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

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" />.

While the mutations in B.1.1.7 seem unlikely to make current anti-COVID-19 vaccines less effective, there is more concern regarding the additional mutations in 501Y.V2<ref name="smc1">[https://www.sciencemediacentre.org/expert-reaction-to-the-south-african-variant/ Expert reaction to the South African variant], Science Media Centre of the UK, January 4, 2021.</ref>. Unfortunately, poor management of COVID-19 and inconsistent therapy maneuvers have favored development of mutations that may evade the initial wave of vaccines<ref name="bieniasz">[https://www.virology.ws/2021/01/05/musings-of-an-anonymous-pissed-off-virologist/ Musings of an anonymous, pissed off virologist] by Paul Bieniasz, Professor at Rockefeller University, January 5, 2021.</ref>. Antibodies in the blood of half of people who have recovered from COVID-19 are unable to neutralize 501Y.V2<ref name="wibmer">[https://www.biorxiv.org/content/10.1101/2021.01.18.427166v1 SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma], preprint posted January 19, 2021.</ref>, but other forms of immunity, such as T-cells, may still be protective. On January 28, 2021, Novavax reported that its vaccine, which was 90% effective in the UK, was '''only 50% effective in South Africa''', where ~90% of cases were 501Y.V2<ref name="novavax1">[https://ir.novavax.com/node/15506/pdf Novavax COVID-19 Vaccine Demonstrates 89.3% Efficacy in UK Phase 3 Trial], posted January 28, 2021 by Novavax.</ref>. The next day, Johnson and Johnson announced similar results<ref name="jnj1">[https://www.jnj.com/johnson-johnson-announces-single-shot-janssen-covid-19-vaccine-candidate-met-primary-endpoints-in-interim-analysis-of-its-phase-3-ensemble-trial#_ftn1 Johnson & Johnson Announces Single-Shot Janssen COVID-19 Vaccine Candidate Met Primary Endpoints in Interim Analysis of its Phase 3 ENSEMBLE Trial], January 29, 2021.</ref>. Experts believe that present vaccines could be modified for greater effectiveness against these mutants, if necessary, withinin a few months<ref name="smc1" />. Moderna began development of a vaccine modified to combat 501Y.V2 in January, 2021<ref name="moderna-501.v2">[https://www.businessinsider.com/moderna-to-test-coronavirus-vaccine-to-fight-south-africa-variant-2021-1 Moderna is designing a new version of its COVID-19 shot to fight the variant first found in South Africa] by Andrew Dunn and Allison DeAngelis, ''Business Insider'', January 25, 2021.</ref>. On March 26, 2021, public health officials in the UK announced a plan to begin booster vaccinations in September with variant-adapted vaccines<ref name="ukboosters">[https://www.yahoo.com/news/exclusive-over-70s-booster-covid-205453613.html Exclusive: Over-70s to get booster Covid vaccines from September] by Ben Riley-Smith in ''The Telegraph'', March 26, 2021, quoting vaccines minister Nadhim Zahawi.</ref>.

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>.

*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" />.

*May 24, 2021: Added evidence that unvaccinated children are a reservoir of variants<ref name="children" />.