For more information: www.cdc.gov/COVID19

Emerging SARS-CoV-2 Variants: 

Considerations for Vaccine 

ACIP COVID-19 Vaccines

CDR Heather Scobie PhD, MPH

ACIP Meeting

March 1, 2021
Background
SARS-CoV-2 Variants

▪ Multiple SARS-CoV-2 variants circulating globally

– After emerging, some disappear; others persist

▪ CDC and others are studying these variants to understand whether they:

– Spread more easily from person to person

– Cause milder or more severe disease in people

– Detected by available diagnostic tests

– Respond to therapeutics currently used to treat people for COVID-19

– Change effectiveness of COVID-19 vaccines

▪ Variants classified, e.g., "variant of concern"

https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant.html

https://www.who.int/publications/m/item/covid-19-weekly-epidemiological-update
Why are new SARS-CoV-2 variants emerging?

▪ Viruses constantly change through mutation, so new variants are expected

– SARS-CoV-2 has low mutation rate, compared with influenza and HIV

▪ Evolutionary selection — still being characterized, may be driven by:

– Chronic infection (e.g., immunocompromised)

– Interspecies transmission (e.g., minks)

– Therapeutic treatment (e.g., monoclonal antibodies, convalescent sera)

– Prior immunity to strains with limited cross-reactivity

– Increased transmissibility

– Founder effect — small number of genotypes seed a new population
Example of SARS-CoV-2 strain replacement

D614G – worldwide

▪ Greater infectivity, more open 

conformation of viral spike 

protein

▪ Likely increased transmissibility 

(20%)

▪ Not more clinically severe

▪ Current vaccines are still 

highly effective

Figure source: Callaway E. Nature (2020). https://www.nature.com/articles/d41586-020-02544-6

Volz et al. Cell (2021). https://www.sciencedirect.com/science/article/pii/S0092867420315373

https://www.cdc.gov/coronavirus/2019-ncov/more/science-and-research/scientific-brief-emerging-variants.html#ref2
Example of SARS-CoV-2 strain replacement

D614G – worldwide

▪ Greater infectivity, more open 

conformation of viral spike 

protein

▪ Likely increased transmissibility 

(20%)

▪ Not more clinically severe

▪ Current vaccines are still 

highly effective

Figure source: Callaway E. Nature (2020). https://www.nature.com/articles/d41586-020-02544-6

Volz et al. Cell (2021). https://www.sciencedirect.com/science/article/pii/S0092867420315373

https://www.cdc.gov/coronavirus/2019-ncov/more/science-and-research/scientific-brief-emerging-variants.html#ref2

Spike

proteins
SARS-CoV-2 variants of concern

Name

(Pangolin)

Name

(Nextstrain)

First 

Detected

Cases in

the US

Countries

Reporting

Cases

Key Amino Acid 

Mutations

Transmissibility

Rate

B.1.1.7 20I/501Y.V1 United 

Kingdom Y 101

Δ69/70

Δ144Y

N501Y

A570D

D614G

P681H

~50% increase

B.1.351 20H/501Y.V2 South Africa Y 51

K417N

E484K

N501Y

D614G

~50% increase

P.1 20J/501Y.V3 Brazil/

Japan Y 29

E484K

K417N/T

N501Y

D614G

Not determined

https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html

Davies et al. Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England. medrxiv.org/content/10.1101/2020.12.24.20248822v2

Pearson et al. Estimates of severity and transmissibility of novel SARS-CoV-2 variant 501Y.V2 in South Africa. https://cmmid.github.io/topics/covid19/reports/sa-novelvariant/2021_01_11_Transmissibility_and_severity_of_501Y_V2_in_SA.pdf
SARS-CoV-2 variants of concern

Name

(Pangolin)

Name

(Nextstrain)

First 

Detected

Cases in

the US

Countries

Reporting

Cases

Key Amino Acid 

Mutations

Transmissibility

Rate

B.1.1.7 20I/501Y.V1 United 

Kingdom Y 101

Δ69/70

Δ144Y

N501Y

A570D

D614G

P681H

~50% increase

B.1.351 20H/501Y.V2 South Africa Y 51

K417N

E484K

N501Y

D614G

~50% increase

P.1 20J/501Y.V3 Brazil/

Japan Y 29

E484K

K417N/T

N501Y

D614G

Not determined

https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html

Davies et al. Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England. medrxiv.org/content/10.1101/2020.12.24.20248822v2

