Invest Clin 63(3): 262 - 274, 2022 https://doi.org/10.54817/IC.v63n3a05
Corresponding author: Flor H Pujol. Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celu-
lar, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela. E-mail: fhpujol@gmail.com
Sub-lineages of the Omicron variant
of SARS-CoV-2: characteristic mutations
and their relation to epidemiological
behavior.
José Luis Zambrano1, Rossana C Jaspe2, Mariana Hidalgo3, Carmen L Loureiro2,
Yoneira Sulbarán2, Zoila C Moros1, Domingo J Garzaro2, Esmeralda Vizzi4,
Héctor R Rangel2, Ferdinando Liprandi4, and Flor H Pujol2
1Laboratorio de Virología Celular, Centro de Microbiología y Biología Celular,
Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela.
2Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular,
Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela.
3Laboratorio de Inmunoparasitología, Centro de Microbiología y Biología Celular,
Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela.
4Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular,
Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela.
Key words: COVID-19; SARS-CoV-2; Omicron Variant of Concern; mutations; tropism.
Abstract. By the end of 2021, the Omicron variant of SARS-CoV-2, the
coronavirus responsible for COVID-19, emerges, causing immediate concern,
due to the explosive increase in cases in South Africa and a large number of
mutations. This study describes the characteristic mutations of the Omicron
variant in the Spike protein, and the behavior of the successive epidemic waves
associated to the sub-lineages throughout the world. The mutations in the
Spike protein described are related to the virus ability to evade the protec-
tion elicited by current vaccines, as well as with possible reduced susceptibil-
ity to host proteases for priming of the fusion process, and how this might be
related to changes in tropism, a replication enhanced in nasal epithelial cells,
and reduced in pulmonary tissue; traits probably associated with the apparent
reduced severity of Omicron compared to other variants.
Omicron variant 263
Vol. 63(3): 262 - 274, 2022
Sub-linajes de la variante Ómicron del SARS-CoV-2: mutaciones
características y su relación con el comportamiento
epidemiológico.
Invest Clin 2022; 63 (3): 262 – 274
Palabras clave: COVID-19; SARS-CoV-2; variante de preocupación Ómicron;
mutaciones; tropismo.
Resumen. A finales de 2021 surge la variante Omicron del SARS-CoV-2, el
coronavirus responsable de la COVID-19, causando preocupación inmediata,
debido al aumento explosivo de casos en Suráfrica, y a su gran cantidad de
mutaciones. Este estudio describe las mutaciones características de la variante
Ómicron en la proteína de la Espiga (S) y el comportamiento de las sucesivas
olas epidémicas asociadas a la circulación de sus sub-linajes en todo el mundo.
Las mutaciones en la proteína S descritas están relacionadas con su capacidad
para evadir la protección provocada por las vacunas actuales, así como su posi-
ble susceptibilidad reducida a las proteasas del hospedero para la preparación
del proceso de fusión. Se infiere cómo esto podría estar relacionado con su
cambio en el tropismo, con una replicación mayor en las células epiteliales
nasales y menor en el tejido pulmonar, rasgos probablemente asociados a su
aparente menor gravedad en comparación con otras variantes.
Received: 10-07-2022 Accepted: 22-07-2022
INTRODUCTION
SARS-CoV-2 infection, responsible for
the COVID-19 pandemic, has caused more
than 550 million cases and more than 6
million deaths worldwide until June 2022.
This virus belongs to the family Coronaviri-
dae. This family comprises enveloped virus-
es, with a positive sense genome of around
30,000 nt. In the case of SARS-CoV-2, the
genome codes for four structural proteins
(nucleocapsid or N, spike or S, membrane
or M and envelope or E), 15 non-structural
proteins and eight accessory proteins. The S
protein contains two regions: S1, which in-
cludes the receptor-binding domain (RBD),
and S2, with the furin-cleavage site and the
fusion peptide. RBD, specifically the receptor
binding motif (RBM), is the region respon-
sible for the attachment to the angiotensin-
converting enzyme 2 (ACE2) cellular recep-
tor (Fig. 1)1,2. Two other putative receptors
(Asialoglycoprotein Receptor 1 - ASGR1- and
KREMEN1) have been described recently for
SARS-CoV-2, which are not used by the previ-
ous SARS-CoV. The virus appears to interact
with these two additional receptors through
the RBD and also with N-terminal domain of
the S1 region3,4. These new candidates add
to the list of other potential ligands that
may interact with SARS-CoV-25,6.
During these two years of a high rate
of replication, this virus has accumulated
several mutations, allowing for its clas-
sification in more than 2000 lineages by
June 20227-9. Some of these lineages were
denominated as variants by WHO10. These
variants (lineages of viruses sharing partic-
ular types of mutations) emerged since the
end of 2020, and were defined as Variants
Under Monitoring (VUM), Variants of Inter-
est (VOI), and Variants of Concern (VOC),
264 Zambrano et al.
Investigación Clínica 63(3): 2022
when any different phenotypic trait, such as
increased transmissibility or immune eva-
sion, among others, was suspected for the
two firsts and confirmed for the last10. Until
June 2022, five VOCs were described: Al-
pha variant, which emerged in the UK (lin-
eage B.1.1.7), Beta variant in South Africa
(B.1.351), Gamma variant in Brazil (P1),
Delta variant in India (B.1.617.2), and Omi-
cron variant, first identified in South Africa
(B.1.1529). The last one was included in
the list of VOCs very soon after its identi-
fication. By the end of June, only the Omi-
cron VOC and its sub-lineages were present
as a VOC10.
This variant caused immediate concern,
due to the explosive increase in cases in
South Africa11, and the large number of mu-
tations exhibited by this new lineage. In this
study, we describe the characteristic muta-
tions of the Omicron variant of SARS-CoV-2,
and the behavior of the epidemic waves as-
sociated with the dissemination of the differ-
ent sub-lineages throughout the world.
MATERIALS AND METHODS
Description of the mutations charac-
teristic of each sub-lineage of Omicron.
The identification of characteristic muta-
Fig. 1. Mutations of the SARS-CoV-2 Omicron VOC sub-lineages. Venn diagram showing common mutations
between the SARS-CoV-2 Omicron VOC sub-lineages.
