Tag Archives: SIV

New Grant, Post-Doc Opportunity

Biological and Human Dimensions of Primate Retroviral Transmission
One of the great enduring mysteries in disease ecology is the timing of the AIDS pandemic. AIDS emerged as a clinical entity in the late 1970s, but HIV-1, the retrovirus that causes pandemic AIDS, entered the human population from wild primates many decades earlier, probably near the turn of the 20th century. Where was HIV during this long interval? We propose a novel ecological model for the delayed emergence of AIDS. Conceptually, in a metapopulation consisting of multiple, loosely interconnected sub-populations, a pathogen could persist at low levels indefinitely through a dynamic balance between localized transmission, localized extinction, and long-distance migration between sub-populations. This situation might accurately describe a network of villages in which population sizes are small and rates of migration are low, as would have been the case in Sub-Saharan Africa over a century ago.
We will test our model in a highly relevant non-human primate system. In 2009, we documented three simian retroviruses co-circulating in a metapopulation of wild red colobus monkeys (Procolobus rufomitratus) in Kibale National Park, Uganda, where we have conducted research for over two decades. We will collect detailed data on social interactions, demography, health, and infection from animals in a core social group.
We will also study a series of 20 red colobus sub-populations, each inhabiting a separate, isolated forest fragment. We will determine the historical connectivity of these sub-populations using a time series of remotely sensed images of forest cover going back to 1955, as well as using population genetic analyses of hypervariable nuclear DNA markers. We will assess the infection status of each animal over time and use viral molecular data to reconstruct transmission pathways.
Our transmission models will define the necessary conditions for a retrovirus to persist, but they will not be sufficient to explain why a retrovirus might emerge. This is because human social factors ultimately create the conditions that allow zoonotic diseases to be transmitted from animal reservoirs and to spread. We will therefore conduct an integrated analysis of the root eco-social drivers of human-primate contact and zoonotic transmission in this system. We will study social networks to understand how social resources structure key activities relevant to human-primate contact and zoonotic transmission risk, and we will explore knowledge, beliefs, and perceptions of human-primate contact and disease transmission for a broad sample of the population. We will reconcile perceived risk with actual risk through a linked human health survey and diagnostic testing for zoonotic primate retroviruses.
The ultimate product of our research will a data-driven set of transmission models to explain the long-term persistence of retroviruses within a metapopulation of hosts, as well as a linked analysis of how human social factors contribute to zoonotic infection risk in a relevant Sub-Saharan African population. Our study will elucidate not only the origins of HIV/AIDS, but also how early-stage zoonoses in general progress from “smoldering” subclinical infections to full-fledged pandemics.

I am thrilled to report that our latest EID project proposal, Biological and Human Dimensions of Primate Retroviral Transmission, has now been funded (by NIAID nonetheless!).  I will briefly describe the project here and then shamelessly tack on the full text of our advertisement for a post-doc to work as the project manager with Tony Goldberg, PI for this grant, in the College of Veterinary Medicine, University of Wisconsin, Madison.  This project will complement the ongoing work of the Kibale EcoHealth Project. The research team includes: Tony, Colin Chapman (McGill), Bill Switzer (CDC), Nelson Ting (Iowa), Mhairi Gibson (Bristol), Simon Frost (Cambridge), Jennifer Mason (Manchester), and me. This is a pretty great line-up of interdisciplinary scholars and I am honored to be included in the list.

Biological and Human Dimensions of Primate Retroviral Transmission

One of the great enduring mysteries in disease ecology is the timing of the AIDS pandemic. AIDS emerged as a clinical entity in the late 1970s, but HIV-1, the retrovirus that causes pandemic AIDS, entered the human population from wild primates many decades earlier, probably near the turn of the 20th century. Where was HIV during this long interval? We propose a novel ecological model for the delayed emergence of AIDS. Conceptually, in a metapopulation consisting of multiple, loosely interconnected sub-populations, a pathogen could persist at low levels indefinitely through a dynamic balance between localized transmission, localized extinction, and long-distance migration between sub-populations. This situation might accurately describe a network of villages in which population sizes are small and rates of migration are low, as would have been the case in Sub-Saharan Africa over a century ago.

