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Do all +ssRNA viruses have similar structures and life cycles?

Do all +ssRNA viruses have similar structures and life cycles?


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Take HCV for example. HCV doesn't package any enzymes in it's virions. When it infects a cell, it first translates its RNA genome. It's RdRp is synthesized with other non-structural proteins. Then its RdRp began replicating the RNA genome. Newly synthesized RNA are served as either translation templates or genomes of new virions. Finally new virions are assembled and released.

So do all +ssRNA viruses have the same pattern? There's no enzyme in the virions, and all the enzymes are synthesized after entry into the cells. They have the same life cycles: entry→translation(non-structural)→replication→translation(structural)→assembly→release.


What are Viruses?

First described by Martinus Beijerinck, a Dutch scientist, in 1899, viruses are obligate intracellular parasites that are often described as particles. Unlike many other unicellular organisms, viruses can only replicate within living cells (e.g. in bacteria, plant and animal cells).

They also have a very simple structure and lack many of the organelles found in various prokaryotic and eukaryotic cells (e.g. mitochondria, Golgi apparatus, etc). However, each virion/viral particle consists of nucleic acid that serves to classify different types of viruses. While they cause a wide range of diseases in plants and animals, viruses can also be beneficial to man.

Some of the most common viruses include:

  • Epstein–Barr virus
  • Norwalk virus
  • Ebola virus
  • Hepatitis virus
  • Rhinovirus
  • Simian immunodeficiency virus

Abstract

Genetic perturbation screens using RNA interference (RNAi) have been conducted successfully to identify host factors that are essential for the life cycle of bacteria or viruses. So far, most published studies identified host factors primarily for single pathogens. Furthermore, often only a small subset of genes, e.g., genes encoding kinases, have been targeted. Identification of host factors on a pan-pathogen level, i.e., genes that are crucial for the replication of a diverse group of pathogens has received relatively little attention, despite the fact that such common host factors would be highly relevant, for instance, for devising broad-spectrum anti-pathogenic drugs. Here, we present a novel two-stage procedure for the identification of host factors involved in the replication of different viruses using a combination of random effects models and Markov random walks on a functional interaction network. We first infer candidate genes by jointly analyzing multiple perturbations screens while at the same time adjusting for high variance inherent in these screens. Subsequently the inferred estimates are spread across a network of functional interactions thereby allowing for the analysis of missing genes in the biological studies, smoothing the effect sizes of previously found host factors, and considering a priori pathway information defined over edges of the network. We applied the procedure to RNAi screening data of four different positive-sense single-stranded RNA viruses, Hepatitis C virus, Chikungunya virus, Dengue virus and Severe acute respiratory syndrome coronavirus, and detected novel host factors, including UBC, PLCG1, and DYRK1B, which are predicted to significantly impact the replication cycles of these viruses. We validated the detected host factors experimentally using pharmacological inhibition and an additional siRNA screen and found that some of the predicted host factors indeed influence the replication of these pathogens.


1 Introduction

CRISPR-Cas systems are adaptive immune systems that protect bacteria and archaea against phages and other invasive mobile genetic elements (MGEs). [ 1-4 ] The hallmark feature of these systems is the array of genomic DNA known as clustered regularly interspaced short palindromic repeats (CRISPRs), between which memory of previous infections is stored in form of short sequences (spacers) acquired from invading MGEs. [ 5-7 ] Adjoining the CRISPR array are multiple genes encoding CRISPR-associated (Cas) proteins. Cas proteins perform different tasks in the three phases of CRISPR-Cas-driven immunity: adaptation, CRISPR RNA (crRNA) biogenesis, and interference. [ 2, 3, 8-12 ] During the adaptation phase, Cas1 and Cas2 select and modify segments of foreign nucleic acids (termed protospacers), eventually adding them to the CRISPR array. [ 9, 10, 12 ] Upon subsequent infection, spacers are transcribed along with the rest of CRISPR array into a long precursor crRNA (pre-crRNA). pre-crRNA is then processed either by Cas effectors or other endogenous endonucleases into mature crRNAs (also known as guide RNAs, gRNAs) containing a direct repeat and a spacer sequence. [ 13, 14 ] Some systems also require a second small RNA known as transactivating crRNA, which binds with crRNA to form functional gRNA. [ 14 ] gRNAs are then used by Cas interference module as a template that guides the effector to cleave complementary nucleic acid sequences in MGEs, thereby curbing infection. [ 2, 3, 11 ]

The unceasing arms race between prokaryotes and MGEs has led to evolutionary development of a great variety of CRISPR-Cas systems. [ 15-19 ] Currently known CRISPR-Cas systems can be grouped into class 1 and class 2 systems, which are further divided into types and subtypes. Class 1 CRISPR-Cas systems (type I, III, and IV systems) utilize a wide assortment of smaller Cas proteins to form a multi-subunit interference complex. [ 20, 21 ] By contrast, class 2 systems (type II, V, and VI systems) use a single, comparatively larger Cas effector protein for interference and, in certain cases, crRNA biogenesis. [ 22-24 ]

In the years following the discovery of Cas9, the DNA-targeting type II and type V CRISPR-Cas effectors have been successfully harnessed for a variety of applications in genome editing and nucleic acid detection. [ 25-33 ] Engineered and certain naturally occurring variants of Cas9 have also been used for RNA targeting and binding, thus initiating the use of CRISPR-Cas technology in RNA manipulation and potentially advancing this field by overcoming limitations of conventionally used RNA-targeting methods. [ 34, 35 ] However, the fact that Cas9 also retains its ability to target DNA involves risk from undesired off-target effects on genes. [ 36 ] Moreover, Cas9 effectors may not necessarily be efficient in all RNA-targeting applications, so expanding the CRISPR-Cas toolbox with new and diverse effectors would allow greater flexibility and more sophisticated RNA manipulation.

More recently, type VI CRISPR-Cas systems that exclusively target single-stranded RNA (ssRNA) have been discovered. [ 37-40 ] Four subtypes (A–D) have been identified to date, of which subtypes VI-A, VI-B, and VI-D have been functionally characterized along with respective effectors, i.e., Cas13a, Cas13b, and Cas13d (Figure 1A and Table 1). Functionally, all Cas13 effectors are crRNA-guided RNases with two distinct and independent catalytic centers. One catalytic center processes pre-crRNA, and the other is formed by two R-X4-H motifs typical of higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domains that mediate ssRNA cleavage. As opposed to Cas9 that specifically cleaves crRNA spacer-complementary dsDNA sequences (i.e., target DNA) in cis, the activated Cas13-crRNA interference complex cleaves nonspecifically both the crRNA-bound complementary ssRNA sequence (henceforth referred to as activator RNA) in cis and any other encountered RNA (both host and viral RNA) in trans (also known as collateral or bystander cleavage) (Figure 1B). [ 37-40 ] The cleavage preferentially occurs within structurally exposed regions of the RNA secondary structures, usually at uridine (U) or adenosine (A) (Figure 1B). Given their potent performance in mammalian cells, Cas13 effectors have already been used as tools for RNA manipulation, albeit their practical application is still in its infancy. [ 38, 39, 41-49 ]

88 nt (long) e) e) consists of 5′ and 3′ fragments of the 36-nt repeat sequence separated by an intervening repeat region

HEPN nuclease switch region

  • a) cleavage appears to be unrestricted or negligibly affected by protospacer-flanking sequences for certain orthologs or under certain conditions
  • b) confirmed in U-cleaving Cas13a orthologs
  • c) Csx27 represses Cas13b activity and is found inconsistently in type VI-B1 CRISPR loci, whereas, whereas Csx28 enhances Cas13b activity and is universally present in type VI-B2 loci both accessory proteins can regulate orthogonal Cas13b effectors
  • d) WYL domain-containing protein enhances Cas13d activity and is found inconsistently in type VI-D CRISPR loci
  • e) consists of 5′ and 3′ fragments of the 36-nt repeat sequence separated by an intervening repeat region
  • f) may vary between orthologs.

In the light of recent studies on Cas13 effectors, this review article will summarize the current knowledge of structural and mechanistic basis for function of Cas13 effectors, outline the reported applications and point out issues that need to be addressed before these effectors could be used more broadly and efficiently.