Omicron variant 265
Vol. 63(3): 262 - 274, 2022
tions of the five sub-lineages of Omicron
was performed using the following data-
bases: SARS-CoV-2 lineages (Cov-lineages.
org), Outbreak.info and, GISAID EpiFlu™
(https://www.gisaid.org/). The Venn dia-
gram was made in Bioinformatics & Systems
Biology UGent/VIB (bioinformatics.psb.
ugent.be), and edited in Illustrator CC (ver.
23.0.1).
Analysis of the frequency of Omicron
VOC in the world from November 2021 to
May 2022. The number of sequences of Omi-
cron VOC available at the GISAID database
(https://www.gisaid.org/) on June 26, 2022
was compared to the total number of se-
quences foe each month, between November
2021 and May 2022.
Frequency of Omicron VOC sub-lineag-
es in the world. The number of sequences
reported for each Omicron VOC sub-lineage,
together with the date of the first and peak
detection, were analyzed from “SARS Cov2-
Lineages.” https://cov-lineages.org/lineage_
list.html9, and accessed on June 26, 2022.
Analysis of the epidemic waves caused
by the Omicron VOC in different coun-
tries. The peak number of cases caused by
the circulating Omicron VOC was analyzed
in selected countries, and compared with
the previous highest peak of cases occurring
in the same country, using the Worldometer
database (https://www.worldometers.info/
coronavirus/, accessed on July 1, 2022).
RESULTS
Key mutations of the Omicron variant
The Omicron variant exhibits a large
number of mutations in its genome, par-
ticularly in the S protein (Fig. 1). Five sub-
lineages of the Omicron variant have already
been identified, which exhibit some differ-
ences with the original B.1.1.529 lineage
and between them (Figs. 1 and 2). Addition-
ally, a recombinant BA.1/BA.2 sub-lineage
has also been described (Table 1).
The number of mutations exhibited by
the different sub-lineages of Omicron VOC
ranges from 22 for BA.3 to 57 in BA.4. Key
mutations of the S protein and present in al-
most all the sub-lineages are shown in Fig.
2. The S371L, K417N, and N440K muta-
tions, although not present in all the BA.1
isolates, are however also frequently found,
according to a search in GISAID database
(data not shown) In the case of BA.3, many
key mutations present in the other lineages
of Omicron, such as D405N, K417N, N440K,
T478K, E484A and N501Y, were found in
most sequences of lineage BA.3 available in
the GISAID database (data not shown).
Of particular relevance is the absence
of the deletion of the amino acids 69 and
70 in the S protein in the BA.2 sub-lineage,
which instead possesses a deletion of the
amino acids 25 to 279 (Fig. 1). Another im-
portant mutation acquired by the BA.4 and
Fig. 2. Key mutations in the different Omicron VOC sub-lineages.
266 Zambrano et al.
Investigación Clínica 63(3): 2022
BA.5 sub-lineages is the L452R mutation
(Fig. 2), a key mutation in the Delta VOC,
which was previously identified, particularly
in some Californian variants. The sub-lin-
eage BA.2.12.1 carries the mutation L452Q,
previously described in the C.37 VOI9.
Omicron dissemination and sub-lineages
Soon after its emergence, the Omicron
VOC displaced very rapidly the other lineag-
es circulating in the world, mainly the Delta
VOC (Fig. 3). At the end of June 2022, the
Omicron VOC was the only VOC recognized
by the WHO, although some Delta VOC iso-
lates were still described in the GISAID da-
tabase.
At the end of June 2022, the most fre-
quent lineages found in several parts of the
world were the sub-lineages BA.2.12.1, BA.4
and BA.5. These 3 lineages are expected to
circulate abundantly in the next months of
2022. Very few sequences of sub-lineage BA.3
were available at GISAID database (Table 1).
Table 2 shows some representative pat-
terns of the epidemic waves caused by the
Omicron VOC and its successive sub-linea-
ges. Generally, the Omicron VOC dissemi-
nation caused an epidemic wave of unprece-
dented magnitude, when compared to the
previous waves. Exceptions to this are India
and Iran, for which the ratio of Peak number
of cases with Omicron VOC/Peak number
of cases before Omicron VOC (PNO/PNBO)
was below 1 (Table 2). Additionally, this ratio
is highly variable between countries, being
generally lower in American countries, com-
pared to European ones, for example. The
second epidemic wave of Omicron VOC, due
to the dissemination of sub-lineages such as
BA.2, BA.4 and BA.5, was observed earlier in
many countries of Europe, while in America,
for example, some countries were suffering
an ongoing peak at the end of June 2022
(Table 2).
Several factors may have affected the
analysis. The testing capacity of each cou-
ntry, which ranged in July 1, 2022, from
five tests/million inhabitants in Algeria,
to 21,890,462 tests/million inhabitants in
Denmark (https://www.worldometers.info/
coronavirus/), may have limited more accu-
rate estimation of cases during the epidemic
waves, particularly during the Omicron VOC
one. With the highest testing capacity, Den-
mark exhibited a high PNO/PNBO of 11.54
(Table 2). The intensity of the Delta VOC
epidemic wave, which was particularly high
in some Asian countries, like India and Iran,
Table 1
Description of Omicron VOC sub-lineages.
Omicron main
lineage
Sub-lineages1Date of first
detection
Date of peak
detection2
Number of
sequences3
BA.1 50 (54) 2/9/21 4/1/22 2166293
BA.2 53 (108) 11/10/21428/3/22 1625851
BA.3 2 23/11/21 3/2/22 745
BA.4 1 (4) 10/1/22 25/5/22 13334
BA.5 2 (15) 5/1/22 30/5/22 27560
XE51 19/1/22 28/3/22 2438
Information from (9), accessed on June 26, 2022.
1 The effective number of sub lineages is shown, with the number of proposed ones indicated under parentheses.
2Date when the highest number of sequences were available was June 26, 2022. This date may change,
particularly for lineages BA.4 and BA.5, which are more actively disseminating in June 2022.
3The number of total sequences tentatively assigned to this lineage is shown.
4An earlier date of detection is reported for sub-lineage BA.2.3 (29/9/21).
5Recombinant BA.1/BA.2.
