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The n e w e ng l a n d j o u r na l of m e dic i n e

Spe ci a l R e p or t

SARS-CoV-2 Variants and Vaccines


Philip R. Krause, M.D., Thomas R. Fleming, Ph.D., Ira M. Longini, Ph.D., Richard Peto, F.R.S.,
Sylvie Briand, M.D., David L. Heymann, M.D., Valerie Beral, F.R.C.P., Matthew D. Snape, M.D.,
Helen Rees, M.R.C.G.P., Alba‑Maria Ropero, B.Sc., Ran D. Balicer, M.D., Jakob P. Cramer, M.D.,
César Muñoz‑Fontela, Ph.D., Marion Gruber, Ph.D., Rogerio Gaspar, Ph.D.,
Jerome A. Singh, Ph.D., Kanta Subbarao, M.B., B.S., Maria D. Van Kerkhove, Ph.D.,
Soumya Swaminathan, M.D., Michael J. Ryan, M.D., and Ana‑Maria Henao‑Restrepo, M.D.

Summary sequencing and sharing. A SARS-CoV-2 risk-moni-


toring and evaluation framework is being devel-
Viral variants of concern may emerge with dan- oped and continually improved by the WHO to
gerous resistance to the immunity generated by identify and assess variants of concern. This
the current vaccines to prevent coronavirus dis-
ease 2019 (Covid-19). Moreover, if some variants
of concern have increased transmissibility or viru- Table 1. Vaccine-Related Priorities to Control Viral Variants.*
lence, the importance of efficient public health Evaluate existing vaccines for efficacy against variants
measures and vaccination programs will increase. Randomize vaccine schedules (e.g., agents and timing) during deployment
The global response must be both timely and and study postexposure prophylaxis
science based. Perform observational studies to estimate variant-specific vaccine effectiveness
Expand worldwide capacity for sequencing of virus isolates

I n addition to continuing to track the emer-


gence of new variants of severe acute respira-
tory syndrome coronavirus 2 (SARS-CoV-2), there
Obtain sequences of clinical isolates from postlicensure studies, clinical
trials, and vaccinees with serious breakthrough infections
If current vaccines are inadequate, assess the effectiveness of new vaccines
are four major priorities for the global response or modified vaccines against variants
to variants of concern (Table 1). These priorities, Evaluate new vaccines, ideally in randomized, placebo-controlled trials with
which involve scientific approaches for evaluat- clinical end points
ing existing vaccines and developing modified Develop and evaluate modified vaccines to achieve adequate efficacy against
and new vaccines, are to determine whether ex- variants of concern
isting vaccines are losing efficacy against vari- Reduce the risk that additional variants of concern will emerge
ants, to decide whether modified or new vac- Promote public health measures (e.g., masking, social distancing, and vac‑
cines are warranted to restore efficacy against cination) to reduce viral transmission
variants, to reduce the likelihood that variants of Avoid the use of treatments with uncertain benefit that could drive the evolu‑
concern will emerge, and to coordinate interna- tion of variants
tional research and the response to new vari- Consider targeted vaccination strategies to reduce community transmission
ants, both in general and in relation to vaccines, Coordinate the worldwide response
through the World Health Organization (WHO). Identify and characterize viral variants of concern
Efforts to track viral mutations and variants Select antigens for modified or new vaccines
are ongoing. The aim is to detect new changes
Share research results, including methods to link genetic sequence data
quickly and to assess their possible effects. Many with the antigenic characteristics of circulating SARS-CoV-2
research groups are sequencing virus isolates and
Decide whether the variant data warrant modification of existing vaccines
sharing these sequences on public databases
Promote convergence of regulatory assessments
such as GISAID (Global Initiative on Sharing All
Influenza Data).1 This collaboration helps scien- Establish a global data repository
tists track the ways in which the virus is evolv- * An existing vaccine is one that has been shown to be effective in clinical tri‑
ing. In order to help monitor and respond to the als, a modified vaccine one in which a new antigen is delivered through an
evolving pandemic, it is important that all coun- existing vaccine, and a new vaccine a completely new vaccine. SARS-CoV-2
denotes severe acute respiratory syndrome coronavirus 2.
tries increase the collection of virus isolates for

