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General description of viruses

Viruses has been found to be highly abundant in Arctic ecosystem, and they play an important role in the control of microbial communities, in these ecosystems, with low nutrients and under extreme environmental conditions (Rastojo and Alcami 2018). Viruses are infectious agents that replicate exclusively within a living cell. Viruses can infect all types of organisms, from animals and plants to bacteria and archaea. They consist of a viral particle that protects the viral genome from degradation in the extracellular environment and allows the infection of another cell. The viral particle often referred to as virion is composed of genetic material, a protein coat and, in some cases, a lipid envelope. Viruses are highly diverse genetically and structurally, and many different virus families have been described to date (www.viralzone.expasy.org). Viral genomes are formed by either single strand (ss) or double strand (ds) DNA or RNA. Single stranded genomes are divided into positive or negative strand types, depending on whether or not they are complementary to the viral messenger RNA. The mechanism of replication is diverse and depends on the nature of the viral genome, requiring RNA or DNA polymerases of viral or host origin, and the mechanism of messenger RNA production (Baltimore classification of viruses). Viral particles are also diverse, with a size ranging from 20 to 300 nm in diameter, a helical or icosahedral morphology, and an additional lipid envelope in some cases.

Viruses cannot replicate on their own and need to infect a host cell for replication. Upon virus attachment and entry, viruses take full control of the host cell and use the host cells machinery and cellular compartments to produce copies of the viral genome and synthesize new virus particles. We divide the virus infection in two different cycles. The lytic cycle leads to the death of the infected cell and the release of high numbers of infectious virus particles into the environment that are ready to infect neighbouring cells. Alternatively, viruses may introduce their viral genome into the host cell and remain silent within the infected cell in a latent state, where the viral genome is integrated into the host genome or maintained as an episome (a genetic element inside a bacterial cell). This type of infection is known as lysogenic infection for bacterial viruses (bacteriophages). Viruses that establish lysogeny or latency may later become activated to induce a lytic replication cycle that will destroy the infected cell and produce new virus particles that will infect new cells, ensuring the transmission and persistence of the virus in the host population.

In the past, only viruses known to be pathogenic were isolated and studied. More recently, with the advancement of methodology, it has been realized that viruses constitute the most abundant and diverse biological entities on Earth (Suttle 2005; Rohwer 2009), and more focus has been directed towards them. Viral abundances in aquatic ecosystems are usually quantified using epifluorescent microscopy counting stained virus-like particles (VLPs), but virus particles have also been visualized by electron microscopy (Kepner 1998; Wilson 2000) and flow cytometry analyses. Environmental samples contain 1000-10000 million VLPs per litre of water in the oceans, 100-1000 VLP in aquatic habitats and 1000 million VLPs per cubic cm of soil (Sawstrom 2007, Sawstrom 2008, Suttle 2005). This is typically about 10 times the number of bacteria for aquatic habitats and it is estimates that they outnumber bacteria in the soil 5- to 1000-fold (William et al 2013). It has been estimated that there are 4 x 1030 virus particles in the oceans, equivalent to the carbon mass of 75 millions of blue whales (Suttle 2005). If all these viral particles were aligned in a single column, they would extend 10 million light years, 100 times the distance across our galaxy. This extraordinary abundance of viruses has changed our view of the role of viruses in ecosystems.

Later analyses using metagenomics has enabled unprecedented insight into viruses allowing the genetic identification of thousands to millions of viral sequences and the discovery of new viruses. Viral metagenomics of environmental samples generally identify a low percentage of viral sequences related to viruses previously sequenced and deposited in databases, and 80-90% of the viral sequences are new and unrelated to previously identified viruses (e.g., Angly 2006).

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