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Ebola Updates: Still no reason to panic

Another big headline at the NYTimes: A Second Healthcare worker in Dallas has tested positive for ebola.

Is anyone shocked?  Please raise your hand where I can see you.

Didn’t think so.

Update: So, now we find that the second nurse who was infected was on a plane from Cleveland to Dallas the day before she reported symptoms.  Ahhh, now here is where Americans should start to get concerned.  Americans get around.  That is, it’s  relatively easy to jump on a plane for a weekend getaway, though why anyone would want to go to Cleveland is beyond me.  Sorry about that, Cleveland.  And Pittsburgh is only a few hours from Cleveland by car.  Nevertheless, there is still no reason to panic, though the CDC seems to think the passengers on that flight need to be tracked down. The nurse landed in Dallas-Ft. Worth on Monday night at 8:16pm and reported symptoms on Tuesday. That is a very tight timeframe so passengers probably have more of a reason to be concerned but not panicked. But the bigger problem is that it will be harder to keep ebola in Texas if infection rates blossom.

Reminder: Back in May, I went to a user group meeting in Cambridge, MA where I met several researchers who had just come back from a visit to the CDC.  They reported that the budget cuts had demoralized the CDC and researchers there sometimes didn’t know who they reported to or who was in their group.  That’s not a slight on the CDC.  It has been a world renowned institution but if you starve it for funds, it is going to have problems.  If you do it over a period of 14 years, it’s going to have BIG problems.

I’m copying a few comments I made in a previous thread on the latest ebola news.

On the CNN report about the Nurses Union that is speaking out for the Dallas health care workers, Katiebird may be posting on this later once she has tracked down some information.  These are just my uninformed, idle speculations to the news that Texas Health Presby Hospital may have put its employees and others at risk:

I read that CNN article late last night and I was shocked but not surprised, if that makes any sense. Shocked because the hospital was caught so unprepared and was really botching it. But unsurprised because it made a lot of sense in how the infection was spread to this nurse. No health care worker in their right mind wouldn’t take the utmost precautions given the media frenzy over ebola.

I could only conclude that the hospital itself was at fault for being caught off guard and, probably, considering cost over treatment protocol. After all, who was going to pay to isolate Thomas Duncan? Rick Perry turned down medicaid expansion and the Texas legislature has severely cut back on state board of health offices. Laissez faire apparently means anything goes when it comes to profiting off of health care and Duncan was a money sink.

The 90 minutes gap where Duncan was with other patients before he was isolated may have referred to the emergency room. Here’s my best guess: The ambulance dumps Duncan off at the ER with a barf bag. He has to sit there with other sick patients while calls are being made to the hospital administrative staff to decide how to admit him. He’s a foreign visitor, not even an immigrant, with no health insurance, dumped on Texas Health Presby Hospital. He doesn’t qualify for Obamacare, there’s no medicaid for him either because, hellloooo, Americans, especially those living in the south, don’t want to pay for the health care needs of foreigners. Are there funds set aside in Texas to manage a highly infectious disease like ebola? Are you kidding?? Decisions, decisions. The hospital might have thought of transferring him elsewhere but I’m betting the other facilities said they were no better able to care for him. It’s your problem.
Damn, Duncan could wipe out the profit for the entire year, what with the isolation and ruining ventilation and dialysis equipment, not to mention how to get rid of hazardous waste.

So, he sat in the ER for 90 minutes, vomiting and sweating all over the chairs and gurneys, before the hospital decides it doesn’t have a choice anymore and has to take him. Who knew how many people came in contact with him while he was shedding billions of viruses? Poor Nina Pham probably did what she was instructed to do with very little CDC oversight.

On the ebola forum symposium held yesterday at the Johns Hopkins School of Public Health that was held yesterday:

Peter Jahrling showed all of the possible drug treatments in the pipeline. It’s a joke. No, seriously. ZMapp looks like the best bet but the company can only make about 20 doses in its next batch. It’s not their fault. They’re just overwhelmed by the scale and logistics.

A couple of vaccines are being tested in the field. And they have to have a control group so 1/3 of the participants are getting Hepititis C vaccine. It can’t be helped but the participants must know that some of these people are going to die. There’s no way around it. That’s the way science is done. And these vaccines are not in anyway ready for FDA approval.

