basin for decades, if not centuries. CDC has a blood sample in their freezer from an adult male from Kinshasa taken in the 1950’s that contains HIV. Genetic evolutionists put the origin far far before that. And that should not be surprising. Imagine some hunter butchers a chimp and cuts his hand, he gets something close to HIV… maybe it makes him sick, maybe his wife dies too, who would ever know that one or two people died of some slow funky illness in that Congolese village? It was not until HIV got into a hyper-sexually active cohort that enough “infectious momentum” could be in place to get the disease into blood supplies, commercial sex workers, and all those footholds that HIV gained on the road to becoming a major global burden. I am quite sure: what San Francisco bath houses were to HIV, West African funerals have been to Ebola.

There are widespread traditions in Sierra Leone that suggest the body of your loved one needs to be washed to cleanse the spirit so they will be accepted by the ancestors. Allowing them to be buried unwashed would be for many something akin to Christians damning someone to hell. Funeral attendees often kiss the corpse as well… like in the US. Thus, people, usually women, commonly cleanse and wash the body after death. They will then often pour the rinse water over themselves to bask in, and respect, the decedent’s spirit. And, as if that wasn’t microbiologically disastrous enough, then these women usually prepare food for the large number of people coming to the funeral. This is a virus whose concentration in the body spikes with the acute phase of illness and where death often releases millions of viruses that ooze out afterwards. It would be hard to dream up a more perfect way to spread this virus around than the traditional West African wash & rinse funeral. For the first months of this outbreak, almost all big transmission chains were associated with funerals and in the CDC’s VHF dataset, the majority of cases through September reported recently attending a funeral. That fraction has dropped dramatically! Maybe less than 10% now. It may be that the outbreak has enough “momentum” to keep running wild without funeral transmission, but no one knows.

When I got here two months ago, of the major elements needed to achieve the two major UN goals (70% of bodies buried safely and 70% of cases isolating themselves early in the course of illness by seeking treatment), almost nothing was functioning well. Now, major progress has been made on the safe burial front. There are lots of articles written about the burial system falling apart (e.g. http://www.bbc.com/news/world-africa-30191938 ) but those are the exception. The safe burial effort is perhaps the major success. The bad centralized data suggest about half of all deaths are buried by safe burial teams (which is on paper required by law for all deaths) but I suspect the fraction of Ebola deaths buried safely is significantly higher. In our surveillance sensitivity exercises, out in the smallest villages far from the paved roads, most chiefs are adamant about calling burial teams if they think they have an Ebola death. Does the family wash the body before the teams come? Yes, probably. But, it may not be such a huge deal if there are no funerals, no meals, and no kissing the corpse components to the burial. It is stunning how in our field work often eight, ten, or all of a household can get infected with no neighbors getting the disease. Funerals somehow seem to be an incredibly powerful mechanism to move this reluctant but pernicious disease between houses and villages.

Recently, in the most out of the way village I have visited, there were four families out in the fields in the mile before the village and we saw those people as we approached but they always hid as we got close. I am not sure if they fled from Ebola laden villages or were driven out because a family member got sick. Then when our car rolled into this village of around 200 people, everyone slipped inside and there was suddenly no one to be seen. It was only because the driver was from that Chiefdom and spoke with the perfect dialect that people could be lured out. They were scared… scared of anyone from outside and the risk they might bring Ebola. Things are not as they were in July!

By and large, people don’t go to funerals now. Certain people don’t tolerate commercial sex with outsiders. There is a lot changing and I am convinced that in the few weeks to come the outbreak will peak… not because of what the health community has done, but because people have changed their behaviors and thus changed that interaction between virus and culture that determines the R₀. With flu, R₀ is largely determined by the intrinsic nature of the virus and people talk about it, and model it, as if it is an internal characteristic. With suicide, no one would consider the degree to which is contaminable or transmissible some fixed internal characteristic, because, to the extent suicides come in clusters, it is viewed as a social and psychological contagion. In this regard (the degree to which the R₀ is intrinsically or socially determined) , I am convinced that Ebola is far closer to suicide than flu. I am frustrated by our (my!) inability to get NGO’s to step-up and operate treatment centers and the ability to make treatment beds available. (But, our former Emergency Medicine Fellow, Trina Helderman has just come this week bringing the NGO Medair…sort of a Swiss based mini-MSF, so hope lingers.) But, I expect history to show that the outbreak turned around because the people of Sierra Leone changed the communicability of the disease. When that happens, I hope the American public will be able to be convinced that Ebola would almost certainly have an R<1 in the US and spend their fear and energy on more dangerous socially induced diseases, like fat intake, or lack of exercise, or Governors who want to be President.

Onward!

