Living Evidence - SARS-CoV-2 variants

Living evidence tables provide high level summaries of key studies and evidence on a particular topic, and links to sources. They are reviewed regularly and updated as new evidence and information is published.

Viruses constantly change through mutation and over time, new variants of a virus are expected to occur. Some variants have characteristics that have a significant impact on transmissibility, severity of disease and effectiveness of vaccines.  This table includes information on variants that are currently causing concern in the scientific community.

Currently, the World Health Organization  has identified five variants of concern: Alpha, Beta, Gamma, Delta and Omicron.

Daily checks are conducted for new content and any updates that occur during the week are highlighted. All highlights are removed each Monday.

 Alpha (B.1.1.7) Beta (B.1.351) Gamma (P.1) Delta (B.1.617.2)Omicron  (B.1.1.529)
WHO label Alpha Beta Gamma Delta Omicron
Scientific names

B.1.1.7

GRY (formerly GR/501Y.V1)

20I/S:501Y.V1

B.1.351

GH/501Y.V2

20H/S:501Y.V2

B.1.1.28.1 (P.1)

GR/501Y.V3

20J/S:501Y.V3

B.1.617.2

G/452.V3

21A/S:478K

B.1.1.529

GR/484A

21K

First detected

UK

September 2020

South Africa

May 2020

Brazil

November 2020

India

October 2020

Botswana, South Africa

November 2021


Reports  Omicron was in the Netherlands before South Africa alerted WHO*^
Mutations 23 (17 of which change amino acids)

Includes N501Y substitution

21 (8 of which change amino acids)

Includes N501Y substitution

17 (11 of which change amino acids)

Includes N501Y substitution

12

Includes spike mutation profiles L452R, E484Q and D614G and lacks mutations at amino acid positions 501 or 484 in its ACE2 receptor.

P681R change is a crucial feature of Delta*^

~50 mutations, including 32 mutations on its spike protein and 15 on the receptor binding domain*^

Omicron has been separated into 2 clades: BA.1 and BA.2

Transmissibility compared with wild type

Reproduction number ~3.5-5.2*^

Increased transmissibility and secondary attack rate compared with wild type*^

Estimated 43–90% higher reproduction number than wild type and transmission advantage at warmer temperatures *^

Estimated higher rates of transmission in children aged 0 to 9 years. Reports of high seroprevalence rate in secondary school-aged children*^ and some studies inferring an increase in within-school transmission*^

Increased transmissibility and estimated to be 2.5 times greater than wild type*^

Increased transmissibility and secondary attack rate compared with wild type^

Reproduction number ranges from 3.2 to 8, with a  mean of 5.0.

Increased transmissibility and secondary attack rate compared with wild type*^ for household and non-household contacts.

Estimated 2.5-fold higher viral loads compared to other variants*^, and 15-fold higher saliva viral loads compared to wild type*^ Similar viral loads between vaccinated and unvaccinated individuals*^

Virological characteristics of vaccine breakthrough infections suggest  Ct-values decreased throughout the first three days of illness*^.  

Estimated mean of the latent period and the incubation period are 4.0 days and 5.8 days, respectively*^

Several reports suggest overall growth advantage*^

Factors contributing to the growth rate  include immune evasion and potential intrinsic increased transmissibility*^

One study estimates that Omicron is 36.5% more transmissible than Delta*^

Reproduction number ranges from 2.6 to 4.0, with an estimate of 3.06 from WHO*^ The doubling time is 1.5-3 days.

Preliminary data suggests that the amount of viral RNA is highest three to six days after diagnosis or symptom onset*^.

Data suggests an increased risk of household transmission*^. 

Household secondary attack rate estimates range from 15.8% to 31% for Omicron compared to 10.3% to 21% for Delta. One study suggests increased transmission for unvaccinated individuals, and reduced transmission for booster-vaccinated individuals, compared to fully vaccinated individuals*^

Epidemiological data in the Gauteng Province, South Africa, showed SARS-CoV-2 infection rates increased more rapidly than in previous waves but have now plateaued.*^

Virulence / severity or duration of disease / reinfection

Increased risk of hospitalisation, possible increased risk of severity and mortality*^

Average infections last 13.3 days compared with 8.2 days for other variants*^ and Alpha does not appear to influence patient trajectories including onset to hospitalisation and length of stay*^

Reports of breakthrough infections*^

Possible increased risk of severe disease and in-hospital mortality*^

Possible increased risk of hospitalisation and severity of disease *^

Increased risk of emergency care and hospitalisation, including higher odds of oxygen requirement, admission to an intensive care unit, and possible increased risk of mortality*^

Studies show hospitalisation rates for unvaccinated individuals are higher compared with vaccinated individuals*^

Summary of vaccine effectiveness against different outcomes: infection, symptomatic disease, hospitalisation and morality*^. Estimated vaccine effectiveness against hospitalisation and ICU admissions*^

Estimated reinfection risk of ~46% *^. Prior infections result in less severe disease against subsequent infections*^.  One study suggests that vaccine-induced immunity provides greater protection than infection-induced immunity against laboratory-confirmed COVID-19*^

Some studies suggest symptoms can differ to wild type*^.

