Quan Ke Thai,
Department of Saigon University, 273 An Duong Vuong, Ward 3 District 5, Ho Chi
Minh city, Vietnam. Phuoc Huynh, department of aVNU HCMC University of Science,
227 Nguyen Van Cu, Ward 4 District 5, Ho Chi Minh city, Vietnam. Yen Le Thi,
department of DSI1191, Saigon University, 273 An Duong Vuong, Ward 3 District
5, Ho Chi Minh city, Vietnam. Huyen
Nguyen Thi Thuong, department of Department of Biology, HCMC University of
Education, 280 An Duong Vuong Ward 4 District 5, Ho Chi Minh city, Vietnam. Wrote
a research article about, Genetic Diversity of Omicron Spike Variants in
Vietnam. Entitled, Genetic diversity of SARS-CoV-2 Omicron variants’ spike gene
in Vietnam. This research paper published by the International Journal of Biosciences | IJB. an open access scholarly research journal on Biosciences.
under the affiliation of the International Network For Natural Sciences|
INNSpub. an open access multidisciplinary research journal publisher.
Abstract
The recently emerging Omicron is of prime concern because this variant has been the cause of current large outbreaks. Omicron becomes more dangerous when numerous content mutations in the Spike (S) gene lead to more than 30 substitutions of amino acids in spike protein. Omicron variant had been identified as Variants Of Concern (VOC) when it had transmission rate overtake previous VOCs. In this report, we focus on analyzing the genetic diversity of the S gene of Omicron variants in Vietnam. Our results indicate the high level of haplotype diversity when confirmed 362 haplotypes and the haplotype diversity index at 0.9160 ± 0.0037. The analysis of nucleotide diversity display nucleotide diversity at 0.0053 ± 0.0026 and recorded 318 polymorphic sites with the average number of mutations of 40 ± 9. Almost missense mutations appeared in the RBD region, and deletion and insertion occurred in the NTD region. Besides, we note conserved mutation in the S gene of Omicron in Vietnam, namely C21618T G21987A T22200G G22578A C22674T T22679C C22686T A22688G G22775A A22786C G22813T T22882G G22992A C22995A A23013C A23040G A23055G A23063T T23075C A23403G C23525T T23599G C23604A C23854A G23948T A24424T T24469A, and C25000T. Furthermore, the genetic networks of the S gene provided more correlation between infection and mutation in this gene. Ultimately, we propose the close relation between BA.2 and BA.4, BA.5 through the network, in which necessary focus T22917G (L452R), T23018G (F486V), and other novel mutations will appear in the S gene. The network provided the whole picture of Omicron variants in Vietnam, supporting the tracing of the source of a new outbreak in the future.
Introduction
The recently emerging
Omicron is of prime concern because this variant has been the cause of current
large outbreaks. Omicron becomes more dangerous when numerous content mutations
in the Spike (S) gene lead to more than 30 substitutions of amino acids in
spike protein. Omicron variant had been identified as Variants Of Concern (VOC)
when it had transmission rate overtake previous VOCs. In this report, we focus
on analyzing the genetic diversity of the S gene of Omicron variants in
Vietnam. Our results indicate the high level of haplotype diversity when
confirmed 362 haplotypes and the haplotype diversity index at 0.9160 ± 0.0037.
The analysis of nucleotide diversity display nucleotide diversity at 0.0053 ±
0.0026 and recorded 318 polymorphic sites with the average number of mutations
of 40 ± 9. Almost missense mutations appeared in the RBD region, and deletion
and insertion occurred in the NTD region. Besides, we note conserved mutation
in the S gene of Omicron in Vietnam, namely C21618T G21987A T22200G G22578A
C22674T T22679C C22686T A22688G G22775A A22786C G22813T T22882G G22992A C22995A
A23013C A23040G A23055G A23063T T23075C A23403G C23525T T23599G C23604A C23854A
G23948T A24424T T24469A, and C25000T. Furthermore, the genetic networks of the
S gene provided more correlation between infection and mutation in this gene.
