challenge to viral discovery and identification, because only portions of a novel virus
might yet have been identified. Furthermore, viral sequences detected in
metagenomic sequencing studies often have no related reference entry in established
viral databases and are referred to as viral dark matter (Waldron 2015;
Krishnamurthy and Wang 2017). It should be noted that the viral sequence database
in GenBank (Benson et al. 2000) for example is biased toward mammalian, plant,
and bacteria that either cause disease in humans or impact animal farms and crop
production. Sequences for viruses that use archaea or protists as hosts comprise only
a fraction of the database (currently less than 10%) and more research has to be
accomplished to reveal the true extent of viral diversity (Krishnamurthy and Wang
2017; Greninger 2018). In addition to sequencing and aligning viral genomes with
known database entries, other methods are available to identify and characterize
virions, exploring their diversity and also revealing modes of entry and replication;
the gold standard among them is viral culturing that allows the researcher to
determine if an unknown sequence is indeed of viral origin and to observe potential
cytopathic effects of viral infection. Classical viral isolation relies upon membrane
filtration using 0.2 μm filters which allow the separation of viral agents from
prokaryotes and eukaryotic cells, followed by RNAse and DNAse treatment that
has no effect on virions protected by protein coats but will destroy any genetic
material from lysed cells or viroids. In addition, viral tagging with fluorescent dyes
can be useful to investigate viruses if they are permeable to the dye being used. For
additional methods used by virologists to target and detect viruses please refer to
(Boonham et al. 2014; Krishnamurthy and Wang 2017) and other references mentioned within this chapter. For the future, we will rely on improvements of viral
culture methods to distinguish the so-called genetic dark matter from sequences of
known viral origin and perhaps develop improved molecular methods that allow
more sensitive and reliable cluster and differentiation analyses leading to the identification of as yet unknown viral lineages.
So, what do we know about the viral diversity in the environment? Studying the
virome of different environments has continued to attract substantial U.S. and
European government funding in recent years, as a result of major threats to
humanity, to mention only the Ebola epidemic in West Africa in 2014–2016
(Matz et al. 2019) and the Coronavirus epidemic that started in Wuhan, China, in
2019 (Ralph et al. 2020). Research is needed because of difficulties in identifying the
natural reservoirs of the pathogens and strategies to identify and successfully treat
the patient zero of an outbreak. Furthermore, funds to develop new vaccines against
these beforementioned emerging pathogens and others, such as viruses that cause
livestock abortion storms (Dun 2019), and encephalitis in humans and animals
(Centers for Disease Control and Prevention 2020a, b) are desperately needed.
Recently, the Global Virome Project was launched with the goal of identifying yet
unknown viral agents and their natural reservoir over a 10-year schedule, aiming to
reduce global vulnerability to known and yet unknown potentially emerging viral
zoonotic agents and to provide timely data for epidemiologists and other healthcare
providers to prevent future pandemics. First results revealed hundreds of new viruses
and their animal reservoirs (http://www.globalviromeproject.org/overview, see also
28 Viruses, Underestimated Drivers of Ecology and Evolution of Life
621
might yet have been identified. Furthermore, viral sequences detected in
metagenomic sequencing studies often have no related reference entry in established
viral databases and are referred to as viral dark matter (Waldron 2015;
Krishnamurthy and Wang 2017). It should be noted that the viral sequence database
in GenBank (Benson et al. 2000) for example is biased toward mammalian, plant,
and bacteria that either cause disease in humans or impact animal farms and crop
production. Sequences for viruses that use archaea or protists as hosts comprise only
a fraction of the database (currently less than 10%) and more research has to be
accomplished to reveal the true extent of viral diversity (Krishnamurthy and Wang
2017; Greninger 2018). In addition to sequencing and aligning viral genomes with
known database entries, other methods are available to identify and characterize
virions, exploring their diversity and also revealing modes of entry and replication;
the gold standard among them is viral culturing that allows the researcher to
determine if an unknown sequence is indeed of viral origin and to observe potential
cytopathic effects of viral infection. Classical viral isolation relies upon membrane
filtration using 0.2 μm filters which allow the separation of viral agents from
prokaryotes and eukaryotic cells, followed by RNAse and DNAse treatment that
has no effect on virions protected by protein coats but will destroy any genetic
material from lysed cells or viroids. In addition, viral tagging with fluorescent dyes
can be useful to investigate viruses if they are permeable to the dye being used. For
additional methods used by virologists to target and detect viruses please refer to
(Boonham et al. 2014; Krishnamurthy and Wang 2017) and other references mentioned within this chapter. For the future, we will rely on improvements of viral
culture methods to distinguish the so-called genetic dark matter from sequences of
known viral origin and perhaps develop improved molecular methods that allow
more sensitive and reliable cluster and differentiation analyses leading to the identification of as yet unknown viral lineages.
So, what do we know about the viral diversity in the environment? Studying the
virome of different environments has continued to attract substantial U.S. and
European government funding in recent years, as a result of major threats to
humanity, to mention only the Ebola epidemic in West Africa in 2014–2016
(Matz et al. 2019) and the Coronavirus epidemic that started in Wuhan, China, in
2019 (Ralph et al. 2020). Research is needed because of difficulties in identifying the
natural reservoirs of the pathogens and strategies to identify and successfully treat
the patient zero of an outbreak. Furthermore, funds to develop new vaccines against
these beforementioned emerging pathogens and others, such as viruses that cause
livestock abortion storms (Dun 2019), and encephalitis in humans and animals
(Centers for Disease Control and Prevention 2020a, b) are desperately needed.
Recently, the Global Virome Project was launched with the goal of identifying yet
unknown viral agents and their natural reservoir over a 10-year schedule, aiming to
reduce global vulnerability to known and yet unknown potentially emerging viral
zoonotic agents and to provide timely data for epidemiologists and other healthcare
providers to prevent future pandemics. First results revealed hundreds of new viruses
and their animal reservoirs (http://www.globalviromeproject.org/overview, see also
28 Viruses, Underestimated Drivers of Ecology and Evolution of Life
621