Discussion

Most of the current antiviral therapeutics act for inhibiting specific viral proteins, e.g. essential viral enzymes. Unfortunately, this approach has been ineffective because of drug resistance developed by viruses, especially in the case of RNA viruses which can mutate very rapidly. The next‐generation antiviral therapeutics are emerging which target host proteins required by the pathogens, instead of targeting pathogen proteins. If these host factors are indispensable for pathogens, but not essential for host cells, their silencing may effectively inhibit infections without developing drug resistance rapidly 1, 21, 22. Another alternative approach is to inhibit the interactions between these host factors and pathogen proteins, instead of targeting the proteins 23. The development of these novel strategic therapeutic approaches against infectious diseases raises the need for enlightening the infection mechanisms through PHIs, in order to identify putative host‐oriented anti‐infective therapeutic targets. To understand the complex mechanisms of infections, computational analysis of underlying protein interaction networks may serve crucial insights to develop non𠄌onventional solutions 2, 14, 24. This study of computational analysis of virus–human interactomes aims to provide initial insights on the infection mechanisms of DNA and RNA viruses, comparatively, through the observation of the characteristics of human proteins interacting with viral proteins. The common and special infection strategies of DNA and RNA viruses found here may lead to the development of broad and specific next‐generation antiviral therapeutics.

Highly targeted human proteins

As the main viral infection strategy, all viruses manipulate cellular processes to proliferate within the host. Therefore, viral proteins highly interact with human proteins functioning in cell cycle, human transcription factors to promote viral genetic material transcription, nuclear membrane proteins for transporting viral genetic material across the nuclear membrane, and also regulatory proteins for translation and apoptosis 3, 15, 25, 26. We identified human proteins that are highly interacting with viral proteins, sequentially based on the total number of targeting virus families (Table 4 ). The list includes the top viral targets which interact with multiple viral families, within the most comprehensive PHI data. Some of these human proteins were previously reported as targets for multiple viruses, i.e. P53, NPM, ROA2, GBLP, and HNRPK 3, 15.

Our analyses revealed that there are six heterogeneous nuclear ribonucleoproteins (HNRPs) in the highly targeted human proteins list (HNRPK, ROA1, HNRPC, HNRH1, HNRPF, ROA2). HNRPs are RNA𠄋inding proteins, which function in processing heterogeneous nuclear RNAs into mature mRNAs and in regulating gene expression. Specifically, they take role in the export of mRNA from the nucleus to the cytoplasm. They also recruit regulatory proteins associated with pathways related to DNA and RNA metabolism 27, 28. Being targeted by multiple viruses, HNRPU was reported as a hotspot of viral infection, and proposed as a potential antiviral human protein 4. In the present study, HNRPU is found to be targeted by five viral families (see Data S3). Our data additionally indicate several other HNRPs, targeted by viral proteins (see Data S1–S3). For all virus‐targeted HNRPs, the number of targeting RNA virus families is found to be higher than that of DNA virus families (see Data S3), revealing that they may play crucial roles in viral RNA processing. The protein family of HNRPs may serve as host‐oriented antiviral drug targets.

Moreover, our analyses also reflected that proteins functioning in transport and localization related processes within the cell are targeted highly by both DNA and RNA viruses, i.e. IMA1, ADT2, TCPG, and TCPE. IMA1 (Karyopherin alpha 2, KPNA2) functions mainly in nuclear import as an adapter protein for nuclear receptor KPNB1 (Karyopherin beta 1). Interacting with IMA1 enables viruses to enter the nucleus and consequently to use the host's transcriptional machinery. Besides, viruses may interact with IMA1 in order to inhibit the host antiviral response, since nuclear import factors regulate the transport of innate immune regulatory proteins to the nucleus of cells to activate the antiviral response 3, 29, 30, 31. The transmembrane transporter activity of ADT2 is responsible for the exchange of cytoplasmic ADP with mitochondrial ATP across the mitochondrial membrane, serving crucial roles in metabolic processes 32. Attacking to human metabolic processes was reported as a common infection strategy of bacteria and viruses 15. The proteins, TCPG and TCPE are responsible for RNA localization activity and our results reveal that they are targeted by larger number of RNA families (Table 4 ). Highly targeted transporter proteins should be investigated further for their potential to be next‐generation antiviral target, because of their crucial roles in viral life cycle within the host organism.

EF1A1 and EF1A3 function as translation elongation factors in protein biosynthesis. EF1A proteins promote the GTP�pendent binding of aminoacyl‐tRNA to the A‐site of ribosomes during protein biosynthesis with a responsibility of achieving accuracy of translation 33. Translation elongation factors were reported as targets for viruses, in early studies 34, 35, 36. Since they are essential components of the cellular translational machinery, viruses interact with them for biosynthesis of viral proteins within the host cell. We found translational elongation as the top biological process, commonly targeted by both DNA and RNA viruses (Table 7 ).

Interacting with human transcription factors was reported as one of the main viral infection strategies 3, 15. Among the highly targeted human proteins, YBOX1 and P53 have transcription factor activity. Both of these proteins are multifunctional. YBOX1 functions in transcription of numerous genes, as a transcription factor. It also contributes to the regulation of translation. On the other hand, P53 is the famous tumor supressor acting as an activator for apoptotic cell death. Apoptosis is a very crucial process during the viral infection progress, and should be strategically controlled by viruses for a successful viral infection. Apoptosis is an innate immune response to viral infection. In the early stage of viral life cycle in the host cell, apoptosis is inhibited by corresponding virus–human protein interactions. After completion of transcription and translation of viral genetic material, viruses try to induce apoptosis to assist virus dissemination 37, 38, 39.

Among the highly targeted human proteins in Table 4 , EF1A1, ADT2, TBA1C, GRP78, TBB5, P53, TCPG, HS90B, and TBA1A were found as drug targets listed in DrugBank 40. However, only ADT2, GRP78, TBB5, P53, and TBA1A are approved for commercial drugs. Nevertheless, no antiviral therapeutic usage is available for these drug targets yet. Above‐mentioned human proteins ribonucleoproteins, proteins functioning in intracellular transport and localization, translation elongation factors and transcription factors require further investigation for their potential for serving as antiviral drug targets.

Targeted human mechanisms

Gene ontology and pathway enrichment analyses of pathogen‐targeted host proteins are widely used in bioinformatic analysis of PHI networks to understand the attack strategies of pathogens 3, 4, 15, 41, 42 as well as in verification of computationally predicted PHIs 43. Additionally, GO and pathway terms are widely used as features in computational PHI prediction studies 44, 45.

Our observation of the enriched GO process terms for human proteins targeted by only DNA viruses (Table 5 ) may lead to the conclusion that DNA viruses have specifically evolved to be able to attack human cellular and metabolic processes simultaneously, during infections. Using this PHI mechanism, DNA viruses can finely exploit the cellular and metabolic mechanisms of infected cells to their own advantage, generally resulting in chronic infections in human. On the other hand, GO process terms enriched in human proteins targeted by only RNA viruses are mostly related to RNA processing, intracellular transport and localization within the cell (Table 5 ). It was reported that RNA viruses extensively target human proteins that are involved in RNA metabolism and also protein and RNA transport to promote viral RNA processing for a successful infection 4.

Further investigation of the enriched processes of human proteins attacked by multiple DNA viruses (Table 6 ) pointed out their high preference to target cellular processes. It was reported that DNA viruses tend to target crosstalking human proteins linking the cell cycle with either transcription or chromosome biology, with a possible aim of promoting viral replication instead of cellular growth 4. For the RNA viruses, we found that the human proteins attacked by multiple RNA virus families are enriched in specific processes within the cellular mechanisms (Table 6 ). All viruses need host's transcriptional machinery for viral genetic material transcription.