Pearson et al. Estimates of severity and transmissibility of novel SARS-CoV-2 variant 501Y.V2 in South Africa. https://cmmid.github.io/topics/covid19/reports/sa-novelvariant/2021_01_11_Transmissibility_and_severity_of_501Y_V2_in_SA.pdf
SARS-CoV-2 variants of concern

Name

(Pangolin)

Name

(Nextstrain)

First 

Detected

Cases in

the US

Countries

Reporting

Cases

Key Amino Acid 

Mutations

Transmissibility

Rate

B.1.1.7 20I/501Y.V1 United 

Kingdom Y 101

Δ69/70

Δ144Y

N501Y

A570D

D614G

P681H

~50% increase

B.1.351 20H/501Y.V2 South Africa Y 51

K417N

E484K

N501Y

D614G

~50% increase

P.1 20J/501Y.V3 Brazil/

Japan Y 29

E484K

K417N/T

N501Y

D614G

Not determined

https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html

Davies et al. Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England. medrxiv.org/content/10.1101/2020.12.24.20248822v2

Pearson et al. Estimates of severity and transmissibility of novel SARS-CoV-2 variant 501Y.V2 in South Africa. https://cmmid.github.io/topics/covid19/reports/sa-novelvariant/2021_01_11_Transmissibility_and_severity_of_501Y_V2_in_SA.pdf
SARS-CoV-2 variants of concern

Name

(Pangolin)

Name

(Nextstrain)

First 

Detected

Cases in

the US

Countries

Reporting

Cases

Key Amino Acid 

Mutations

Transmissibility

Rate

B.1.1.7 20I/501Y.V1 United 

Kingdom Y 101

Δ69/70

Δ144Y

N501Y

A570D

D614G

P681H

~50% increase

B.1.351 20H/501Y.V2 South Africa Y 51

K417N

E484K

N501Y

D614G

~50% increase

P.1 20J/501Y.V3 Brazil/

Japan Y 29

E484K

K417N/T

N501Y

D614G

Not determined

https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html

Davies et al. Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England. medrxiv.org/content/10.1101/2020.12.24.20248822v2

Pearson et al. Estimates of severity and transmissibility of novel SARS-CoV-2 variant 501Y.V2 in South Africa. https://cmmid.github.io/topics/covid19/reports/sa-novelvariant/2021_01_11_Transmissibility_and_severity_of_501Y_V2_in_SA.pdf

Glutamic Acid (E) to Lysine (K) 

replacement at spike position 484:

− to + charge change
U.S. COVID-19 cases caused by 

variants of concern

https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant-cases.html; data as of 02/28/2021

B.1.1.7

Variant Reported 

cases

No. of states

B.1.1.7 2,400 46

B.1.351 53 16

P.1 10 5

B.1.351

P.1

Reporting sources vary, so calculating 

proportions is not possible
B.1.1.7 trajectory in the United States

▪ First identified in Dec. 2020, but likely 

arrived in Nov. 2020

– Multiple introductions

▪ Current prevalence estimated 1-2%

– Commercial diagnostic data suggest 

early phase logistic expansion

▪ Two models suggest B.1.1.7 may 

predominate by March 2021

– One suggests high vaccine coverage will 

blunt impact of higher transmissibility

https://www.cdc.gov/coronavirus/2019-ncov/more/science-and-research/scientific-brief-emerging-variants.html

Figure source: Washington et al. medRxiv preprint (Feb 7 2021): https://www.medrxiv.org/content/10.1101/2021.02.06.21251159v1

Galloway et al. MMWR 2021;70:95–99. https://www.cdc.gov/mmwr/volumes/70/wr/mm7003e2.htm?s_cid=mm7003e2_w
Changes in receptor-binding domain (RBD) of spike protein

▪ RBD binds host ACE2 receptor – essential for infection

▪ Majority of neutralizing antibodies bind RBD in most 

convalescent human sera

▪ Convergent evolution of several RBD mutations

– ↑ binding, ↑ infectivity, ↓ efficacy of antibody therapies

https://www.nytimes.com/interactive/2021/health/

coronavirus-variant-tracker.html
Changes in receptor-binding domain (RBD) of spike protein

▪ RBD binds host ACE2 receptor – essential for infection

▪ Majority of neutralizing antibodies bind RBD in most 

convalescent human sera

▪ Convergent evolution of several RBD mutations

– ↑ binding, ↑ infectivity, ↓ efficacy of antibody therapies

https://www.nytimes.com/interactive/2021/health/

coronavirus-variant-tracker.html

P.2
Vaccine effectiveness data
Review of 26 studies: Vaccine sera neutralization of 

