🦠 VIROME ANALYSIS | DNA EXTRACTION

Viruses are suggested to be the most abundant and diverse biological entities on our planet, with an estimated 10^31 particles on Earth.
While it's been demonstrated that the human body hosts vast microbial communities (termed the microbiome), the fact that the human body also hosts vast numbers of different viruses, is less well known. The collective community of viruses in a given environment is called the 'virome'. mammalian viral families in rodents
Virome refers to the assemblage of viruses[ that is often investigated and described by metagenomic sequencing of viral nucleic acids that are found associated with a particular ecosystem or organism . The word is frequently used to describe environmental viral shotgun metagenomes. Viruses, including bacteriophages, are found in all environments, and studies of the virome have provided insights into nutrient cycling,development of immunity,[6] and a major source of genes through lysogenic conversion.
Some scientists are interested in understanding viral communities present in wildlife, as well as the prevalence, genetic diversity, and geographical distribution of these viruses, as it could be valuable for prevention and control of wildlife-origin Emerging Infectious Diseases. Comprehensively studying the faecal viromes of laboratory rats under different dietary conditions could also be useful in understanding how the virome affects health.
In this video, we go over the preparation of viruses (bacteriophages) from enteric bacteria, followed by DNA extraction and next generation sequencing for studying metagenomes, viromes, viruses, gut virome, viral infections, etc.
Typical enteric viruses found in rodents include hantaviruses, mammarenaviruses and coronaviruses.

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A 2018 paper in the journal Microbiome, where Wu et al. look at viral diversity in rodents to assist efforts to predict and reduce the risk of future emergence of zoonotic viral diseases: microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0554-9

[@drshinwarishinwari1253]

That would be very useful

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The goal in DNA extraction is to break open cells: this involves breaking open not only the cell membrane but also the nuclear membrane (nuclear envelop in the case of viruses). This is achieved with reagents such as detergents; which are added to a buffer to help make holes in the cell membrane (permeabilises the membrane). This permeabilisation allows the contents of the cell to spill out. The next steps are to remove the protein fractions of the cell. The process includes heating the lysate so that the proteins denature and become single threads of amino acid. In this process, chloroform is then added. THe purpose of the Chloroform is to emulsify the mixture so that we can separate it into an organic and aqueous layer. The proteins move into the organic layer, while the nucleic acids move into the aqueous layer on top. In between the aqueous and organic layer is a very thin interface layer which contains lipids and other insoluble matter.
The aqueous layer is removed to a separate tube and ethanol is added to precipitate the DNA out of solution and concentrate it. The purpose of the ethanol (or isopropanol) is to reduce the solubility of the nucleic acid, allowing it to pellet out of solution when centrifuged.
Several wash steps (with ethanol or isopropanol) is further performed to remove salts that are soluble in alcohol.
Finally, the DNA is resolubilised in a small volume of MiliQ water or salt buffer such as Tris EDTA, in order to have concentrated nucleic acids for use in other applications.

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