Nearly two years after the first case of COVID 19 we are still dealing with massive human health impacts and changes in our daily lives, but how can digitising bats help prevent future pandemics?
Like many of us, when the world went into lockdown, scientists involved in the Consortium of European Taxonomic Facilities (CETAF) wanted to know how they could help. The CETAF COVID-19 taskforce was set up in April 2020 to anticipate and prevent the occurrence and propagation of future health crises.
The Digital Collections programme have working alongside eight other European institutions on a project initiated by the CETAF COVID19 taskforce and funded by SYNTHESYS+. This project will gather and release data on three families of bats; the Horseshoe bats (family Rhinolophidae) and their close relatives the Old World Leaf-nosed bats (family Hipposideridae) and Trident bats (family Rhinonycteridae). The data will be released onto the Museum’s Data Portal and contribute to a COVID-19 Knowledge base with the other European institutions involved.
Although scientists 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 (Rhinolophus affinis).
The ability to fly requires bats to be incredibly metabolically active. Animals that have a high metabolic rate often live short lives because of the cellular damage that this can cause, however bats can live for up to 40 years. Bats have enhanced cellular mechanisms to repair damaged cells – because of this, bats have incredible immune systems. It is thought that coronaviruses have co-evolved with bats for thousands of years.
Viruses developing within an organism with an enhanced immune system become a problem when they jump into different species (known as a spillover event). Diseases that are transmitted from animals to humans are known as zoonotic. It is therefore pressing to study bats, and especially their distribution and their relationship to viruses.
The Museum’s bat data will help global researchers studying the origins of the virus. Data from Natural History Museums is an important and often untapped resource. Specimens in Museum collections have been collected over hundreds of years. This means that the collections hold vast quantities of data from across time and space, which can be used in scientific research from figuring out where and when specific species lived, to identifying viruses in historic specimens and using modelling to predict future pandemics.
There are approx. 8,200 specimens that we are gathering data from for this project. However, this is over three parts of the collections; skulls and skeletons, skins and specimens stored in spirits and we have around 11,300 items. When researching bats, the skull and teeth are very important and have defining characteristics for each species. In many cases, the skull will be separated from the rest of the animal, or the skin and skeleton will be separated. In some cases this means we may have two or three items that relate to the same original specimen.
For this project we gathered our existing specimen records to create a database and we revisited our collections to enhance those records with all the information we could find. Each item was checked for where and when the specimens were collected, who collected them, their age and sex, as well as any ecological and behavioural information about these bat species.
We have now completed this audit with some time to spare on the project, so we are able to do some enhanced digitisation photographing the type specimens. Type specimens are example specimens for which a species is names. We have 190 type specimens. Some have both skull and spirit, so this amounts to around 275 items in total. We will be taking photos of our skull types, as well as close-up photos of the nose-leaf of the type specimens preserved in spirit. These photos will be useful as reference for specimen identification and other studies.
Last but not least, we are going to examine the notebooks that the collectors kept to find any other information about the ecology and behaviour of the bats that didn’t fit on the specimen labels. When we have collected all information we can get, we are going to share our data on the Museum’s Data Portal and our data will be shared with CETAF project initiators so that it will join data from the other eight European institutions to form the Covid-19 Chiroptera Knowledge Base.
Battling future Pandemics
Once the data from this collection is online researchers, at the University of Nottingham are hoping to use this to locate specific specimens for ongoing virus discovery projects. As the Museum’s collections date back over 100 years, this provides a unique record of recent evolution of bat virus species. Next generation sequencing can be applied to small samples of specimens that have been kept in spirit to extract viral genome fragments. These can then be analysed to look for the presence of novel viruses – and potential ancestral viruses to things like Ebola and Coronaviruses – and assess how human activity has potentially impacted on disease emergence. It can also provide insights into the range of viruses that have the potential to cause future outbreaks in humans, their livestock and companion animals.
Commenting on this work, Prof Jonathan Ball, from the Wolfson Centre for Emerging Virus Infections at Nottingham University said, “This expansive and well-documented collection of preserved samples can give us unique insights into the array of viruses that were present in bat populations over the past hundred years or so. It represents an important archive to study of the evolution of bat viruses to try to understand factors that might influence disease emergence.”