Ultimately, we propose the close relation between BA.2 and BA.4, BA.5 through
the network, in which necessary focus T22917G (L452R), T23018G (F486V), and
other novel mutations will appear in the S gene. The network provided the whole
picture of Omicron variants in Vietnam, supporting the tracing of the source of
a new outbreak in the future.
appearance of the Delta
variant is almost eliminated, breaking the achievements preventing the pandemic
in some countries. Delta's rapid transmission is determined mainly by the spike
protein's L452R, T478K, and E484Q N501Y mutations (Kumar, Singh et al., 2021)
(Fan, Hu et al., 2021). In addition, some substitutions, such as E484K, D614G,
and P681H/R, have also been conserved in many different VOC variants
(Papanikolaou, Chrysovergis et al., 2022) (Lubinski, Frazier et al., 2021) .
Recently, a new variant is thought to be more infectious than the Delta variant
and maintains from 30 to 45 mutations in the spike protein (Wei, Shan et al.,
2021) (Kumar, Thambiraja et al., 2022). According to PANGO Lineages, this
variant belongs to lineage B.1.1.529, named Omicron by WHO and classified as a
VOC variant. Since December 2021, Omicron has almost replaced Delta as the
primary source of infection infections in the United States (Fall, Eldesouki et
al., 2022). After that, the Omicron variant became almost universally dominant
and gradually replaced the previously dangerous Delta variant (Chaguza, Coppi
et al., 2022).
Vietnam is one of the
infrequent countries that has succeeded in controlling the epidemic situation
in the early stages of the pandemic outbreak in the world. Vietnam has
successfully gone 99 days with no community transmission, and most cases (60%)
in Vietnam are due to entry from China, Europe, and the United States (Thai,
Rabaa et al., 2021). Examination of genomics indicated that the nucleotide
similarity of the sequences in Vietnam in the two outbreaks was very high
(minimum 99.96%, mean 99.97%), combined with familiar mutation exhibiting that
virus is not competent to silently infect the community from April 2020
(Phuong, Tung et al., 2021). In Vietnam, each epidemic wave corresponds to the
emergence of a new variant with a more robust infectious fitness. During the
third wave of epidemics (beginning on January 28, 2021), the outbreak in
northern Vietnam occurred rapidly with the main contribution of Alpha variants
(Chau, Hong et al., 2021). Then, the fourth wave (beginning on April 27, 2021)
had been the worst ever experienced by the country. In May 2021, all patients
in Vietnam were derived by the Delta variant (Nguyen, Wong et al., 2021). In
November, this wave had caused 99.9% of total deaths in the country (Hoang,
Pham et al., 2022). The Vietnamese government has had to implement
unprecedented strict epidemic prevention measures, including encouraging people
to isolate themselves at home, mobilizing the participation of the army and
military medics, and setting up field hospitals. However, the epidemic
situation had been still difficult to control because the Delta variant has
high transmissibility.
After November 2021,
when the vaccination rate in Vietnam reached a relatively high threshold,
government took to restore social life under "new normal" conditions.
The gradual easing of
epidemic prevention measures has facilitated the spread of the virus in the
community. The first case confirmed that the Omicron variant was recorded in
Vietnam on December 19, 2021. Until March 2022, the Omicron became the primary
circulating variant and the cause of infections in the Hanoi capital. On March
12, 2022, Vietnam recorded the highest number of infections ever at 454,179
cases/day. This number is much larger than the previous wave of epidemics
caused by the Delta variants. Proposes that Omicron will become the dominant
variant in Vietnam shortly. Despite the sudden increase in cases, the mortality
rate tends to be the opposite.
The number of deaths
caused by the Omicron on March 13, 2022, is 95 cases, and the average of the
last seven days is 82. These concerns were lower than Delta's 803 cases on
September 1, 2021, and the average of the last seven days in 360 cases
(according to Vietnam's Ministry of Health). The current research literature
indicates that the Omicron variants are more infectious than previously
recorded variants (Ren, Wang et al., 2022) (He, Hong et al., 2021). On the
other hand, Omicron can cause symptoms less severe (Callaway and Ledford, 2021)
(Kupferschmidt and Vogel, 2021) (Ren, Wang et al., 2022). Even so, the high
transmission rate of Omicron will pose a significant challenge for diagnostics
and vaccine strategies. Therefore, tracking the genetic shifts of these
variants is significant. For these reasons, the genetic diversity of the S gene
of Omicron variants isolated in Vietnam was investigated. By constructing a
network, the genetic relationship of Omicron variants would be revealed,
supporting the tracing of a infection source of a new outbreak in the future.
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