User:AlveoliRavioli/New sandbox

This sandbox is for editing the Norovirus Article

Continued Rewrite: -- Diagnosis -- Current Entry:
"Specific diagnosis of norovirus is routinely made by polymerase chain reaction (PCR) assays or quantitative PCR assays, which give results within a few hours. These assays are very sensitive and can detect as few as 10 virus particles.

Tests such as ELISA that use antibodies against a mixture of norovirus strains are available commercially, but lack specificity and sensitivity.

Due to a lack of specific therapy, the need for expensive stool diagnostics is being questioned by experts if gastroenteritis by noroviruses has already been detected in the environment."

Diagnosis Addition:

 * Refer to Kaplan's the 4 diagnostic symptoms of an outbreak
 * Explain cell culture methods are not available

My re-write: (Underline = not changed)
Specific diagnosis of norovirus is routinely made by reverse transcriptase quantitative PCR assays, which give results within a few hours. These assays are very sensitive and can detect as few as 10 virus particles, but for quickly identifying the etiological agent of an outbreak, molecular tests may prove difficult to acquire before many people are infected. ELISA tests use antibodies against a mixture of norovirus strains are commercially available but lack specificity and sensitivity. Generally, investigation of a Norovirus outbreak should commence if an illness reveals Kaplan's four criteria for Norovirus-induced gastroenteritis. Vomiting should be a symptom in more than half of infected individuals, the mean/median incubation time and duration of illness should be about 48 hours and 12-60 hours respectively, and no bacterial pathogen should be detected in stool samples.

Many viral contagions in research labs are able to be grown and cultivated in mammalian or other cell lines, leading to cytopathic effects (CPE) that can be used in the identification process of etiological agents. However, after almost 50 years of identifying the Norwalk agent, human noroviruses have only recently been successfully cultured in mammalian B-cells and enteroids, producing small replication numbers. This makes identifying molecular mechanisms of disease difficult, but also the development of effective antivirals.

Current entry in Norovirus article on Replication:
"Viral replication is cytoplasmic. Entry into the host cell is achieved by attachment to host receptors, which mediates endocytosis. Positive-stranded RNA virus transcription is the method of replication. Translation takes place by leaky scanning and RNA termination-reinitiation. Humans and other mammals serve as the natural host. Transmission routes are fecal-oral and contamination."

Norovirus Replication Cycle Addition:

 * Talk about glycan, non-glycan, and the potential proteinaceous receptors known to MuNV and FCV, but not clearly identified yet in humans (CD300lf receptor -- has an immunoglobulin family)
 * HBGA -- can be secreted into body fluids, unless a person possesses a FUT2 mutation. This effectively leads to the inability for secreting cells to produce the free-floating A,B,O antigens that may bind NoV capsids. These people are more resistant to HuNoV infection, although, it does not mean they will never contract NoV illness.

My re-write: (Underline = not changed)
Viral replication is cytoplasmic. Entry into the host cell is achieved be attachment to host receptors, which mediates endocytosis. Glycan receptors have also been implicated in Norovirus entry, primarily human blood-group antigen or HBGA HBGA are found on the surfaces of red and white blood cells, intestinal epithelium, and mucosal membranes. Therefore, Norovirus is capable of not only targeting enterocytes entry, but it may also target immune cells such as B-lymphocytes, macrophages, and dendritic cells in immunocompromised individuals. Research has yet to indicate with certainty the proteinaceous receptor that allows entry into host cells, but work with mouse noroviruses and feline calcivirus (FCV) provide strong evidence for entry via the C300fl receptor. The C300fl receptor is thought to play a role in the penetration of Norovirus genome into host cells after entry via clathrin and caveolin-independent endocytosis. The proposed mechanism in FCV studies is that once inside the endosome, the acidic pH causes the VP1 protein on the nucleocapsid to change conformation, but more specifically a P domain rotation. A pore is created in the endosomal membrane that allows the internal VP2 protein to escape and interact with both motifs of the P domain, the insertion of hydrophobic residues into the endosomal membrane, and the resulting formation of a pore in which genomic RNA exits to the cytoplasm for translation.

Translation takes place by leaky scanning and RNA termination-reinitiation. Because the +ssRNA genome can act as mRNA, translation of ORF1 immediately follows genome entry. ORF1 codes for a polyprotein that codes for at least 6 different protein products: p48 (NS1/2), NTPase (NS3), p22 (NS4), viral-genome linked protein (NS5), 3C-like protease (NS6), and an RNA-dependent RNA-polymerase (NS7). Notably, the NS6 protease undergoes autocleavage, and this allows the individual protein products to be released from the original polyprotein. This is critical for genome replication, as it releases the RNA-dependent RNA-polymerase for viral genomic transcription. Replication of Norovirus does not occur in the nucleus, but in the cytoplasm within structures known as viral factories. It is thought that p48 plays a critical role in the construction of viral factories to protect dsRNA intermediates from host cell recognition (citation). ORFs 2 and 3 code for the major capsid protein VP1 and minor VP2, respectively. ORF3 is translated in a reinitiation event where the ribosome detaches from the viral bicistronic RNA after ORF2 translation, but then associates again with the RNA for ORF3 translation. Once the genome and capsid proteins have assembled in the cell cytoplasm, the virions exit the cell through cell lysis and set out to infect more host cells.