Other treatments are even less ready. Interferon actually makes the infection worse. There’s an interesting research topic. What is it about the cell signaling that makes interferon treatment worse? Then there are a couple of “drugs”. Honestly, I think biologists are analyzing the high throughput data. They think any hit is a drug. The compounds presented may have some efficacy (probably in the millimolar range from the looks of them) but they’re not very bioavailable and the toxicity could be a major problem.
So, in short, we’re pretty much screwed if we can’t get West Africa back under control and the infection spreads.

Not that we have much to worry about here in the US. We don’t. But it’s not very reassuring to me that we are sooooo far behind in the drug discovery area on infectious diseases. Again, shocked but not surprised.

The symposium can be found here. Most of it is School of Public Health academics trying to one up each other on modeling the progress of the disease. It got to be too insidery and less informative after awhile. Jahrling’s presentation was more straightforward, to the point and alarming. If the general public truly understood what Jahrling’s presentation was saying, they’d never vote for another budget slashing Republican. Ebola is only one of a number of devastating infectious diseases that we are not prepared to deal with because we cut funding, blocked nominations, and let private industry, dominated by shareholders and billionaires, dictate the research and manage the pipeline portfolios. It’s baaaaad.

About quick and dirty drug design using publicly available ebola virus crystal structures and the funky vocabulary that goes with it, this is a little primer on what I was initially thinking and about some of the obstacles:

FASTA is a format for amino acid sequences. Every protein has a sequence of amino acids and they are all unique. Families of proteins are related to one another. You can perform an evolutionary trace on a single protein if the sequence of that protein over time has been determined. The FASTA sequence is stored in publicly available databases. The NIH allows access to these sequences for researchers and provides tools to search them. One of these search tools is called BLAST. It can do sequence alignments. So, if you have a fragment of a sequence or a new sequence, you can search the database to find the entire sequence or similar sequences. I used to use a related tool called BLASTp. That allows the user to find protein sequences that have been crystallized and are stored at the RCSB.

So, let’s say you have a protein that you know has mutated away from its original source. In this case, we are talking about the ebola viral proteins. The crystal protein I referred to last night was from a strain found in Zaire, in a place called named after a nurse called Mayinga. But the newest outbreak of ebola is located in West Africa and it is a different strain, therefore, different mutations in the amino acid sequence.

If you designed a drug based on the Zaire Mayinga strain, it may not be effective against the West Africa strain because the amino acid sequences may be different. But we can make a homology model of the new viral protein structure if we know where the new mutations are. It’s the next best thing to a experimentally determined crystal structure.

The questions to ask are: do all of the viral proteins mutate at the same rate? We would know by looking at the latest FASTA sequences and mapping them onto the structure. Can we identify a binding site? The protein I looked at yesterday processed RNA. I can make an educated guess as to where this occurs. But when it oligomerizes, that is, forms a new structure by self assembly, it has a couple of different binding sites. That is, the binding sites of each subunit to the subunits adjacent to it can also be targeted for drug design. I worked briefly on a different oligomer previously and it was possible to create a drug like entity called a paptamer by extracting a chunk of the secondary structure of the subunit and modifying it very slightly. This prevented the subunits from self assembly, or so the theory goes.

But in the ebola protein I looked at yesterday, the protein-protein interactions between subunits appeared to be dominated by beta sheets, which relate to one another along parallel and antiparallel strands. So, extracting a piece of this binding surface would be difficult if not impossible. Another, more complex and time consuming drug design process would need to be done. If it were just a matter of a helix, it might have been a different story. So, this viral protein target might not be amenable to quick and dirty drug design work and it might have to be abandoned for another ebola protein.

In any case, the FASTA sequence is very informative. It has likely been deposited at the NIH. They usually do that for Flu viruses and you can track mutations as they zip around the world. But I’m not sure we have the very latest info for ebola.

Ok, that was long.  I’m going to eat lunch.