In the case of human proteins targeted by both DNA and RNA viruses, the P‐values of the enriched GO process terms are very low, indicating statistically strong results (Table 7 ). The most highly‐targeted human process is translational elongation. Translational control of viral gene expression in eukaryotic hosts was reported repeatedly 46, 47, 48. Here, we presented translational elongation as the top GO process term enriched in human proteins targeted by both DNA and RNA viruses within the current experimental PHI data. The remaining list includes cellular and metabolic processes, which can be considered as targets of both virus types. Based on these observations, we can state that the common viral infection strategy is to target human proteins functioning within the processes of gene expression and protein synthesis, simply because of the lack of their own such machineries. All viruses depend on the cellular mechanisms for these processes and they recruit host ribosomes for translation of viral proteins.

A comparative investigation of the enriched pathway terms for human protein sets targeted by only DNA viruses and by only RNA viruses (Table 8 ) reveals additional support for the different infection strategies of these viral groups. There is no common term in these two lists of enriched human pathways. Cell cycle pathway targeted by only DNA viruses and RNA‐related pathways targeted by only RNA viruses, provide parallel results with GO enrichment analyses. The enriched pathway terms in 4𠄍NA viruses‐targeted human protein set are only Epstein�rr virus (EBV) infection and viral carcinogenesis (Table 9 ). EBV is a species of DNA virus family Herpesviridae, which constitute nearly half of the DNA viruses–human PHI data (Table 1 ). On the other hand, it is estimated that 15% of all human tumors are caused by viruses, mainly DNA viruses, i.e. Herpesviruses and Papillomaviruses 49. The pathway enrichment analysis of 4‐RNA viruses‐targeted set brings the terms of protein processing and immune system related terms forward (Table 9 ). Finally, for the common targets of two virus types, we obtained ribosome term enriched with a very small P‐value (Table 10 ). Both viruses use host ribosome for viral protein synthesis.


Classification of Animal Viruses | Microbiology

In this article we will discus about the classification of animal viruses.

Baltimore (2008) classified the animal viruses in the following seven groups according to the relationships between virion, nucleic acid and mRNA transcription Table (17.1).

The RNA within the virion is known as plus (+) or sense strand because it acts as mRNA, whereas the newly synthesized RNA which is complementary in base-sequence to the original infectious strand is called minus (-) or antisense strand. It acts as template to produce additional (+) strand which may act as mRNA.

Class 1. dsDNA viruses:

The mRNA is synthesized on a dsDNA genome template (± dsDNA → (+) mRNA) which usually occurs in a cell.

Following are the example of some viruses:

Papova-viruses: Polyomavirus, SV40

Poxviruses: Vaccinia virus

Adenoviruses: Human adenovirus

Herpes-viruses: Herpes simplex virus type I and type II, Epstein-Barr virus.

Class 2. (+) ssDNA viruses:

In such viruses an intermediate DNA is synthesized before the synthesis of mRNA transcript (+ ssDNA → + mRNA). The mRNA has the same polarity as the DNA.

Parvoviruses: Adeno-associated viruses, mouse minute virus.

Class 3. (+) ssRNA viruses:

The RNA has similar polarity as the mRNA.

Viruses of this class have been grouped into the following two classes:

Subclass 3a: Individual mRNA encodes a polyprotein which is broken later on to form viral proteins.

Picornaviruses: e.g. polio virus.

Subclass 3b: From (+) ss RNA two types of mRNA molecules are transcribed, one is of same length as virion RNA and the other is a fragement of virion RNA.

Togaviruses: Alpha viruses (group A), sindbis virus, semliki forest virus, Haviviruses (group B) e.g. dengue virus, yellow fever, St. Louis encephalitis virus are the important examples.

Class 4. (-) ssRNA viruses:

The virion RNA is complementary to mRNA.

Following two types of viruses are found in this class:

Subclass 4a: The ssRNA genome encodes a series of monocistronic mRNA. Rhabdoviruses: e.g. Mumps virus, measles virus, sendai virus.

Subclass 4b: Each segment molecule of the genome acts as template for the synthesis of mRNA which are monocistronic or encodes polyprotein.

Orthomyxo-viruses: e.g. Human influenza virus

Bunya viruses: e.g. Bunyawera virus

Arena-viruses: e.g. Lassa virus

Class 5. dsRNA viruses:

All the viruses of this class have segmented genome. Each chromosome encodes a single polypeptide. The dsRNA acts as template and asymmetrically synthesize (+) mRNA. Reoviruses: e.g. reovirus of humans.

Class 6. (+) ssRNA-RT viruses:

In these viruses (+) ssRNA directs the synthesis of (-) DNA which in turn acts as template for the transcription of mRNA (RNA→ (-) DNA→ + RNA). Virion RNA and mRNA are of the same polarity.


​Life Cycle of Viruses with Animal Hosts

Lytic animal viruses follow similar infection stages to bacteriophages: attachment, penetration, biosynthesis, maturation, and release (see Figure 4). However, the mechanisms of penetration, nucleic-acid biosynthesis, and release differ between bacterial and animal viruses. After binding to host receptors, animal viruses enter through endocytosis (engulfment by the host cell) or through membrane fusion (viral envelope with the host cell membrane). Many viruses are host specific, meaning they only infect a certain type of host and most viruses only infect certain types of cells within tissues. This specificity is called a tissue tropism. Examples of this are demonstrated by the poliovirus, which exhibits tropism for the tissues of the brain and spinal cord, or the influenza virus, which has a primary tropism for the respiratory tract.

Figure 4. In influenza virus infection, viral glycoproteins attach the virus to a host epithelial cell. As a result, the virus is engulfed. Viral RNA and viral proteins are made and assembled into new virions that are released by budding.​

​Animal viruses do not always express their genes using the normal flow of genetic information—from DNA to RNA to protein. Some viruses have a dsDNA genome like cellular organisms and can follow the normal flow. However, others may have ssDNA, dsRNA, or ssRNA genomes. The nature of the genome determines how the genome is replicated and expressed as viral proteins. If a genome is ssDNA, host enzymes will be used to synthesize a second strand that is complementary to the genome strand, thus producing dsDNA. The dsDNA can now be replicated, transcribed, and translated similar to host DNA.

If the viral genome is RNA, a different mechanism must be used. There are three types of RNA genome: dsRNA, positive (+) single-strand (+ssRNA) or negative (−) single-strand RNA (−ssRNA). If a virus has a +ssRNA genome, it can be translated directly to make viral proteins. Viral genomic +ssRNA acts like cellular mRNA. However, if a virus contains a −ssRNA genome, the host ribosomes cannot translate it until the −ssRNA is replicated into +ssRNA by viral RNA-dependent RNA polymerase (RdRP) (see Figure 5). The RdRP is brought in by the virus and can be used to make +ssRNA from the original −ssRNA genome. The RdRP is also an important enzyme for the replication of dsRNA viruses, because it uses the negative strand of the double-stranded genome as a template to create +ssRNA. The newly synthesized +ssRNA copies can then be translated by cellular ribosomes.

Figure 5. RNA viruses can contain +ssRNA that can be directly read by the ribosomes to synthesize viral proteins. Viruses containing −ssRNA must first use the −ssRNA as a template for the synthesis of +ssRNA before viral proteins can be synthesized.​

​An alternative mechanism for viral nucleic acid synthesis is observed in the retroviruses, which are +ssRNA viruses (see Figure 6). Single-stranded RNA viruses such as HIV carry a special enzyme called reverse transcriptase within the capsid that synthesizes a complementary ssDNA (cDNA) copy using the +ssRNA genome as a template. The ssDNA is then made into dsDNA, which can integrate into the host chromosome and become a permanent part of the host. The integrated viral genome is called aprovirus. The virus now can remain in the host for a long time to establish a chronic infection. The provirus stage is similar to the prophage stage in a bacterial infection during the lysogenic cycle. However, unlike prophage, the provirus does not undergo excision after splicing into the genome.

Figure 6. HIV, an enveloped, icosahedral retrovirus, attaches to a cell surface receptor of an immune cell and fuses with the cell membrane. Viral contents are released into the cell, where viral enzymes convert the single-stranded RNA genome into DNA and incorporate it into the host genome. (credit: modification of work by NIAID, NIH)​

Do all +ssRNA viruses have similar structures and life cycles? - Biology

Pre-requisites: read Virus_Tech page 1.

