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The world has been uprooted by the COVID-19 pandemic, but the specific origin of the virus remains unknown. Museum collections can help to solve these kinds of natural world mysteries.
Scientists are creating a knowledge base using data from bat specimens held in natural history collections.
Data on three bat families will be released on an open platform and made available to researchers all over the world. It could be used to discover the origins of the COVID-19 virus, and even help mitigate the risk of future pandemics.
Approximately 75% of all emerging infectious diseases are zoonotic, meaning they are transmitted from animals to humans. Examples of zoonotic diseases include rabies caught from dogs, Ebola virus disease transmitted from bats, HIV from apes, and now COVID-19.
Although we are not certain which species passed on the organism that causes COVID-19 in humans, genome sequences of the virus from the beginning of the pandemic are 95% identical to that of a bat coronavirus. It was found in populations of a common Southeast Asian horseshoe bat species called the intermediate horseshoe bat.
Bats, which form the group Chiroptera, account for around 20% of all mammal species, and are an essential part of the ecosystems we live in and rely on. They help control populations of crop-damaging insects, pollinate over 500 species of plants and their seed-filled droppings help with seed dispersal and reforestation.
Bat populations are also known to be natural reservoirs of viruses, meaning they are populations of animals in which a virus naturally lives and reproduces.
Our troubled relationship with nature brings increasing numbers of people into direct contact with animals like bats that carry diseases. Human activity such as deforestation and intensive farming have brought us close to wild animals and created the perfect conditions for diseases to jump from wildlife to people in what is known as a spillover event.
Unless we study and protect nature, we will experience more spillover events and more frequent pandemics in the future.
Being prepared with data can help us plan for future outbreaks. The specimens held in natural history collections represents a huge and often untapped resource that can contribute to this knowledge, from figuring out where and when specific species lived, to identifying viruses in historic specimens.
There are millions of specimens in the collections of natural history museums around the world that hold vast amounts of information which is useful for research. But not every specimen has its data neatly and consistently recorded, nor are these data always openly available. This is where digitisation comes in.
Digitising natural history collections involves creating a digital record of a specimen, which can consist of all sorts of information such as images, when and where it was collected, its taxonomy, and who it was collected by.
The Museum's Digital Collections Programme (DCP) began in 2014 to digitise the 80 million items in the collection and release the data on open platforms such as the Data Portal where anyone can access it.
How is digitisation and the data held in natural history collections useful for studying viruses?
Firstly, it is about knowing what we have in collections and making this knowledge available to the scientific community.
The Museum already has more than 30,000 records for bat specimens in online databases, but there are about 6,000 other specimens of interest in the collection that are yet to be digitised. These are made up of skins, skeletons and fluid preserved specimens.
Roberto Portela Miguez, Senior Curator in Charge of Mammals at the Museum, says, 'We are not fully exploring the potential of this collection simply because it is not visible.
'This is what makes digitising the collections and making the data freely available so important, as more access to data means more research can be done globally.'
Collections can contain large samples of species from the same places over a period of hundreds of years. Put simply, they help us track where bats live.
Cristiane Bastos Silveira is a researcher at the Centre for Ecology, Evolution and Environmental Changes, University of Lisbon.
'Every specimen collected is a point on a map,' says Cristiane. 'Imagine that a species is suddenly found in a specific city. If you have these data from a museum, you can know if that species has just arrived, or if it has always been there but that no one had noticed.
'Museum collections are a library of time and space that can answer these questions'.
Other information that accompanies specimens can increase our understanding of the ecosystem they live in.
For example, if a bat was collected on a specific expedition, we can learn more about the ecosystem it lived in by looking at the other species collected at the same time or perhaps reading the descriptions of the field in collectors' notebooks.
As many spillover events typically occur within a defined timeframe and location, this extra information is crucial for understanding the world at the time the spillover event occurred. This can help researchers link these events to specific environmental situations. So, we can predict when they might happen again.
Finally, in some cases specimens may be able to be tested for viruses themselves.
Just recently, coronaviruses that are closely related to that which causes COVID-19 were identified in two Rhinolophus shameli bats sampled in Cambodia in 2010, over ten years after they arrived in the collections of the National Museum of Natural History in Paris.
Likewise, in the early 1990s an unknown lethal disease emerged in the southwestern United States, and researchers used specimens from the Museum of Southwestern Biology to identify deer mice as the species it emerged from. They were even able to show that the virus had been circulating in local rodent populations for years and that its emergence in humans was linked to El Niño climate cycles.
