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sars-cov-2 [2022/01/24 14:28]
mathew
sars-cov-2 [2022/09/19 04:39] (current)
pamela
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 ====== SARS-CoV-2 ====== ====== SARS-CoV-2 ======
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 +{{ ::screen_shot_2022-03-03_at_3.16.04_am.png?400|}}
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 **SARS-CoV-2** is a humanborne [[coronavirus]] in the //[[betacoronavirus]]// family. The emergence of SARS-CoV-2 led to the [[SARS-CoV-2 pandemic]] to be declared by the [[World Health Organization]]. **SARS-CoV-2** is a humanborne [[coronavirus]] in the //[[betacoronavirus]]// family. The emergence of SARS-CoV-2 led to the [[SARS-CoV-2 pandemic]] to be declared by the [[World Health Organization]].
  
 +SARS-CoV-2 stands for Severe Acute Respiratory Syndrome Coronavirus 2. It is named as such due to its relative similarity to the [[SARS-CoV-1|SARS coronavirus]] that led to a public health emergency in parts of the world in 2003.((Wu, Y., Ho, W., Huang, Y., Jin, D.-Y., Li, S., Liu, S.-L., Liu, X., Qiu, J., Sang, Y., Wang, Q., Yuen, K.-Y., & Zheng, Z.-M. (2020). //SARS-CoV-2 is an appropriate name for the new coronavirus.// The Lancet, 0(0). https://doi.org/10.1016/S0140-6736(20)30557-2)) ((Feng, D., De Vlas, S. J., Fang, L., Han, X., Zhao, W., Sheng, S., Yang, H., Jia, Z., Richardus, J. H., & Cao, W. (2009). //The SARS epidemic in mainland China: bringing together all epidemiological data.// Tropical Medicine & International Health, 14(Suppl 1), 4–13. https://doi.org/10.1111/j.1365-3156.2008.02145.x))
 +
 +The SARS-CoV-2 virus is a close genetic relative of two other infamous viruses from recent history: [[SARS-CoV-1|SARS-CoV]] and [[MERS-CoV]].((Rabaan, A. A., Al-Ahmed, S. H., Haque, S., Sah, R., Tiwari, R., Malik, Y. S., Dhama, K., Yatoo, M. I., Bonilla-Aldana, D. K., & Rodriguez-Morales, A. J. (2020). //SARS-CoV-2, SARS-CoV, and MERS-COV: A comparative overview.// Le infezioni in medicina, 28(2), 174–184.))
 +
 +
 +{{ ::sars-cov-2_genome_match_2015_studies.png?400|}}
 Related Pages: Related Pages:
   * [[SARS-CoV-2:Origins]]   * [[SARS-CoV-2:Origins]]
 +  * [[SARS-CoV-2:Genetics of SARS-CoV-2]]
   * [[SARS-CoV-2:Spike Protein]]   * [[SARS-CoV-2:Spike Protein]]
   * [[SARS-CoV-2:Surveillance and Testing]]   * [[SARS-CoV-2:Surveillance and Testing]]
   * [[SARS-CoV-2:Variants]]   * [[SARS-CoV-2:Variants]]
- +    * [[SARS-CoV-2:Omicron]] 
 +  * [[COVID-19]] 
 +    * [[COVID-19 Pandemic]] 
 +    * [[COVID-19 Vaccines]] 
 +threadreader for inage ((https://web.archive.org/web/20220917230646/https://threadreaderapp.com/thread/1571168157754089479.html))
 ===== SARS-CoV-2 Viral Mechanisms and Characteristics ===== ===== SARS-CoV-2 Viral Mechanisms and Characteristics =====
 SARS-CoV-2 is a positively charged, single-stranded [[RNA virus]]. SARS-CoV-2 is a positively charged, single-stranded [[RNA virus]].
  
 ==== Features ==== ==== Features ====
 +  * [[SARS-CoV-2:Genetics of SARS-CoV-2]]
   * [[SARS-CoV-2:Spike protein]]   * [[SARS-CoV-2:Spike protein]]
   * [[SARS-CoV-2:Furin Cleavage Site]]   * [[SARS-CoV-2:Furin Cleavage Site]]
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 ==== Pathology ==== ==== Pathology ====
   * Dec, 2020 - Liao et al; SARS-CoV-2 in the bile of a patient with COVID-19-associated gallbladder disease.((December, 2020 | Liao et al | Endoscopy (journal) | SARS-CoV-2 in the bile of a patient with COVID-19-associated gallbladder disease | [[https://www.thieme-connect.de/products/ejournals/abstract/10.1055/a-1290-7446|doi: 10.1055/a-1290-7446]]))   * Dec, 2020 - Liao et al; SARS-CoV-2 in the bile of a patient with COVID-19-associated gallbladder disease.((December, 2020 | Liao et al | Endoscopy (journal) | SARS-CoV-2 in the bile of a patient with COVID-19-associated gallbladder disease | [[https://www.thieme-connect.de/products/ejournals/abstract/10.1055/a-1290-7446|doi: 10.1055/a-1290-7446]]))
 +
 +Researchers have found in autopsies that SARS-CoV-2 does get into brain tissue, and can be present for months after infection, though inflammation outside of the lungs was mild.((December 20, 2021 | Daniel Chertow et al | Nature Portfolio (journal) | SARS-CoV-2 infection and persistence throughout the human body and brain | [[https://www.researchsquare.com/article/rs-1139035/v1|doi.org/10.21203/rs.3.rs-1139035/v1]]))
 +
 +See [[SARS-CoV-2:Spike Protein]] for a discussion of [[:toxins]].
  