Many viruses carry RNA rather than DNA as their genetic material. This RNA may be single or double-stranded .
Like DNA viruses, RNA viruses come in a wide variety of forms. The model above is a togavirus (such as Semliki
Forest Virus (SFV) or Sindbis virus).The core of the virus is the nucleocapsid - single-stranded RNA (ssRNA)
packaged inside a protein capsid with icosahedral symmetry (not an icosahedron, in this instance as there are
more than 20 triangular faces, but the symmetry is icosahedral).

The nucleocapsid is partially covered by a coat of C protein and enveloped by a phospholipid bilayer viral
membrane or envelope ) derived from the host cell's membrane lipids which contains the viral protein spikes.

Adhesion and Injection of DNA

The protein spikes adhere to specific receptors on the target cell surface-membrane. The nucleocapsid,
with its C protein shell enters the host cytosol and the RNA is released and escapes from the capsid.

The replication of the RNA and the protein capsid and their packaging are summarised in the diagram below.
The single-stranded RNA is a plus or positive-strand , meaning that it is of the right sense to be immediately
t ranslated as mRNA. [Some ssRNA viruses carry negative-strand RNA , which must first be copied or
transcribed into the complementary (+)-strand which is then t ranslated .] The (+)-RNA contains two START
(AUG) codons and transcription from each of these results in the synthesis of a different set of proteins.

In the early phase of infection, translation proceeds from the first AUG codon, resulting in the synthesis of a
long polyprotein (using the host's ribosomes) which is then cleaved into separate early protein polypeptides
which fold into enzymes and proteins needed for RNA replication, producing the complementary (-)-strand
RNA, using the original (+)-strand as a template.

Part of this (-)-strand is then copied to produce a short (+)-strand mRNA which lacks the first START codon.
This is translated from the second START codon, producing a different polyprotein which is cleaved to
produce the late proteins which form the virus particle, and include the C protein. In the meantime, the
(-)-RNA is copied repeatedly to produce lots of (+)-strand RNA genomes which are packaged into the
assembling virions. The nucleocapsid is assembled in the host cytosol, where the C protein coat is added.
Spike proteins are manufactured by the rough endoplasmic reticulum and Golgi apparatus of the host cell
before being added to the host cell-surface membrane, where they form patches (excluding host proteins) to
which the assembled virions add and bud from the cell, acquiring their envelope as they do so.

Viroids are plant pathogens that consist of circular ssRNA of about 300b (220 to 380 bases, the smallest is
220b). E.g. potato spindle tuber viroid (PSTVd) which causes infectious disease in potato plants. They code
for no proteins and have no protein capsid or protein-coat at all: they are naked infectious RNA molecules
and thus one of the simplest parasites conceivable. Their replication requires RNA polymerase II, provided
by the host cell and occurs by rolling circle replication . The RNA has a 2D/3D structure, with some
regions pairing by hydrogen-bonding between the bases to give double-stranded regions, and the molecule
is rod-shaped. Some are ribozymes , meaning that they fold to form structures with enzymatic activity, such
as catalysis of cutting the concatemers (produced by rolling circle replication) into individual viroids.

Hepatitis D virus (HDV) is the smallest known animal virus and has a small genome of circular
single-stranded RNA or (-)sscRNA of 1.7 kb, in which about 70% of the nucleotides pair with other bases in
the molecule, forming a rod-like molecule. This virus is not able to complete its life-cycle without a helper
virus
, in this case hepatitis B virus (HBV). HDV must coinfect the same cell as HBV in order to complete its
development as it requires some of the HBV genes. A virus like HDV is called a satellite virus (or subviral
satellite) and is thus parasitic on HBV. It is possible that HDV evolved from a viroid or similar infectious RNA
(it is thought that undiscovered viroids may infect and cause disease in animals).

Like a viroid, the HDV RNA has regions that can form catalytically active ribozymes, which are required to cut
the concatemers produced during genome replication (by (+)RNA to (-)RNA rolling-circle replication, which
first requires synthesis of the (+)RNA antigenome from the original (-)RNA genome) into individual genomes.
This is the fastest known self-cleaving ribozyme in nature, cutting the RNA in less than one second. Neither
encode their own RNA polymerase, required for RNA genome replication, but use host RNA polymerase.

The HDV genome encodes only two proteins: the large and small delta antigens (HDAg-S and HDAg-L) from
a single open reading frame (ORF). HDAg-S is produced early in infection and is required for viral
replication. HDAg-L appears in the later stages and inhibits viral replication and instead promotes viral
particle assembly.

Classification of Viruses

The Baltimore scheme classifies viruses into the following groups, based upon the nature of their genomic
material (different sources number the groups in different orders):

1. dsDNA viruses, with linear dsDNA: e.g. adenovirus (icosahedral symmetry), T4 bacteriophage (binary
symmetry) and poxviruses (complex structure), or with circular dsDNA: e.g.hepatitis B virus.

2. ssDNA , e.g. parvoviruses (icosahedral) such as adenoassociated virus.

3. dsRNA , e.g. reovirus (icosahedral).

4. (+)ssRNA , e.g. togaviruses (icosahedral), coronaviruses.

5. (-)ssRNA , e.g. rhabdoviruses (helical).

6. RNA, with a DNA step in replication, e.g. retroviruses (e.g. HIV-1).

Influenza virus is a (-)ssRNA virus whose genome is divided into 8 separate chromosomes (unusual for a
virus!). Influenza B, which infects humans, has a genome size of 14.648 kb and forms particles which are
spherical to filamentous). These 8 RNA segments are packaged into 8 helical ribonucleoprotein particles
(RNPs) enclosed in a protein capsid (made of the matrix or M1 protein ) surrounded by a phospholipid
bilayer envelope (with the M protein lining the inside of the envelope). Embedded in the envelope are two
types of glycoprotein spike: haemagluttinin (HA or H) so-called because it will cause red blood cells to stick
together, and neuraminidase (NA or N) . The virus is 80-120 nm in diameter and up to 2000 nm long
(variable length).

Function of the HA spikes

The haemagluttinin is involved in cell binding and each strain of influenza has one of 16
subtypes of H (designated H1 to H16). Human influenza is characterised by possessing H1, H2
or H3. Three identical copies of the haemagluttinin polypeptide form a single haemagluttinin
spike (it is trimeric, specifically a homotrimer).

HA binds sialic acid-containing receptors on the target cell surface membrane. This is referred to
as docking, binding or adsorption. Sialic acid is a component of carbohydrate chains borne on
the cell surface (the glycocalyx) and also of mucus (mucoproteins).

The virus then tricks the target cell to take it up (by activating the receptor upon binding to it)
and it is taken-up by (coated-pit) endocytosis into a vesicle called a coated vesicle. Acidic
endosomes fuse with this vesicle, as the cell attempts to digest the virus. HA then facilitates the
fusion of the viral and endosome vesicle membranes. This happens when endosomes fuse with
the coated-vesicle, acidifying it. When the pH drops below 6, the HA changes shape, partially
unfolding, which exposes a hydrophobic region (hydrophobic literally means 'water-fearing' and
refers to substances that prefer to dissolve in lipids, rather than water) which attaches to the
endosome membrane, like a grappling hook, then the HA stabilises and refolds, retracting as it
does so and bringing the viral membrane so close to the endosomal membrane that the two
membranes fuse.

Function of the N spikes

The neuraminidase is a sialidase, an enzyme which cuts sialic acid residues from the ends of
carbohydrate chains. This breaks-up the long carbohydrate chains that form the slimey lining of
respiratory airways and makes the mucus of the respiratory tract more watery, which helps the
virus move easily to its target cells (one of the functions of mucus is to entangle foreign
particles, such as viruses, and the N spikes counter this by cutting the entangling threads). The
N spikes help new virus progeny spread from cell to cell. The N spikes will also cleave sialic acid
residues to which HA binds, if the target is inappropriate (such as a mucoprotein in the mucus
layer rather than the cell receptor).

There are also several types of N and the H and N types carried by a particular strain
charcterise the virus. For example, avian flu is H5N1 (avian influenza has one of H1 to H16 and
one of N1 to N9).

Role of the M2 ion channels

These are activated by the low pH when the endosome fuses with the coated-vesicle containing
the virus. They import protons and are involved in triggering uncoating - the disassembly of the
protein capsid which allows the RNPs to enter the host cytosol.