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The n e w e ng l a n d j o u r na l of m e dic i n e

framework, which involves enhanced surveil-


lance, research on variants of interest and vari-

transmission
ants of concern, and evaluation of the effect of

Increase
P681

H
variants on diagnostic tests, therapeutic agents,

R
and vaccines, will assist in global decision mak-
ing regarding changes in vaccines that may be
necessary.
transmission

Variants of concern with increased transmis-


Increase

sibility are contributing to the reversal of the


D614
Amino Acid Position in Prototype Virus and Proposed Effect of Changing It*

G
G

R
decreases in Covid-19 case counts that occurred
in many countries earlier this year.2 The B.1.1.7
(or alpha) variant of concern increases viral
transmission

transmissibility3 and is emerging as an increas-


Increase

ingly common variant. The P.1 (or gamma) vari-


N501

Y
Y

ant may cause severe disease even in persons who


have been previously infected, although definitive
information is lacking.4 The B.1.351 (or beta)
K (later change)

variant is less easily neutralized by convalescent


neutralization
Decrease

plasma obtained from patients infected with


E484

Q
K

previous variants and by serum obtained from


vaccinees than the prototype virus on which vac-
cine antigens are based,5 and preliminary evidence
(based on data from post hoc subgroups in pla-
neutralization

cebo-controlled vaccine trials) suggests reduced


Decrease
L452

efficacy of some vaccines against mild or moder-


R

* Single letter codes of amino acid changes at specified positions for the listed variants are shown.

ate disease caused by this variant.6-8 Additional


variants that are responsible for many deaths,
such as B.1.617.2 (or delta),9 continue to emerge.
neutralization

So far, there is no good evidence that currently


Decrease
K417

N/T

identified variants of concern evade the most


N

important vaccine effect — that of prevention of


severe disease. Table 2 describes key properties
of and mutations in five selected variants. The fact
69–70 deleted
transmission

that a few key amino acids in the spike protein


Increase
Table 2. Key Spike Protein Mutations in Five SARS-CoV-2 Variants.

Δ69–70

have changed independently in variants identi-


fied in various parts of the world indicates that
these are convergent changes and suggests that
vaccines that incorporate these selected residues
Increase transmission

Increase transmission
Increase transmission
Phenotypic Change

decrease neutral‑

could cover several variants.


Increase transmis‑

Increase transmis‑
sion, decrease

sion, decrease
and virulence,

neutralization
and virulence

virulence

E valuating E xis ting Vaccine s


ization

for Effic ac y ag ains t Variant s

Although animal models and in vitro studies


can provide important information, clinical data
B.1.1.28.1 (or gamma or

will continue to be needed to determine whether


B.1.617.1 (or kappa)

existing vaccines are losing efficacy against vari-


B.1.617.2 (or delta)
B.1.1.7 (or alpha)
B.1.351 (or beta)

ants. While existing vaccines are being deployed,


clinical data can be sought not only from care-
fully planned observational studies, but also from
P.1)
Variant

randomized trials of vaccines versus placebo, of


one vaccine versus another, or of different vac-

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SARS-CoV-2 Variants and Vaccines

cination regimens (e.g., different doses, numbers


of doses, and intervals between doses). Vaccination
Trial Researchers Vaccinees Personnel
In areas where the vaccine supply or delivery
Instead of usual
capacity is limited, instead of letting operational vaccine allocation
decisions determine the order in which people procedures, use
randomization to
are vaccinated, making first vaccine doses avail- Planning
determine which
able to some of the target population on a ran- persons to vaccinate
and when and where
domized basis could provide useful information they will be vaccinated
about efficacy against major variants. This is
Inform the vaccinators Receive detail Administer vaccine
especially true if the numbers of participants and participants when about and attend and record vaccina-
Implementation
who undergo randomization are large enough to and where vaccine vaccination tion in accordance
will be delivered appointment with usual procedures
allow assessment of “hard” end points such as
hospitalization or severe disease. Monitor vaccination
status and incidence
If large-scale randomization were used dur- Follow-up
of Covid-19 from
ing vaccine deployment to compare the effects of health records

