“In the jungle, the mighty jungle, the virus hunters will not sleep tonight.” They may not be the original lyrics from the song, but I could not help but sing them to myself as we set up our small mammal and bat traps in the Kuamas Forest Reserve – an area of jungle near Kampung Baba in the Telupid District, in the middle of Sabah.

When you are working to find zoonotic viruses, sleepless nights in the jungle are necessary. The field team always set the traps before dusk to enable us to spend the night catching and sampling the animals we are studying for the Deep Forest Project – part of the USAID funded PREDICT program.

Deep Forest was started in 2012 to explore the impact of increasing land-use change on patterns of animal biodiversity, the viruses they carry, and patterns of human occupancy, abundance and behaviour that may influence contact rates with wildlife in these dynamic landscapes. Understanding all these factors is key to preventing zoonotic disease spillover.

Preventing zoonotic spillover events - setting up bat trap in the forest

A bat trap is erected in the Kuamas Forest Reserve before the long night begins.

The aim of the Deep Forest Project

The aim of the Deep Forest Project is to gain a better understanding of the potential hotspots for zoonotic diseases and create an early warning system to prevent zoonotic virus transmission. We are working at preventing zoonotic spillover events such as the SARS-CoV-1 outbreak in 2003, that spread from China to Singapore, to Canada and beyond, killed more than 700 people and cost the global economy USD$ 30-50 billion.

You may wonder how this happened, where did the virus come from? Well, it started in a wildlife market in Guangzhou, China, that was selling a variety of wildlife and domestic animals including civets and bats. Initially it was believed that civets were the reservoir for this new emerging virus, but we now know that a species of horseshoe bat were the natural reservoir. The mixing of different wildlife and domestic animals in a wet market creates the ideal circumstances for a virus spillover event as animals that would never normally meet in the wild come into close contact with each other. Animals are often in poor health, being kept in unhygienic and stressful conditions with cages stacked on top of each other. In 2003 in Guangzhou this led to a horseshoe bat passing the SARS-CoV-1 virus onto a civet that amplified the virus and passed it on to a human allowing this new emerging virus to start its journey around the world.

Loss of habitat brings wildlife into closer contact with human populations, increasing the chances of zoonotic spillover. Placing them in unhygienic conditions in wildlife markets brings them closer to other species which they would not normally encounter, increasing the risk of disease transmission between animals and then into the human population. If we can identify zoonotic viruses carried by the wildlife in Sabah that have the potential to spillover and become a public health threat, we can use this risk to strengthen the case for conserving their environment, and for increased regulation of the legal wildlife trade as well as lobby for more action to help end the illegal wildlife trade.

"Loss of habitat brings these animals into closer contact with human populations, increasing the chances for zoonotic disease spillover."

Catching animals in the Deep Forest

Nine sampling sites with different human disturbance grades were selected, at each site we set up an area to catch bats with 8 mist nets and 2 harp traps and an area to trap rodents and small mammals with 100 small mammal traps.

The sampling team stayed in the jungle from dusk to dawn to capture and collect biological samples from the bats. After the mammal traps were baited for the night, the team would return to check them in the morning and sample anything we trapped before releasing them back into the forest.

“Hey Jimmy, we’ve got one”, one of our rangers shouted from afar. We were lucky, and had captured a Malayan civet – a magnificent creature with black spots on its body, black and grey stripe on its tail and stunning black lines on its neck (which I think looks like a fancy necklace).

We would carefully transfer the civet into a cloth bag to minimize its stress – who wouldn’t be afraid when surrounded by a bunch of people wearing weird layers of blue plastic on their hands, a white cloth covering their nose and mouth and shiny pieces of glass on their eyes? – before transferring it to our temporary lab in the forest.

A bat is caught in the Kuamas Forest Reserve during the Deep Forest Project. The animals were sampled for potential viruses before being released back into the forest.

A bat is caught in the Kuamas Forest Reserve during the Deep Forest Project. The animals were sampled for potential viruses before being released back into the forest.

Deep Forest Project sampling

After the animals arrived at the temporary lab, the field veterinarian would start to anaesthetize them. As soon as the animals started to fall asleep, the sample collection process was started.

Samples including swabs samples, a small amount of blood and ectoparasite are collected. During the sampling process the animal’s welfare is monitored by a veterinarian or trained field biologist. Once the sampling process is complete, the animal is returned to where they were caught to be released.

The samples are then transported back to the Wildlife Health, Genetic and Forensic Laboratory – the first Biosafety Level 2 biocontainment Laboratory dedicated to wildlife work in South East Asia – for zoonotic virus surveillance. The testing results are vital to help us to understand the zoonotic viruses carried by the wildlife in Sabah and the risk of transmission.

Some of you reading this blog may wonder why we are not wearing the white Tyvek protective suits to carry out this work. Well working in the forest wearing a white Tyvek suit poses a range of problems, they stand out at night and make a lot of noise which can spook bats, they restrict our movement which can make it hard to run away from a charging elephant (something I have had to do on more than one occasion) and they are easy to rip making them impractical in certain environments. So, while in an outbreak situation or dealing with certain wildlife species we would always wear a Tyvek suits there are times when our Risk Assessments determine that using dedicated clothing is the safer option. These dedicated clothes are water resistant just like the Tyvek suit so prevent any body fluids from the animals we work with contacting our skin, but they do not restrict our movement or make us stand out like aliens in the forest. At the end of each sampling session the dedicated clothing is removed in the same way as a Tyvek suit, but rather than being disposed of they are disinfected and cleaned before being used again. This allows us to work safely and reduces the amount of waste from a sampling trip which is better for the environment.