Les

Les Roberts – “Day 51: Protecting the public from epidemiological data”

Les Roberts – Freetown, Sierra Leone – November 24^th, 2014

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Day 51: Protecting the public from epidemiological data

It is rather astonishing here how much of the data I and others collect cannot be shared. It is not that the data is about things people don’t know. It is not that the data is about secret findings… it is about keeping the press and academics from saying stupid things and attributing it to WHO.

We have done a series of sensitivity analyses of the major CDC created surveillance system, the VHF, that everyone knows is incomplete. It is consistently 10 or 20% lower than the weekly district reports probably because somehow 10 or 20% of cases fail to be properly documented and transferred on through the steps of the surveillance process (e.g. the case report does not get filled out, or gets lost, or gets missed at the data entry office on the district level….or because half the freakin’ country have one of about six first and last names so they see 17 people named Mohammed Kumara from that district and think that their Mohammed Kumara has already been entered…). But, say out loud with data what everyone knows, for example that most of the cases are not being detected, and wow do the cheap seats in Atlanta and New York start rattling.

The most stunning censorship is the reluctance of anyone to show the epidemic curve. This is because the data takes time to get into the system (both the CDC VHF system and the MoHS “call to the Districts every day” system). It takes days for suspect cases to be tested and confirmed or sent home. It takes days for the data to get entered into the database. There are all kinds of delays… that when presented as an Epi curve, constantly give the impression that the outbreak has peaked and is coming down over the last two weeks.

Above is a classic example from this past Friday’s local Sit-rep. It is mostly based on the MoHS data so the dip is not as dramatic as the VHF database. Most every reporter and fancy-pants modeler that has never done contact tracing or data entry form hospital forms will be tempted to report that the outbreak appears to be going down. This is actually what going up looks like. It would be fine if poorly informed people misinterpreted and then moved on to the crossword puzzle, but more often, the press officer and we in the office need to squander time explaining about data flow and delays. And then there are aberrant events.

If one looks at the week of September 21 above, it looks like there was a spike in suspected cases and then a dip. In fact, there was an outbreak of coding errors combined with the largest lab near Port Loko (the district with the highest incidence) shutting down for the week. Thus, those suspected cases from the week of September 21 mostly died without ever being laboratory confirmed and thus they will stay suspect forever. Since back in September, it took 4 or 5 days to get a lab test back (it is much shorter now), and then the data record had to be updated, typically cases that appeared as suspect in the week of Sept. 21 would mostly change to confirmed in the week of Sept. 28, but that never happened that week resulting in an artifact of apparently elevated numbers of suspect cases one week and fewer cases the next. There are issues like this or bigger in every data source I see every day… so people just do not share data and findings… not with the press, not with your peers who might share it with the press, and heaven knows not with Geneva!

Ah, the things they don’t teach you in intro Epi!

Les

Les Roberts – “Day 49: Each in their own way”

Les Roberts – Freetown, Sierra Leone – November 22nd, 2014

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Day 49: Each in their own way

I went to a house a couple weeks ago. We were trying to see if household quarantine caused or prevented secondary cases in the home. We went to a house that was not quarantined and where over a four week period, 14 out of 16 household members had developed ebola and 12 had died. Only about four ever went to a clinic because there were no beds free.

There was a neighbor….he reminded me of my late father-in-law. He was just a regular guy. If he was in the US, he would own a hardware store or be a little league baseball coach. At the outbreak peak of the neighboring house that we went to see, the 13 year old girl in the house started to show symptoms. This neighbor went and took the girl to his house and put her in the cooking hut and made her drink. When another sister got sick, he brought her over too. When the second sister started vomiting blood, he cleaned out a bedroom and moved the 13 year old into his house… and she lived. Now, the family is disbanded and the 13 year old lives with this neighbor. She got teary eyed as we discussed her family… but those two now have a lovely bond that is clear for all to see. I am sure that the neighbor didn’t really know exactly what he was doing, but he just desperately needed to help, and help he did. That is a really nice aspect of this crisis. As with all crises, little people are doing their part for the big picture, even if it is trying to help by the most indirect of means like teaching children at night in this chapter of closed schools or cooking for others.

John doing his thing.

Every day, seven days per week, John makes me breakfast. He stands out in the meal area at my hotel cooking eggs and making sure the spread is proper. He is the master chef of the hotel and very witty and good natured. Every morning, we have a little shtick that we go through where I ask him what will we be having for breakfast and every day the answer is something else: a Lapland omelet, a hopeful omelet, an Australian omelet (from way south, with a pouch, that has a little baby omelet inside). It is always the same omelet, just with a different name and explanation. He speaks Japanese with my Japanese colleague, he speaks French well, he speaks Spanish. It turns out that he is a Sierra Leone born, high end chef from London. When Ebola arrived here, he just had to come home to help. His 15 year old daughter thinks it is fine he is here. His 23 year old daughter was visiting for the summer when the war broke all those years ago and was pretty traumatized; she is not at all understanding about John being here. He cooks here at a hotel filled almost exclusively with WHO employees and members of a Scandinavian logistical group call IHP (who are unfalteringly reliable and competent in a way WHO and most everyone else is not). Being a chef is not very logically related to stopping ebola… but John wants to help and what he knows how to do is cook, so he is cooking. And my life is richer for it in many ways.