SARS-CoV-2 variants

▪ 8 published studies and 18 preprint studies; all small sample sizes (n=5−50)

▪ 13 studies only Pfizer; 3 studies only Moderna; 2 studies on AstraZeneca; 7 

studies on ≥1 vaccine; 1 study on unspecified mRNA vaccine

▪ 8 studies on single/limited sets of mutations – generally minimal impact

– E484K and E484K-K417N-N501Y larger effects*

▪ Largest impacts: B.1.351 (South Africa) > P.1, P.2 (Brazil) > B.1.1.7 (UK)

– Most B.1.351 studies: 3−11-fold reduction, ranged up to 97-fold

– Most B.1.1.7 studies: <3-fold reduction, ranged up to 9-fold

* Mutations found in South Africa (B.1.351) and Brazil (P.1, P.2) References in Appendix
1

10

100

Fold reduction

Reduced neutralization activity of vaccine sera relative 

to wildtype/dominant strain, by study (n=22)

B.1.1.7 

UK

B.1.351

S. Africa

P.1

Brazil

P.2

Brazil 

E484K B.1.1.7 

+ E484K

mRNA (Pfizer or Moderna)

Novavax

AstraZeneca

Studies by vaccine type

References in Appendix

No effect =
Neutralization of variants after 1 & 2 vaccine doses

▪ Postponing 2nd mRNA dose may leave 

some less protected against variants

▪ Minimal/no neutralization of B.1.351 

after one dose

– History of COVID-19 + 1 dose → 

moderate protection against B.1.351

▪ Improved neutralization of B.1.1.7 and 

B.1.351 after 2nd dose

▪ Delayed antibody response against 

variants

1 dose

Week 2 Week 3

Figure Source: Planas et al. bioRxiv preprint (Feb 12 2021: https://doi.org/10.1101/2021.02.12.430472

Skelly et al. Res square preprint (Feb 9 2021); https://www.researchsquare.com/article/rs-226857/v1

Garcia-Beltran et al. medRxiv preprint (Feb 14 2021): https://doi.org/10.1101/2021.02.14.21251704

Shen et al. bioRxiv preprint (Jan 28 2021); https://doi.org/10.1101/2021.01.27.428516

Collier et al. medRxiv preprint (Feb 15 2021): https://doi.org/10.1101/2021.01.19.21249840

Stamatatos et al. medRxiv preprint (Feb 5 2021): https://doi.org/10.1101/2021.02.05.21251182

Supasa et al.Cell (2021): https://doi.org/10.1016/j.cell.2021.02.033

Pfizer vaccine 
Neutralization of variants after 1 & 2 vaccine doses

▪ Postponing 2nd mRNA dose may leave 

some less protected against variants

▪ Minimal/no neutralization of B.1.351 

after one dose

– History of COVID-19 + 1 dose → 

moderate protection against B.1.351

▪ Improved neutralization of B.1.1.7 and 

B.1.351 after 2nd dose

▪ Delayed antibody response against 

variants

1 dose 2 doses

Week 2 Week 3 Week 4

Figure Source: Planas et al. bioRxiv preprint (Feb 12 2021: https://doi.org/10.1101/2021.02.12.430472

Skelly et al. Res square preprint (Feb 9 2021); https://www.researchsquare.com/article/rs-226857/v1

Garcia-Beltran et al. medRxiv preprint (Feb 14 2021): https://doi.org/10.1101/2021.02.14.21251704

Shen et al. bioRxiv preprint (Jan 28 2021); https://doi.org/10.1101/2021.01.27.428516

Collier et al. medRxiv preprint (Feb 15 2021): https://doi.org/10.1101/2021.01.19.21249840

Stamatatos et al. medRxiv preprint (Feb 5 2021): https://doi.org/10.1101/2021.02.05.21251182

Supasa et al.Cell (2021): https://doi.org/10.1016/j.cell.2021.02.033

Pfizer vaccine 
Discussion of lab studies

▪ Difficult to estimate how laboratory results might translate to clinical protection

– No immunological correlate of protection for SARS-CoV-2

▪ Neutralization antibodies in sera from mRNA vaccine recipients generally shown to be 

higher than COVID-19 convalescent sera

▪ Variation in results may be explained by differences in experimental conditions

– Neutralization assays — replicating & nonreplicating pseudovirus vs. SARS-CoV-2

– Sera — time post-vaccination, or population (e.g., age, COVID-19 history)

– Use of limited or full sets of spike mutations vs. clinical isolates of variants