 

 

14 Responses

  1. Dr. Thomas Frieden, CDC Director: Countdown to resignation.

    • Do you think so? I’m listening to the CDC briefing right now and I don’t get the idea that he is incompetent. But do you remember when I said I’d heard some stuff about the CDC when I was in Cambridge in May? What I’d heard was that scientists who had visited there found the staff demoralized by the budget cuts and they didn’t know who was in their group. I found that information to be alarming but I wasn’t surprised. The CDC is a VERY important agency and it has a world wide reputation. The rest of the world looks to the CDC for information and guidance and we have decided, well, it’s not that crucial to keep the place fully funded. I guess private industry is supposed to pick up the slack.
      So, I feel for Friedan. He is under a lot of pressure right now and much of it was thrust upon him by that slathering, insensible mob known as the Republican party.
      I’d just like to ask the WaPo and WSJ opinion pages, was it worth it? I mean, even if we can get ebola under control in the US, which I don’t doubt we can, look at what this limited outbreak has exposed. I have been saying for years that our research infrastructure is a mess but it takes only a few cases of ebola to show what a house of cards it actually is.
      I mean, think about it. *I* am out of work. I might not have a PhD but I have over 20 years of experience in drug design and all I can do is look at public structures and speculate on design strategy. Why are so many of us sidelined like this??

      • I think he’s a visible symbol that the Centers for Disease Control haven’t exactly controlled this disease in the US. He’s been on TV virtually everyday for a while now and I think someone’s going to be fired for this. Most likely him.

        • NOT that I believe we’re going to get an epidemic here. I don’t.

        • And my point is that it’s really hard to do your job if you have to worry about whether the budget is going to be there or whether you’ll have to stop taking on new PhDs or let some positions go vacant for years at a stretch or whether you can update your database because you can’t afford to hire anyone to code. Do you see where I’m going? This is the kind of crap I’ve been warning about for several years.
          And it’s ridiculous to expect the private sector to pick up the slack. They don’t want to. It would eat into shareholder value.
          So, we’re stuck.
          Firing him is not going to make this better. A huge infusion of cash *might* make it better in a couple of years.

          • Oh, I totally agree with you — I should have said that.

            Still. The administration is going to make someone take the fall. This issue is spinning out of control (note, I didn’t say the crisis is spinning out of control) And we don’t seem to have a Surgeon General.

          • I know who should take the fall! Every politician and legislator who promoted and then voted for that reckless sequester. Everyone of them should lose their jobs.

          • Instead, we’ll probably set sequester II as soon as the election is over.

        • He accused the nurse of causing her own ebola through “lack of adherence to protocol”. So nurses as a group are severely upset by that blameshifting diversionary accusation and are going public with their complaints about systemic pre-sabotage of protocol systems to begin with.

        • That was very bad. If I was a nurse, I’d be Seriously enraged.

      • “Why are so many of us sidelined like this??”

        Because FreeDUMB says:

        [wingnut] “It’s worth it if I risk an agonizing death from one plague microbe or another, in order to eliminate the chance that somewhere, some ‘unworthy’ subhuman from a tribe I don’t like might manage to chisel a few cents of my tax money!

        And never mind how much more the ‘defense’ contractors take from me in order to make gold-plated weapons systems which don’t work half the time, and when they do work are used to slaughter as many brown people as necessary to make the survivors submit to brigandage by our righteous masters, the rich! They earned every bit of their money, dammit!” [/wingnut]

        Oh my dear Haruhi-kami-sama, am I showing too much contempt for my fellow Murkans here? 😉

  2. RD:
    Thank you for your reports and qualified info…it helps tremendously to some of us to get better picture of mishandling priorities of our -bureaucratic- government.

    • I hope you don’t get the wrong idea. I am completely in favor of vastly increased funding for the CDC, NIH and the FDA. We need those institutions to be able to function optimally. They can’t do it when research and safety is compromised by these ridiculous and harmful budget battles.
      You know by now that I am no fan of the current administration or the complacent Democrats who go along to get along. But the way the Republicans have behaved in the past 14 years has put all of our lives at risk, and not just from ebola. You should be very angry at the way our functioning government has been gutted. They work for you and they can’t do their jobs.
      Doesn’t that piss you off?

      • The Democrats didn’t just go along. They actively co-conspired with malice aforethought to help Obama make the Bush Tax Cuts permanent and to help Obama make the Sequester permanent.
        The Democratic Party itself is an “ebola hut”. it should be locked and burned down with every faithful party member trapped inside it.
        The space it occupied should then be decontaminated like any Political/Ideological Superfund Site would be decontaminated. Then perhaps a legitimate political party can be built on the cleared and decontaminated space.

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