Taking on HIV Local Epidemic with Local Epidemiology

World AIDS day is about one week away and I think it is important to thing about progress against this infectious disease. While HIV/AIDS does not grab headlines in the manner of Ebola, foodborne outbreaks, or AFM (acute flaccid myelitis) it is important to realize that it is still very impactful in the US and in the world.

In 2018, though there still remains no feasible cure or vaccine there are a few important tools that have reshaped the way it approached.


One such tool is antiretroviral therapy. Many people realize that effective treatment cocktails have transformed HIV from a death sentence to a manageable chronic illness, but they do more than that. When someone is on antiretroviral therapy and their viral load (the amount of virus detectable in their blood) is undetectable. They are no longer contagious. Undetectable = Untransmittable (U = U). This means that treatment is prevention as those on therapy are unable to infect others.

A second tool, is pre-exposure prophylaxis (PrEP). PrEP is a means of protecting oneself from contracting HIV by taking two antiretroviral medications on a regular basis so if one encounters the virus during an activity such as sex, the drugs prevent infection from taking hold. While not a panacea, it is an unequivocal advance in HIV prevention and its scale up could make a significant dent in new HIV infections.

When most people think of HIV, they think of it is as the global problem that it is. However, the global pandemic is really the aggregation of local cases and outbreaks. In the Pittsburgh area, where I live and practice, there are several groups working to curtail infections locally. One such group, that I am part of, is AIDS Free Pittsburgh. This organization’s aim is to decrease new HIV diagnoses in Allegheny County, in which Pittsburgh is located, by 75% from 2015 levels (142 cases) and eliminate AIDS in the county by 2020.

Recent data shows that their concentrated approach of working with strategic partners to increase testing, increase linkage to care, and enhance PrEP prescribing has been effective. In 2017, just 100 new diagnoses of HIV were made in the county — representing a 30% decrease since the formation of the organization — with 26 new AIDS diagnoses.

Looking at the data, however, there clearly are epidemiological opportunities to further decrease the force of infection in the county. For example, 80% of new infections were in males with 61% being in men who have sex with men — a prime target for PrEP. In fact, it seems the 75% goal could almost be met with prevention activity in this subgroup. Injection drug use accounted for 8% of new infections — another transmission category easily amenable to interdiction through needle exchange.

The point I am trying to make is that the HIV crisis can be addressed in a meaningful way just by looking at one’s local epidemiology and tailoring approaches to address the nuances of the area. Other communities, would do well to learn from the example of AIDS Free Pittsburgh.

Controversies & False Alternatives: A Review of Biosecurity Dilemmas

The field of biosecurity is fairly new and for such a new field it is remarkable that so many scholarly works have appeared. I recently completed reading one such work, Biosecurity Dilemmas: Dreaded Diseases, Ethical Responses, and the Health of Nations by Christian Enemark. The theme of this book, published in 2017, is to “highlight and explain the tension between differing values and interests that are generated or exacerbated by the practice of ‘biosecurity’.”

For those that track the field, it comes as no surprise that tensions exist in the field and a constant risk-benefit calculus is always at play. Biosecurity Dilemmas accurately (but selectively) reflects the tension and is divided into four parts that highlight major debates in the field: “Protect or Proliferate,” “Secure or Stifle,” “Remedy or Overkill,” and “Attention or Neglect. Each of the eight chapters explores in detail important events to concretize the concepts being discussed.

My colleague, Gigi Gronvall, has already reviewed this book for Science and highlighted her concerns regarding the selective attention the book pays to arguable the largest biosecurity issue and the heightened attention given to American programs. As she writes:

Although U.S. biodefense efforts are worthy of critical analysis, they are largely transparent. The book would have benefited from more critical attention to a nation that is not nearly as open and that has a long history of flouting biosecurity norms: Russia.

To not recapitulate her review, I want to focus on one specific aspect of Enemark’s analysis that I do not believe to be valid.

Biosecurity, in its original conception, addresses the threat of intentional infectious disease releas. As such, it must be viewed as a national security issue despite the fact that many actions involved may have substantial overlap with public health and ordinary healthcare activities (e.g. disease surveillance, vaccination, diagnostic testing). However, it is indisputable that gains in biosecurity positively impact and synergize with “ordinary” public health and medical activities, involve many of the same people, and have “all hazards” preparedness implications. What, in my analysis, has happened is that because of these synergies, it becomes easier for people to lose the distinctions and muddle the concepts.


Cashing in on this conflation, Enemark to advocate a “security sensitive” approach that attempts to create a middle way between what he characterizes as the “dispassionately evidence-based” and “people’s dread of being attacked.” This “security sensitive utilitarianism” underlies his call to require that all “civilian biodefense projects…afford protection against natural as well as as intentional infectious disease risks” as measured by a “dual-benefit” test.