Omicron variant 267
Vol. 63(3): 262 - 274, 2022
led to a reduction of this ratio in these cou-
ntries, probably combined with saturated
testing capacities. PNO/PNBO is of parti-
cular interest in countries like South Korea
(83.58), Australia (59.61) and New Zealand
(unassigned since no peak in the number of
cases was observed before the Omicron wave
(Table 2). In Colombia and Venezuela, for
example, the PNO/PNBO was close to 1 (Ta-
ble 2). In addition to possible testing satura-
tion during the Omicron VOC wave in these
countries, the lower severity associated with
this variant, particularly in young persons,
may have reduced the demand for testing in
some groups.
DISCUSSION
Soon after its identification, the Omi-
cron variant was declared as a VOC, especia-
lly due to the huge number of mutations it
harbors11. Of the more than 30 mutations
present in the Omicron variant in the S pro-
tein, around half of them are located in the
RBD12. Some of these mutations can be used
detecting of this VOC by rapid methods13. Se-
ven produce a modest increase in the affinity
of the RBD for the ACE2 receptor: Q493R,
N501Y, S371L, S373P, S375F, Q498R, and
T478K12,14. It has been shown that Omicron
VOC can infect murine cell lines15. At least
two of the substitutions responsible for the
increase in affinity for the human ACE2 re-
ceptor are also responsible for the increa-
se in binding to mouse ACE2: Q493R and
Q498R15,16. Furthermore, the molecular
spectrum of Omicron-acquired mutations
was significantly different from the spectrum
for viruses that evolved in human patients.
However, it resembles the spectra associa-
ted with virus evolution in a mouse cellular
environment. These observations lead to the
suggestion that the progenitor of Omicron
might have jumped from humans to mice,
accumulating mutations conductive to in-
fecting that host, then jumping back into
humans, indicating an interspecies evolutio-
nary trajectory for the Omicron outbreak15.
Thus, this increased propensity for reverse
zoonosis makes this variant more likely than
previous variants to establish an animal re-
servoir of SARS-CoV-2.
Recent studies show that Omicron VOC
exhibit a replication enhanced in human
primary nasal epithelial cells, and reduced
in pulmonary cells17-20. This trait appears
to be related to the fact that, unlike other
SARSCoV-2 variants, Omicron is capable of
efficiently entering cells in a TMPRSS2-in-
dependent manner, via the endosomal rou-
te. This enables Omicron to infect a greater
number of cells in the respiratory epithe-
lium, allowing it to be more infectious at
lower exposure doses and resulting in en-
hanced transmissibility17. Syncytia forma-
tion depends on the fusogenic activity of the
S2 region of the S protein after cleavage by
the TMPRSS2. The Omicron also forms fewer
syncytia than other lineages20,21. The authors
suggest that this phenotypic trait may be
due to the presence of the mutation N969K.
The role of syncytia formation in the patho-
genic effect of SARS-CoV-2 remains a mat-
ter of debate22. Other substitutions, such as
N679K and H655Y, may be contributing to
Fig. 3. Frequency of Omicron VOC around the world
from November 2021 to May 2022. Green:
Omicron VOC. Red: other lineages, mainly
Delta VOC. From GISAID (https://www.gisaid.
org/accessed on June 26, 2022). In November
2021, only 3217 sequences of Omicron were
available out of 810820 total sequences.
268 Zambrano et al.
Investigación Clínica 63(3): 2022
this particular phenotype in Omicron VOC.
The N679K substitution is located in the
QTQTN motif upstream of the furin cleavage
site (QTQTK in the Omicron VOC). The clea-
vage site is known to play an important role
in viral pathogenesis. Its deletion attenuates
viral replication in respiratory cells in vitro
and attenuates disease in vivo22. The subs-
titution N679K in the QTQTN motif of the
Omicron VOC has been shown to reduce the
affinity of the protein for furin, resulting in
a reduced susceptibility to serine proteases
on the cell surface for entry23,24. The substi-
tution H655Y, in contrast, has been shown to
enhance viral replication and spike protein
cleavage25.
One of the most striking characteris-
tics of the Omicron VOC is its ability to eva-
de protective immunity induced by previous
infection or vaccination26,27. In fact, it is be-
lieved that the increase in transmissibility of
this variant is primarily due to its ability to
Table 2
Omicron VOC epidemic waves in selected countries.
Country Pop
(M hab)
Cases1
(M)
PNBO2PNO3PNO
/PNBO
SOP4
America
USA 334.9 89.4 (1) 310,438 (8/1/21) 908,909 (14/1/22) 2.93 140,047 (23/6/22)
Brazil 215.6 32.4 (3) 115,041 (23/6/21) 282,050 (3/2/22) 2.45 75,106 (30/6/22)
Argentina 45 9.4 (13) 41,080 (27/5/21) 139,853 (14/1/22) 3.40 8,314 (26/5/22)
Colombia 52 6.2 (18) 33,594 (26/6/21) 35,575 (15/1/22) 1.06 3,403 (28/6(22)
Mexico 131.6 6 (20) 28,953 (19/8/21) 60,552 (20/1/22) 2.09 32,216 (30/6/22)
Chile 19.4 4 (31) 9151 (9/4/22) 39,840 (10/2/22) 4.35 13,104 (17/5/22)
Venezuela 28.3 0.5 (86) 1,786 (4/4/21) 2,646 (30/1/22) 1.48 199 (24/6/22)
Africa
South Africa 60.8 4 (30) 26,645 (3/7/21) 37,875 (12/12/22) 1.42 10,017 (11/5/22)
Asia
India 1,407 43.5 (2) 414,433 (6/5/21) 347,254 (20/1/22) 0.88 19118 (30/6/22)
South Korea 51.3 18.4 (9) 7434 (17/12/21) 621,328 (17/3/22) 83.58 10,437 (29/6/22)
Iran 86.1 7.2 (17) 50,228 (17/8/21) 39,819 (7/2/22) 0.79 4,615 (5/4/22)
Hong Kong 7.6 1.2 (55) absent 79,876 (3/3/21) +++ 2,352 (30/6/22)
Europe
France 65.6 31.1 (4) 83,321 (7/11/20) 501,635 (25/1/22) 6.02 217,480 (29/3/22)
UK 68.6 22.7 (6) 83,088 (30/12/20) 275,618 (5/1/22) 3.32 109,320 (22/5/22)
Italy 60.3 18.6 (7) 41,386 (13/11/20) 228,740 (18/1/22) 5.53 100,823 (20/4/22)
Denmark 5.8 3 (39) 4,508 (18/2/20) 52,009 (10/2/22) 11.54 2,407 (28/6/22)
Oceania
Australia 26.1 8.2 (16) 2,528 (9/10/21) 150,702 (13/1/22) 59.61 67,379 (30/3/22)
New Zealand 5 1.3 (53) absent 24,106 (2/3/22) +++ 8,331 (28/6/22)
1Cases: Total number of cases in millions (M) until July 1, 2022 (position in the ranking of cases).