▪ AstraZeneca — not prefusion stabilized spike, limited generalizability to other vaccines

▪ Limitation for all studies — small sample sizes and lack generalizability

– Many studies are preprints not yet peer-reviewed
Vaccine efficacy or effectiveness (VE) against variants

Hall et al. Lancet preprint (Feb 22 2021): https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3790399; *VE for symptomatic & asymptomatic infection

Dagan et al. NEJM (2021). https://www.nejm.org/doi/full/10.1056/NEJMoa2101765?query=TOC

https://www.fda.gov/media/146217/download

Novavax.: https://ir.novavax.com/news-releases/news-release-details/novavax-covid-19-vaccine-demonstrates-893-efficacy-uk-phase-3

Madhi et al. medRxiv preprint (Feb 12 2021): https://doi.org/10.1101/2021.02.10.21251247

Emary et al. Lancet preprint (Feb 4 2021): https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3779160

Vaccine Study type VE

Pfizer Post-licensure • 86% in UK (predominate B.1.1.7 circulation)*

• 94% in Israel (up to 80% of cases from B.1.1.7)

Janssen Pre-licensure • 74% in U.S.

• 66% in Brazil (69% of cases from P.2)

• 52% in S. Africa (95% of cases from B.1.351)

Novavax Pre-licensure

Pre-licensure

• 96% against non-B.1.1.7 in UK

• 86% against B.1.1.7 in UK

• 60% in S. Africa (93% of cases from B.1.351)

AstraZeneca Pre-licensure

Pre-licensure

• 84% against non-B.1.1.7 in UK

• 75% against B.1.1.7 in UK

• 10% against B.1.351 in South Africa
Vaccine efficacy or effectiveness (VE) against variants

Hall et al. Lancet preprint (Feb 22 2021): https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3790399; *VE for symptomatic & asymptomatic infection

Dagan et al. NEJM (2021). https://www.nejm.org/doi/full/10.1056/NEJMoa2101765?query=TOC

https://www.fda.gov/media/146217/download

Novavax.: https://ir.novavax.com/news-releases/news-release-details/novavax-covid-19-vaccine-demonstrates-893-efficacy-uk-phase-3

Madhi et al. medRxiv preprint (Feb 12 2021): https://doi.org/10.1101/2021.02.10.21251247

Emary et al. Lancet preprint (Feb 4 2021): https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3779160

Vaccine Study type VE

Pfizer Post-licensure • 86% in UK (predominate B.1.1.7 circulation)*

• 94% in Israel (up to 80% of cases from B.1.1.7)

Janssen Pre-licensure • 74% in U.S.

• 66% in Brazil

• 52% in S. Africa

Novavax Pre-licensure

Pre-licensure

• 96% against non-B.1.1.7 in UK

• 86% against B.1.1.7 in UK

• 60% in S. Africa (93% of cases from B.1.351)

AstraZeneca Pre-licensure

Pre-licensure

• 84% against non-B.1.1.7 in UK

• 75% against B.1.1.7 in UK

• 10% against B.1.351 in South Africa

73-82% for severe/critical 

disease in each country
Summary of preliminary data: Implications of SARSCoV-2 variants of concern on vaccine effectiveness

▪ B.1.1.7 (first detected in the United Kingdom)

– Exponential increase in prevalence in United States

– Minimal impact on vaccine effectiveness, but attention needed for variants 

with additional substitutions in RBD, such as E484K

▪ B.1.351 (first detected in South Africa)

– Currently low prevalence in United States

– Moderate impact on vaccine effectiveness, suggests it’s prudent to start 

evaluating variant vaccines in case prevalence substantially increases

▪ P.1 (first detected in Brazil/Japan)

– Very low prevalence in United States, but same three RBD mutations as B.1.351

– Additional data needed on potential impact on vaccine effectiveness
Modifying vaccines to target SARS-CoV-2 variants

▪ Current prevention measures and licensed vaccines offer protection against 

SARS-CoV-2 variants

– Efforts needed to increase speed and degree of uptake

▪ Periodic update of SARS-CoV-2 vaccines likely needed

▪ Modeling study predicts changing COVID-19 vaccines to target faster 

spreading viral variants more effective than targeting the slower dominant 

strain, despite initial prevalence 1

1. Bedwick et al. medRxiv preprint (Feb 8 2021); doi: https://doi.org/10.1101/2021.01.05.21249255
Response to variants
SARS-CoV-2 Interagency Group (SIG)

▪ Established by Dept. of Health & Human Services to improve coordination

– CDC

– National Institutes of Health (NIH)