We will test our model in a highly relevant non-human primate system. In 2009, we documented three simian retroviruses co-circulating in a metapopulation of wild red colobus monkeys (Procolobus rufomitratus) in Kibale National Park, Uganda, where we have conducted research for over two decades. We will collect detailed data on social interactions, demography, health, and infection from animals in a core social group.

We will also study a series of 20 red colobus sub-populations, each inhabiting a separate, isolated forest fragment. We will determine the historical connectivity of these sub-populations using a time series of remotely sensed images of forest cover going back to 1955, as well as using population genetic analyses of hypervariable nuclear DNA markers. We will assess the infection status of each animal over time and use viral molecular data to reconstruct transmission pathways.

Our transmission models will define the necessary conditions for a retrovirus to persist, but they will not be sufficient to explain why a retrovirus might emerge. This is because human social factors ultimately create the conditions that allow zoonotic diseases to be transmitted from animal reservoirs and to spread. We will therefore conduct an integrated analysis of the root eco-social drivers of human-primate contact and zoonotic transmission in this system. We will study social networks to understand how social resources structure key activities relevant to human-primate contact and zoonotic transmission risk, and we will explore knowledge, beliefs, and perceptions of human-primate contact and disease transmission for a broad sample of the population. We will reconcile perceived risk with actual risk through a linked human health survey and diagnostic testing for zoonotic primate retroviruses.

The ultimate product of our research will a data-driven set of transmission models to explain the long-term persistence of retroviruses within a metapopulation of hosts, as well as a linked analysis of how human social factors contribute to zoonotic infection risk in a relevant Sub-Saharan African population. Our study will elucidate not only the origins of HIV/AIDS, but also how early-stage zoonoses in general progress from “smoldering” subclinical infections to full-fledged pandemics.

Post Doctoral Opportunity

The Goldberg Lab at the University of Wisconsin-Madison invites applications for a post-doctoral researcher to study human social drivers of zoonotic disease in Sub-Saharan Africa.   The post-doc will be an integral member of a new, international, NIH-funded project focused on the biological and human dimensions of primate infectious disease transmission in Uganda, including social drivers of human-primate contact and zoonotic transmission.  This is a unique opportunity for a post-doctoral scholar with training in the social sciences to study human-wildlife conflict/contact and health and disease in a highly relevant ecological setting.  The following criteria apply.

  1. Candidates must have completed or be near to completing a PhD in the social sciences, in a discipline such as anthropology, geography, sociology, behavioral epidemiology, or a relevant discipline within the public health fields.
  2. Candidates must have a demonstrated interest in health and infectious disease.
  3. Candidates must have prior field experience in Sub-Saharan Africa.
  4. Candidates must be willing to relocate to Madison, Wisconsin for three years.
  5. Candidates must be willing to spend substantial time abroad, including in Sub-Saharan Africa and at partner institutions in the United Kingdom.
  6. Candidates must have experience with collection and analysis of both quantitative and qualitative data.  Familiarity with methods such as social network analysis, GIS, participatory methods, and survey design would be advantageous.

The successful candidate will help lead a dynamic international team of students and other post-docs in a multi-institutional, multidisciplinary project.  Duties involve a flexible combination of fieldwork, analyses, and project coordination, in addition to helping to mentor students from North America, Europe, and Africa.  The successful applicant will be expected to explore new research directions of her/his choosing, assisted by a strong team of collaborators.

University of Wisconsin-Madison is a top-notch institution for research and training in the social and health sciences.  Madison, WI, is a vibrant city with outstanding culture and exceptional opportunities for outdoor recreation.

Applicants should send a current CV, a statement of research interests and qualifications (be sure to address the six criteria above), and a list of three people (names, addresses, e-mails) who can serve as references.

Materials and inquiries should be sent to Dr. Tony L. Goldberg (tgoldberg@vetmed.wisc.edu).  Application materials must be received by September 12, 2011 for full consideration; the position is available starting immediately and requires a three-year commitment.