Function of the three polymerase peptides

Once in the cytosol the nucleoprotein which packages the RNA of each RNP, allows movement
of the RNPs into the host cell nucleus. Once inside the nucleus, the three polymerase units (PA,
PB1 and PB2) initiate transcription of the viral RNA. PB2 attaches to the cap present at the head
end (5') of host mRNA, PB1 then cleaves this cap which attaches to PB2 - the virus steals the 5'-
cap off host RNA to make itself look like mRNA! PB1 also adds the usual 3' tail to the end of the
viral RNA, so now it resembles host mRNA ready to be transcribed! PB1 and PA then synthesise
more viral RNA, both mRNA ((+)ssRNA) which is translated by host ribosomes in the cytoplasm
to make viral proteins, and new copies of the viral genome, which remain in the nucleus.

Once synthesis results in a high concentration of NP protein in the cytoplasm, viral mRNA
synthesis stops but synthesis of genomic RNA continues - this occurs in the late phase of
infection and switches the virus from protein synthesis mode, into assembly mode, in which the
synthesised components are assembled into new virus particles. RNPs are assembled in the
host cell nucleus and are then exported to the cytoplasm.

M protein, HA and N accumulate together in the host cell-surface membrane (after being
processed and delivered there by the rough endoplasmic reticulum and Golgi apparatus of the
host cell). The RNPs assemble here and then the virus buds from the host cell surface,
becoming enclosed in the phospholipd envelope containing the viral protein spikes.

  1. Chill, fever (38-39 C)
  2. severe weakness, fatigue, aches and pains in joints and especially in the back and legs,
    sore throat, headache, eye irritation and reddening, reddening of the face and nose.
  3. Abdominal pain in children.
  4. complications that may occur include pneumonia, bronchitis, sinus and ear infections and
    death.

Several chemotherapeutic agents have been developed to combat influenza. These include:

  • M2 inhibitors, block the M2 proton channels with the aim of preventing the viral RNA
    entering the cell cytosol, e.g. amantadine (1-aminoadamantane).
  • Neuraminidase inhibitors, e.g. Tamiflu (Oseltamivir) and relenza (Zanamivir) which
    competes with sialic acid for the enzyme, slowing-down the action of the enzyme.

Influenza replication cycle

The replication or life cycle of influenza is illustrated below. This illustrates many of the features
of a 'typical' animal cell virus, such as:

  1. Adhesion (attachment) of the virus particle (virion) to specific receptors (glycoproteins)
    on the target cell surface.
  2. This adhesion triggers uptake (endocytosis) of the virion by the target cell.
  3. Uncoating and release of the genetic material into the host cell cytoplasm, and
    subsequently nucleus in this case. This genetic material commandeers the machinery of
    the host cell to make more proteins and replicate the viral genome.
  4. Assembly of new virions on the host cell membrane and their eventual budding from the
    host cell, taking host cell phospholipid, modified with virus proteins, with them as the viral
    envelope.

Above: a retrovirus of the lentivirus type, e.g. human immunodeficiency virus (HIV) . HIV has
two (+)ssRNA molecules in its genome, represented above as the spirals (red) in the centre of
the elongated inner core (yellow) which are both identical copies of the genome wound with
packaging proteins to form ribonucleoprotein . The elongated conical core shell (the shape
of which is characteristic of the lentivirus variety of retrovirus, the core being icosahedral in
some retroviruses). HIV is enveloped, that is it is enclosed in a phospholipid bilayer membrane
(cyan) derived from the host cell-surface membrane. This envelope contains glycoprotein
spikes. Just beneath the envelope is a protein shell 9inner shell or matrix) which stabilises the
structure of the envelope.

HIV is well-known as the causative agent of AIDs (Acquired-immunodeficiency syndrome or
acquired immune-deficiency syndrome) in which destruction of key components of the body's
immune system leaves it very susceptible to many other infections. This occurs because HIV
targets certain immune cells, especially T-helper cells (cells that act as alarms and 'officers' for
the immune system - activating and directing other immune cells). HIV will target these cells,
enter them and turn them into virus factories!

Retrovirus Cycle - example HIV

1. Adsorption/adhesion and entry

As usual, the virus must bind to specific receptors on its target cell. These receptors are more-
or-less specific, since viruses infect only one or a few cell types. In the case of HIV, the gp120
spikes bind to CD4 receptors on T-cells (HIV can also infect a few other cell types, such as
macrophages). This is the initial adhesion, which is transient and unstable. This is followed by a
secondary and more stable adhesion between the vrius and a second receptor on the cell
surface (CCR5 or CXCR4). Once stably bound or adsorbed, the lipid envelope of the virus
fuses with the host cell membrane (this fusion is triggered by gp41). The inner core is then
released into the cell.

2. Replication of viral genome

Retroviruses replicate their RNA via a DNA intermediate. They use their RNA as a template to
synthesise first a complementary ssDNA molecule (creating an RNA/DNA hybrid molecule with
the RNA then be degraded leaving ssDNA) and then the ssDNA is used as a template to
generate a dsDNA intermediate. To complete this unusual task, of synthesising dsDNA from a
ssRNA template, HIV carries the viral enzyme reverse transcriptase (RT) - blue spheres
inside inner core in the diagram above. This enzyme is responsible for:

i) Synthesising the ssDNA complementary strand by using the RNA as a template, that is
working as an RNA-dependent DNA polymerase, resulting in the formation of an RNA/DNA
hybrid molecule.

ii) Digesting away the RNA strand of the RNA/DNA hybrid duplex ( RNAse activity, present as a
separate enzyme or bound to RT and called RNase H) producing ssDNA.

iii) Synthesising the second DNA strand, using the ssDNA as a template, that is working as a
DNA-dependent DNA polymerase, producing dsDNA.

This dsDNA can then be integrated into the host chromosome - it inserts into the DNA of the
host-cell, with the help of the viral enzyme integrase . In this integrated dsDNA state the virus is
called a provirus . Note that as this step proceeds efficient gene expression, the virus must
carry integrase, RNase and reverse transcriptase with it. All these enzymes are represented by
the blue spheres inside the viral core.

HIV is unusual in that it can insert its provirus and replicate inside non-dividing cells. To do this
it has to gain access to the nucleus by passing the nuclear pore complex (NPC). It does this
with the help of at least two viral proteins: MA, which apparently acts as a key granting access
past the NPC and Vpr. replication of the viral RNA takes about 6 hours after cell-infection.

3. Transcription and expression of viral genes

The synthesis of virus proteins only begins efficiently once the provirus is integrated into the
host DNA. The primary transcript (the RNA initially produced by transcription by RNA
polymerase) covers all nine or so genes of the HIV genome and is spliced (cut-up by enzymes)
into more than 30 separate mRNA - 9 genes produce more than 9 proteins, many of which have
multiple functions - a way of minimising on the amount of DNA that must be packaged and
carried by the virion.

