Virus Hunters: Searching for Microbes in the Wild

We’re just a big, hairy afterthought to life on earth. This world belongs to microbes; we just live on it, and not always comfortably. If the viral particles (which are just a fraction of all microbes) on Earth− a staggering 1 x 1031− were laid end to end, they would stretch 100 million light years away. Yet while we know that there are tons of microbes on earth, we don’t know how much diversity there is among their ranks. The total number of microbial species is unclear and the estimates vary widely, ranging from a low of around 120,000 to tens of millions or more.3 Regardless of the exact number, it is obvious that−to date− we have only scratched the surface of microbial diversity.

Unfortunately, in this case, what we don’t know can hurt us. While the vast majority of microbes are benign, there are plenty that can do us ill, literally. There are currently about 1,400 known human pathogens (microbes that cause disease, including viruses, bacteria, fungi, protozoa, and helminthes). While that’s far less than 1% of the microbial species on the planet, they do plenty of damage.3 Searching for new microbes promises not only to increase our knowledge of life on earth, it may also be a chance to safeguard human life.

Virus hunters

In recent years, we have heard a lot about zoonoses (diseases that spillover from animals to humans), and with good reason (see my post on the issue). Of the 335 novel (new) infectious disease that were reported from 1940-2004, 60.3% came from animals, and most of those came from wildlife.2 Although the exact origins of some pathogens are hard to trace, it’s clear that many of the most lethal diseases afflicting humans (e.g. SARS, Ebola, etc.) have come from our wild or domesticated brethren. With increasing agricultural intensification and greater and greater encroachment into natural areas, there is every reason to expect the future to hold more of the same.

While that is a terrifying fact, it shouldn’t be paralyzing. So why aren’t we acting against these microbial horrors now, while we have the chance? Well there’s a rub: normally we have to wait until someone gets sick to identify a pathogen or even recognize the start of an epidemic5, especially of a new disease, and by then it’s (by definition) too late.

That’s all beginning to change. Over the past two decades, several groups of scientists have started to turn the tables on microbial pathogens, especially viruses. Instead of waiting for them to find us, these researchers are setting out to find them.

virus hunters

On the hunt

Perhaps the most prominent virus hunter is Dr. Nathan Wolfe, a visiting professor at Stanford University who has dedicated his career to seeking out pathogens around the globe.5 He works with a large team; in 2007, Wolfe founded the Global Virus Forecasting Initiative, a nonprofit research institute, and in 2008, he founded Metabiota, Inc., a for-profit sister company that provides disease surveillance, forecasting, and epidemic data.1,5 Wolfe and his collaborators work in more than 20 countries, focusing on Central Africa and South Asia, regions where large groups of people live cheek by jowl with the animals they depend on, either for bushmeat (tropical wild game, including monkeys, gorillas, and chimpanzees, among many other species) or for agriculture.4,5

The group has set up listening posts across their study regions where they survey for pathogens, regularly sampling animals and humans alike. Possibly more importantly, they educate locals about the risks of exposing themselves to the bodily fluids of animals.4 What they have found in the course of their work is both surprising and disturbing. Along with discovering several new viral species, they have uncovered much more viral spillover between animals and humans than anyone expected. Their results from Central Africa are particularly alarming: 1% of hunters sampled in Cameroon had simian foamy virus (SFV), a retrovirus that is a relative of HIV.5 Although thankfully SFV doesn’t cause illness in those infected, it’s presence shows that the barrier between humans and animals is more permeable than we thought.

These findings have made a significant impact, inspiring greater surveillance efforts and raising awareness. But despite the best efforts and frightening discoveries of Wolfe and his team, we will all remain at risk while we allow large chunks of humanity to suffer, impoverished and ignored. In Central Africa, bushmeat is a principal protein source; the region consumes at least 2 million tons per year. This may seem unthinkable or willfully self-destructive, given what we now know may be lurking in the meat, but although many residents of the region are no longer ignorant of the risks, they still have no other options. The alternative is often hunger or malnutrition for themselves and their families.4 So while the risks of illness are potentially enormous, they aren’t as immediate or as certain as an empty stomach.

Make no mistake: we may die of disease, but it’s poverty that’s killing us.


  1. Hope, B. Virus Hunter Metabiota Finds Niche in Epidemic Research. The Wall Street Journal Online. 20 May 2015. Web. 23 October 2015.
  1. Langreth, R. Finding the Next Epidemic Before It Kills. 6 November 2009. Web. 23 October 2015.
  1. Editorial Staff. 2001. Microbiology by numbers. Nature Reviews, 9: 628.
  2. Specter, M. The Doomsday Strain. The New Yorker Online. 20 December 2010. Web. 23 October 2015.
  1. Wolfe, A. Nathan Wolfe: On the Hunt for New Viruses. The Wall Street Journal Online. 12 December 2014. Web. 23 October 2015.

Image source: NIAID,

For more on Dr. Wolfe’s work, check out his TED talk.