The collections might be finite, but the potential uses of them are infinite. As technology and scientific techniques evolve, so too do the uses of our collections.
'Not long ago we thought we couldn't get any DNA from museum specimens, but recent advances in technology have now made this possible,' says Roberto. 'We shouldn't stop ourselves dreaming about what could be learnt from collections.'
Alongside eight institutions, the DCP is taking part in a project that aims to gather the data held in natural history collections on horseshoe bats (Rhinolophidae) and their closely related families Old World leaf-nosed bats (Hipposideridae) and trident bats (Rhinonycteridae).
These families were chosen because a coronavirus most like the one that has caused the current pandemic was found in a species of bat belonging to the horseshoe bat family.
This data will be released on an open platform as a COVID-19 Chiroptera knowledge base, making it available to researchers all over the world who are studying the origins of the virus.
Cristiane is leading on the project with Gabor Csorba, a Senior Researcher and bat expert at the Hungarian Natural History Museum.
'We were caught unprepared by the COVID lockdown,' says Gabor. 'Very suddenly, all of the laboratories and the collections were closed, and in many cases the information we needed lay in personal notes, unpublished datasets or in isolated collections.'
Early in the pandemic, it was clear that there was a relationship between bats and the disease.
'This put more pressure on needing the Chiroptera data to be available,' explains Cristiane.
The pandemic highlighted the lack of access to the bat data that was needed and, more broadly, illustrated the importance of digitising natural history collections.
'We have to seize this opportunity to make databases which are openly accessible and useable for the whole scientific community,' says Gabor. 'This situation that we find ourselves in is a great stimulus to produce this huge database.'
While this project is working on creating new public records for bat specimens that do not currently have one, there are thousands of specimen records for bats that have already been digitised and are available in databases such as the Global Biodiversity Information Facility (GBIF) and iDigBio. These data also have huge potential for research into the pandemic, and so the National Science Foundation (NSF) have funded a grant to make these data as useful as possible.
This is being lead by Florida State University, with Austin Mast as Principal Investigator and Deborah Paul as Co-Principal Investigator.
'Listening to bat researchers, disease ecologists and microbiologists in the CETAF COVID-19 taskforce and ViralMuse taskforce, the idea arose that currently published museum records, if further enhanced, could potentially add valuable information needed to help scientists with this pathogen spillover event,' explains Deborah.
Enhancing the data to make them more useful involves trying to refine the records, such as by figuring out where specimens were collected (known as geocoding or georeferencing), standardising collection dates, updating taxonomic names and adding identifiers to who collected and identified the specimens.
Sharing these enhanced data with the International Union for Conservation of Nature (IUCN) has the potential to help scientists revise what they know about where bats lived in the past and where they live now. This information can support conservation, pandemic mitigation, and policy development efforts.
Cleaning and making the data more useful should also help projects such as the SYNTHESYS+ Virtual Access project to work more efficiently.
'Our work to update the taxon names applied, our georeferencing work, our efforts to enhance the people data,' says Deborah. 'All of this information can be used in the SYNTHESYS project to potentially speed up their work, making it possible to get this vital data to researchers faster. '
Regardless of which species passed the virus to humans, human behaviour is really the culprit behind the COVID-19 crisis.
Bats have often been portrayed as the villain in this pandemic, and fear of bats has sometimes led to them being killed and persecuted. Yet indiscriminately eradicating bats will only lead to more negative consequences.
Cristiane talks about an ecosystem as if it is a tower of playing cards. She says, 'You have to take care, because if you remove one card, everything collapses.'
If we remove bats then the ecosystem is disrupted, potentially leading to ecosystem collapse or exacerbating the very factors that increase the likelihood of pandemics in the first place.
The pandemic has served as a reminder that the health of humanity relies on a healthy environment. Protecting nature is the only way forward, and data freed from museum collections is a vital tool for informing planning and decision-making into how we protect it.
'You make better decisions if you have better knowledge,' says Cristiane. 'This is the key, and you can make better decisions when they are based on data.'
Re-watch our discussion with Prof Kate Jones, world-leading professor of ecology and biodiversity at University College London (UCL), for an exploration of why viral outbreaks happen and why we need to re-evaluate our relationship with nature.