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severe acute respiratory syndrome coronavirus 2; SARS-CoV2; Wuhan coronavirus

- Covariants is a free & open source resource that provides an overview of SARS-CoV2 variants & mutations [21] Epidemiology: - see SARS Cov2 epidemiology Pathology: - see COVID-19 Genetics: - SARS-CoV2 is an RNA virus that appears most similar to 2 SARS-like coronaviruses that originated in bats [1] === alpha === - mutation VUI-202012/01 (B.1.1.7 dubbed 'alpha') discovered in the United Kingdom [9,33] - has been found in Australia, Denmark, Iceland, Italy. the Netherlands, Japan, Australia, & Lebanon - first case in U.S. found in Colorado [10] - > 10% of all U.S. COVID-19 infections March 2021 [22] - does not appear to cause more severe disease than other variants [9,24] - English variant B.1.1.7 may be associated with higher risk of mortality than wild type SAS CoV2 (RR=1.6) [11,18,21] - both vaccines being used in the U.K. are effective against the variant. - appears to be a more transmissible (contagious) variant [9,10] - 43-90% higher transmissibility than earlier strains [17] - affects higher proportion of younger persons < 20 years of age [10] - predicted to become most prevalent strain of virus in U.S. by March [12] === beta === - spike protein mutations called 501Y.V2 (K417N, E484K, & N501Y) discovered in South Africa (B.1.351 variant dubbed 'beta') [8,33] - may cause more severe disease in younger patients - neutralizing titers of Moderna's vaccine 6 fold lower than other strains - still believed to be susceptible to the 2 FDA-approved mRNA vaccines - detected in U.S., including California [8] - neutralizing antibodies against B.1.351 reduced 20-40 fold with Moderna & Pfizer vaccines [20] - reported susceptible to J&J Ad26.COV2.S vaccine (see COVID-19 vaccine) - AstraZeneca's COVID-19 vaccine does not appear to prevent infection from the B.1.351 variant [19] - the B.1.351 strain appears to elicit a strong antibody response against several other strains [23] - two linked clusters of B.1.351 infection identified in Maryland 2021 involving 17 individuals, two had received the 1st of a of a two-dose vaccine & one who had been diagnosed with COVID-19 5 months earlier, none with travel history [26] - two people were hospitalized, one death [26] - hospital admissions, & in-hospital mortality increased during the 2nd wave of COVID-19 in South Africa, when the Beta variant (B.1.351) was predominant [42] === gamma === - variant 20J/501Y.V3 or P.1 variant dubbed gamma discovered in Brazil - P.1 variant is related to South African B.1.351 [5,20] - found in U.S. & is more transmissible [14,28] - neutralizing antibodies from Moderna & Pfizer vaccines 5- to 6-fold less effective against the variants discovered in Brazil [20] - breakthrough infections in fully vaccinated in French Guiana (87% symptomatic, no severe infections) 56% had received Pfizer vaccine [47] - rapid spread of Gamma variant in Brazil, replaced other variants in < 3 months [59] === delta === - B.1.617.2 (dubbed 'delta') found in India carries 13 mutations, 7 in the spike protein, including the L452R mutation also found in CAL.20C & the E484Q mutation similar to the E484K mutation found in B.1.351 (South African) & P.1 (Brazilian) variants [27] - found in Lancaster County, Nebraska May 2021 [29] - dominant variant in U.S, July 2021 [40] - to become the dominant variant globally due to increased transmissibility [37,39] - one of the most infectious respiratory viruses known [45] - people infected with the Delta variant carry ~1000 times more virus compared with previous versions of the virus [45] - delta variant accounts for 83% of US Covid-19 cases July 2021 [35] - WHO reports delta makes up 99.5% of all genomic sequences reported to public databases Nov 2021, excepting South America where Gamma, Lambda & Mu contribute to cases [63] - delta variant can cause symptoms 2-3 days sooner than the original coronavirus [63] - people shed the Delta variant 2 days prior to onset of symptoms [52] - the Delta variant