early second doses with those of delayed second Report vaccination


doses, any differences in efficacy could be reli- compliance; analyze
outcomes according
ably assessed not only overall but perhaps with Analysis
to assigned vaccine
respect to certain common variants. In some (intention-to-treat
principle)
populations, random assignment of the vaccina-
tion date or location might be built into public
Figure 1. Roles of Researchers, Vaccinees, and Vaccinators in Simplified
health programs, and persons who become eli- Randomized Trials Conducted during Vaccine Deployment.
gible for vaccination (according to vaccine prior- In trials to assess vaccine efficacy, work performed by trial researchers is
ity groupings) could be randomly assigned to re- considerably more simplified than work in a standard trial, with no extra
ceive appointments to be vaccinated with a longer effort required from vaccinees or vaccination personnel. Covid-19 denotes
or a shorter gap between doses or to receive one coronavirus disease 2019.
vaccine or another. This strategy might allow
many hundreds of thousands of persons to un-
dergo randomization with little cost to the vac- ies could also detect loss of protection against
cination program and with little or no distur- variants of concern in previously infected persons.
bance of the existing vaccination capacity (Fig. 1). Observational studies lack precision when
At the opposite extreme of trial size, if any vac- either vaccine uptake or variant prevalence is too
cines were known to have the potential to pre- low or too high for statistical stability, but they
vent Covid-19 even when administered after an could provide insights if cases and controls are
exposure to SARS-CoV-2, relatively small, ran- adequately matched for potential confounders
domized studies of postexposure prophylaxis (e.g., in a “test-negative design”10). There are
could provide important insights about vaccine ways to at least limit confounding for such stud-
efficacy (or relative efficacy) against different ies in general11 and for test-negative studies in
strains. particular.12,13
Nonrandomized observational studies that Creative methodologic approaches are still
attempt to estimate vaccine effectiveness are all needed to assess any influences of variants of con-
prone to some bias. Nevertheless, in areas where cern on vaccine efficacy and durability. In studies
several variants are cocirculating and some but of vaccine efficacy and effectiveness against vari-
not all of the population has been vaccinated, ants of concern, near-complete sequencing of
carefully designed observational studies of the isolates from selected sentinel sites can reduce
distribution of viral genotypes among cases in biases in the selection of samples for sequenc-
vaccinated and unvaccinated persons could yield ing. Sequencing capacity is lacking in many parts
fairly reliable estimates of relative vaccine efficacy of the world and should be increased. Samples
against various variants. Such studies should ac- obtained from unselected vaccine recipients with
count for potential confounding if the level of breakthrough infection and from matched un-
vaccination is correlated with the relative preva- vaccinated controls could be used to assess the
lence of variants across sites. Observational stud- influence of particular genomic or antigenic

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The n e w e ng l a n d j o u r na l of m e dic i n e