On Newspaper Front Pages

Expert wrangler of predicaments Phillip Mendonça-Vieira has put together a very cool time-lapse movie from about 12,000 screenshots of the front page of the nytimes.com.  The movie is interesting to watch in a Koyaanisqatsi kind of way, but what I find most poignant is his commentary that accompanies the movie. Mendonça-Vieira writes,

Having worked with and developed on a number of content management systems I can tell you that as a rule of thumb no one is storing their frontpage layout data. It’s all gone, and once newspapers shutter their physical distribution operations I get this feeling that we’re no longer going to have a comprehensive archive of how our news-sources of note looked on a daily basis. Archive.org comes close, but there are too many gaps to my liking.

This, in my humble opinion, is a tragedy because in many ways our frontpages are summaries of our perspectives and our preconceptions. They store what we thought was important, in a way that is easy and quick to parse and extremely valuable for any future generations wishing to study our time period.

This really resonated with me.  Some time back, we wrote a paper that garnered quite a lot of media coverage. Indeed, we even got the ‘front page’ of the nytimes.com, if only fleetingly. I am very glad that I had the presence of mind to save that screen shot as a pdf so I would be able to preserve this 15 minutes of fame for posterity. If they had been available, I would have bought lots of paper copies.  However, what I am left with is this:

NYTimes_Front_Page

This really is a shame and clearly represents a serious challenge for the historians of tomorrow and the archivists of today.

Chimpanzees and Biomedical Research

I have now been asked a perfectly reasonable question that arises from our recent paper on chimpanzee “AIDS” several times (see previous entry). The question is, should we reinvigorate biomedical testing of SIV infection in chimpanzees as a model for HIV?  The simple answer is no. There are several compelling reasons for this.

First, there are the ethical considerations.  Given the genetic and phylogenetic closeness of chimpanzees to humans and their complex psychology and social behavior, the use of chimpanzees in experimental medical studies is not an ethically viable practice. Second, there is the legal fact that chimpanzees are an endangered species and therefore protected from such uses by international law. Third, is the simple economic argument.  Chimpanzees are too expensive to maintain for the types of insights biomedical research on them is likely to yield.  Fourth, they are impractical as an animal model.  Chimpanzees live for 40 years or more in captivity and the time course of SIV pathology — while still not entirely understood — is certainly slow (remember the lenti– in lentivirus means slow).  Remember, the surprising thing about our paper is that no one noticed AIDS-like pathology either in the wild or in experimentally infected chimps in captivity.  Finally, we have much better animal models.  SIVmac infection of rhesus monkeys provides an excellent model of infection and pathogenesis.  Rhesus macaques are much less long-lived, are not endangered, have a much shorter time-course of pathogenesis, and their social systems make them far easier to manage in captivity. Of course, parallel ethical arguments can be used against biomedical research on any primate species as those for chimpanzees, but I’m going to duck that for the time being since this is a post on chimpanzees.

That’s the take on invasive, laboratory-based, biomedical research. Naturalistic studies of SIVcpz are another story altogether. We strongly believe that field studies of naturally infected ape populations (western lowland gorillas also have naturally acquired SIV infection) should be expanded. These studies would help us understand HIV pathogenesis by providing fecal, urine, and post-mortem samples for virological and immunological analysis. With regard to post-mortem samples, it is particularly important to have a constant field presence.  Even when the mortality hazard is 16 times the baseline, death is a relatively rare event and bodies disappear amazingly fast in tropical forests (perhaps I’ll post some day about the maddening difficulty of trying to collect feces in a rainforest).

Our results open up an opportunity to compare pathogenesis in two closely related species. We hope that this will accelerate the identification of both viral and host factors responsible for disease progression.  This, in turn, could lead to the development of novel therapeutic or preventative measures that have the potential to benefit both chimpanzees and humans. I am particularly sanguine about the possibilities of finding host factors that are protective against infection.  With my former post-doc and current NCEAS scholar, Sadie Ryan, I have been doing some analysis of chimpanzee sexual networks. I don’t want to spill the beans here before we submit the paper, but suffice it to say, there is a lot of exposure to SIVcpz in chimpanzee sexual networks.  This shouldn’t be surprising to anyone who has even a passing familiarity with chimpanzee mating systems, but the formalization makes it particularly striking.