Invasive Species and Disease: Rabbit, Rabbit

New isn’t always better. Invasive species, those entering an environment for the first time, are often unwelcome visitors; because they are free from their native predators and pathogens, their populations can reach extraordinarily high numbers, usually to the detriment of native species. Humans are often the cause of invasive species introductions, and at times, we try to cure the disastrous results, attempting control by any means, including unleashing disease.

Australia is famous for its native marsupials, from koalas to kangaroos. Historically, because its wilderness was chockablock full of creatures with pouches, it had little ecological space for placental mammals. That all changed in 1859, when a wealthy grazier, hoping to lay the foundation for the refined sport of rabbit shooting, released two dozen rabbits on his estate in southern Victoria. The rabbits bred like, well, rabbits, and within 10 years they had become a major agricultural pest across the subtropical regions of the country. By 1888, both the Australian and New Zealand governments were offering a substantial reward for a winning rabbit control strategy2.

What doesn’t kill you

As early as 1918, myxoma virus, the cause of a fatal South American rabbit disease called myxomatosis, was suggested as a means to cull the Australian rabbit population. The idea took a while to gain traction; testing under quarantine didn’t begin until 1937, and field trials weren’t underway until 1949. A year later, the disease spread way past the trial area, and caused high rabbit mortality. Since that was in fact the goal, the authorities quickly abandoned containment efforts and continued to release the virus through the 1950s, while monitoring the disease through laboratory testing. That’s when things went awry. Evolution, pushing its nose in where it wasn’t wanted, took action, and by 1957, it was clear that less virulent strains of myxoma were outcompeting the more virulent ones in the wild, reducing the rate of mortality. Not only that, but the 10% or so of infected rabbits that survived the epidemic continued to breed like, well, rabbits, and produced offspring that were more resistant to the disease2.

Despite this Darwinian turn of events, the campaign against rabbits wasn’t a total failure. The rapid reduction of the rabbit population gave the Australian landscape some much needed ecological breathing room, and cut rabbit populations down to 5-25% of their pre-1950 numbers. The program’s early success even inspired other countries to follow suit. In 1952 myxomatosis was released in France. Over the following decade, it spread across Europe (it’s actually still spreading), until the inevitable happened: the same evolutionary processes at work in Australia took hold in the Old World. But by the time the virus’ virulence declined and the rabbits’ resistance rose, the French rabbit population had been reduced by 90-98%. Unfortunately, there also appear to be some serious side effects. The devastation of rabbits in the Iberian peninsula, where they are a keystone species, has threatened the survival of the regions apex predators, the imperial eagle and the lynx3.

invasive species
It begins.

If you can’t beat them

In the 1980s, a different rabbit pathogen, rabbit haemorrhagic disease virus (RHDV), went from being unknown to having a global spread. RHDV is terrifyingly lethal; it can cause death within 24 hours. In 1988, after outbreaks among wild rabbits in Spain, RHDV was suggested for rabbit control in Australia. Things moved along more quickly this time, and by 1995, field trials were underway. Despite taking greater precautions (such as hosting the field trials on an island offshore, delightfully named Wardang Island), RHDV escaped the quarantine area and spread to the adjacent mainland. Within six months it had spread about 360km from the quarantine site. None of the carefully planned containment measures got the disease under control, so it was declared endemic, and the measures were abandoned. By 1996, RHDV was being deliberating released into wild Australian rabbit populations1.

Although it had been a party to the RHDV field trials, the New Zealand government decided against using the disease on their own rabbits. This decision did not sit well with farmers, who promptly ignored it, and within a month of the announcement, released RHDV on their own. After a month of failing to contain the disease (largely due to the fact that farmers continued to deliberately spread it), the government relented and legalized its use.

While it is too early to predict the long-term outcomes of releasing RHDV, it has clearly had a large ecological and economic impact: changing rabbit population cycles and reducing the population in affected areas by 85% (it has been particularly successful in hot, arid regions), increasing vegetation and the amount of grazable land (at least temporarily). But again, there are side effects. RHDV may have negatively impacted native wildlife, because it has left behind a legion of hungry domestic cats; the cats (another invasive species) had been feeding on rabbits, and have begun preying on native species in their stead1.

Novelty can come at a high price, as invasive species show. New ideas and approaches are inherently challenging, because we have no way to gauge what will happen, leaving only our best guess to guide us. Ecological systems are particularly delicate; they are extremely complex, and often precariously balanced. Adding anything to the mix can cause the whole thing to collapse, so the stakes of intervention (even when well-intentioned) are high. What else is new?


  1. Cooke, BD, and F Fenner. (2002). Rabbit haemorrhagic disease and the biological control of wild rabbits, Oryctolagus cuniculus, in Australia and New Zealand. Wildlife Research, 29:689-706.
  1. Fenner, F. (2000). Adventures with poxviruses of vertebrates. FEMS Microbiology Reviews, 24:123-133.
  1. Kerr, P. (2012). Myxomatosis in Australia and Europe: A model for emerging infectious diseases. Antiviral Research, 93:387-415.

Image source: Creative Commons,