features of interest on vaccine efficacy. With the example, the magnitude of the immune re-
use of such approaches (i.e., “sieve analyses”14) sponse against one or more variants of concern
in trials or in studies conducted after vaccine after a person has received a modified vaccine
deployment, important insights could be gleaned could be compared with that against the proto-
about the relevance of particular viral features, type virus after a person has received the origi-
and these insights may lead to improved strain nal vaccine that is known to be effective. Assess-
selection in the formulation of modified vaccines. ment of neutralizing responses against several
How reliably any immune biomarker can variants of concern and against the prototype
serve as a “correlate of protection” is not yet virus may help to determine whether more than
known. The effects of vaccination on such bio- one vaccine (or, ultimately, a polyvalent vaccine)
markers (as surrogate end points) — if those is needed.
biomarkers prove to be reliably predictive of the There has been consensus in recent regula-
effects of vaccine on the incidence or outcome of tory discussions15 and in WHO guidance that
breakthrough infections — could provide sup- conventional, large, clinical end-point trials are
port for regulatory action regarding new candi- probably not necessary in order to introduce
date vaccines. However, caveats include the modified vaccines against variants of concern.
potential dependence of immune correlates of Because differences among assays of immune
protection on vaccine-specific factors, viral strain, responses may complicate direct comparisons,
and the choice of Covid-19 study end points the Food and Drug Administration (but not the
(i.e., any infection vs. symptomatic infection vs. European Medicines Agency) has proposed that
severe disease). animal models16 could be used to provide fur-
ther support for the effectiveness of modified
vaccines against variants of concern.
E valuating Ne w or Modified
Vaccine s ag ains t Variant s Even with the deployment of some safe and
effective vaccines, more will be needed to ad-
Although there will be reluctance to deploy vac- dress the international pandemic. New vaccines
cines that are based on new sequences before may be more effective than previous vaccines
there is clear evidence that the original vaccines against emerging viral variants, and they may be
are failing, there will also be reluctance to allow administered in a single dose, be noninjectable,
prolonged circulation of vaccine-resistant vari- avoid cold-chain constraints, or have improved
ants while new vaccines or modified vaccines are manufacturing scalability. The design of modified
being developed, if this can be avoided. Now is vaccines or of completely new vaccines should
the time to plan for the development of modi- leverage international recommendations regard-
fied vaccines that could protect against vaccine- ing antigenic composition.
resistant variants, because such variants may well Trials of new vaccines can still yield reliable
emerge. Planning should include the effect of and interpretable results in an efficient manner
vaccine modification on timelines for vaccine by using randomization, by evaluating effects not
supply and rollout. only on immunologic but also on clinical end
Studies of modified vaccines (i.e., vaccines in points, and by using placebo controls when ethi-
which a new antigen is delivered through a vac- cally appropriate,17,18 perhaps in communities
cine that has already been shown to be effective where vaccine supply is very limited or in sub-
against previously circulating viral variants) should populations (e.g., young adults) in which even if
address the ability of these vaccines to elicit re- infection occurs, the probability of progression
sponses in persons who have not previously had to serious disease is very low.19,20 Randomized
an immunologic response against SARS-CoV-2 trials require additional planning, but when
and in previously vaccinated persons. Changes in practicable they prevent unidentified trial de-
the in vitro neutralization of circulating strains sign–related differences from confounding the
by vaccine-induced antibodies may not imply study results.21 Viral genotyping in persons with
waning effectiveness. Although neutralizing re- breakthrough infection (during or after trials)
sponses may not be reliably predictive of vaccine can support multiple analyses, including assess-
efficacy, striking differences may well provide ment of the influence of viral variants on vaccine
sufficient support for regulatory decisions. For efficacy. In randomized, controlled studies, such

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SARS-CoV-2 Variants and Vaccines

Table 3. Randomized Trials to Determine the Efficacy of New Vaccines.

Trial Design Trial Conduct Ethical Considerations


Randomization of participants to Rapid enrollment of trial participants Trial participants gain either immedi‑
receive one or more new vaccines with high adherence and retention ate or delayed access to experi‑
or a common control vaccine mental vaccines
Use of placebos, if appropriate, or Data monitoring committee safe‑ Participating communities or coun‑
use of active control vaccines guards participants and enhances tries have priority access to vac‑
with established efficacy19 trial integrity cine if it has a good safety profile
and is effective
Monitoring of symptomatic disease, Samples are obtained at diagnosis Vaccine efficacy is assessed in the
severe disease, durability of ef‑ visits from trial participants with context of whatever viral strains
fect, influence of variants on infection, and sequencing of sam‑ are circulating in the communities
efficacy (“sieve analysis”), and ples obtained from recipients of of trial participants; results with
immunologic responses as po‑ control vaccines and new vaccines global relevance are provided
tential correlates of protection* is used to assess the influence of
viral variants on vaccine efficacy