– Food and Drug Administration (FDA)

– Biomedical Advanced Research and Development Authority (BARDA)

– US Department of Agriculture (USDA)

– Department of Defense (DoD)

▪ Focuses on rapid characterization of emerging variants and monitors 

potential impact on SARS-CoV-2 diagnostics, therapeutics, and vaccines

Walensky, Walke and Fauci. JAMA (2021): https://jamanetwork.com/journals/jama/fullarticle/2776739
CDC approaches to genomic surveillance and 

epidemiology

▪ National SARS-CoV-2 Strain Surveillance (NS3)

– Approximately 3,000 random specimens/month regularly submitted from public 

health laboratories across U.S.

▪ Partnership with commercial diagnostic laboratories

– Scaling to 6,000 sequences/week

▪ Contracts and partnerships with state and local health departments and universities

▪ SPHERES* Consortium of ~170 domestic partners — open sharing of sequencing data

▪ Focused molecular epidemiologic studies

https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance.html

https://www.aphl.org/programs/preparedness/Crisis-Management/COVID-19-Response/Pages/Sequence-Based-Surveillance-Submission.aspx

https://www.cdc.gov/coronavirus/2019-ncov/covid-data/spheres.html

* SPHERES= SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance
U.S. sequences available in public repositories

https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/genomic-surveillance-dashboard.html as of 2/28/21

National Center for Biotechnology Information (NCBI); GISAID, a global initiative maintaining a repository of viral sequencing data 

Data 

collection

ongoing

0

20,000

40,000

60,000

80,000

100,000

120,000

140,000

160,000
Investigating COVID-19 vaccine breakthrough cases

▪ Despite high vaccine efficacy, vaccine breakthrough cases expected

– Some will be caused by variants, even if vaccine has similar effectiveness against variants

▪ Vaccine breakthrough case: person with SARS-CoV-2 RNA or antigen detected 

in respiratory specimen collected ≥14 days after completing primary series of 

an FDA-authorized COVID-19 vaccine

▪ Cases identified from national case-based surveillance, Vaccine Adverse 

Events Reporting System (VAERS), health departments, healthcare providers

– Working with state health departments on case investigation

– Respiratory specimens used for whole genome sequencing to identify variants

▪ Data from investigations will be posted or published when available
Boosters and second-generation vaccines against SARSCoV-2 variants

▪ Moderna and Pfizer launching booster studies of current vaccines in U.S. and 

developing second-generation vaccines against B.1.351

– Moderna: Variant-specific vaccine (mRNA-1273.351) and multivalent vaccine 

with original authorized vaccine and variant vaccine (mRNA-1273.21)

▪ Yet to be defined:

– Evidence indicating need for a modified vaccine

– Process for evaluating, deciding and recommending whether a modified 

vaccine is needed 

▪ World Health Organization (WHO) has likely role in global coordination —

developing framework for risk assessment

https://investors.modernatx.com/news-releases/news-release-details/moderna-covid-19-vaccine-retains-neutralizing-activity-against

https://investors.modernatx.com/news-releases/news-release-details/moderna-announces-it-has-shipped-variant-specific-vaccine

https://www.pfizer.com/news/press-release/press-release-detail/pfizer-and-biontech-initiate-study-part-broad-development
FDA: Data needed to support EUA amendment for 

a vaccine addressing emerging SARS-CoV-2 variants

1. Good manufacturing practices and controls

2. Nonclinical data, e.g., laboratory studies, animal models

3. Clinical data from immunogenicity studies — noninferiority with licensed 

vaccine

– Primary series or booster dose

– Could be single age group with extrapolation to other age groups

– Safety data from during the immunogenicity evaluation period

4. Laboratory assays and immunogenicity endpoints

– Correlates of protection not yet established

https://www.fda.gov/regulatory-information/search-fda-guidance-documents/emergency-use-authorization-vaccines-prevent-covid-19
Variants: Implications for vaccine policy

▪ Continue to monitor evidence:

– Emergence and spread of SARS-CoV-2 variants

– Vaccine effectiveness

– Breakthrough infections in vaccinated or previously infected persons

– Ability of postvaccination serum to neutralize emerging variant viruses

▪ Work Group and ACIP will review evidence submitted for any next 

generation vaccines
For more information, contact CDC

1-800-CDC-INFO (232-4636)

TTY: 1-888-232-6348 www.cdc.gov

The findings and conclusions in this report are those of the authors and do not necessarily represent the 

official position of the Centers for Disease Control and Prevention.

Thank you