2PNBO: Peak number of cases before Omicron VOC (date). 3PNO: Peak number with Omicron VOC (date).
4SOP: Secondary Omicron VOC peak (date).
Omicron variant 269
Vol. 63(3): 262 - 274, 2022
evade previous protective immunity rather
than to of a higher affinity of its S protein
for the ACE2 receptor28. Several mutations
of Omicron VOC could impair neutralizing
antibodies (Nabs) with different specifici-
ties. Specifically, mutations K417N, G446S,
E484A, and Q493R induce escape of NAbs
in Group A-D, whose epitope overlaps with
the ACE2-binding motif. Group E (S309
site) and F (CR3022 site) NAbs, which of-
ten exhibit broad Sarbecovirus neutralizing
activity, are still somehow effective against
the Omicron VOC, but mutations G339D,
N440K, and S371L may induce resistance to
a subset of Nabs27.
The Omicron VOC also exhibits an inser-
tion of 3 amino acids (EPE) in the N-terminal
region of the S protein, at residue 214. This
insertion of EPE has not been observed in
other major variants of SARS-CoV-2 and may
induce a structural change, which might be
associated with a decrease in neutralizing
antibody binding ability to this region. This
genomic insertion has also been suggested to
be incorporated into SARS-CoV-2 by recombi-
nation with another coronavirus or even oth-
er respiratory pathogens29,30. The mutation
L452R present in sub-lineages BA.4 and BA.5,
may confer to these Omicron VOC sub-lineag-
es an increased immune evasion31,32, and may
also contribute to the dissemination of these
lineages. The sub-lineages more frequent in
June 2022, BA.2.12.1, BA.4 and BA.5, exhibit
an increased potential of breakthrough in-
fection after vaccination and infection, even
with a previous infection with another Omi-
cron VOC33-35.
In contrast, the sub-lineage BA.3 of the
Omicron VOC did not exhibit wide dissemi-
nation, compared to the other ones. This
may be related to the absence of many key
mutations exhibited by the other sub-lineag-
es, related to increased transmissibility and
immune evasion (Figs. 1 and 2). However,
the number of mutations found in this sub-
lineage is also variable among different iso-
lates, and some of those key mutations are
also frequently found.
Several lines of evidence suggest that
the Omicron VOC is highly more transmis-
sible than all previous variants, in addition
to the reduced sensitivity to the immune
protection conferred by vaccines and previ-
ous infections. The effective and basic re-
production numbers of the Omicron variant
have been estimated to be 3.8 and 2.5 times
higher than that of the Delta variant, respec-
tively, which was the previous VOC display-
ing the highest reproduction numbers36.
From this significant increase in trans-
missibility and resistance to previous immu-
nity, it could be inferred at a first glance,
that the clinical course of the Omicron VOC
might be more severe. However, the changed
tropism of this variant, to a virus infecting
more the upper respiratory airway, com-
pared to the lungs, suggests that is the con-
trary. Indeed, several studies point to a less
severe clinical course of infection with the
Omicron VOC, compared to the infection
caused by the Delta VOC.
The first evidence comes from in vitro
and animal model infections, where the Omi-
cron VOC exhibited an attenuated pheno-
type37. The early studies of the Omicron VOC
in South Africa also suggested a reduced odd
of severity for the patients infected with this
VOC38. This trend was confirmed in a retro-
spective observational study39. The same ob-
servation was found among US Veterans40.
Children in Israel were less prone to develop
multisystem inflammatory syndrome (MISC),
a common sequel of COVID-19 in children,
during the Omicron VOC wave, than during
the Delta and Alpha VOC waves41.
The emergence of Omicron VOC and
its sub-lineages led to an abrupt epidemic
peak worldwide42. However, differences in
the intensity of the epidemic peak caused
by the Omicron VOC were however observed
between countries. For example, countries
such as South Korea, Australia, and New Zea-
land were characterized by a successful con-
trol of COVID-19 during the pandemic43-45,
until the Omicron VOC wave. The increased
transmission ability of the Omicron VOC al-
270 Zambrano et al.
Investigación Clínica 63(3): 2022
lowed it to spread widely even in countries
with previous highly successful control mea-
sures. Finally, the great disparities in vac-
cination coverage between countries46, also
had a profound influence on the intensity of
the Delta and Omicron VOC waves.
In conclusion, the Omicron VOC displays
a great number of mutations, some of them
already present in previous lineages. Although
associated with a high attack rate and im-
mune evasion, this variant seems to be associ-
ated with lower severity, compared to previous
ones. A probable explanation for this somehow
attenuated phenotype could be related to its
resistance to the cleavage of TMPRSS2 and
probably furin, and its reduced ability to form
syncytia, leading to increased tropism for epi-
thelia over the lungs. The reduced effectivity
observed for various vaccines to protect against
infection with this variant has not hampered
its effectiveness in reducing the morbidity
and mortality of COVID-19, particularly with a
booster dose, which still induces neutralizing
antibodies47. The well-known non-pharmaco-
logical preventive interventions (mask, social
distancing, ventilation and frequent hand hy-
giene), together with vaccination, are still the
most effective measures to reduce the burden
of this highly contagious variant.
Funding
This study was supported by IVIC, Min-
isterio del Poder Popular de Ciencia, Tec-
nología e Innovación de Venezuela.
Conflict of interest
The authors declared that they have no
competing interests.