New Publication: Chimpanzee "AIDS"

keele_etal2009-first-pageA long-anticipated paper (by me anyway!) has finally been published in this week’s issue of Nature.  In this paper, we show that wild chimpanzees living in the Gombe National Park in western Tanzania on the shores of Lake Tanganyika appear to die from AIDS-like illness when infected with the Simian Immunodeficiency Virus (SIV).  Many African primates harbor their own species-specific strain of SIV and chimpanzees are no exception.  The host species for a particular SIV strain is indicated by a three letter abbreviation (all in lower-case) following the all-caps SIV. So, for chimpanzees, the strain is called SIVcpz. It turns out that there are two distinct HIVs, known as HIV-1 and HIV-2. HIV-1 is the virus that causes the majority of the world’s deaths.  It is what we call the “pandemic strain.” HIV-2 is less pathogenic and has a distinct geographic focus in West Africa.  The HIVs and the various SIVs belong to a larger group of viruses that infect a wide range of mammals known as the lentiviruses (lenti– meaning slow, referring to the slow time course of the pathology typically caused by these viruses). Collectively, we call the SIVs and HIVs “primate lentiviruses.”  Both HIV-1 and HIV-2 have well-documented origins in nonhuman primate reservoirs.  HIV-2 is most closely related to SIVsmm, a virus that infects sooty mangebeys (a type of West-African monkey).  HIV-1, on the other hand, is most closely related to SIVcpz, the virus that infects central and east African chimpanzees.  We believe that both HIV-1 and HIV-2 entered humans hosts when hunters were contaminated with the blood of infected monkeys (HIV-2) or chimpanzees (HIV-1). Note that this means that our terminology for the primate lentiviruses is polyphyletic.  SIVsmm and HIV-2 are sister species, while SIVcpz and HIV-1 are sister species.  Yet we call all the viruses that infect nonhuman primates simian and all the viruses that infect humans human immunodeficiency viruses.  It seems to me the best way to fix this would be to call the viruses that infect humans SIVhum1 and SIVhum2.  Of course, that will never happen, but I do think that it’s important to clarify the evolutionary history of these viruses.

The conventional wisdom regarding primate lentiviruses is that, with the exception of HIV, they are not pathogenic in their natural host.  The reasoning for why HIV causes the devastating pathology that characterizes AIDS goes that HIV-1 is a relatively new infection of humans, having just spilled over into the human population recently.  Pathogens that have recently crossed species boundaries are frequently highly pathogenic because neither the new host nor the pathogen has a history of coevolution with its new partner.  While it is a pernicious myth (that just won’t seem to die) that pathogens necessarily evolve toward a benign state, it is true that they frequently evolve a more intermediate level of virulence from their initial spillover virulence.  There are a number of problems with the idea that HIV causes AIDS because it is poorly adapted to human physiology.

The first of these is that HIV-1 is not that recent an infection of humans.  Sure, we didn’t notice it until 1983 but careful molecular evolutionary analysis by Bette Korber of the Santa Fe Institute and my collaborator Beatrice Hahn and her group at the University of Alabama Birmingham puts the most likely date for the emergence of HIV-1 in humans to be 1931.  That means that HIV-1 was being transmitted from human-to-human for over fifty years before it was ever noticed by western science. Fifty years, while certainly brief in evolutionary terms, is still long enough to lead to some reduction in virulence or host evolution.