Reports that asymptomatic cases clear more quickly, 11 days compared to 1 day, and had higher mean antibody levels than symptomatic cases *^

Estimated illness duration for children is 5 days, with symptoms including headache and fever*^.  Reports of low hospital presentation and the presence of long illness*^It is not yet clear whether Omicron causes more severe disease, compared to infections with other variants, including Delta*^

Preliminary data from South Africa, England, Scotland and Denmark show that people infected with the Omicron variant are less likely to require hospitalisation compared with Delta. This ranges from 40-45%, up to 80% less likely.*^

Early estimates of disease severity suggest the risk of hospitalisation and death is 65% lower for Omicron compared to Delta, and 83% lower for intensive care unit addmission or death*^.  Another study suggests significantly less severe outcomes for paediatric age groups, adults and older adults.

Preliminary data  indicates a 2.4 to 5.4-fold increased risk of reinfection*^. Reinfection has been reported in several countries including South Africa, Denmark, Israel and the UK.

Currently no information to suggest symptoms differ to other variants. However, one study suggests increased reports of sore throat and a marked reduction in reporting of loss of smell and taste in PCR-positive cases.

Evidence suggests higher proportions of asymptomatic infections compared to other variants*^

Immune escape (vaccines / previous infections will not be protective)
Comirnaty (Pfizer - BNT162b2)

Estimated <2-fold reduction in neutralisation*^

Full vaccination (≥7 days after dose 2) up to 89% vaccine effectiveness against symptomatic infection*^

Estimated 5 to <10-fold reduction in neutralisation*^

Full vaccination (≥7 days after dose 2) up to 84% vaccine effectiveness against symptomatic infection*^

Neutralisation increased with prior COVID-19 infection*^

Estimated 2 to <5-fold reduction in neutralisation

Full vaccination (≥7 days after dose 2) up to 84% vaccine effectiveness against symptomatic infection*^

Neutralisation increased with prior COVID-19 infection*^

Estimated 5 to <10-fold reduction in neutralisation with some studies suggesting an 11.30-fold reduction^*

Full vaccination (≥7 days after dose 2) up to 87% vaccine effectiveness against symptomatic infection^*. Another study suggests  ~90%, ~85% and 79% effectiveness after 30, 60 and 90 days respectively*^

Reports suggest a strong effect of waning immunity*^ Evidence of waning across all age groups following a second dose of vaccine and some reports suggest a decline after four months*^. However, there is evidence for the maintenance of protection against severe disease*^ including hospitalisation and mortality*^

Evidence suggests ~90% lower mortality following a third dose (booster) at least 5 months after the second dose*^ One study suggests vaccine effectiveness from 14 days after the booster was ~93.1% when the primary course was Vaxzevria (AstraZeneca) and ~94% for Comirnaty (Pfizer) against symptomatic disease*^.

A 20- to 40-fold reduction in neutralising activity by two doses of Comirnaty compared with other strains^

A booster dose of Comirnaty resulted in an increase in neutralising activity irrespective of primary vaccination type (approximately 71% for
those who received Vaxzevria as the primary course and approximately 76% for those who received Comirnaty)^

Two doses of Comirnaty offers 70% protection against hospitalisation.^
Vaxzevria (AstraZeneca -ChAdOx1))

Estimated 5 to <10-fold reduction in neutralisation*^

Vaccination (≥14 days after dose 1 only) up to 64% vaccine effectiveness against symptomatic infection*^

Estimated 5 to <10-fold reduction in neutralisation*^

Vaccination (≥14 days after 1 dose only) up to 48% vaccine effectiveness against symptomatic infection*^

Estimated 2 to <5-fold reduction in neutralisation*^

Vaccination (≥14 days after dose 1 only) up to 48% vaccine effectiveness against symptomatic infection*^

Vaccine effectiveness profile

Estimated 2 to <5-fold reduction in neutralisation*^

Vaccination (≥14 days after one dose only) up to 67%  vaccine effectiveness against symptomatic infection*^.  Another study suggests ~69% effectiveness after 14 days after the second dose, and  61% at 90 days*^

Breakthrough infections may cause asymptomatic or mild disease, but are associated with high viral loads, prolonged PCR positivity and low levels of vaccine-induced neutralising antibodies*^

Reported drops in vaccine effectiveness, however, there is evidence for the maintenance of protection against severe disease*^

Estimated vaccine effectiveness from 14 days after the booster was ~93.1% when the primary course was Vaxzevria (AstraZeneca) and ~94% for Comirnaty (Pfizer) against symptomatic disease*^Early reports of breakthrough infections*^

Preliminary studies suggest reduced effectiveness against symptomatic disease at 15 weeks after the second dose*^, however, a booster dose of Comirnaty resulted in an increase in neutralising activity irrespective of primary vaccination type (~71% for those who received Vaxzevria)*^

Spikevac (Moderna -mRNA-1273)

Estimated <2-fold reduction in neutralisation*^

Full vaccination (≥7 days after dose 2) up to 92% vaccine effectiveness against symptomatic infection*^