Authors contribution
Design of the study and writing of the
manuscript: JLZ, RCJ, FL, FHP. Data analy-
sis: JLZ, RCJ, MH, YS, CLL, ZCM, DJG, EV,
HRR, FHP. All the authors read and approved
the final version of the manuscript.
Author’s ORCID numbers
José Luis Zambrano:
0000-0001-9884-2940
Rossana C Jaspe:
0000-0002-4816-1378
Mariana Hidalgo:
0000-0002-8307-8254
Yoneira Sulbarán:
0000-0002-3170-353X
Carmen L Loureiro:
0000-0003-3665-1107
Zoila C Moros:
0000-0001-6322-9230
Domingo J Garzaro:
0000-0002-9956-5786
Esmeralda Vizzi:
0000-0001-6865-1617
Héctor R Rangel:
0000-0001-5937-9690
Ferdinando Liprandi:
0000-0001-8084-8252
Flor H Pujol:
0000-0001-6086-6883
REFERENCES
1. V’kovski P, Kratzel A, Steiner S, Stalder
H, Thiel V. Coronavirus biology and repli-
cation: implications for SARS-CoV-2. Nat
Rev Microbiol 2020; 19(3): 155–170. Doi:
10.1038/s41579-020-00468-6.
2. Pujol FH, Zambrano JL, Jaspe RC, Lourei-
ro CL, Vizzi E, Liprandi F, Rangel HR. Bio-
logía y evolución del coronavirus causante
de la COVID-19. Rev Soc Venezol Microbiol
2020; 40:63-73.
3. Gu Y, Cao J, Zhang X, Gao H, Wang Y,
Wang J, He J, Jiang X, Zhang J, Shen G,
Yang J, Zheng X, Hu G, Zhu Y, Du S, Zhu
Y, Zhang R, Xu J, Lan F, Qu D, Xu G, Zhao
Y, Gao D, Xie Y, Luo M, Lu Z. Receptome
profiling identifies KREMEN1 and ASGR1
as alternative functional receptors of SARS-
CoV-2. Cell Res 2022;32(1):24-37. Doi:
10.1038/s41422-021-00595-6.
Omicron variant 271
Vol. 63(3): 262 - 274, 2022
4. Hoffmann M, Pöhlmann S. Novel SARS-
CoV-2 receptors: ASGR1 and KREMEN1.
Cell Res 2022;32(1):1-2. Doi: 10.1038/
s41422-021-00603-9.
5. Rangu R, Wander PL, Barrow BM, Zraika
S. Going viral in the islet: mediators of
SARS-CoV-2 entry beyond ACE2. J Mol
Endocrinol 2022;69(2):R63-R79. Doi: 10.
1530/JME-21-0282.
6. Eslami N, Aghbash PS, Shamekh A, En-
tezari-Maleki T, Nahand JS, Sales AJ,
Baghi HB. SARS-CoV-2: Receptor and Co-
receptor Tropism Probability. Curr Micro-
biol 2022;79(5):133. Doi: 10.1007/s00284-
022-02807-7.
7. Rambaut A, Holmes EC, O’Toole Á, Hill V,
McCrone JT, Ruis C, du Plessis L, Pybus
OG. A dynamic nomenclature proposal for
SARS-CoV-2 lineages to assist genomic epi-
demiology. Nat Microbiol. 2020;5(11):1403-
1407. Doi: 10.1038/s41564-020-0770-5.
8. O’Toole Á, Scher E, Underwood A, Jack-
son B, Hill V, McCrone JT, Colquhoun
R, Ruis C, Abu-Dahab K, Taylor B, Yeats
C, du Plessis L, Maloney D, Medd N, Att-
wood SW, Aanensen DM, Holmes EC,
Pybus OG, Rambaut A. Assignment of
epidemiological lineages in an emerging
pandemic using the pangolin tool. Virus
Evol 2021;7(2):veab064. Doi: 10.1093/ve/
veab064.
9. “SARS Cov2-Lineages.” https://cov-linea-
ges.org/lineage_list.html. [Accessed on
June 26, 2022].
10. World Health Organization. “Tracking
SARS-CoV-2 variants.” https://www.who.
int/en/activities/tracking-SARS-CoV-2-va-
riants/. [Accessed on June 26, 2022].
11. Viana R, Moyo S, Amoako DG, Tegally H,
Scheepers C, Althaus ChL, Anyaneji UJ,
Bester PhA, Boni MF, Chand M, Choga
WT, Colquhoun R, Davids M, Deforche
K, Doolabh D, du Plessis L, Engelbrecht
S, Everatt J, Giandhari J, Giovanetti M,
Hardie D, Hill V, Hsiao NY, Iranzadeh A,
Ismail A, Joseph Ch, Joseph R, Koopile
L, Kosakovsky Pond SL, Kraemer MUG,
Kuate-Lere L, Laguda-Akingba O, Lese-
tedi-Mafoko O, Lessells RJ, Lockman
Sh, Lucaci AG, Maharaj A, Mahlangu B,
Maponga T, Mahlakwane K, Makatini Z,
Marais G, Maruapula D, Masupu K, Mats-
haba M, Mayaphi S, Mbhele N, Mbulawa
MB, Mendes A, Mlisana K, Mnguni A, Mo-
hale Th, Moir M, Moruisi K, Mosepele M,
Motsatsi G, Motswaledi MS, Mphoyakgosi
Th, Msomi N, Mwangi PN, Naidoo Y, Ntuli
N, Nyaga M, Olubayo L, Pillay S, Radibe
B, Ramphal Y, Ramphal U, San JE, Sco-
tt L, Shapiro R, Singh L, Smith-Lawrence
P, Stevens W, Strydom A, Subramoney K,
Tebeila N, Tshiabuila D, Tsui J, van Wyk
S, Weaver S, Wibmer CK, Wilkinson E,
Wolter N, Zarebski AE, Zuze B, Goedhals
D, Preiser W, Treurnicht F, Venter M, Wi-
lliamson C, Pybus OG, Bhiman J, Glass
A, Martin DP, Rambaut A, Gaseitsiwe S,
von Gottberg A, de Oliveira T. Rapid epi-
demic expansion of the SARSCoV-2 Omi-
cron variant in Southern Africa. Nature
2022;603(7902):679-686. Doi: 10.1038/
s41586-022-04411-y.