What Enemark fails to realize is that government, properly understood, has specific roles that are delegated to it. These roles are limited to the protection of individual rights. Individual rights are violated through the use of physical force or fraud. When it comes to biosecurity this means government’s role is to protect individuals from being endangered by the use of microorganisms or their toxins, just as they do with bullets and bombs. Naturally occuring infectious diseases, outside of quarantine and related matters, are can not really be seen in the same manner. Biosecurity is a core function of government. As such, no “dual-benefit test” or calculation involving natural infections should be performed. Biodefense, whether civilian or military, is a policing function of the government and must be evaluated in that context, not in the context of seasonal influenza, HIV, and non-communicable diseases. While it is ideal when biosecurity is integrated with other overlapping domains, it is still distinct. To construct a false alternative obscures this fact.

Overall, despite my disagreements with the philosophical framework of the book, I believe that those wanting to deepen their understanding of aspects of the field of biosecurity would benefit from the book.

Thinking Hard and Deep about the Very Small: A Review of Philosophy of Microbiology

I think it is generally true that all infectious disease physicians love microbiology. However, it is also probably true that most infectious disease physicians think of medical microbiology as their handmaiden — a powerful tool that allows them to make diagnoses, treatment decisions, and predictions. Microbiology as such is something that is often neglected not only by physicians but also by philosophers of science who are often focused on “bigger” entities when they delve into the philosophical questions posed by biology.


Philosopher Maureen A. O’Malley addresses these issues and much much more in an intellectually challenging and rigorous book aptly entitled Philosophy of Microbiology. O’Malley motivates her call for more attention to the philosophy of microbiology by calling to attention the fact that microbes are the “most important, diverse and ancient life forms on our planet. The science of these organisms, microbiology, is the science of the most significant living entities and their influence on all the rest of life.” Additionally if one looks at eukaryotes, it is the single-celled protists that dominate multicellular organisms.

The book provides great amounts of information on just how important microbial life is to all ote life and is full of facts that should be kept in mind such as the diversity of metabolic pathways possessed by bacteria, the role of cyanobacteria in the Great Oxidation Event, the oxygenation power of plants being derived from endosymbiont bacteria, conversion of carbon, nitrogen fixation, and much more.

One of the most fascinating discussions in the book is that on teleosemantics, “the philosophical study of how mental content can be explained naturalistically” and its relationship with magnetotactic bacteria, that “sense” the planet’s geomagnetic field.

There are also fascinating sections that deal with the implications of lateral gene transfer (LGT), phylogeny/classification, the pangenome, and microbial “communities.” Not only does the book prompt the reader to think harder about microbiology, it prompts one to consider well-established facts from a wider context.

It’s hard to do give O’Malley’s book the justice it is due in a brief blog post but it is really a clarion call to take microbiology much more seriously from a philosophical standpoint. As she writes:

“There are no eukaryotes without mitochondria, and (within eukaryotes) no plants without chloroplasts”

“The origins of life are exclusively microbial; life until recently was exclusively microbial; life in the future will most probably be exclusively microbial too. If there is indeed life on other planets in other galaxies, it is most likely to be exclusively microbial”

For those who want to think rigorously, endlessly, and deeply about microbiology, I highly recommend the book.

Getting Sour on Lyme: A Review of Lyme: The First Epidemic of Climate Change

I devour infectious disease books however the latest one has given me a bit of indigestion. I recently read Lyme: The First Epidemic of Climate Change by investigative reporter Mary Beth Pfeiffer. I came across this book after seeing it mentioned favorably in the premiere scientific journal, Nature. I don’t share their enthusiasm for the book.

For those who follow infectious disease news, the controversies and mythologies surrounding Lyme Disease are nothing new despite the fact that they seem to multiply, become more complex, and become more insoluble day-by-day.

Pfeiffer’s book is written from the viewpoint of someone who gives a lot of credence to alternative therapies for nebulous conditions that may or may not be related to Lyme infection. The best aspects of Pfeiffer’s book are its chronicling of the increasing geographic range of the Ixodes scapularis deer tick responsible for Lyme Disease transmission and explicitly linking it to suburban reforestation plans that put people into much greater contact with ticks.

She also deserves credit for cataloging the other important infections that can be spread by the deer tick such as Powassan virus, babesiosis, ehrlichiosis, and anaplasmosis — all of which are important for doctors to consider when evaluating someone with a potential tick-borne illness.

However there are several areas with which I strongly disagree with the book. Not surprisingly, much of my disagreement deals with her disparagement of the Infectious Diseases Society of America (IDSA) and major academic Lyme Disease researchers which she basically describes as a involved in a vast conspiracy to hide the truth about Lyme. This ire is focused almost entirely on the contentious subject of “chronic Lyme Disease” — an impossible to define concept that centers on the belief that ongoing damage-causing Lyme infection continues after sufficient antibiotic therapy and merits further antibiotics, hyperbaric oxygen, or other therapies.