The following structural proteins are produced:

  • Gag (p55) - associates with the host cell-surface membrane and recruits two copies of
    the viral RNA genome and other structural proteins for virion assembly and budding from
    the host. It is then cleaved, after the virus has budded and while it is maturing, into the
    following proteins: MA (matrix or p17) which forms the inner protein shell beneath the
    viral envelope which stabilises the virion structure and is also involved in transport of the
    viral RNA to the nucleus, CA (capsid or p24) which forms the conical core or capsid , NC
    (nucleocapsid) which coats the genomic RNA during packaging into the virion and p6 , a
    viral protease required for the incorporation of the viral protein Vpr into the virion and
    efficient release of budding virus.
  • Gag-Pol - a protein produced from mRNA that encodes the gag and adjacent pol
    (polymerase) genes. Some 95% of the time, Gap is produced, but 5% of the time, the
    ribosome shifts frame (due to a signal carried on the Gag mRNA and so misses the Gag
    STOP codon and continues onto pol which is encoded on the same mRNA, producing
    Gag-Pol. A viral protease (Pro) then cleaves the Gag from the Pol and cuts up the Pol
    polypeptide into RT (reverse transcriptase, p50), In (integrase, p31), Pro (protease) and
    RNase H (p15, 50% of which remains linked to RT). Pro cleaves Gag and Gag-Pol.
    About 20 Gag are produced to every Gag-Pol.
  • Env - envelope glycoprotein -Env is sent to the host cell's Golgi apparatus where
    carbohydrate chains are added to it (glycosylation) to convert it into a glycoprotein (gp).
    A host cell protease then cleaves Env into gp41 and gp120. These form the envelope
    spikes of HIV: gp41 spans the envelope membrane and the gp120 ligand binds to gp41
    (by a non-covalent bond).
  • Tat (transcriptional transactivator) which binds HIV genomic RNA and increases the
    efficiency of its replication 1000-fold.
  • Rev - switches from early to late gene expression.
  • Nef (negative factor) which is produced early and downregulates the CD4 receptor from
    the infected cell (preventing superinfection?). It is also packaged into virions and cleaved
    by viral protease during virion maturation and greatly increases virion infectivity
    (mechanism?).
  • Vpr - incorporated/pacakged into virions helps the viral DNA gain access to the cell
    nucleus (binds the DNA to the NPC?).
  • Vpu - essential for release of budding virus from the host cell surface prevents CD$
    inside the cell from binding to Env and blocking its incorporation into developing virions
    by causing the cell to degrade any CD4 bound to Env.
  • Vif - essential for replication incorporated into the virion facilitates nucleoprotein
    pacakaging and possibly counters a host cell antivirus mechanism.

Gag, gp41 and gp120 gather in patches in the host cell membrane and recruit viral RNA and
other components of the virion. The virus then buds from the host cell, acquiring the lipid
envelope and then completes its maturation.


Virion Structure

A study done by Prasad and colleagues in 1994 revealed that the Norovirus capsid has a diameter of 38.0nm and exhibits T=3 icosahedral symmetry, with a defined surface structure that resembles typical animal and human caliciviruses, in which cup-like depressions or hollows are evident at the three- and fivefold axes of symmetry. Each virus particle is composed of 180 molecules of the capsid protein, which form 90-arch-like capsomers at all the local and strict twofold axes surrounding the hollows(Bertolotti-Ciarlet et al., 2002). The capsid protein folds into two principal domains, a shell (S) domain and a protruding (P) domain, which contains two subdomains, P1 and P2 (Bertolotti-Ciarlet et al., 2002). Studies done by Bertolotti-Ciarlet and colleagues indicate that the shell domain of the Norovirus capsid protein contains everything required to initiate the assembly of the capsid, whereas the entire protruding domain contributes to the increased stability of the capsid by adding intermolecular contacts between dimeric subunits—which may control the size of the capsid. In the modular structure of the Norovirus capsid protein, the S domain is typically involved in the icosahedral contacts, and the P domains are involved in the dimeric contacts (Prasad et al., 1999).

Noroviruses and other caliciviruses are unique among the animal viruses because they posses a capsid composed of a single major structural protein. Because of this, all the functional entities required for calicivirus structural integrity, immunogenicity, and infectivity are encoded in one structural protein. It is believed that the capsid protein not only provides shell structure for the virus but also contains cellular receptor binding site(s) and viral phenotype or serotype determinants. The function of VP2 associates with upregulation of VP1 expression in cis and stabilization of VP1 in the virus structure (Bertolotti-Ciarlet et al., 2002). Understanding the structure and functions of this viral capsid protein should facilitate the development of antiviral strategies for caliciviruses (Bertolotti-Ciarlet et al., 2002).


Life Cycle of Viruses with Plant Hosts

Plant viruses are more similar to animal viruses than they are to bacteriophages. Plant viruses may be enveloped or non-enveloped. Like many animal viruses, plant viruses can have either a DNA or RNA genome and be single stranded or double stranded. However, most plant viruses do not have a DNA genome the majority have a +ssRNA genome, which acts like messenger RNA (mRNA). Only a minority of plant viruses have other types of genomes.

Plant viruses may have a narrow or broad host range. For example, the citrus tristeza virus infects only a few plants of the Citrus genus, whereas the cucumber mosaic virus infects thousands of plants of various plant families. Most plant viruses are transmitted by contact between plants, or by fungi, nematodes, insects, or other arthropods that act as mechanical vectors. However, some viruses can only be transferred by a specific type of insect vector for example, a particular virus might be transmitted by aphids but not whiteflies. In some cases, viruses may also enter healthy plants through wounds, as might occur due to pruning or weather damage.

Viruses that infect plants are considered biotrophic parasites, which means that they can establish an infection without killing the host, similar to what is observed in the lysogenic life cycles of bacteriophages. Viral infection can be asymptomatic (latent) or can lead to cell death (lytic infection). The life cycle begins with the penetration of the virus into the host cell. Next, the virus is uncoated within the cytoplasm of the cell when the capsid is removed. Depending on the type of nucleic acid, cellular components are used to replicate the viral genome and synthesize viral proteins for assembly of new virions. To establish a systemic infection, the virus must enter a part of the vascular system of the plant, such as the phloem. The time required for systemic infection may vary from a few days to a few weeks depending on the virus, the plant species, and the environmental conditions. The virus life cycle is complete when it is transmitted from an infected plant to a healthy plant.


Do all +ssRNA viruses have similar structures and life cycles? - Biology

All viruses depend on cells for reproduction and metabolic processes. By themselves, viruses do not encode for all of the enzymes necessary for viral replication. But within a host cell, a virus can commandeer cellular machinery to produce more viral particles. Bacteriophages replicate only in the cytoplasm, since prokaryotic cells do not have a nucleus or organelles. In eukaryotic cells, most DNA viruses can replicate inside the nucleus, with an exception observed in the large DNA viruses, such as the poxviruses, that can replicate in the cytoplasm. RNA viruses that infect animal cells often replicate in the cytoplasm.

The Life Cycle of Viruses with Prokaryote Hosts

The life cycle of bacteriophages has been a good model for understanding how viruses affect the cells they infect, since similar processes have been observed for eukaryotic viruses, which can cause immediate death of the cell or establish a latent or chronic infection. Virulent phages typically lead to the death of the cell through cell lysis. Temperate phages , on the other hand, can become part of a host chromosome and are replicated with the cell genome until such time as they are induced to make newly assembled viruses, or progeny virus es.

The Lytic Cycle

During the lytic cycle of virulent phage, the bacteriophage takes over the cell, reproduces new phages, and destroys the cell. T-even phage is a good example of a well-characterized class of virulent phages. There are five stages in the bacteriophage lytic cycle (see [link]). Attachment is the first stage in the infection process in which the phage interacts with specific bacterial surface receptors (e.g., lipopolysaccharides and OmpC protein on host surfaces). Most phages have a narrow host range and may infect one species of bacteria or one strain within a species. This unique recognition can be exploited for targeted treatment of bacterial infection by phage therapy or for phage typing to identify unique bacterial subspecies or strains. The second stage of infection is entry or penetration . This occurs through contraction of the tail sheath, which acts like a hypodermic needle to inject the viral genome through the cell wall and membrane. The phage head and remaining components remain outside the bacteria.

A virulent phage shows only the lytic cycle pictured here. In the lytic cycle, the phage replicates and lyses the host cell.

The third stage of infection is biosynthesis of new viral components. After entering the host cell, the virus synthesizes virus-encoded endonucleases to degrade the bacterial chromosome. It then hijacks the host cell to replicate, transcribe, and translate the necessary viral components (capsomeres, sheath, base plates, tail fibers, and viral enzymes) for the assembly of new viruses. Polymerase genes are usually expressed early in the cycle, while capsid and tail proteins are expressed later. During the maturation phase, new virions are created. To liberate free phages, the bacterial cell wall is disrupted by phage proteins such as holin or lysozyme. The final stage is release. Mature viruses burst out of the host cell in a process called lysis and the progeny viruses are liberated into the environment to infect new cells.