Estimated 5 to <10-fold reduction in neutralisation*^

Vaccination (≥14 days after dose 1 only) up to 77% vaccine effectiveness against symptomatic infection*^

Estimated 2 to <5-fold reduction in neutralisation*^

Vaccination (≥14 days after dose 1 only) up to 77% vaccine effectiveness against symptomatic infection*^

Estimated 2 to <5-fold reduction in neutralisation*^

Vaccination (≥14 days after dose 1 only) up to 72% vaccine effectiveness against symptomatic infection*^

Reports that two-dose vaccine effectiveness was ~86.7% against Delta infection and ~97.6% against hospitalisation; however, declined with increasing time since vaccination*^

Reported drops in vaccine effectiveness*^ However, there is evidence for the maintenance of protection against severe disease*^

Preliminary studies suggest low-absent neutralisation; however, a booster mRNA may reduce risk of symptomatic breakthrough infections and prevent hospitalisation*^

A booster dose of Spikevax at 50 microgram (ug) level increases Omicron neutralising antibody levels approximately 37-fold compared to pre-boost level. A booster dose at 100ug increased the Omicron neutralising antibody levels approximately 83-fold.^

Johnson & Johnson (Ad26.COV2.S)

Estimated 2 to <5-fold reduction in neutralisation*^

≥10-fold reduction in neutralisation*^

Estimated 2 to <5-fold reduction in neutralisation*^

Estimated  <2-fold reduction in neutralisation^* 

One study suggests a booster (third) dose increases neutralising antibodies and different immune phenotypes following heterologous (“mix-and-match”) compared with homologous boost strategies for COVID-19*^

Immune escape - other

Elicits cross-reactive neutralising antibodies*

Elicits cross-reactive neutralising antibodies^

Elicits cross-reactive neutralising antibodies^

Transmission is associated with an escape to antibodies targeting non-RBD and RBD Spike epitopes*^

Prior infection prevented symptomatic reinfection with Omicron (~60%) to a much lesser extent than other variants (Alpha, Beta and Delta ~ 90%).  Neutralisation capacity against Omicron was maintained best against sera from individuals infected and vaccinated or vaccinated and infected*^

Data suggests that the T-cell immune response in previously infected, and most likely vaccinated individuals, should still be effective against Omicron*^

Treatment   

review study found that monoclonal antibodies had reduced efficiency in neutralising variants^.  One study suggests Delta is resistant to bamlanivimab*^

Therapeutic interventions for the management of severe or critical COVID-19 that target host responses (such as corticosteroids, interleukin 6 receptor blockers and prophylaxis with anticoagulation) are expected to remain effective*^

Early findings suggests the mutations in Omicron will likely compromise the binding of many monoclonal antibodies; however, residual binding should provide protection from severe disease*^

Preliminary data  suggests sotrovimab retains activity, while early tests show Regen-Cov (imdevimab and casirivimab failed to neutralise the Omicron variant*^

Testing and detection

Limited impact.

S gene target failure; no impact on the overall result from multiple target RT-PCR, no impact on Ag RDTs observed.

No impact on RT-PCR or Ag RDTs*^

No reported impacts on diagnostics*^

Lateral flow devices effective in detecting*^

Estimated lower PCR Ct values and significantly longer duration of Ct value ≤30. One study suggests higher loads do not translate into different testing  scenarios*^.  Another study suggests no significant differences in the duration of RT-PCR positivity among fully vaccinated individuals versus not fully vaccinated individuals, or in duration of culture positivity*^

The diagnostic accuracy of routinely used PCR and antigen-based rapid diagnostic test (Ag-RDT) assays does not appear to be influenced by Omicron*^

S gene target failure  from a widely used PCR test (ThermoFisher TaqPath) is indicated for Omicron, and can be used as the marker for this variant, which may lead to efficient detection of Omicron*^

Preliminary data suggests four RT-qPCR assays enabled rapid identification of Omicron and early reports of detection in the wastewater*^

Countries reporting detection (not necessarily local transmission) Detected in ~175 countries Detected in ~114 countries Detected in ~72 countries    

Detected in ~162 countries

Detected in ~149 countries

The World Health Organization (WHO) announced the Variant naming system on 1 June 2021. The labels do not replace existing scientific names. Designations include Variant of Concern (VOC), Variant of Interest (VOI) and Variants Under Monitoring (VUMs). A previously designated VOC or VOI can also be reclassified if it no longer poses a major added risk to global public health.

Details are tabulated when Variants meet the World Health Organization (WHO) definition of Variant of Concern (VOC).

Reports of Variants of Interest (VOI) are updates identified in the grey literature are below:

Notes

*Preliminary data, not fully established, in some cases small numbers or short follow up; interpret with caution

^ Commentary grey literature, pre-peer review or news

Background

Evidence check - SARS-CoV-2 variants (PDF)

Living evidence tables include some links to low quality sources and an assessment of the original source has not been undertaken. Sources are monitored daily but due to rapidly emerging information, tables may not always reflect the most current evidence. The tables are not peer reviewed, and inclusion does not imply official recommendation nor endorsement of NSW Health.

Last updated on 19 Jan 2022

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