12. Kumar S, Thambiraja TS, Karuppanan K,
Subramaniam G. Omicron and Delta va-
riant of SARS-CoV-2: A comparative com-
putational study of spike protein. J Med
Virol 2022;94(4):1641-1649. Doi: 10.1002/
jmv.27526.
13. Jaspe RC, Zambrano JL, Hidalgo M, Sul-
baran Y, Loureiro CL, Moros ZC, Garza-
ro DJ, Liprandi F, Rangel HR, Pujol FH.
Detection of the Omicron variant of SARS-
CoV-2 by restriction analysis targeting the
mutations K417N and N440K of the Spike
protein. Invest. Clin 2022;63(1):92-99. Doi:
10.54817/IC.v63n1a08.
14. Ortega JT, Jastrzebska B, Rangel HR.
Omicron SARS-CoV-2 Variant Spike Pro-
tein Shows an Increased Affinity to the Hu-
man ACE2 Receptor: An In Silico Analysis.
Pathogens 2021;11(1):45. Doi: 10.3390/
pathogens11010045.
15. Wei C, Shan KJ, Wang W, Zhang S, Huan
Q, Qian W. Evidence for a mouse origin of
the SARS-CoV-2 Omicron variant. J Genet
Genomics 2021;48(12):1111-1121. Doi:
10.1016/j.jgg.2021.12.003.
16. Yan K, Dumenil T, Le TT, Tang B, Bis-
hop C, Suhrbier A, Rawle DJ. Passage
of SARS-CoV-2 in cells expressing hu-
man and mouse ACE2 selects for mou-
se-adapted and ACE2-independent viru-
ses. bioRxiv 2021; 12.16.473063. doi:
10.1101/2021.12.16.473063.
272 Zambrano et al.
Investigación Clínica 63(3): 2022
17. Peacock TP, Brown JC, Zhou J, Thakur
N, Sukhova K, Newman J, Kugathasan
R, Yan AWC, Furnon W, De Lorenzo G,
Cowton VM, Reuss D, Moshe M, Quan-
trill JL, Platt OK, Kaforou M, Patel AH,
Palmarini M, Bailey D, Barclay WS. The
altered entry pathway and antigenic dis-
tance of the SARS-CoV-2 Omicron variant
map to separate domains of spike pro-
tein. bioRxiv 2021;12.31.474653; Doi: 10.
1101/2021.12.31.474653.
18. Hui KPY, Ho JCW, Cheung MC, Ng KC,
Ching RHH, Lai KL, Kam TT, Gu H, Sit
KY, Hsin MKY, Au TWK, Poon LLM, Peiris
M, Nicholls JM, Chan MCW. SARS-CoV-2
Omicron variant replication in human
bronchus and lung ex vivo. Nature 2022;
603(7902):715-720. Doi: 10.1038/s41586-
022-04479-6.
19. Abdelnabi R, Foo CS, Zhang X, Lemmens V,
Maes P, Slechten B, Raymenants J, André
E, Weynand B, Dallmeier K, Neyts J. The
omicron (B.1.1.529) SARS-CoV-2 variant of
concern does not readily infect Syrian ham-
sters. Antiviral Res. 2022; 198:105253. Doi:
10.1016/j.antiviral.2022.105253.
20. Zhao H, Lu L, Peng Z, Chen LL, Meng
X, Zhang C, Ip JD, Chan WM, Chu AW,
Chan KH, Jin DY, Chen H, Yuen KY, To
KK. SARS-CoV-2 Omicron variant shows
less efficient replication and fusion ac-
tivity when compared with Delta variant
in TMPRSS2-expressed cells. Emerg Mi-
crobes Infect. 2022;11(1):277-283. Doi:
10.1080/22221751.2021.2023329.
21. Rajah MM, Hubert M, Bishop E, Saunders
N, Robinot R, Grzelak L, Planas D, Dufloo
J, Gellenoncourt S, Bongers A, Zivaljic
M, Planchais C, Guivel-Benhassine F, Po-
rrot F, Mouquet H, Chakrabarti LA, Bu-
chrieser J, Schwartz O. SARS-CoV-2 Alpha,
Beta, and Delta variants display enhanced
Spike-mediated syncytia formation. EMBO
J 2021; 40(24):e108944. Doi: 10.15252/
embj.2021108944.
22. Koch J, Uckeley ZM, Lozach PY. SARS-
CoV-2 variants as super cell fusers: cause or
consequence of COVID-19 severity? EMBO
J 2021;40(24):e110041. Doi: 10.15252/
embj.2021110041.
23. Vu MN, Lokugamage KG, Plante JA,
Scharton D, Johnson BA, Sotcheff S,
Swetnam DM, Schindewolf Cr, Alvarado
RE, Crocquet-Valdes PA, Debbink K, Wea-
ver SC, Walker DH, Routh AL, Plante KS,
Menachery VD. QTQTN motif upstream
of the furin-cleavage site plays key role
in 9SARS-CoV-2 infection and pathoge-
nesis. bioRxiv 2021;12.15.472450; Doi:
10.1101/2021.12.15.472450.
24. Jawaid MZ, Baidya A, Jakovcevic S, Lusk
J, Mahboubi-Ardakani R, Solomon N,
Gonzalez G, Arsuaga J, Vazquez M, Da-
vis RL, Cox DL. Computational study of
the furin cleavage domain of SARS-CoV-2:
delta binds strongest of extant variants.
bioRxiv 2022; 01.04.475011. doi: 10.
1101/2022.01.04.475011.
25. Escalera A, Gonzalez-Reiche AS, Aslam S,
Mena I, Laporte M, Pearl RL, Fossati A,
Rathnasinghe R, Alshammary H, van de
Guchte A, Farrugia K, Qin Y, Bouhaddou
M, Kehrer T, Zuliani-Alvarez L, Meekins
DA, Balaraman V, McDowell C, Richt JA,
Bajic G, Sordillo EM, Dejosez M, Zwaka
TP, Krogan NJ, Simon V, Albrecht RA,
van Bakel H, García-Sastre A, Aydillo T.
