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

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Introduction

  • Covariants is a free & open source resource that provides an overview of SARS-CoV2 variants & mutations[21]

Epidemiology

Pathology

Genetics

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]
    • 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

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

epsilon

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

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

Omicron variant

  • variant, called B.1.1.529 1st identified in Botswana
  • data suggest Omicron may be less severe variant than Delta[71]
  • 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]
  • 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 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]
    • 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]
  • 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]
    • XBB is 17% of strains in Singpore with 92% vaccination rate Oct 18 2022[108]
  • 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]

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

R.1 variant 1st reported in Japan

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

human genetic factors

other issues

Can SARS CoV2 RNA genes insert into human DNA?[31]

Clinical manifestations

Laboratory

Diagnostic procedures

Radiology

Complications

Management

Comparative biology

More general terms

More specific terms

Additional terms

References

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