has a transmissibility Ro of 6.4 higher than the Ro of 2-4 of the original SARS-CoV2 [52] - vaccinated persons 65% less likely than unvaccinated persons to transmit infection [52] - vaccinated persons can still carry high viral loads in their nasopharynx [58] - levels of virus decline more rapidly in vaccinated persons [63] - vaccinated individuals infected with Delta variant carry high viral loads (CDC) [48] - Delta easily transmits from vaccinated people to household contacts [62] - contacts less likely to become infected if vaccinated themselves [62] - both mRNA vaccines likely effective against B.1.617.2 variant [30,39] - Pfizer mRNA vaccine produces 3-5 fold lower levels of antibodies against B.1.617.2 [34,44] - 1 dose of Pfizer vaccine marginally effective; 2 doses effective in 95% [44] - BNT162b2 (Pfizer) or ChAdOx1 (Astra-Zeneca) nCoV-19 vaccines only modestly less effective against delta variant than alpha variant after 2 doses [46] - B.1.617.2 found in the U.K. [32] - delta variant doubles risk for hospitalization vs alpha variant [36] - delta variant not more virulent in U.S. adults than previous variants [69] - 2 vaccine doses provides strong protection against the Delta variant, albeit less than against the Alpha variant [36] - Moderna vaccine appears to be 2-fold more effective against Delta variant in preventing breakthrough infections than the Pzifer vaccine [49] - no differences in complications from Delta variant with either mRNA vaccine, with similar 21-day hospitalizations, 21-day ICU admissions, & 28-day mortality [49] - since the Delta variant has become the dominant strain - vaccine effectiveness against hospitalization has ranged from 75%-95%. [53] - for adults > 75 years, vaccine effectiveness against hospitalization is > 80% at the end of July 2021; for ages 18-49, efficacy is ~94% - unvaccinated adults 17 times more likely to be hospitalized than vaccinated adults - vaccine effectiveness against preventing infection ranges from 39%-84% - delta variant B.1.617.2.1 (delta plus) with K417N mutation in spike protein also present in B.1.351 (South African or beta) variant may be even more transmissible [37] - fully vaccinated adults can carry the same nasopharygeal viral load of delta variant as unvaccinated adults [51] - delta variant infected 6 of 92 fully vaccinated guests at an outdoor wedding under a large, open-air tent in Texas. 1 of 6 died. 2 guests from India likely source. [43] - teams made up of health & logistics experts from several federal agencies will conduct coronavirus testing, distribute medicines designed to fight the virus, & boost local & state efforts to increase vaccinations in 1000 counties where the delta variant is spreading rapidly June 2021 [40] === epsilon === - CAL.20C (B.1.427/B.1.429) variant(s) (dubbed 'epsilon') or 'West Coast Strain' - originated in California - found in > 1/3-1/2 of samples collected in January 2021 in Los Angeles [4] - no evidence that CAL.20C is more lethal than other variants [4] - found in several states nation wide [4] - ~20% increased transmission - reduced efficacy of some antibody treatments - clade 20G (lineage B.1.2) with amino acid 677 substitution in spike protein [13] - Q677P, Q677H === Eris === - Eris named for a dwarf planet in the solar system between Neptune & Pluto [118] - EG.5 accounts for 17% of all U.S. COVID infections Aug 7, 2023 - up 12% from previous week [118] - the most prevalent COVID-19 variants globally one August 23, 2023 were XBB.1.16 & EG.5 each comprising 25% of total [121] - EG.5 is a descendant of the XBB strains - same makeup as XBB.1.9.2 but carries an extra spike protein mutation [118] - variants include EG.5.1 & EG.5.1.1 - no indication so far that EG.5 is more contagious or severe than other variants - current vaccines protect against the variant (CDC) [118] === iota === - B.1.526 (dubbed 'iota'): reduced efficacy of some antibody treatments - found in New York Feb 2021 [16] - most common mutations L5F, T95I, D253G, E484K or S477N, D614G, & A701V [16] === eta === - B.1.526.1 & B.1.525 (dubbed 'eta'): decreased response to some antibody treatments === zeta === - P.2 (dubbed 'zeta'): decreased response to some antibody treatments. - B.1.617.1 (dubbed 'kappa'): decreased response to some antibody treatments - B.1.617.3 (no designation): decreased response to some antibody treatments === mu === - variant mu (B.1.621) first identified in Colombia - since confirmed in at least 39 countries including US & UK [54] - reduction in neutralization capacity of convalescent & vaccine sera similar to that seen for the Beta variant (unconfirmed) [54] - 7 residents of a nursing home (all in 80s & 90s, some in poor conditiono) in Belgium have died after infection with B.1.621, despite being fully vaccinated [50] - global prevalence has declined, currently < 0.1%; however prevalence in Colombia & Ecuador has consistently increased [54] - Mu has mutations from Delta & also mutations from Alpha [57] - World Health Organization (WHO) is monitoring mu as a variant of interest [57] === Omicron variant === - variant, called B.1.1.529 1st identified in Botswana - has been detected in Netherlands, South Africa, Hong Kong, Belgium, Israel & 17 states in the U.S., including California (12/6/21) [64] - named Omicron variant by WHO - variant contains > 30 mutations to the spike protein [64] - Omicron variant may be more transmissible (WHO) [68] - patients infected with Omicron remain contagious as long as patients infected with earlier variants >= 6 days [88] - CDC estimates 95% of Covid-19 cases in U.S. due to Omicron variant Jan 5, 2022 [75] - data suggest Omicron may be less severe variant than Delta [71] - Omicron variant appears to cause less damage to the lungs in studies with mice & hamsters where disease appears to be largelyt confined to upper airway [73] - risk of hospitalization with Omicron 1/3 that of Delta [74] - Omicron variant accountd for almost 100% of COVID-19 cases in the United States Feb 2022 - the 7-day average of daily COVID-related deaths hit 2,600 in Feb 2022, the highest rate in about a year - Omicron appears to be less severe than Delta, but is not 'mild' (WHO) [76] - Omicron ~1/2 as likely as Delta to cause long Covid-19 (~5%) [96] - Omicron variant could make it more likely that people will need a 4th Covid-19 vaccine earlier than expected [67] - Fauci says that boosters are effective against Omicron variant [67] - prior SARS-CoV-2 infection less effective at preventing reinfection with Omicron vs prior variants; 56% for Omicron, 90% for Alpha, 86% for Beta, 92% for Delta [82] - however, no reinfections resulted in death - prior Omicron infection 88% effective at preventing severe/critical reinfection [82] - Regen-Cov less effective against Omicron variant in preliminary tests [65] - Pfizer CEO thinks it unlikely Paxlovid will be less effective against Omicron [66] - Moderna 50 ug booster increases antibodies to Omicron by 37-fold within 1 month [70] - a 100 ug booster increases neutralizing antibodies 87-fold [70] - a 3rd dose of Pfizer or Moderna mRNA vaccine increases cross-reactive antibody responses sufficient to neutralize Omicron [77] - majority of T cell response, induced by vaccination or natural infection, cross-recognises the Omicron variant [72] - new, highly contagious subvariant of Omicron has emerged BA.2, or 'son of Omicron' [78] - Omicron BA.1 is the original Omicron [86] - Omicron subvariant BA.2 1.5-fold more contagious than BA.1 [80] - Omicron subvariant BA.2 23% of SARS-CoV2 variants in U.S. March 16, 2022 [87], 55% of COVID variants in the U.S. March 26, 2022 according to CDC estimates - BA.5 Omicron subvariant makes up ~80% of COVID-19 cases July 21, 2022 [102] - BA.5 Omicron subvariant makes up ~68% of COVID-19 cases Oct 17, 2022 [107] - BA.2 may cause more severe disease than BA.1 [84] - BA.2 causes less severe disease than BA.1 [89] - BA.2 known as stealth variant because it is more difficult to detect [86] - BA.2.12.1 accounts for 26% of sequenced genomes in North America May 2022 [94] - no real-world evidence that BA.2 causes more severe disease than BA.1 [85] - BA.2.75 first detected in India in May 2022, by July 2022 found in least 10 countries in Asia, Europe, North America, & Australia [100] - more worrisome BA.2.75.2 [107] - BA.2.86 is a highly mutated variant - detected in the United States, Denmark & Israel [119] - may be more more capable than older variants in causing infection in previously infected or vaccinated persons [120] - too soon to know if BA.2.86 causes more severe illness than previous variants [120] - Omicron variants BA.3 & BA.4 identified [86] - Omicron variants BA.4 & BA.5 identified in U.S. [95] - prior Omicron infection provides some protection against BA.4 & BA.5 variants [103] - recovery from Omicron BA.2 or BA.2.12.1 probably does not confer protection against Omicron BA.4 or BA.5 [95,101] - BA.5=83%, BA.4.6=12%, BF.7=2.3%, BA.4 & BA.2.76 each=1.4% of circulating strains in U.S. Sept 18-24 2022 [106] - Omicron BA.2.12.1, BA.4,& BA.5 subvariants escape neutralizing antibodies induced by both vaccination & infection [97,104] - similar protection against severe, critical, or fatal Omicron infection conferred by previous infection, vaccination, or a combination of both [99] - a third vaccine dose results in recall & expansion of SARS-CoV-2 Spike protein- specific memory B cells, leading to neutralizing antibodies with enhanced potency & breadth against variants [104] - night sweats associated with Omicron infection, especially BA.5 [98] - Omicron XE a combination of the original Omicron strain & subvariant Omicron BA.2 identified in the United Kingdom [92] - speculation that it may be more contagious than BA.2 - BQ.1.1, BA.2.3.20, & XBB variants of concern [107] - BQ.1 & BQ.1.1 make up ~20% of COVID-19 cases in the New York & New Jersey region, as of Oct 17, 2022 & 12% of strains in U.S. [108] - BQ.1 is a BA.5 sub-lineage, thus some cross protection anticipated for the current (October 2022) Pfizer & Moderna bivalent vaccines [107] - Omicron BQ & XBB subvariants may be resistant to Pfizer & Moderna bivalent vaccines [112] - XBB is 17% of strains in Singpore with 92% vaccination rate Oct 18 2022 [108] - XBB was estimated to account for 18.3% of the COVID-19 cases in the United States & 50% of cases in the Northeast in the week ended Dec. 24, 2022 [113] - XBB.1.5 40%, BQ.1.1 27%, BQ.1 18% of US cases in week ending Dec. 31, 2022 [114,115] - XBB.1.5 (Kraken variant) may be most infectious SARS CoV2 variant yet [115] - XBB.1.5 is so transmissible that everyone is at risk of infection, even if prior infection & fully vaccinated [115] - XBB.1.16 Arcturus (formally, Omicron subvariant XBB.1.16) - reported in India: children with conjunctivitis, pink eye or 'sticky' eyes [117] - the most prevalent COVID-19 variants globally one August 23, 2023 were XBB.1.16 & EG.5 each comprising 25% of total [121] - Omicron BN.1 linked to ~4.3% of cases in U.S. Nov. 2022 [109] - during Omicron predominance, COVID-19 hospitalization rates in Los Angeles County among unvaccinated persons were 23.0 times those of fully vaccinated persons with a booster, & 5.3 times those among fully vaccinated persons without a booster [81] - Omicron survives ~ as long as Alpha on plastic (193 hours average) & 21 hours on skin [79] - Omicron variant CH.1.1 'Orthrus' named after a monster canine in Greek mythology has a mutation, L452R, present in the Delta variant & Omicron variants BA.4 & BA.5 - CH.1.1 emerged in Southeast Asia in November 2022, now accounts for ~ 1/4 of cases in Feb 2023 in the U.K. & New Zealand [116] - Omicron variant HV.1 major circulating strain in U.S. Fall of 2023 - sublineage of omicron XBB.1.9.2 & a direct descendent of EG.5, - subvariants XBB.1.5, EG.5 & FL.1.5.1 on the rise in U.S. Fall of 2023 [122] - JN.1 declared variant of interest by WHO in Dec 2023 [123] - new variant FLiRT identified in U.S. 2024 [124] - KP.3 & KP.3.1.1 account for almost 1/2 of all COVID-19 cases in the U.S. in August 2024 [125] - KP.3.1.1 (25% COVID-19 cases in the U.S. August 2024) may be more of a challege to our immune system than other variants - KP.2 circulating