Mutations in SARS-CoV-2 variants of con-
cern link to increased spike cleavage and
virus transmission. Cell Host Microbe
2022; 30(3):373-387.e7. Doi: 10.1016/j.
chom.2022.01.006.
26. Dejnirattisai W, Huo J, Zhou D, Zahradník
J, Supasa P, Liu C, Duyvesteyn HME, Ginn
HM, Mentzer AJ, Tuekprakhon A, Nutalai
R, Wang B, Dijokaite A, Khan S, Avinoam
O, Bahar M, Skelly D, Adele S, Johnson
SA, Amini A, Ritter TG, Mason C, Dold C,
Pan D, Assadi S, Bellass A, Omo-Dare N,
Koeckerling D, Flaxman A, Jenkin D, Aley
PK, Voysey M, Costa Clemens SA, Naveca
FG, Nascimento V, Nascimento F, Fernan-
des da Costa C, Resende PC, Pauvolid-Co-
rrea A, Siqueira MM, Baillie V, Serafin N,
Kwatra G, Da Silva K, Madhi SA, Nunes
MC, Malik T, Openshaw PJM, Baillie JK,
Semple MG, Townsend AR, Huang KA, Tan
TK, Carroll MW, Klenerman P, Barnes E,
Dunachie SJ, Constantinides B, Webster
H, Crook D, Pollard AJ, Lambe T; OP-
TIC Consortium; ISARIC4C Consortium,
Paterson NG, Williams MA, Hall DR, Fry
EE, Mongkolsapaya J, Ren J, Schreiber G,
Stuart DI, Screaton GR. SARS-CoV-2 Omi-
Omicron variant 273
Vol. 63(3): 262 - 274, 2022
cron-B.1.1.529 leads to widespread escape
from neutralizing antibody responses. Cell
2022;185(3):467-484.e15. Doi: 10.1016/j.
cell.2021.12.046.).
27. Cao Y, Wang J, Jian F, Xiao T, Song W, Yi-
simayi A, Huang W, Li Q, Wang P, An R,
Wang J, Wang Y, Niu X, Yang S, Liang H,
Sun H, Li T, Yu Y, Cui Q, Liu S, Yang X, Du
S, Zhang Z, Hao X, Shao F, Jin R, Wang
X, Xiao J, Wang Y, Xie XS. Omicron es-
capes the majority of existing SARS-CoV-2
neutralizing antibodies. Nature. 2022;
602(7898):657-663. Doi: 10.1038/s41586-
021-04385-3.
28. Yao L, Zhu KL, Jiang XL, Wang XJ, Zhan
BD, Gao HX, Geng XY, Duan LJ, Dai EH,
Ma MJ. Omicron subvariants escape anti-
bodies elicited by vaccination and BA.2.2
infection. Lancet Infect Dis. 2022; S1473-
3099(22)00410-8. Doi: 10.1016/S1473-
3099(22)00410-8.
29. Nersisyan S, Zhiyanov A, Zakharova M,
Ishina I, Kurbatskaia I, Mamedov A, Ga-
latenko A, Shkurnikov M, Gabibov A,
Tonevitsky A. Alterations in SARS-CoV-2
Omicron and Delta peptides presentation
by HLA molecules. PeerJ 2022;10:e13354.
Doi: 10.7717/peerj.13354.
30. Qin S, Cui M, Sun S, Zhou J, Du Z, Cui
Y, Fan H. Genome Characterization and
Potential Risk Assessment of the Novel
SARS-CoV-2 Variant Omicron (B.1.1.529).
Zoonoses 2021; Vol. 1(1). Doi: 10.15212/
ZOONOSES-2021-0024.
31. Motozono C, Toyoda M, Zahradnik J, Sai-
to A, Nasser H, Tan TS, Ngare I, Kimura I,
Uriu K, Kosugi Y, Yue Y, Shimizu R, Ito J,
Torii S, Yonekawa A, Shimono N, Nagasaki
Y, Minami R, Toya T, Sekiya N, Fukuhara
T, Matsuura Y, Schreiber G. Genotype to
Phenotype Japan (G2P-Japan) Consortium,
Ikeda T, Nakagawa S, Ueno T, Sato K. SARS-
CoV-2 spike L452R variant evades cellular
immunity and increases infectivity. Cell
Host Microbe 2021; 29(7):1124-1136.e11.
Doi: 10.1016/j.chom.2021.06.006.
32. Deng X, Garcia-Knight MA, Khalid MM,
Servellita V, Wang C, Morris MK, Sotoma-
yor-González A, Glasner DR, Reyes KR,
Gliwa AS, Reddy NP, Sanchez San Martin
C, Federman S, Cheng J, Balcerek J, Ta-
ylor J, Streithorst JA, Miller S, Sreekumar
B, Chen PY, Schulze-Gahmen U, Taha TY,
Hayashi JM, Simoneau CR, Kumar GR,
McMahon S, Lidsky PV, Xiao Y, Hemarajata
P, Green NM, Espinosa A, Kath C, Haw M,
Bell J, Hacker JK, Hanson C, Wadford DA,
Anaya C, Ferguson D, Frankino PA, Shi-
vram H, Lareau LF, Wyman SK, Ott M, An-
dino R, Chiu CY. Transmission, infectivity,
and neutralization of a spike L452R SARS-
CoV-2 variant. Cell 2021;184(13):3426-
3437.e8. Doi: 10.1016/j.cell.2021.04.025.
33. Qu P, Faraone J, Evans JP, Zou X, Zheng YM,
Carlin C, Bednash JS, Lozanski G, Mallampa-
lli RK, Saif LJ, Oltz EM, Mohler PJ, Gumina
RJ, Liu SL. Neutralization of the SARS-CoV-2
Omicron BA.4/5 and BA.2.12.1 Subvariants.
N Engl J Med 2022; 386(26):2526-2528. Doi:
10.1056/NEJMc2206725.
