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The Ebola epidemic was caused in part because of the destruction of bat habitats, which meant bats lived closer to humans.CELLOU BINANI/AFP / Getty Images

Science journalist and author Sonia Shah has spent her career studying history's most disruptive diseases and contagions, trying to figure out how some of the most deadly turned into full-blown pandemics that have wiped out hundreds of thousands of lives. Her previous book, The Fever, was touted by The New York Times as a "tour-de-force history of malaria." Her new book, Pandemic: Tracking Contagions, from Cholera to Ebola and Beyond, provides engrossing insight into the hot spots where viruses thrive, how they mutate, and ultimately travel around the globe, potentially infecting population centres around the world. In an interview with The Globe and Mail, Shah discusses what new pathogens stalk humankind today, from Ebola, avian influenza, and now the mosquito-carried Zika virus, which emerged in Brazil and is associated with alarming defects in the fetuses of pregnant women. It has since spread to more than 30 countries, mostly in the Americas. The origins of epidemics is both fascinating and grim, but Shah says there are steps we can take to protect future generations from the next epidemic.

In a recent survey of epidemiologists, 90 per cent of them said a pandemic would leave one billion people sick; kill 165 million; and cost the world economy $3-trillion (U.S.) over the next two generations. Which pathogen will do this?

That's the million-dollar question and we don't know the answer. Most virologists expect it will be a new kind of avian influenza. If a new kind of avian influenza were to emerge and spread as effectively as existing influenza viruses do already, we will see a huge increase in sickness, hospitalizations and death. More novel forms of influenzas are emerging. And the frequency with which they're emerging is due to the changed economy and ecology of South China and large parts of Asia – areas where most of our wild waterfowl live. With the intense invasion of agriculture going on there, combined with the destruction of wildlife habitats – these have become the ultimate reservoirs for these viruses to mutate and change in new ways. Another candidate for the next pandemic is highly drug-resistant bacterial pathogens, which resist all antibiotics. In this scenario, where there is nothing medicine can do, global health – and the traditional practice of medicine – would be altered in a huge way.

You started researching this book six years ago, just after the 2010 publication of The Fever. How did you become interested in the history of cholera as the starting point to talk about the threat of a new pandemic?

Cholera started as a harmless microbe and turned into a world-changing pandemic. It still exists today and its latest beachhead is Haiti – 400 miles off Florida. Cholera has caused seven pandemics. We think of it as a poor person's disease, which it is, but it didn't start out that way. When it first emerged in the 19th century it hit some of the most prosperous, technically advanced cities in the world such as New York, Paris and London. In 2009, we had the H1N1 pandemic [also known as swine flu that began circulating in pigs]. My sons were also infected with MRSA virus [a staph infection that often begins as a painful skin boil]. Cholera had just broken out in Haiti, where it hadn't been seen in 100 years. And it struck me. What is going on with all these new pathogens that can cause so much death and destruction? My previous book was on malaria, the oldest infectious pathogen known to human kind. The malarian pathogens started out, evolutionarily speaking, as something in a plant and then turned into this thing that has had such a huge impact on human history. With Ebola, and possibly the Zika virus, we can see that process happening right now in front of us. I wanted to study how we can try to prevent pandemics.

How big of a threat is the Zika virus?

It emerged in the tropics – specifically Brazil – and there's been huge urban expansion into the Americas. It's allowed highly urbanized mosquitoes to dramatically expand their territory, which has been happening over the past few decades. We know those mosquitoes carry diseases, they've done so with dengue fever and now the outbreak of Zika, a virus associated with microcephaly [infections in mothers linked to births of babies born with abnormally small heads] and Guillain-Barre, a rare syndrome where the immune system attacks nerves. If those two complications are found to be caused by Zika then this situation is very serious. If they're not, if it's some other thing, an anomaly cause by some third factor we don't know of yet, then Zika is a very mild disease we don't have to worry about. But it is still a pandemic. If there is a link to microcephaly it's going to lead to birth rates declining because it may cause some women to put off pregnancy if they're afraid they won't be able to carry a healthy pregnancy to term. That affects the population's health. Whether death rates go up or birth rates fall, either way you can see a shrinkage in the population.

Can you explain what you mean when you say new diseases aren't just potentially deadly but also socially disruptive?