* Sieve analysis is a statistical method that is used to infer the way in which vaccine efficacy varies with viral variants or
genotypes.14

genotyping also yields unbiased information abouttive advantage generally favoring more transmis-
variant-specific efficacy. Countries that participate
sible variants. Variants of concern with resistance
in such trials may assess vaccine efficacy against
against natural or vaccine-induced immunity
locally prevalent viral strains and should receive
would probably supplant previously circulating
priority access to trial vaccines if they have been
strains only if this immune evasion capability
shown to have an acceptable safety profile and resulted in increased fitness, including trans-
to be efficacious (Table 3). In areas where place-
missibility. Given the emergence of immunity-
bo-controlled trials of new vaccines are not ap- evading variants even before vaccines were
propriate, the use of an active comparator could broadly deployed, it is hard to implicate vaccines
still yield important results.22 However, the valid-
or vaccine deployment strategies as the major
ity of a noninferiority trial in which an active drivers of immune evasion.
comparator vaccine is used as the control is de- However, prolonged viral replication in the
pendent on the ability of the previous studies ofpresence of partial immunity in immunocompro-
the active comparator to provide investigators with
mised persons or circumstances in which rapid
reliable insights about the efficacy of the active
transmission of high titers of virus occurs (e.g.,
comparator vaccine against viral variants that crowded living conditions23) could have contrib-
are currently present in communities engaged in uted to the development of variants that can at
the trial. least partially escape human immune responses.
Once modified vaccines or completely new vac-The use of antibody-based treatments (e.g., mono-
cines that address new variants have been intro- clonal antibodies or convalescent plasma) in cir-
duced, the cycle can begin anew with monitoring cumstances in which they are of limited or un-
for even newer variants that might necessitate demonstrated efficacy may further contribute to
further changes in the vaccine antigen sequence. the evolution of variants of concern that could
Development and deployment strategies should evade not only these but also other antibody re-
account for the possibility that multiple variants
sponses.24 Partially effective interventions may
may circulate in the same area. Studies in which therefore encourage viral evolution. In addition,
one vaccine is boosted with a later dose of an- the larger the number of infected persons, the
other would also be valuable. greater the chance that new variants of concern
will arise. Hence, effective public health strate-
gies such as social distancing, the use of masks,
Red ucing the Risk That Variant s
of Concern Will Emer ge and the targeted use of effective vaccines that
reduce both infection and transmission can help
Variants of concern have been evolving since the to limit viral evolution. Limiting transmission in
beginning of the Covid-19 pandemic, with selec- the general population is extremely important

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The n e w e ng l a n d j o u r na l of m e dic i n e