 ==== Transmission and Infectivity ==== ==== Transmission and Infectivity ====
 Nearly two years into the [[COVID-19 pandemic]], some aspects of transmission is still debated. Contact tracing research out of [[China]] showed no asymptomatic viral transmission at all.((November 20, 2020 | Cao et al | [[Nature Communications]] | [[https://www.nature.com/articles/s41467-020-19802-w|Post-lockdown SARS-CoV-2 nucleic acid screening in nearly ten million residents of Wuhan, China]])) Other research indicates that symptomatic transmission drives the pandemic, but there may be smaller amounts of asymptomatic and presymptomatic spread.((April, 2021 | Nakajo and Nishiura | [[International Journal of Infectious Disease]] | [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7894083/|doi: 10.1016/j.ijid.2021.02.065]])) ((https://swprs.org/pre-symptomatic-transmission-is-very-real/| Pre-symptomatic transmission is very real | Swiss Policy Institute | Aug, 2021)) ((Mar 4, 2020 | Nishiura et al | [[International Journal of Infectious Diseases]] | [[https://www.ijidonline.com/article/S1201-9712(20)30119-3/fulltext|doi.org/10.1016/j.ijid.2020.02.060]])) Nearly two years into the [[COVID-19 pandemic]], some aspects of transmission is still debated. Contact tracing research out of [[China]] showed no asymptomatic viral transmission at all.((November 20, 2020 | Cao et al | [[Nature Communications]] | [[https://www.nature.com/articles/s41467-020-19802-w|Post-lockdown SARS-CoV-2 nucleic acid screening in nearly ten million residents of Wuhan, China]])) Other research indicates that symptomatic transmission drives the pandemic, but there may be smaller amounts of asymptomatic and presymptomatic spread.((April, 2021 | Nakajo and Nishiura | [[International Journal of Infectious Disease]] | [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7894083/|doi: 10.1016/j.ijid.2021.02.065]])) ((https://swprs.org/pre-symptomatic-transmission-is-very-real/| Pre-symptomatic transmission is very real | Swiss Policy Institute | Aug, 2021)) ((Mar 4, 2020 | Nishiura et al | [[International Journal of Infectious Diseases]] | [[https://www.ijidonline.com/article/S1201-9712(20)30119-3/fulltext|doi.org/10.1016/j.ijid.2020.02.060]]))
 +
 +Further reading:
 +  * Jan 7, 2021 - Johansson et al; Asymptomatic and presymptomatic spread 25% less.((January 7, 2021 | Johansson et al | [[JAMA Network]] | SARS-CoV-2 Transmission From People Without COVID-19 Symptoms | [[https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2774707|doi:10.1001/jamanetworkopen.2020.35057]]))
  
 === Aerosolization and Transmissibility === === Aerosolization and Transmissibility ===
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 == Indoor/Outdoor Transmission == == Indoor/Outdoor Transmission ==
 SARS-CoV-2 is a highly aerosolized virus, and research shows that nearly all transmission takes place in indoor settings where a poorly ventilated room can fill to a pressurized level with virions. One study (preprint) found that 95% of primary case transmission in [[Japan]] took place in closed environments.((Apr 16, 2020 | Nishiura et al | [[https://www.medrxiv.org/content/10.1101/2020.02.28.20029272v2|https://doi.org/10.1101/2020.02.28.20029272]])) SARS-CoV-2 is a highly aerosolized virus, and research shows that nearly all transmission takes place in indoor settings where a poorly ventilated room can fill to a pressurized level with virions. One study (preprint) found that 95% of primary case transmission in [[Japan]] took place in closed environments.((Apr 16, 2020 | Nishiura et al | [[https://www.medrxiv.org/content/10.1101/2020.02.28.20029272v2|https://doi.org/10.1101/2020.02.28.20029272]]))
 +
 +https://www.irishtimes.com/news/ireland/irish-news/outdoor-transmission-accounts-for-0-1-of-state-s-covid-19-cases-1.4529036
  
 = Transmission among Children and in Schools = = Transmission among Children and in Schools =
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     * School closures had no significant impact on spread of SARS-CoV-2 either among the children in spill-over effects to older generations. School opening had no impacts, and lower transmission incidence was seen.     * School closures had no significant impact on spread of SARS-CoV-2 either among the children in spill-over effects to older generations. School opening had no impacts, and lower transmission incidence was seen.
  