Comparison: Norovirus article vs. Rotavirus article

 * Introduction/ Teasers
 * Rotavirus intro -- who gets the virus, how does one become immune, transmission, epidemiology stats of death and hospitalizations, vaccine introduction decreases childhood disease and death risk
 * Norovirus intro -- symptoms, illness described, transmission, risk and prevention, epidemiology stats, where the Norwalk virus originated
 * VIROLOGY
 * Rotavirus
 * Begins immediately talking about the virology (types --> structure --> proteins structural and nonstructural --> replication)
 * Has a separate section for TRANSMISSION
 * Norovirus
 * Opens with a brief overview of SIGNS AND SYMPTOMS and mentions rare, but severe instances of illness. Then, it talks about the virology (transmission --> classification --> structure --> genome   --> evolution --> only a few sentences on the replication process).
 * Other section comparisons after the virology component
 * Rotavirus
 * SIGNS AND SYMPTOMS
 * DISEASE MECHANISMS -- I like this section a lot because it actually explains why the symptoms are present with this viral infection. The Norovirus lacks a section like this.
 * IMMUNE RESPONSES -- I also really like this section. For Norovirus, I could make a section similar to this one, but I would add what I have learned about the interferon response...although...that article was a primary source, so probably not :(
 * DIAGNOSIS AND DETECTION -- similar to the Norovirus article
 * TREATMENT AND PROGNOSIS
 * PREVENTION
 * EPIDEMIOLOGY
 * OTHER ANIMALS -- this section is not in the Norovirus article, but it may not be necessary (at least, for my contribution). There are mouse strains of the virus for Norovirus, but the immune response is different for mice than for humans. It could be worth adding or mentioning, but I may do that as a last resort if my other ideas for entries fall though
 * HISTORY -- I do not think this makes sense to put history at the end of an article. The "story" of the virus does not flow well whenever the past comes at the end. Why should people be concerned with the virus other than it makes people sick?
 * Norovirus
 * PATHOPHYSIOLOGY -- Not very helpful in understanding why symptoms arise after infection. Merely restates the symptoms of the virus and some epidemiology data. Consider eliminating this section and moving the info to other defined sections ( SIGNS AND SYMPTOMS & EPIDEMIOLOGY )
 * DIAGNOSIS -- similar info to the Rotavirus article, but I think I could make the wording better (more "flowy").
 * PREVENTION -- I think this section should go after the treatment section, like in the Rotavirus article
 * TREATMENT
 * EPIDEMIOLOGY -- I may try to move this section before the diagnosis section. Because people will have read about the virology and how the virus enters
 * HUMAN GENETICS -- I like that this article dives into the "exceptions" of people who are not as likely to contract an illness from Norovirus. However, it may be wise to put this section close the "virology" section of the article so that they see the larger impact of that information right away. Also, if people are worried that they are infected with the virus, seeing how rare or common it is in certain parts of the world may calm their nerves or make them more curious.
 * HISTORY -- Same thing as for Rotavirus. This section should be at the beginning of the article because the virus has a story. I do not think it is inconvenient to scroll past the "history" section if people are curious about personal symptoms or the virology of this bug.

Revised Norovirus Article Format:

 * Intro paragraph (keep the same)
 * HISTORY
 * Move the information from the transmission section into this section (as long as it is relevant to historical outbreaks). The outbreak can be introduced here, while the reason there was an outbreak can be explained in the transmission subsection!
 * VIROLOGY
 * Classification/Genome
 * Add what genes encode which proteins
 * Structure
 * Replication cycle -- this part is lacking
 * Include information of a cytoplasmic body that protects the genome as it replicates
 * attachment and entry
 * Immune cell and enterocyte tropism
 * May exploit M cells, which surround Peyer's patches, to infect the intestinal epithelium
 * Transmission
 * There is an example of fecal-oral transmission in this section. Honestly, I think it should be put in the history section or omitted.
 * HGBA receptor information
 * HUMAN GENETICS
 * People with the FUT2 gene mutation do not present an antigen for norovirus binding, and people with this mutation are less susceptible to Norovirus infection
 * EPIDEMIOLOGY
 * SIGNS AND SYMPTOMS
 * Maybe go in depth about why the signs and symptoms are present (what is happening molecularly?)
 * DIAGNOSIS
 * Cell culture methods are not readily available because there is not a method to grow Norovirus in cell culture
 * TREATMENT
 * PREVENTION
 * Lettuce binding (would require a primary source)
 * Lettuce binding (would require a primary source)