This outbreak is really ugly and is out of control. But, there are a lot of nice faces of human nature in Sierra Leone these days.

Cheers,

Les

Les Roberts – “Day 40: KB”

Les Roberts – Freetown, Sierra Leone – November 13th, 2014

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Day 40: KB

I work with a guy named Kyobe Bosa. Everyone calls him KB. One of my colleagues was at a public event, a Community care Center (CCC) opening last week, and an official walked up to KB and said, “Good morning Chief.” He was standing next to a Paramount Chief, a Chief of perhaps 100 villages who is elected for life. The Paramount Chief wryly looked over at KB and said, “Not yet he’s not!”

KB has worked for years on infectious disease control issues at the WHO headquarters in Geneva. I suspect, WHO will be his career path for a long time to come. He is from Port Loko District where he is now the WHO field coordinator. When the outbreak happened, he just told his boss, and the Ebola Response crowd in Geneva that he needed to go home.   It is a beautiful thing, how he just has to be home at this moment of extreme need. But what is even more beautiful, is how unabashedly angry he is at the international response. He is perhaps the angriest person I have met here. He laughs a lot. He smiles a lot. But, don’t get him started on the issue of quarantined households not getting food, or how long it takes to have dead bodies picked up, or the contact tracers. Anger, it can be a really constructive thing. People in the relief world talk a lot about local empowerment as if it is a gift from the donors. It is really inspiring to see a local-lad take power!

Les

KB in Port Loko: the revolution will not be televised!

Les Roberts – “Day 39: The plural of anecdote is not data”

Les Roberts – Freetown, Sierra Leone – November 12th, 2014

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Day 39: The plural of anecdote is not data

This past week, I was assessing the completeness of the main case listing database (a sensitivity analysis) which involved going to villages and asking if there had been any suspected cases in the village during the month of October. In one village, there had been a woman and her two small children who had returned from Freetown just after the three day lockdown (September 28-30). She was originally from the town, was married to a man from the town, but had been living in Freetown for a while. When she returned, the village quarantined her in a store. It is against the law to allow a visitor to stay in your house in Bombali District. But she was from the village so they could not turn her away. Quarantine in a non-house building seemed like the right thing to do in this village that had reportedly never had an Ebola case and was officially closed to outsiders. I am sure they saw this as a humane compromise.

On day 18 of the quarantine, one of the 18 month-old children died in the morning and the other twin died in the evening.  The village chief reported to us that they were Ebola cases. The bodies were swabbed before burial and one is listed as a positive swab in the official CDC VHF database (I am sure you are asking why one and not two….that is the sensitivity part, and I wonder the same thing). The mother supposedly was never sick? Was she an asymptomatic case? Hard to say. The kids could have been infected 19 days earlier (unlikely, but a theoretical possibility). The mother could have really been a case, was discharged and did not tell anyone and somehow infected the kids. Again, unlikely as the very limited fluid sampling I have heard about suggests the virus disappears from breast milk quickly, making it safe, while other fluids like sperm remain deadly for months (Therese McGinn has been saying variations of that same theme for years!). Whatever happened, it was a pretty odd case. As we drove back, a colleague told me one of the guards at a holding center in Makeni had developed fever, been tested, was positive, but never developed serious illness. The next day, another colleague told me of a family where a mother was ill, there were no open beds at treatment centers or holding centers so she was quarantined in the house with her two small children and her sister. The woman died; a week later a kid died, and then the other while the sister spent perhaps 30 days in a house caring for three people as they died, a house that was never disinfected, and she never fell ill. I have now heard perhaps a dozen stories like this.  No one story is very convincing that it was an asymptomatic or mild infection. Taken together, the likelihood that this is not a disease like measles (where virtually everyone can get it) seems to be growing in lots of people’s minds. There are supposedly almost no villages where the attack rate has been more than 20 or 30%. These are often really humble villages where no children have shoes and feces flow like social media in New York. Lots of us are lamenting that there is so much work to do, that there is no time to learn the lessons that are passing before us (like drawing blood in these high attack villages to see if people who report never being sick have antibodies). Maybe next year, when the outbreak has passed…

Instead, tomorrow I am off with my Ministry Of Health mates to measure if quarantine causes or prevents infections within a home. We are planning to interview most of 100 homes… Finally, there will be something more than anecdotes linking quarantine and secondary household deaths. Either way (and I have no idea what we will find) a lot of people are going to be annoyed with the results. Ebola, the rift that keeps on rifting!

Les