for slowing the emergence of additional variants ployment should be viewed as international en-
of concern. terprises, with international coordination by the
Globally, vaccines are being rolled out slowly, WHO helping benefits to accrue throughout the
partly because of limitations on production ca- world.
pacity and “vaccine nationalism,”25 and in many Coordination is essential in assessing the
countries supplies will probably be limited even need for new or modified vaccines, in evaluating
in late 2021. Currently, the main strategy is to them, and in facilitating scientific understand-
protect critical services, persons in whom severe ing of the risk posed by novel variants and of the
disease is most likely to develop (e.g., older adults), relationships between genetic variation and anti-
and persons who are likely to transmit the virus genic escape. Open and frequent scientific dis-
to vulnerable populations (e.g., health care, front- cussion is necessary to identify which variants of
line, and essential workers), and to contain the concern require attention. Criteria are needed to
spread of the virus in the general population. The assess the appropriateness of given vaccines and
balance between using vaccines to protect per- the likely effect of emerging variants on vac-
sons from disease and using vaccines to target cines, as well as to support recommendations on
prevention of spread involves a strategic decision the development and evaluation of modified vac-
that should be informed by reliable epidemio- cines and new vaccines and the timing of their
logic information. deployment. This process can build on the global
In some epidemics, complete disease elimina- framework used periodically by the WHO to
tion has been achieved efficiently by using an coordinate the selection of antigens in influenza
epidemiologic understanding of transmission to vaccines (Fig. 2).
target the deployment of vaccines (e.g., vaccinat- Decision making about which antigens should
ing “rings” of contacts and contacts of contacts be included in vaccines against SARS-CoV-2 will
around cases of smallpox or Ebola26-28). Together need to involve epidemiologic data, data from
with other public health measures, targeting vac- evolutionary biology, and clinical, animal, and
cination to persons in certain areas or to demo- in vitro data that are pertinent to immune re-
graphic groups with a high incidence of infec- sponses and to continued vaccine efficacy in the
tion rather than focusing only on persons at high face of changing viral sequences and the possi-
risk for serious disease could slow transmission ble waning of vaccine-induced immunity. Meet-
and reduce the risk of development of additional ing these challenges efficiently will require en-
variants of concern, although no strategy can hanced surveillance with continued sharing of
work if adequate vaccine supplies are unavail- data (including viral sequences and correspond-
able. Targeted approaches are now being inves- ing antigens that are linked to clinical and epi-
tigated. For example, in certain areas, the de- demiologic information) and samples (including
ployment of some vaccines in a modified ring new viral variant isolates and serum samples
vaccination strategy has been suggested.29 Stud- obtained from vaccinated persons). It will also
ies of the effectiveness of such targeted strate- require the use of standardized reference reagents
gies could be of global relevance, especially if and models to evaluate viruses and modified vac-
groups or areas with consistently high and low cines. With collaborative, open discussion of re-
rates of transmission can be identified. sults, this data sharing will help foster consistent
and thoughtful public communications about
Co ordinating the Worldwide new variants and help maintain appropriate con-
Re sp onse fidence in vaccines and in the processes used to
develop, test, and deploy them.
New variants of concern may emerge in any cor- Although Covid-19 continues to present pub-
ner of the world and spread quickly, and conver- lic health challenges, including the emergence
gent changes have been noted in variants of of new variants, great progress has been made
concern identified in various parts of the world. in understanding this disease and how to pro-
The modification of sequences targeted by a vac- tect against it. Even though existing vaccines are
cine to meet the needs of one country could have helping to bring the pandemic under control in
repercussions elsewhere. Therefore, vaccine de- some locations, it is also necessary to plan for
velopment, vaccine modification, and vaccine de- unsatisfactory outcomes. As this planning con-

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SARS-CoV-2 Variants and Vaccines

Evaluate efficacy of existing vaccines


against variants of concern

Evaluate efficacy of
modified vaccines against
variants of concern

Decide whether Promote convergence


a new antigen of regulatory
is warranted assessments
Determine which new
antigen should be used Evaluate efficacy of
completely new vaccines
against variants of concern

Figure 2. A Framework for Evaluating Vaccines against Variants of Concern.


After variants of concern are designated, the efficacy of existing vaccines is evaluated with the use of in vitro data,
animal models, randomized evidence, observational studies, and surveillance.

tinues, international coordination by the WHO 1. Global Initiative on Sharing All Influenza Data (GISAID).
of research efforts and sharing of data and hCoV-19 tracking of variants. 2021 (https://www​.­gisaid​.­org/​­).
2. World Health Organization. WHO coronavirus (COVID-19)
specimens should be a priority. Maintaining the dashboard. 2021 (https://covid19​.­who​.­int/​­).
efficacy of vaccines against emerging variants 3. Volz E, Mishra S, Chand M, et al. Assessing transmissibility
and achieving equitable access to effective vac- of SARS-CoV-2 lineage B.1.1.7 in England. Nature 2021;​593:​266-
9.
cines in all countries will be of utmost impor- 4. Faria NR, Mellan TA, Whittaker C, et al. Genomics and epi-
tance as a sustainable response is built. demiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Sci-
The opinions expressed in this article are those of the authors ence 2021 April 14 (Epub ahead of print).
5. Wang P, Nair MS, Liu L, et al. Antibody resistance of SARS-
and not necessarily those of their organizations or of the World
Health Organization. CoV-2 variants B.1.351 and B.1.1.7. Nature 2021;​593:​130-5.
6. Madhi SA, Baillie V, Cutland Cl, et al. Safety and efficacy of
Disclosure forms provided by the authors are available with
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B.1.351 variant in South Africa. February 12, 2021 (https://www​
From the Office of Vaccines Research and Review, Center for .­medrxiv​.­org/​­content/​­10​.­1101/​­2021​.­02​.­10​.­21251247v1). preprint.
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