In this brief review, it is impossible to rebut everything she asserts (with backing from certain physicians) but I would just point out that almost every patient I have seen who has this constellation of symptoms has no objective evidence of immune system response (i.e. C-reactive protein levels are completely normal) indicating that, even if remnants of the Lyme bacteria are present, there is no inflammation associated with and hence it does not make biological sense to attribute symptoms to something that the immune system itself is not attributing symptoms to. Furthermore, antibiotic therapy — which Pfeifer discounts the danger of — is not warranted.

One of my other problems with the book is how Pfeiffer conflates different diseases spread by ticks which could be confusing to the non-medical reader. While it is definitely the case that multiple infections with tick-borne pathogens can occur in the same person, it is not the usual case and lumping them all into the “Lyme” problem makes matters worse. For example, Borrelia miyamotoi does not cause Lyme Disease — it causes a distinct clinical syndrome — as does Babesia microti. The reader is left with dread feeling that every tick bite will unleash a Pandora’s Box of pathogens upon them and that of all infectious disease threats, this is the most pressing (while she discounts the arguably largest threat of antibiotic resistance fueled by antibiotic overuse).

I also have a lot of objections to what she writes about standard testing, its limitations, and the clinical diagnosis of Lyme by its characteristic rash.

I fear this book will make the field even more contentious and give patients, who desperately want answers for their symptoms, to continue down the wrong lane lined with those will not offer any evidence-based, scientific answers or therapies.

2 Years and 10 Questions: Remembering DA Henderson

It’s been 2 years since the founder of the Center for Health Security, DA Henderson, died. Like I wrote then and last year, it is an incalculable loss to the field of infectious disease that such a giant voice speaks no more. Personally, it’s rare that I go a day without thinking about him and the wisdom he always about all things infectious.


Last year to commemorate DA, and concretize how pressing public health and infectious disease issues are, I listed things that happened since he died that I — and the world — desperately needed his expert opinion about. So in that spirit, here are my new set of questions for DA.

1. What do you think about Russia and the current state of their former bioweapons program? There’s been a recent book about this topic and you personally debriefed some of the highest level defectors from the Soviet Union. Also, Putin has shown no qualms about using Novichok agents (as well as dioxin and polonium) so is their anything different about biological agents?

2. What’s your take on the number of food borne outbreaks? We had cyclospora and a big E.coli outbreak this year. Is it that surveillance is capturing what we never knew about or is the risk increasing or is it both?

3. The cholera outbreak in Yemen is the biggest ever and compounded by war. How would you tackle it? You dealt with conflict when you eradicated smallpox. Would you advise vaccines? Antibiotics? 

4. Back-to-back Ebola outbreaks have occurred in the DRC. The first one came and went but the second is a lot more scary because of the conflict zone in which it occurred. The vaccine seems excellent and was used in the ring vaccination manner — which you developed to beat smallpox — but they can’t find the contacts of cases so well in this 2nd outbreak. Should they just blanket immunize ? What priority should vaccination have when you can’t do contact tracing? 

5. Measles elimination in the Americas is no more. Venezuela and their totalitarian government have seen outbreaks of malaria, diphtheria, and now measles transmission for over a year. How can we fix this? You were never a fan of eradication and now it seems measles, which was on the list, is slipping away. 

6. We had a bad seasonal flu year and it had hospitals inundated. We seem no where near able to cope with a pandemic and H7N9 looms. I know you don’t have an easy answer but when this pandemic occurs not having you to lead will make it much worse.  

7. We have a new smallpox antiviral. I know you had issues with this drug and didn’t have a good idea for how it would be used and definitely opposed it’s research program being used as an excuse not to destroy the samples of the virus but it’s here now. How should we use it? Individual cases? The vaccine should still be the cornerstone of response, right? 

8. Horsepox was artificially synthesized in the quest for a better vaccine. I know you would  have something to say about that. The standard vaccine’s cardiac side effects weren’t something you thought was significant enough to scrap it and this is the reason cited for the horsepox version. There’s also the debate about this event lowering the threshold for those who want to synthesize smallpox. What do you think about all this? We really missed your voice on this.

9. Polio eradication is still faltering. Just Afghanistan and Pakistan have wild cases and it looks like type 2 polio is gone the way of 3 and we’re just contending with type I. The Taliban hasn’t stopped their anti-vaccine push either. People are getting hyper about vaccine-derived cases and we’re still using the Sabin vaccine in many parts of the world. I know you taught me to think of vaccine-derived cases entirely separately and I’ve been saying that to people. This is the way to do it right? Wild polio first then switch to Salk and deal with vaccine-cases separate, right?

10. What do you think about my Pandemic Pathogens report? I know this is my own vanity but I spent a lot of time thinking about this topic and really want it to impact the field. It hopefully would be something that would make you proud of the time you spent teaching me. 

As is apparent, DA’s intellect is needed just as much now as it was when he beat smallpox off the planet. I don’t know if humans will ever produce another DA. It seems like a dream that he existed, but we should all remember him and how the insoluble problems of infectious diseases fell away when his mind faced them.