Through history, there have been xenophobic reactions at the feet of pathogens. Peoples' fears of outsiders. Fears of invasion of germs. It's irrational, but we usually blame the wrong people. Sometimes we go for the marginalized in society. But it's not always the poorest of the poor who are blamed, but also those who seem mysteriously powerful, including clinicians and doctors. When a new pathogen emerges there are always these questions: Where did it come from? Who is responsible? Let's get to the bottom of this and find the cause so we can cast blame. The reaction is due to feeling essentially powerless in the face of these new pathogens. We saw this with the Ebola epidemic in South Africa where clinicians and aid workers were blamed for bringing cholera, some of them were even violently assaulted and murdered.

For decades, private and economic interests have trumped public health interests. Explain?

One example in the United States is antibiotic-resistant bacteria. We've known since the 1940s if we use antibiotics for anything other than medically necessary purposes we can trigger the evolution of resistant bugs and yet to this day, 70 years later, 80 per cent of antibiotics used in the U.S. are for commercial purposes. They're not medically necessary at all. Farmers use antibiotics, for instance, to make livestock grow faster. We have increasingly difficult problems with antibiotic-resistant pathogens in livestock as a result. We've taken only the tiniest of baby steps to rectify this. You can also see our global health agencies, like the World Health Organization, which have been steadily defunded in recent decades to the point where they now get most of their budget from non-government sources, whose donations are appreciated, but whose priorities can be earmarked by the people or group giving the money. So, in effect, the agencies aren't in charge. In other words, public health priorities in this instance might not be coming first.

Can you give a current example of how the invasion of natural habitats has played a huge role in contagions and pandemics?

We're invading wild habitats on a massive scale, as farms, mines, cities grow. We're losing a lot of biodiverse species and of those that remain, the microbes in animals we are in far closer contact with them. Today over 60 per cent of our emerging pathogens originate in the bodies of animals and 70 per cent from wild animals. Prime example is the Ebola virus.

We know that Lyme disease is caused by bacteria in rodents from Northeastern forests in the United States, as well as elsewhere. When the forests are intact, the tick population (which transports Lyme bacteria) is relatively low because there is diversity of animals living in those forests, such as opossums, which help control the tick population (opossums destroy 6,000 a week). When we invade those forests, the opossums and chipmunks et cetera disappear because they can't be sustained in the patchwork we leave behind. So we lose them, and we gain more ticks. That's how Lyme disease spread steadily in North America in the seventies. In the States, we now have 300,000 diagnoses of Lyme every year. We also have a whole new range of tick-born pathogens that are starting to infect people. Ebola, which comes from bats, is another example. We've steadily destroyed bat habitats, which means bats now roost in gardens and farms and in places near human habitation because the wild habitat is gone. The microbes in their bodies start to come into our bodies through this kind of novel, intimate contact.

How does the burgeoning domestication of livestock (and demand for meat) spread contagions?

Right now there are more animals domesticated than in the past 10,000 years of domestication combined through 1960. This is crucial to the pandemic equation. We also keep a lot of them in factory farms where millions of animals are crowded very closely together – like humans living in slums, where there is very poor sanitation. When pathogens are introduced into environments like this, where animals are exposed to each others' waste, they replicate wildly and mutate. They evolve into more virulent streams, and those streams don't die out because those huge crowds of captive individuals are susceptible. We saw this with avian influenza where wild waterfowl migrate, and drop viruses into these giant factory farms. Factory farms. which are so crowded, offer all kinds of novel amplication opportunities for pathogens: One example is avian influenza. H5N1 broke out in 1997 and is still making the rounds to this day. Although H5N1 does not usually infect humans, nearly 650 cases of human cases of H5N1 have been reported from 15 countries since 2003.

What can we do to decelerate the spread of contagions and pandemics?

There is a lot. Let's prepare hospitals better by stockpiling vaccines. Let's improve infection control in hospitals. Let's spend more on potentially pinpointing new pathogens by doing active surveillance in places we know are likely to be disease hot spots. In those hot spots, let's actively collect samples and look at the microbes in them, and study how they're changing. People are starting to do that, but we need to invest more in potentially pinpointing a pathogen with pandemic potential before it starts to spread. It's like stamping out an ember before it lights into a fire. We have to restore wild habitats. Protect people in slums and animals in factory farms. We have to keep up with vaccinations. Don't go to school or work when you're sick. Most important, remain informed. Because so much of a pathogen becoming a pandemic is really shaped by human behaviour. It's really up to us.

This interview has been edited and condensed.