New tools for pandemic prevention research: DNA sequencing from water
and leeches

Date:
June 28, 2021
Source:
Leibniz Institute for Zoo and Wildlife Research (IZW)
Summary:
In new research, water from African and Mongolian waterholes as
well as bloodmeals from Southeast Asian leeches were assessed for
the ability to retrieve mammalian viruses without the need to find
and catch the mammals. The scientists analyzed the samples using
high-throughput sequencing to identify known viruses as well as
viruses new to science.



FULL STORY ==========================================================================
In a new scientific investigation headed by the German Leibniz Institute
for Zoo and Wildlife Research (Leibniz-IZW), water from African and
Mongolian waterholes as well as bloodmeals from Southeast Asian leeches
were assessed for the ability to retrieve mammalian viruses without the
need to find and catch the mammals. The scientists analysed the samples
using high throughput sequencing to identify known viruses as well as
viruses new to science. Both approaches proved to be suitable tools
for pandemic prevention research as they allow finding and monitoring reservoirs of wildlife viruses. For example, a novel coronavirus most
likely associated with Southeast Asian deer species was identified. The
results are published in the scientific journal "Methods in Ecology
and Evolution".


========================================================================== Finding and monitoring reservoirs of wildlife viruses such as
SARS-CoV-2 -- for which the reservoir has yet to be discovered -- is challenging. Many areas which wildlife inhabit are difficult to access
and the species in question are hard to find or catch. In order to
prevent future pandemics such as COVID-19, new and effective methods
to discover and monitor viruses circulating in wildlife are urgently
needed. Environmental DNA (eDNA) and invertebrate-derived DNA (iDNA) based approaches may enhance the available toolkit to overcome these challenges,
when coupled with high throughput sequencing. The team of scientists
assessed water from African and Mongolian waterholes and bloodmeals from Southeast Asian leeches for the ability to retrieve viruses from both
sample types. The usual limitation of such samples is that they contain
only tiny amounts of low-quality DNA, particularly pathogen DNA. The
author therefore used a modern "hybridisation capture" approach to fish
out sequences similar to those from currently known vertebrate viruses and
then sequenced them using sophisticated high-throughput techniques. This approach was successful in that it allowed the identification of known
and novel viruses in both water and leech samples.

The DNA from water samples yielded several viruses common to zebras
and wild ass, which were expected as these animals frequently visit the waterholes in large numbers. In the case of the viruses found in African
water holes, the authors demonstrated in a related publication that the
viruses are still infectious, suggesting that the water itself may be
a source of viral transmission. From the Southeast Asian leeches, many
known as well as novel viruses were identified. Of particular interest
was a novel coronavirus previously unknown to science, which potentially represents an entirely new genus in the Coronaviridae family and seems
to be associated with deer species.

"For many of the deadliest viruses such as Ebola we still don't know
where they come from," says Prof Alex Greenwood, head of the Department
of Wildlife Diseases. "The current pandemic demonstrates that we still
know very little about the viral diversity in nature. New methods might
help us to identify novel viruses and their potential hosts without
the usual logistical and ethical problems associated with collecting
wildlife samples directly." Environmental DNA is proving useful in
a number of contexts including the characterisation of the diversity
of wildlife species from inaccessible regions, the study of ancient
populations and more recently in pathogen research. Environmental DNA
from water and DNA derived from blood-sucking invertebrates can be useful
in different environments. "Water is an essential resource for life and, particularly in areas of seasonal shortages, a concentration point for animals," Greenwood says.

"Terrestrial leeches are often highly abundant in areas of previous
viral emergence in Southeast Asia and their bloodmeals can be used to
identify their mammalian hosts, including the pathogens contained in their blood," adds Dr Niccolo` Alfano, a former PostDoc from the Leibniz-IZW Departments of Wildlife Diseases and Ecological Dynamics, now working
at the University of Pavia in Italy. "We identified mammalian viruses
from five different viral families in our leech samples and more than
50 % of the samples contained mammalian viruses. Some of these, such
as a porcine circovirus or a bear annellovirus could be assigned to the
bearded pig and sun bear, their mammalian hosts which were also detected
in the leech samples. Most interesting was the discovery of the novel coronavirus, as this showed that with our method we are able to discover
viral pathogens previously unknown to science circulating in wildlife,"
Alfano adds. This may help to identify potentially infectious viruses
at an early stage which may help to prevent potential future epidemics." Further work will be needed to characterise the newly discovered viruses,
such as sequencing their complete genomes and confirming their host-virus relationships. In addition, waterholes or leeches are not found in all environments. Soil, faeces and other invertebrates represent additional
sources of nucleic acids that could be used to supplement direct animal sampling and enhance our ability to discover and monitor viruses as we
go forward from the current pandemic and hopefully learn to prevent them
in the future.

========================================================================== Story Source: Materials provided by Leibniz_Institute_for_Zoo_and_Wildlife_Research_(IZW).

Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Niccolo` Alfano, Anisha Dayaram, Jan Axtner, Kyriakos Tsangaras,
Marie‐Louise Kampmann, Azlan Mohamed, Seth T. Wong,
M. Thomas P.

Gilbert, Andreas Wilting, Alex D. Greenwood. Non‐invasive
surveys of mammalian viruses using environmental DNA. Methods in
Ecology and Evolution, 2021; DOI: 10.1111/2041-210X.13661 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2021/06/210628124949.htm

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