Nel 2020-21 abbiamo imparato tutto sui virus, una infinità di cose che prima ci erano poco conosciute o completamente sconosciute.
Cioè, immagino che voi avrete imparato tutto sui virus, io mi rendo conto che ancora ne so poco o nulla.
Questo non è un post ironico o allegro ma è un post con il massimo rispetto per i malati e per le vittime da virus.
No, nn credo che abbiamo imparato tutto ... anzi anzi. Ma proprio nn lo credo per nulla.
Guarda questo è un testo abbastanza elementare per chi è addetto ai lavori, parla della classificazione per via della struttura genomica ... immaginiamo quelli complessi ...
Classification of Viral Genomes
Currently, over 4000 viruses have been described, classified into 71 families. Even though viruses possess small genomes, they exhibit enormous diversity compared with plants, animals and even bacteria. With respect to the genome, viruses are broadly divided into DNA viruses and RNA viruses. Both DNA and RNA viruses can either single stranded or double stranded, with a circular, linear or segmented arrangement. DNA and RNA viruses are distinguished by their features, such as monopartite or multipartite. In monopartite, their genome is having a single nucleic acid molecule. All double stranded DNA genomes contain only a single nucleic acid molecule and few of the viruses with single stranded genomes are reported to have multiple segments. In contrast, RNA viral genomes are generally multipartite, with more frequency for single stranded RNA viruses. Additionally, single stranded virus genomes may be either positive sense (+) where the RNA present in the genome will of the same polarity as mRNA and will encode the genes or negative sense (−), where the entire ssRNA genome must be copied and the copied strand is transcribed. Some single stranded viruses are ambisense (a mixture of + and − sense). Bacteriophages such as MS2, Qb, and Mimivirus belonging to family Leviviridae consists of ambisense viral genomes. Size of the DNA viruses is larger than that of RNA viruses. Few DNA viruses can be as large as 305,000 nucleotides. DNA viruses are called large viruses and RNA viruses are small. Size of a few single stranded RNA genomes is up to 31,000 nucleotides. The small size of the single-stranded virus might be limited due to the fragility of the RNA, which provides the tendency of the large RNA strands to break and also due to the fact that RNA viruses are more susceptible to mutations than DNA viruses. Single stranded DNA and RNA viruses are fragile than double stranded viruses.
The genomes of the largest double-stranded DNA viruses such as herpesviruses and poxviruses are quite complex, resembling their host cells. Genomes of Polyomavirus are complexed with cellular histone proteins, which form a chromatin-like structure inside the virus particle. After infecting the host cell, these genomes behave like miniature satellite chromosomes inside the host cell following the dictates of cellular enzymes and the cell cycle. mRNAs of Vaccinia virus were polyadenylated at their 3¢. The genome of Adenovirus consists of split genes with non-coding introns, protein-coding exons, and spliced mRNAs. In order to streamline the replication cycle, the Adenovirus takes control of many biological processes in the cell, such as alternative RNA splicing and polyadenylation for expanding the coding potential of the limited viral genome.
Phage genomes are simple and least complex. Introns in prokaryotes were first discovered in the genome of T4 phage in 1984. The genome of T4 phage is 160 kbp double-stranded DNA, highly compressed with promoters and sequences that control translation are nested within the coding regions of overlapping upstream genes. It consists of three self-splicing group I introns, located in the genes that codes for thymidylate synthase (td), aerobic ribonucleotide reductase (nrdB) small subunit and the anaerobic ribonucleotide reductase (nrdD). Like any other group I introns, the td and nrdD introns each contain an open reading frame encodes for a homing endonuclease that renders the introns mobile and they can be inserted into new phage genomes. The nrdB intron is non-mobile due to a deletion in the intron-borne homing endonuclease gene. It was speculated that the presence of in these introns may confer a selective advantage to the phage by offering the possibility of regulating the expression of the intron-containing genes by the regulation of splicing. It was also believed that horizontal transfer of the introns between phages through homing has played a significant role in the evolution of group I introns in T-like phages.
The size of viral genomes also depends on the type of host cell. Viruses with prokaryotic host cells tend to replicate quickly to keep up with their host cells, which are reflected in the compact nature with overlapping genes of many bacteriophages, leading to the minimum genome size. Viruses with eukaryotic cells as hosts show tremendous compression while the core is getting packed into the capsid so that only optimum amount of genome can be packed. Viruses pack their genomes into protective protein contained capsids. Packaging strategies of viruses are related to the type of genome. Viruses with double stranded DNA genomes use a molecular motor with a spool like structure to pack their genomes into the capsid. In contrast, viruses with single stranded DNA or RNA genomes employ a co-operative mechanism, in which package and assembly of the genome into the capsid will occur simultaneously, enhancing the assembly efficiency of the capsid. In bacteriophage MS2, genomic RNA sequence will form a short term loop, for its interaction with the capsid proteins. This interaction will trigger conformational changes that convert symmetric protein dimers into asymmetric form, needed to build the capsid. Some bacteriophages of the family Myoviridae, such as T4 contain relatively large genomes, up to 170 kbp. The largest viral genome currently is known that of Mimivirus, ~1.2 Mbp, consisting of 1200 open reading frames, with only 10% of them showing the similarity with proteins of known function. Among the eukaryotic viruses, herpesviruses and poxviruses possess relatively large genomes, up to 235 kbp. These genomes contain genes involved in their own replication, particularly enzymes concerned with nucleic acid metabolism. Therefore, these viruses can partially escape the restrictions of the host cell biochemistry by encoding additional biochemical apparatus with the penalty of encoding all information necessary for a genome to pack into the capsid, which also causes upward pressure on its size. Whatever might be the composition of a genome, all viruses are obligate intracellular parasites, which can replicate only inside the appropriate host cells, their encoded genomes must be recognized by a specific host cell, which is getting parasitized. For that, the genetic code employed by the virus must either match or recognized by the host cell. Similarly, the signals that regulate the expression of viral genes must be inappropriate to the host. The general features of viral genomes sequenced are displayed in Table 1.1.