34. Cao Y, Yisimayi A, Jian F, Song W, Xiao
T, Wang L, Du S, Wang J, Li Q, Chen X,
Yu Y, Wang P, Zhang Z, Liu P, An R, Hao
X, Wang Y, Wang J, Feng R, Sun H, Zhao
L, Zhang W, Zhao D, Zheng J, Yu L, Li C,
Zhang N, Wang R, Niu X, Yang S, Song X,
Chai Y, Hu Y, Shi Y, Zheng L, Li Z, Gu Q,
Shao F, Huang W, Jin R, Shen Z, Wang Y,
Wang X, Xiao J, Xie XS. BA.2.12.1, BA.4
and BA.5 escape antibodies elicited by Omi-
cron infection. Nature 2022. Doi: 10.1038/
s41586-022-04980-y.
35. Hachmann NP, Miller J, Collier AY, Ventu-
ra JD, Yu J, Rowe M, Bondzie EA, Powers
O, Surve N, Hall K, Barouch DH. Neutrali-
zation Escape by SARS-CoV-2 Omicron Sub-
variants BA.2.12.1, BA.4, and BA.5. N Engl
J Med 2022. Doi: 10.1056/NEJMc2206576.
36. Liu Y, Rocklöv J. The effective reproducti-
ve number of the Omicron variant of SARS-
CoV-2 is several times relative to Delta. J
Travel Med; 29(3): taac037. Doi: 10.1093/
jtm/taac037.
37. Shuai H, Chan JF, Hu B, Chai Y, Yuen TT,
Yin F, Huang X, Yoon C, Hu JC, Liu H, Shi
J, Liu Y, Zhu T, Zhang J, Hou Y, Wang Y,
Lu L, Cai JP, Zhang AJ, Zhou J, Yuan S,
Brindley MA, Zhang BZ, Huang JD, To KK,
Yuen KY, Chu H. Attenuated replication
and pathogenicity of SARS-CoV-2 B.1.1.529
Omicron. Nature 2022; 603(7902):693-
699. Doi: 10.1038/s41586-022-04442-5.
38. Wolter N, Jassat W, Walaza S, Welch R,
Moultrie H, Groome M, Amoako DG, Eve-
274 Zambrano et al.
Investigación Clínica 63(3): 2022
ratt J, Bhiman JN, Scheepers C, Tebeila
N, Chiwandire N, du Plessis M, Govender
N, Ismail A, Glass A, Mlisana K, Stevens
W, Treurnicht FK, Makatini Z, Hsiao NY,
Parboosing R, Wadula J, Hussey H, Da-
vies MA, Boulle A, von Gottberg A, Cohen
C. Early assessment of the clinical severi-
ty of the SARS-CoV-2 omicron variant in
South Africa: a data linkage study. Lancet
2022;399(10323):437-446. Doi: 10.1016/
S0140-6736(22)00017-4.
39. Jassat W, Abdool Karim SS, Mudara C,
Welch R, Ozougwu L, Groome MJ, Go-
vender N, von Gottberg A, Wolter N, Wol-
marans M, Rousseau P; DATCOV author
group, Blumberg L, Cohen C. Clinical se-
verity of COVID-19 in patients admitted to
hospital during the omicron wave in South
Africa: a retrospective observational study.
Lancet Glob Health 2022;10(7):e961-e969.
Doi: 10.1016/S2214-109X(22)00114-0.
40. Mayr FB, Talisa VB, Castro AD, Shaikh
OS, Omer SB, Butt AA. COVID-19 disea-
se severity in US Veterans infected during
Omicron and Delta variant predominant pe-
riods. Nat Commun. 2022;13(1):3647. Doi:
10.1038/s41467-022-31402-4.
41. Levy N, Koppel JH, Kaplan O, Yechiam
H, Shahar-Nissan K, Cohen NK, Shavit I.
Severity and incidence of multisystem in-
flammatory syndrome in children during 3
SARS-CoV-2 pandemic waves in Israel. JAMA
2022; 327(24):2452-2454. Doi: 10.1001/
jama.2022.8025.
42. Jaspe RC, Sulbaran Y, Loureiro CL, Mo-
ros ZC, Marulanda E, Bracho F, Ramírez
NA, Canonico Y, D’Angelo P, Rodríguez
L, Castro J, Liprandi F, Rangel HR, Pu-
jol FH. Detection of the Omicron variant
of SARS-CoV-2 in international travelers
returning to Venezuela. Travel Med In-
fect Dis 2022; 48:102326. Doi: 10.1016/j.
tmaid.2022.102326.
43. Kang J, Jang YY, Kim J, Han SH, Lee KR,
Kim M, Eom JS. South Korea’s responses
to stop the COVID-19 pandemic. Am J In-
fect Control. 2020; 48(9):1080-1086. Doi:
10.1016/j.ajic.2020.06.003.
44. Baker MG, Wilson N, Anglemyer A. Suc-
cessful Elimination of Covid-19 Transmis-
sion in New Zealand. N Engl J Med. 2020;
383(8):e56. Doi: 10.1056/NEJMc2025203.
45. Paterson DL, Rickard CM. Letter From
Australia: A Never-Ending Pandemic? Ann
Intern Med. 2021; 174(12):1743-1744. Doi:
10.7326/M21-3295.
46. Chen Z, Zheng W, Wu Q, Chen X, Peng
C, Tian Y, Sun R, Dong J, Wang M, Zhou
X, Zhao Z, Zhong G, Yan X, Liu N, Hao F,
Zhao S, Zhuang T, Yang J, Azman AS, Yu
H. Global diversity of policy, coverage, and
demand of COVID-19 vaccines: a descripti-
ve study. BMC Med. 2022; 20(1):130. Doi:
10.1186/s12916-022-02333-0.
47. Bowen JE, Addetia A, Dang HV, Stewart C,
Brown JT, Sharkey WK, Sprouse KR, Walls
AC, Mazzitelli IG, Logue JK, Franko NM,
Czudnochowski N, Powell AE, DellotaJr E,
Ahmed K, Ansari AS, Cameroni E, Gori A,
Bandera A, Posavad CM, Dan JM, Zhang Z,
Weiskopp D, Sette A, Crotty S, Iqbal NT,
Corti D, Geffner J, Snell G, Grifantini R, Chu
HY, Veesler D. Omicron spike function and
neutralizing activity elicited by a compre-
hensive panel of vaccines. Science. 2022;
19 Jul. Doi: 10.1126/science.abq02.