The Lysogenic Cycle

In a lysogenic cycle , the phage genome also enters the cell through attachment and penetration. A prime example of a phage with this type of life cycle is the lambda phage. During the lysogenic cycle, instead of killing the host, the phage genome integrates into the bacterial chromosome and becomes part of the host. The integrated phage genome is called a prophage . A bacterial host with a prophage is called a lysogen . The process in which a bacterium is infected by a temperate phage is called lysogeny . It is typical of temperate phages to be latent or inactive within the cell. As the bacterium replicates its chromosome, it also replicates the phage’s DNA and passes it on to new daughter cells during reproduction. The presence of the phage may alter the phenotype of the bacterium, since it can bring in extra genes (e.g., toxin genes that can increase bacterial virulence). This change in the host phenotype is called lysogenic conversion or phage conversion . Some bacteria, such as Vibrio cholerae and Clostridium botulinum, are less virulent in the absence of the prophage. The phages infecting these bacteria carry the toxin genes in their genome and enhance the virulence of the host when the toxin genes are expressed. In the case of V. cholera, phage encoded toxin can cause severe diarrhea in C. botulinum, the toxin can cause paralysis. During lysogeny, the prophage will persist in the host chromosome until induction , which results in the excision of the viral genome from the host chromosome. After induction has occurred the temperate phage can proceed through a lytic cycle and then undergo lysogeny in a newly infected cell (see [link]).

A temperate bacteriophage has both lytic and lysogenic cycles. In the lysogenic cycle, phage DNA is incorporated into the host genome, forming a prophage, which is passed on to subsequent generations of cells. Environmental stressors such as starvation or exposure to toxic chemicals may cause the prophage to be excised and enter the lytic cycle.

This video illustrates the stages of the lysogenic life cycle of a bacteriophage and the transition to a lytic phase.

Transduction

Transduction occurs when a bacteriophage transfers bacterial DNA from one bacterium to another during sequential infections. There are two types of transduction: generalized and specialized transduction. During the lytic cycle of viral replication, the virus hijacks the host cell, degrades the host chromosome, and makes more viral genomes. As it assembles and packages DNA into the phage head, packaging occasionally makes a mistake. Instead of packaging viral DNA, it takes a random piece of host DNA and inserts it into the capsid. Once released, this virion will then inject the former host’s DNA into a newly infected host. The asexual transfer of genetic information can allow for DNA recombination to occur, thus providing the new host with new genes (e.g., an antibiotic-resistance gene, or a sugar-metabolizing gene). Generalized transduction occurs when a random piece of bacterial chromosomal DNA is transferred by the phage during the lytic cycle. Specialized transduction occurs at the end of the lysogenic cycle, when the prophage is excised and the bacteriophage enters the lytic cycle. Since the phage is integrated into the host genome, the prophage can replicate as part of the host. However, some conditions (e.g., ultraviolet light exposure or chemical exposure) stimulate the prophage to undergo induction, causing the phage to excise from the genome, enter the lytic cycle, and produce new phages to leave host cells. During the process of excision from the host chromosome, a phage may occasionally remove some bacterial DNA near the site of viral integration. The phage and host DNA from one end or both ends of the integration site are packaged within the capsid and are transferred to the new, infected host. Since the DNA transferred by the phage is not randomly packaged but is instead a specific piece of DNA near the site of integration, this mechanism of gene transfer is referred to as specialized transduction (see [link]). The DNA can then recombine with host chromosome, giving the latter new characteristics. Transduction seems to play an important role in the evolutionary process of bacteria, giving them a mechanism for asexual exchange of genetic information.

This flowchart illustrates the mechanism of specialized transduction. An integrated phage excises, bringing with it a piece of the DNA adjacent to its insertion point. On reinfection of a new bacterium, the phage DNA integrates along with the genetic material acquired from the previous host.

Life Cycle of Viruses with Animal Hosts

Lytic animal viruses follow similar infection stages to bacteriophages: attachment, penetration, biosynthesis, maturation, and release (see [link]). However, the mechanisms of penetration, nucleic-acid biosynthesis, and release differ between bacterial and animal viruses. After binding to host receptors, animal viruses enter through endocytosis (engulfment by the host cell) or through membrane fusion (viral envelope with the host cell membrane). Many viruses are host specific, meaning they only infect a certain type of host and most viruses only infect certain types of cells within tissues. This specificity is called a tissue tropism . Examples of this are demonstrated by the poliovirus , which exhibits tropism for the tissues of the brain and spinal cord, or the influenza virus , which has a primary tropism for the respiratory tract.

In influenza virus infection, viral glycoproteins attach the virus to a host epithelial cell. As a result, the virus is engulfed. Viral RNA and viral proteins are made and assembled into new virions that are released by budding.

Animal viruses do not always express their genes using the normal flow of genetic information—from DNA to RNA to protein. Some viruses have a dsDNA genome like cellular organisms and can follow the normal flow. However, others may have ssDNA , dsRNA , or ssRNA genomes. The nature of the genome determines how the genome is replicated and expressed as viral proteins. If a genome is ssDNA, host enzymes will be used to synthesize a second strand that is complementary to the genome strand, thus producing dsDNA. The dsDNA can now be replicated, transcribed, and translated similar to host DNA.

If the viral genome is RNA, a different mechanism must be used. There are three types of RNA genome: dsRNA, positive (+) single-strand (+ssRNA) or negative (−) single-strand RNA (−ssRNA) . If a virus has a +ssRNA genome, it can be translated directly to make viral proteins. Viral genomic +ssRNA acts like cellular mRNA. However, if a virus contains a −ssRNA genome, the host ribosomes cannot translate it until the −ssRNA is replicated into +ssRNA by viral RNA-dependent RNA polymerase (RdRP) (see [link]). The RdRP is brought in by the virus and can be used to make +ssRNA from the original −ssRNA genome. The RdRP is also an important enzyme for the replication of dsRNA viruses, because it uses the negative strand of the double-stranded genome as a template to create +ssRNA. The newly synthesized +ssRNA copies can then be translated by cellular ribosomes.

RNA viruses can contain +ssRNA that can be directly read by the ribosomes to synthesize viral proteins. Viruses containing −ssRNA must first use the −ssRNA as a template for the synthesis of +ssRNA before viral proteins can be synthesized.

An alternative mechanism for viral nucleic acid synthesis is observed in the retrovirus es, which are +ssRNA viruses (see [link]). Single-stranded RNA viruses such as HIV carry a special enzyme called reverse transcriptase within the capsid that synthesizes a complementary ssDNA (cDNA) copy using the +ssRNA genome as a template. The ssDNA is then made into dsDNA, which can integrate into the host chromosome and become a permanent part of the host. The integrated viral genome is called a provirus . The virus now can remain in the host for a long time to establish a chronic infection. The provirus stage is similar to the prophage stage in a bacterial infection during the lysogenic cycle. However, unlike prophage, the provirus does not undergo excision after splicing into the genome.

HIV, an enveloped, icosahedral retrovirus, attaches to a cell surface receptor of an immune cell and fuses with the cell membrane. Viral contents are released into the cell, where viral enzymes convert the single-stranded RNA genome into DNA and incorporate it into the host genome. (credit: modification of work by NIAID, NIH)

Persistent Infections

Persistent infection occurs when a virus is not completely cleared from the system of the host but stays in certain tissues or organs of the infected person. The virus may remain silent or undergo productive infection without seriously harming or killing the host. Mechanisms of persistent infection may involve the regulation of the viral or host gene expressions or the alteration of the host immune response. The two primary categories of persistent infections are latent infection and chronic infection . Examples of viruses that cause latent infections include herpes simplex virus (oral and genital herpes), varicella-zoster virus (chickenpox and shingles), and Epstein-Barr virus (mononucleosis). Hepatitis C virus and HIV are two examples of viruses that cause long-term chronic infections.

Latent Infection

Not all animal viruses undergo replication by the lytic cycle. There are viruses that are capable of remaining hidden or dormant inside the cell in a process called latency. These types of viruses are known as latent virus es and may cause latent infections. Viruses capable of latency may initially cause an acute infection before becoming dormant.

For example, the varicella-zoster virus infects many cells throughout the body and causes chickenpox , characterized by a rash of blisters covering the skin. About 10 to 12 days postinfection, the disease resolves and the virus goes dormant, living within nerve-cell ganglia for years. During this time, the virus does not kill the nerve cells or continue replicating. It is not clear why the virus stops replicating within the nerve cells and expresses few viral proteins but, in some cases, typically after many years of dormancy, the virus is reactivated and causes a new disease called shingles ([link]). Whereas chickenpox affects many areas throughout the body, shingles is a nerve cell-specific disease emerging from the ganglia in which the virus was dormant.

