SARS-CoV-2 spike protein mutations: Difference between revisions

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Eric Martz

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 '''SARS-CoV-2''' stands for ''Severe Acute Respiratory Syndrome - Corona Virus 2''. The SARS-CoV-2 [[SARS-CoV-2 spike protein priming by furin|coronavirus]] causes '''COVID-19''' ('''CO'''rona '''VI'''rus '''D'''isease 20'''19'''). SARS-CoV-2 was numbered "2" because another coronavirus, [[SARS Coronavirus Main Proteinase|SARS-CoV, caused an epidemic in 2002-2003]]. The genes of SARS-CoV-2 are in [[RNA]]. Viruses with RNA genomes tend to mutate faster than do viruses with DNA genomes<ref "rnamut1">PMID: 30102691</ref><ref name="rnamut2">PMID: 26499340</ref>. For example, a new [[influenza]] vaccine is needed every year due to mutations, and a single drug against [[HIV]] quickly becomes ineffective due to mutations. It is no surprise that SARS-CoV-2 is mutating.
+<table style="background-color:#ffffc0;"><tr><td>
+This page has not been updated since the greek letter terminology was introduced for variants, and it has not been updated since mid-2021.
+</td></tr></table>
 <StructureSection load='' size='340' side='right' caption='' scene='87/870593/Spike_open/6'>
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 In February, 2021, mutations at '''position 677''' (Q677P, Q677H) were reported to have arisen independently (''convergent evolution'') in the south central and southwest USA, where they accounted for 28% (in Louisiana) and 11% (in New Mexico) of sequenced SARS-CoV-2 genomes by late January<ref name="s677">[https://www.medrxiv.org/content/10.1101/2021.02.12.21251658v2.full-text Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677], a preprint by Emma B. Hodcroft ''et al.'', posted February 14, 2021.</ref>. Q677H is present in lineage '''B.1.525'''<ref name="a." />.
+'''B.1.617''' was first detected in October, 2020<ref name="617who">[https://www.who.int/docs/default-source/coronaviruse/situation-reports/20210427_weekly_epi_update_37.pdf COVID-19 Weekly Epidemiological Update for April 25, 2021] from the World Health Organization.</ref>. By the end of April, 2021, B.1.617 was predominant in India, where a devastating surge of COVID-19 was overwhelming hospitals<ref name="617who" /><ref name="617scientist">[https://www.the-scientist.com/news-opinion/what-scientists-know-about-the-b-1-617-coronavirus-variant-68733 What Scientists Know About the B.1.617 Coronavirus Variant] in ''The Scientist'', by Shauna Williams, May 3, 2021.</ref><ref name="617nature">[https://www.nature.com/articles/d41586-021-01059-y India’s massive COVID surge puzzles scientists], ''Nature'', by Smriti Mallapaty, April 21, 2021.</ref>. In addition to India, B.1.617 was identified in the USA, UK, and Singapore<ref name="617who" />.
 ===Mutations Most Concerning===
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 ====Q677P/H====
 Sequence position 677 is close to the [[SARS-CoV-2 spike protein priming by furin|furin cleavage site]] at <span class="text-red">'''PRRAR'''</span> (681-684). The consequences of these mutations are under investigation.
+====B.1.617====
+The defining mutations in B.1.617 include L452R, P681R, and E484Q. '''L452R''' is present in B.1.429 the US "California" lineage, and confers resistance to convalescent serum antibodies<ref name="convalescent" />. '''P681R''' occurs in B.1.1.7, is in the [[SARS-CoV-2 spike protein priming by furin|furin cleavage site]] and is suspected of increasing contagiousness<ref name="617who" />. '''E484Q''' is similar to E484K, present in the "South African" lineage B.1.351 / 501Y.V2, and is thought to contribute to evasion of immunity<ref name="617who" /><ref name="greaney">PMID: 33592168</ref>.
 ===Vaccine Effectiveness Under Investigation===
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 By the end of December, 2020, B.1.1.7 had been detected in at least 18 countries<ref name="18countries">[https://www.businessinsider.com/new-coronavirus-variant-all-the-countries-where-its-been-identified-2020-12 These are all countries that have already reported cases of the new, possibly more infectious coronavirus variant from the UK], Business Insider, December 29, 2020.</ref>, plus the United States<ref name="usa1">[https://www.huffpost.com/entry/new-covid-uk-confirmed-us-colorado_n_5feba1fdc5b66809cb34f0f9 New COVID-19 Variant From U.K. Confirmed In U.S. For First Time], Huffington Post, December 29, 2020.</ref>. By January 18, 2021, B.1.1.7 infections were detected in 20 states of the United States<ref name="20states">[https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant-cases.html US COVID-19 Cases Caused by Variants], update of January 18, 2021. Centers for Disease Control and Prevention, USA.</ref>. By mid-February, 2021, B.1.1.7 was detected in 83 countries<ref name="b.1.1.7">[https://cov-lineages.org/global_report_B.1.1.7.html B.1.1.7 Report], PANGO Lineages, February 17, 2021.</ref>.
+Children, not yet vaccinated, are a dangerous reservoir of variants, according to evidence presented in May, 2021<ref name="children">[https://www.medrxiv.org/content/10.1101/2021.05.22.21257660v1 Emergence of SARS-CoV-2 variants of concern in the pediatric population of the United States], a preprint posted May 24, 2021.</ref>.
 </StructureSection>
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 *February 17, 2021: Cited list of >700 defined lineages<ref name="a." /><ref name="pango" />. Used lineage nomenclature more consistently, where feasible. B.1.1.7 now in 83 countries<ref name="b.1.1.7" />.
 *March 30, 2021: Cited announcement that the UK will start variant-adapted boosters in September, 2021<ref name="ukboosters" />.
+*May 4, 2021: Added information about B.1.617 and the surge in India with several new references.
+*May 24, 2021: Added evidence that unvaccinated children are a reservoir of variants<ref name="children" />.
 ==See Also==