 +=== Animal Transmission ===
 +Early during the [[COVID-19 pandemic]], many laboratories euthanized mice as a preventative measure.((March 23, 2020 | Science.org | [[https://www.science.org/content/article/it-s-heartbreaking-labs-are-euthanizing-thousands-mice-response-coronavirus-pandemic|‘It's heartbreaking.' Labs are euthanizing thousands of mice in response to coronavirus pandemic]]))
  
 === Pathways and Cell Entry === === Pathways and Cell Entry ===
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 == Infectivity in Animal Hosts == == Infectivity in Animal Hosts ==
 +[[https://vis.csh.ac.at/sars-ani/#infections|COVID-19 animal infection tracker]]
 +
 Numerous animals aside from humans have been noted to be susceptible to SARS-CoV-2 infection. Comparative and structural analysis on 410 vertebrate species predicts a broad host range for infection, specifically among mammals.((September 8, 2020 | Damas et al | [[:Proceedings of the National Academy of Sciences|PNAS]] | [[https://www.pnas.org/content/117/36/22311|doi.org/10.1073/pnas.2010146117]])) Numerous animals aside from humans have been noted to be susceptible to SARS-CoV-2 infection. Comparative and structural analysis on 410 vertebrate species predicts a broad host range for infection, specifically among mammals.((September 8, 2020 | Damas et al | [[:Proceedings of the National Academy of Sciences|PNAS]] | [[https://www.pnas.org/content/117/36/22311|doi.org/10.1073/pnas.2010146117]]))
- +One study still in preprint found SARS-CoV-2 moving rapidly into white-tailed deer populations in North America, with over 80% of the deer testing PCR positive for the virus by early 2021.((November 6, 2021 | Kuchipudi et al | preprint | [[https://www.biorxiv.org/content/10.1101/2021.10.31.466677v2|doi.org/10.1101/2021.10.31.466677]]))
- +
-===== Disease ===== +
- +
-==== COVID-19 ==== +
-SARS-CoV-2 is a cause of [[COVID-19]]a disease with wide ranging characteristics primarily affecting the respiratory and vascular sysems.+
  
 ==== Immunity ==== ==== Immunity ====
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 === Natural Immunity === === Natural Immunity ===
 See [[COVID-19:natural immunity]]. See [[COVID-19:natural immunity]].
 +
 +=== Reinfections ===
 +During the early part of the COVID-19 pandemic, physicians and scientists found that reinfections were extremely rare.((May 19, 2020 | ScienceNews.org | [[https://www.sciencenews.org/article/coronavirus-covid19-reinfection-immune-response|New data suggest people aren’t getting reinfected with the coronavirus]]))
 +
 +During the omicron era, reinfections are rapidly on the rise.((March 21, 2022 | [[:Igor Chudov]] | [[https://igorchudov.substack.com/p/uk-short-term-reinfections-exploding?s=r|UK: Short-term Reinfections Exploding]]))
 +
 +=== Transference of Immunity ===
 +Scientists have noted evidence for aerosol transfer of SARS-CoV-2-specific humoral immunity.((May 1, 2022 | Kedl et al | preprint | Evidence for Aerosol Transfer of SARS-CoV2-specific Humoral Immunity | [[https://www.medrxiv.org/content/10.1101/2022.04.28.22274443v1.full#F1|doi.org/10.1101/2022.04.28.22274443]]))
 +
 +
 +
 +===== Disease =====
 +
 +==== COVID-19 ====
 +SARS-CoV-2 is a cause of [[COVID-19]], a disease with wide ranging characteristics primarily affecting the [[respiratory]] and [[vascular]] systems.
 +
 +==== Genetic and Epigenetic Effects of Infection ====
 +
 +=== Chromatin Architecture ===
 +  * SARS-CoV-2 Restructures the Host Chromatin Architecture((July 21, 2021 | Ruoyu Wang et al | preprint | [[https://www.biorxiv.org/content/10.1101/2021.07.20.453146v1.full|doi: https://doi.org/10.1101/2021.07.20.453146]]))
 +
 +
  
 ===== Mutation and Variants ===== ===== Mutation and Variants =====
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 See more at [[SARS-CoV-2:Variants|SARS-CoV-2 Variants]] See more at [[SARS-CoV-2:Variants|SARS-CoV-2 Variants]]
  
 +===== Controversies =====
  
-===== SARS-CoV-2 Origins Story Controversy =====+==== SARS-CoV-2 Origins Story Controversy ====
 The [[SARS-CoV-2:origins|origins of SARS-CoV-2]] are shrowded in mystery, including whether the virus is zoonotic or manmade, or was released accidentially or intentionaly. The [[SARS-CoV-2:origins|origins of SARS-CoV-2]] are shrowded in mystery, including whether the virus is zoonotic or manmade, or was released accidentially or intentionaly.
 +
 +==== Retracted Research ====
 +Many papers have been retracted during the [[COVID-19 pandemic]]. Here are some that relate specifically to SARS-CoV-2, though others may be found at [[Retraction Watch]].
 +  * SARS-CoV-2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro((October 13, 2021 | Jiang and Mei | Viruses (journal) | SARS-CoV-2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro | [[https://pubmed.ncbi.nlm.nih.gov/34696485/|doi: 10.3390/v13102056]]))
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