Table 1.1
General features of viral genomes sequenced
S. No. Class Sequenced genomes Size (Nt) Proteins
1 DsDNA 414 4697–335,593 6–240
2 SsDNA 230 1360–10,958 6–11
3 DsRNA 61 3090–29,174 2–13
4 SsRNA (+) 421 2343–31,357 1–11
5 SsRNA (−) 81 8910–25,142 5–6
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Size, Structure, and Composition of Double Stranded DNA Virus Genomes
Cellular life forms of all categories possess genomes with double stranded DNA and utilize the same as a standard scheme for their replication and expression. In contrast, viruses and other pathogenic and selfish elements exploit all possible inter-conversions of nucleic acids, with their genomes that can be either DNA or RNA, which are single-stranded or double-stranded. Viral genomes that have been sequenced and annotated are compared with genomes of cellular life forms, which were small with unknown gene functions. But, in the past few years, discovery of giant viruses has rapidly expanded the size of viral genomes whose range spans up to 3 orders of their magnitude, from ∼2 kb to ∼2 Mb. Surprisingly, the genomes of giant viruses are larger than the genomes of many bacteria and archaea, obliterating the gulf between cells and viruses in terms of genome size and complexity. A number of viral groups possess double-stranded DNA as their genomes are of considerable complexity, classified into small and large genomes depending on the type of replication. Small genomes use a host DNA polymerase for replication, In contrast, large genomes encode a virus-specific DNA polymerase, responsible for their genome replication. These viruses are genetically similar to the host cells they infect. Large DNA viruses encode more proteins than small DNA viruses.
There are two major viral groups representing the double stranded DNA genomes ie. members of the Adenoviridae and Herpesviridae families. Human adenovirus is one of the most common pathogens that causes minor, self-limiting illness to most of the patients. Adenovirus is one of the very well understood viruses, whose basic biology has been extensively studied over the past 60 years. Human Adenovirus has been isolated in the early 1950s from the adenoid tissue causing respiratory infections. This virus has a remarkable capacity to spread among patients contacting from as few as five virus particles. Adenovirus-induced acute respiratory disease is the most common infection in confined populations of daycare centers, hospitals, retirement homes, and military training venues, accounting for ~8% of all childhood respiratory tract infections, which can lead to bronchitis, bronchiolitis, or pneumonia, requiring hospitalization in ~25% of diagnosed cases. It also causes other localized diseases, such as colitis, hemorrhagic cystitis, hepatitis, nephritis, encephalitis, myocarditis and disseminated disease with multiorgan failure. A few such diseases can be more serious in pediatric and geriatric populations, especially in the individuals with suppressed immune systems, such as transplant recipients or patients suffering from AIDS. Many aspects of Adenoviral life cycle have been completely elucidated in great detail, which has allowed the development of adenoviral vectors that are highly efficient in delivering genes into the mammalian systems, especially human cells for the transgene expression and for delivering therapeutic genes in human gene therapy. Adeno viruses specifically consist of a nucleoprotein core with a 30–40 kb linear double-stranded DNA, surrounded by an icosahedral, non-enveloped capsid of 70 to 100 nm diameter. These viral genomes contain 30–40 genes. The terminal sequence of each DNA strand has an inverted repeat of 100–140 bp. The denatured single strands form a ‘ ’ like structures, which are important for the DNA replication. A 55 kDa protein known as the terminal protein is covalently attached to the 5¢ end of each strand. During the genome replication, this protein might acts as a primer, for initiating the synthesis of new DNA strands. The expression of the genes is rather more complex in Adenoviruses with clusters of genes expressed from a limited number of shared promoters. Multiply spliced mRNAs and alternative splicing patterns are used to express a variety of polypeptides from each promoter.
Apart from the differences in host and tissue tropism, a very less amount of variation is found in the Adenoviral genomes and their structural parameters. Human adenoviral serotype 5, is one of the highly characterized adenovirus, consisting of ~36 kb genome. Its coding region is divided into early (E1–E4) and late (L1–L5) transcripts based on their stage of expression. Essential early E1 region is deleted in most adenoviral vectors, rendering their incapability of replicating in most cell lines. Numerous studies have shown that after the deletion of E1, Adenoviral vectors are more ideal for the in vivo and in vitro studies requiring short-term transgene expression. The Second generation Adenoviral vector constructs are made after deletions in the essential E2 or E4 regions, facilitating the prolonged transgene expression. Helper-dependent Adenoviral vectors (hdAd) are generated by deleting all genes that code for viral proteins for increased cloning capacity. Removal of protein coding sequences in these vectors allows the overall reduction in their genome size from 36 kb for the wildtype to 30 kb in E1/E3-deleted Adenoviruses and ~500 bp for helper-dependent Adenoviral vectors.
Structure and Organization of Virus Genomes