(a) Varicella-zoster, the virus that causes chickenpox, has an enveloped icosahedral capsid visible in this transmission electron micrograph. Its double-stranded DNA genome becomes incorporated in the host DNA. (b) After a period of latency, the virus can reactivate in the form of shingles, usually manifesting as a painful, localized rash on one side of the body. (credit a: modification of work by Erskine Palmer and B.G. Partin—scale-bar data from Matt Russell credit b: modification of work by Rosmarie Voegtli)

Latent viruses may remain dormant by existing as circular viral genome molecules outside of the host chromosome. Others become proviruses by integrating into the host genome. During dormancy, viruses do not cause any symptoms of disease and may be difficult to detect. A patient may be unaware that he or she is carrying the virus unless a viral diagnostic test has been performed.

Chronic Infection

A chronic infection is a disease with symptoms that are recurrent or persistent over a long time. Some viral infections can be chronic if the body is unable to eliminate the virus. HIV is an example of a virus that produces a chronic infection, often after a long period of latency. Once a person becomes infected with HIV, the virus can be detected in tissues continuously thereafter, but untreated patients often experience no symptoms for years. However, the virus maintains chronic persistence through several mechanisms that interfere with immune function, including preventing expression of viral antigens on the surface of infected cells, altering immune cells themselves, restricting expression of viral genes, and rapidly changing viral antigens through mutation. Eventually, the damage to the immune system results in progression of the disease leading to acquired immunodeficiency syndrome (AIDS). The various mechanisms that HIV uses to avoid being cleared by the immune system are also used by other chronically infecting viruses, including the hepatitis C virus.

Life Cycle of Viruses with Plant Hosts

Plant viruses are more similar to animal viruses than they are to bacteriophages. Plant viruses may be enveloped or non-enveloped. Like many animal viruses, plant viruses can have either a DNA or RNA genome and be single stranded or double stranded. However, most plant viruses do not have a DNA genome the majority have a +ssRNA genome, which acts like messenger RNA (mRNA). Only a minority of plant viruses have other types of genomes.

Plant viruses may have a narrow or broad host range. For example, the citrus tristeza virus infects only a few plants of the Citrus genus, whereas the cucumber mosaic virus infects thousands of plants of various plant families. Most plant viruses are transmitted by contact between plants, or by fungi, nematodes, insects, or other arthropods that act as mechanical vectors. However, some viruses can only be transferred by a specific type of insect vector for example, a particular virus might be transmitted by aphids but not whiteflies. In some cases, viruses may also enter healthy plants through wounds, as might occur due to pruning or weather damage.

Viruses that infect plants are considered biotrophic parasites, which means that they can establish an infection without killing the host, similar to what is observed in the lysogenic life cycles of bacteriophages. Viral infection can be asymptomatic (latent) or can lead to cell death (lytic infection). The life cycle begins with the penetration of the virus into the host cell. Next, the virus is uncoated within the cytoplasm of the cell when the capsid is removed. Depending on the type of nucleic acid, cellular components are used to replicate the viral genome and synthesize viral proteins for assembly of new virions. To establish a systemic infection, the virus must enter a part of the vascular system of the plant, such as the phloem. The time required for systemic infection may vary from a few days to a few weeks depending on the virus, the plant species, and the environmental conditions. The virus life cycle is complete when it is transmitted from an infected plant to a healthy plant.

Viral Growth Curve

Unlike the growth curve for a bacterial population, the growth curve for a virus population over its life cycle does not follow a sigmoidal curve. During the initial stage, an inoculum of virus causes infection. In the eclipse phase , viruses bind and penetrate the cells with no virions detected in the medium. The chief difference that next appears in the viral growth curve compared to a bacterial growth curve occurs when virions are released from the lysed host cell at the same time. Such an occurrence is called a burst , and the number of virions per bacterium released is described as the burst size . In a one-step multiplication curve for bacteriophage , the host cells lyse, releasing many viral particles to the medium, which leads to a very steep rise in viral titer (the number of virions per unit volume). If no viable host cells remain, the viral particles begin to degrade during the decline of the culture (see [link]).

The one-step multiplication curve for a bacteriophage population follows three steps: 1) inoculation, during which the virions attach to host cells 2) eclipse, during which entry of the viral genome occurs and 3) burst, when sufficient numbers of new virions are produced and emerge from the host cell. The burst size is the maximum number of virions produced per bacterium.

Ebola is incurable and deadly. The outbreak in West Africa in 2014 was unprecedented, dwarfing other human Ebola epidemics in the level of mortality. Of 24,666 suspected or confirmed cases reported, 10,179 people died. 1

No approved treatments or vaccines for Ebola are available. While some drugs have shown potential in laboratory studies and animal models, they have not been tested in humans for safety and effectiveness. Not only are these drugs untested or unregistered but they are also in short supply.

Given the great suffering and high mortality rates, it is fair to ask whether unregistered and untested medications are better than none at all. Should such drugs be dispensed and, if so, who should receive them, in light of their extremely limited supplies? Is it ethical to treat untested drugs on patients with Ebola? On the other hand, is it ethical to withhold potentially life-saving drugs from dying patients? Or should the drugs perhaps be reserved for health-care providers working to contain the disease?

In August 2014, two infected US aid workers and a Spanish priest were treated with ZMapp , an unregistered drug that had been tested in monkeys but not in humans. The two American aid workers recovered, but the priest died. Later that month, the WHO released a report on the ethics of treating patients with the drug. Since Ebola is often fatal, the panel reasoned that it is ethical to give the unregistered drugs and unethical to withhold them for safety concerns. This situation is an example of “compassionate use” outside the well-established system of regulation and governance of therapies.

On September 24, 2014, Thomas Eric Duncan arrived at the Texas Health Presbyterian Hospital in Dallas complaining of a fever, headache, vomiting, and diarrhea—symptoms commonly observed in patients with the cold or the flu. After examination, an emergency department doctor diagnosed him with sinusitis, prescribed some antibiotics, and sent him home. Two days later, Duncan returned to the hospital by ambulance. His condition had deteriorated and additional blood tests confirmed that he has been infected with the Ebola virus.

Further investigations revealed that Duncan had just returned from Liberia, one of the countries in the midst of a severe Ebola epidemic. On September 15, nine days before he showed up at the hospital in Dallas, Duncan had helped transport an Ebola-stricken neighbor to a hospital in Liberia. The hospital continued to treat Duncan, but he died several days after being admitted.

The timeline of the Duncan case is indicative of the life cycle of the Ebola virus. The incubation time for Ebola ranges from 2 days to 21 days. Nine days passed between Duncan’s exposure to the virus infection and the appearance of his symptoms. This corresponds, in part, to the eclipse period in the growth of the virus population. During the eclipse phase, Duncan would have been unable to transmit the disease to others. However, once an infected individual begins exhibiting symptoms, the disease becomes very contagious. Ebola virus is transmitted through direct contact with droplets of bodily fluids such as saliva, blood, and vomit. Duncan could conceivably have transmitted the disease to others at any time after he began having symptoms, presumably some time before his arrival at the hospital in Dallas. Once a hospital realizes a patient like Duncan is infected with Ebola virus, the patient is immediately quarantined, and public health officials initiate a back trace to identify everyone with whom a patient like Duncan might have interacted during the period in which he was showing symptoms.

Public health officials were able to track down 10 high-risk individuals (family members of Duncan) and 50 low-risk individuals to monitor them for signs of infection. None contracted the disease. However, one of the nurses charged with Duncan’s care did become infected. This, along with Duncan’s initial misdiagnosis, made it clear that US hospitals needed to provide additional training to medical personnel to prevent a possible Ebola outbreak in the US.


Watch the video: Virus Life Cycle for Different Viral Genomes dsDNA, ssDNA, dsRNA, ssRNA, + sense, - sense MCAT (May 2022).


Comments:

  1. Aethelbeorht

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