in summer of 2024 - KP.3.1.1 variant accounts for 53% of positive Covid-19 cases Sept 20, 2024 [126] - XEC is s recombinant or hybrid of the strains KS.1.1 & KP.3.3. - it is allegedly more contagious but not more virulent than previous strains [127] === C.1.2 === - new variant, known as C.1.2 [55] - first detected in South Africa in May 2021 - now spread to most South African provinces & to 7 other countries in Africa, Europe, Asia & Oceania - contains many mutations associated in other variants with increased transmissibility & reduced sensitivity to neutralising antibodies, but in a different mix - most distant variant from the original Wuhan coronavirus, with 44-59 mutations [55] === lambda === - another variant C.37 (dubbed lambda) 1st identified in Peru [41] - spike protein mutations L452Q, F490S, G75V, T76I, D614G, T859N as well as a novel deletion (del246-252) may contribute to increased transmissibility - Pfizer vaccine 3-fold less neutralization, Moderna vaccine 2.3-fold less neutralization; - anti-spike protein monoclonal antibody combination Regenron's casirivimab/imdevimab without loss of activity - variant of interest (WHO) - susceptible to mRNA vaccines === R.1 variant 1st reported in Japan === - 26 residents & 20 healthcare workers tested positive for COVID-19 at a skilled nursing facility in Kentucky March 2021 [61] - vaccination 86.5% protective against symptomatic illness among residents & 87.1% protective for employees - since being reported in Kentucky, R.1 has been detected > 10,000 times in the United States [61] === outlook === - viruses have only been sequenced from ~51,000 of 17 million U.S. cases in Dec 2020 [15] - $1.7 billion national network to identify & track coronavirus mutations in the U.S. is in the works [25] - Covid-19 is likely here to stay as SARS-CoV2 continues to mutate in unvaccinated countries across the world & previous hopes of eradicating it diminish (WHO) [56] === early reports === - WHO looking into the origins of coronavirus in China discovered 13 different strains of SARS-CoV2 in Wuhan China in Dec 2019 [3]] - D614G mutation in the spike glycoprotein region of the SARS CoV-2 genome - known as 'G' or clade 20G initially accounted for 70% of isolates worldwide [4,5,6] - results in more efficient uptake of spike glycoprotein by ACE2-expressing cells - renders virus more infectious - does not render virus nore virulent - other strains include: GR, GH, L, S, V [2] - 382-nucleotide deletion in the open reading frame 8 region of the SARS CoV2 genome appears to be associated with a milder infection [7] === human genetic factors === - see COVID-19 === other issues === Can SARS CoV2 RNA genes insert into human DNA? [31] - probably not, SARS CoV2 does not carry a reverse transcriptase - 2 publications suggest that LINE-1 may fill role of reverse transcriptase - it seems most virologists disagree [31] Clinical manifestations: - see COVID-19 Laboratory: - see SARS Cov2 laboratory Special laboratory: - see COVID-19 Radiology: - see COVID-19 Complications: - see COVID-19 Management: - see COVID-19 management - prevention: - see COVID-19 vaccine - prevention after high-risk exposure: see casirivimab Comparative biology: - see COVID-19

Related

COVID-19 COVID-19 clinical practice guidelines for nursing homes

Specific

SARS CoV2 & pregnancy & breastfeeding SARS Cov2 alpha variant (VUI-202012/01, UK variant) SARS Cov2 beta variant (B.1.351, South African variant) SARS Cov2 delta variant (B.1.617.2, India variant) SARS Cov2 epsilon variant (CAL.20C, B.1.427/B.1.429, West Coast Strain, California variant) SARS Cov2 eta variant (B.1.526.1, B.1.525) SARS Cov2 gamma variant (20J/501Y.V3, P.1, Brazil variant) SARS Cov2 iota variant (B.1.526) SARS Cov2 kappa variant (B.1.617.1) SARS Cov2 omicron variant SARS Cov2 zeta variant (P.2)

General

coronavirus; sarbecovirus

Properties

KINGDOM: virus GENOME-TYPE: RNA SINGLE-STRANDED POSITIVE-STRAND GENOME-SIZE: 16-21 kB ENVELOPE: PRESENT CAPSID-SYMMETRY: HELICAL

References

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