The real nail in the coffin, however, is our new result.  Specifically, we show that SIVcpz causes AIDS-like pathology in the Gombe chimpanzees. This result is surprising because (1) given it’s pathogenicity, one would expect someone to have noticed it before, and (2) chimpanzees infected in captivity do not show obvious AIDS-like illness. I have been collaborating with Anne Pusey, Mike Wilson and their colleagues at the University of Minnesota’s Jane Goodall Institute Center for Primate Studies on the the analysis of the demography of the Gombe chimps for a number of years now. Anne and Mike have, in turn, been collaborating with Beatrice Hahn with her project on monitoring natural SIV infection in wild chimpanzees across Africa. Given my background in HIV epidemiology and statistics, it was only natural that we all join forces to look at the demographic implications of SIV infection among the Gombe chimps.  Jane Goodall famously started chimpanzee research at Gombe in 1960 and since 1964, researchers at Gombe have collected detailed demographic information, documenting all births, deaths, and migration events in the central community and eventually expanding to the peripheral ones in later years. As a result, we have an unmatched level of demographic detail (not to mention behavioral and ecological information) against which to assess the impact of SIV infection.  Using statistical methods known collectively as event-history analysis, we were able to show that the hazard ratio between SIV-infected and SIV-negative chimps is on the order of 10-16.  This essentially means that SIV+ chimps have mortality rates that are 10-16 times higher than uninfected chimps.  The analysis controls for the clear potentially confounding effects of age and sex on overall mortality. The reason why no one ever noticed this heightened mortality rate is really because no one has ever looked for it. Even when a mortality rate is 10 times higher for some segment of a population, when that segment is small and when mortality rates quite low (chimps who survive infancy can live in excess of 40 years) it can be hard to detect even a seemingly large difference.  This is why we do science: because things that seem obvious once we know they are there can be remarkably subtle when we don’t know they’re there.  Science gives us the framework and the tools for studying nature’s subtleties.

This project was absurdly interdisciplinary.  The paper has 22 co-authors, each contributing his or her own particular analytical expertise or providing access to crucial data necessary for the larger narrative.  There are papers in the literature in which people are made co-authors for pretty thin contributions.  This paper has none of that.  It was an extremely complicated story to tell and it really required the collaboration of this large team. Such work is not easy to manage and it’s not at all easy to do well.  I think that Beatrice should be commended for orchestrating all the various major contributions, keeping us in line and on schedule (more or less). It’s really gratifying to see the excellent blog piece by Carl Zimmer in which he notes the virtues — and the difficulty — of combining various scientific styles in pursuit of an important question. The title of Carl’s piece is “AIDS and the Virtues of Slow-Cooked Science.” In addition, there is a nice companion piece in this week’s Nature written by Robin Weiss and Jonathan Heeney.  They too note the strength of the interdisciplinary approach to this problem.

The paper isn’t even officially published until tomorrow and it has already been covered on Carl Zimmer’s blog for Discover Magazine, The New ScientistThe GuardianThe ScientistThe New York Times and MSNBC. Wow.  Weiss & Heeney note a number of questions that are raised by our analysis.  Specifically, they ask “why was the progression to AIDS-like illness not more apparent in chimpanzees in captivity?” My co-author Paul Sharp notes “We need to know much more about whether there are any genetic differences among the chimpanzees, or differences in co-infections with other viruses, bacteria or parasites, which influence whether or not SIV infection leads to illness or death. This presents a unique opportunity to compare and contrast the disease-causing mechanisms of two closely related viruses in two closely related hosts.”  Then, of course, there are the conservation questions that this paper raises.  Chimpanzees in the wild have birth rates that are very nearly balanced out by their death rates.  This difference, called the intrinsic rate of increase, largely determines the probability of extinction of a small population.  When the rate of increase of a population is negative, it is certain to go extinct (assuming the rate remains negative).  However, even if the intrinsic rate of increase is greater than zero, the randomness that besets small populations still means that a population can go extinct.  So, because their average birth and death rates are so close, individual chimp populations are certainly in potential jeopardy of going extinct, and Gombe is no exception to this rule. Now we add to a population something that increases mortality rates 10-16 times.  This is bound to have negative consequences for the persistence of affected chimp populations.  This is a topic that we are exploring even as I write…

Always a Bridesmaid, Never a Bride

Well, it’s happened again.  My work has been written up in Science but I am not mentioned.  I’m actually not that concerned this time — we’re going to submit the paper for publication soon. I’ve been telling myself (and other people) that this thing we’ve ben working on (all the while being very cryptic about what this thing exactly is) is important.  Every once in a while, I wonder if I’ve just been fooling myself.  The fact that this work has been written up in Science the day after the paper was presented at the Montreal Conference on Retroviruses and Opportunistic Infections suggests to me that it is, indeed, important.