PORTFOLIO WAFIQ

PORTFOLIO

NAME: WAFIQ WAJIHUDDIN BIN NOR HAZAN
MATRIC NO : PBA21006
SEMESTER: 3
ESSAY TITLE : COVID 19 VARIANT OMICRON

TABLE CONTENT

Online Article
1. What we know about omicron
2. Update on omicron
3. Decoupling of omicron variant infection and severe covid 19

Journal article
1.broadly neutralizing antibodies overcome SARS omicron antigenic.
2.increased risk of SARS reinfection associated with emergence of the

omicron.
3. population immunity and covid 19 severity with omicron variant.

Newpapers online
1 malaysia is better prepared to deal with omicron surge.
2 omicron sweeps Malaysia.
3 minister urge booster shot as country now facing full omicron.

Magazine online

1 scientists investigate omicron subvariant BA 2
2 how mild is omicron really?

Copies of related book

1 understanding omicron variant
2 omicron covid 19 variant
3 covid 19 omicron variant

Online article

What we know about omicron. Link :

https://www.unicef.org/coronavirus/what-we-know-about-omicron-variant

What is the Omicron variant?

The Omicron variant of COVID-19 has been called a variant of concern
by WHO based on the evidence that it has several mutations that may
have an impact on how it behaves. There is consistent evidence that
Omicron is spreading significantly faster than the Delta variant in
countries with documented community transmission, with a doubling
time of 2-3 days. The overall risk related to this new variant remains
very high.

How did the Omicron variant develop?

When a virus is circulating widely and causing numerous infections,
the likelihood of the virus mutating increases. The more opportunities
a virus has to spread, the more opportunities it has to undergo
changes.

New variants like Omicron are a reminder that the COVID-19
pandemic is far from over. It is therefore essential that people get the
vaccine when available to them and continue to follow existing advice
on preventing the spread of the virus, including physical distancing,
wearing masks, regular handwashing and keeping indoor areas well
ventilated.

It is also crucial that vaccines and other public health measures are
accessible everywhere. Vaccine inequity leaves lower income
countries – many of them in Africa – at the mercy of COVID-19. Well-
supplied countries must urgently deliver the doses they promised.

Update on Omicron

Link : https://www.who.int/news/item/28-11-2021-update-on-omicron

On 26 November 2021, WHO designated the variant B.1.1.529 a variant of concern,
named Omicron, on the advice of WHO’s Technical Advisory Group on Virus
Evolution (TAG-VE). This decision was based on the evidence presented to the
TAG-VE that Omicron has several mutations that may have an impact on how it
behaves, for example, on how easily it spreads or the severity of illness it
causes. Here is a summary of what is currently known.

Decoupling of omicron variant infections and severe
Covid 19

Link : https://www.thelancet.com/journals/lancet/article/PIIS0140-
6736(22)00109-X/fulltext

SARS-CoV-2 omicron (B.1.1.529) was designated a variant of concern by WHO
because of specific mutations that might increase transmissibility, risk of
reinfection, or vaccine breakthrough infection. Many of these mutations affect
the receptor-binding domain and N-terminal domain of the spike protein, which
might, paradoxically, increase binding to ACE-2 while evading antibody
recognition.

Emergence of omicron appears to have parallels with the beta variant (B.1.351)
in South Africa. It was demonstrated that there are decreased neutralising

antibody titres with beta in infection-naive individuals who received two doses
of AZD1222 (ChAdOx1 nCoV-19) or BNT162b.

,

Nevertheless, real-world data showed more than 80% effectiveness against
severe disease and hospitalisations.

Although preliminary evidence suggests booster doses might enhance
protection against omicron,

studies are underway to fully determine vaccine effectiveness. Given the
natural lag between infection and severe outcomes, we await further data on
omicron for effectiveness of vaccinations in preventing severe disease—the key
intended outcome of vaccination.

In the meantime, the South Africa National Institute for Communicable
Diseases has shared preliminary data indicating a decoupling of infection rates
from hospitalisations and deaths with omicron. These data suggest underlying
immune responses following infection and that primary and booster
vaccination might attenuate the course of illness.

Complementary humoral (antibody) and cellular (T cell) immune responses are
activated following natural SARS-CoV-2 infection or vaccination. T-cell
responses encompass a broad range of spike-protein-specific T-cell receptors
that recognise multiple epitopes both within and outside of mutated regions in
variants of concern.

Thus, even if spike protein mutations enable neutralising antibody escape, non-
neutali-sing antibodies or T-cell-mediated responses can provide protection.
The beta variant has only a few mutations in the spike gene that affect T-cell
epitopes, meaning T-cell response is maintained; this is expected to be the case
with omicron.

At this stage of the pandemic, omicron is spreading in populations where many
individuals have been previously infected with SARS-CoV-2 and are now being
vaccinated, or where many have received two or three COVID-19 vaccine doses.
These populations might be expected to have greater depth of antibody
response and a broader and deeper poly-epitopic T-cell response,

which should overcome some of the anticipated antibody evasion of omicron.
In these scenarios, protection against severe disease is anticipated. Most cases
of severe disease and hospitalisation with omicron are among the
unvaccinated; we recommend an accelerated and equitable roll-out of COVID-
19 vaccines, which have a continued role in enhancing protection against

omicron.

Journal onlie article

Broadly neutralizing antibodies overcome SARS omicron antigenic shift.
Link : https://www.nature.com/articles/s41586-021-04386-2

The recently emerged SARS-CoV-2 Omicron variant encodes 37 amino acid
substitutions in the spike protein, 15 of which are in the receptor-binding
domain (RBD), thereby raising concerns about the effectiveness of available
vaccines and antibody-based therapeutics. Here we show that the Omicron RBD
binds to human ACE2 with enhanced affinity, relative to the Wuhan-Hu-1
RBD, and binds to mouse ACE2. Marked reductions in neutralizing activity
were observed against Omicron compared to the ancestral pseudovirus in
plasma from convalescent individuals and from individuals who had been
vaccinated against SARS-CoV-2, but this loss was less pronounced after a third
dose of vaccine. Most monoclonal antibodies that are directed against the
receptor-binding motif lost in vitro neutralizing activity against Omicron, with
only 3 out of 29 monoclonal antibodies retaining unaltered potency, including
the ACE2-mimicking S2K146 antibody1. Furthermore, a fraction of broadly
neutralizing sarbecovirus monoclonal antibodies neutralized Omicron through
recognition of antigenic sites outside the receptor-binding motif, including
sotrovimab2, S2X2593 and S2H974. The magnitude of Omicron-mediated
immune evasion marks a major antigenic shift in SARS-CoV-2. Broadly
neutralizing monoclonal antibodies that recognize RBD epitopes that are
conserved among SARS-CoV-2 variants and other sarbecoviruses may prove
key to controlling the ongoing pandemic and future zoonotic spillovers.

Main

The evolution of RNA viruses can result in immune escape and modulation of
binding to host receptors through the accumulation of mutations5. Previously
emerged SARS-CoV-2 variants of concern (VOCs) have developed resistance
to neutralizing antibodies, including some clinical antibodies that are used as
therapeutics6,7,8. The B.1.351 (Beta) VOC showed the greatest magnitude of
immune evasion from serum neutralizing antibodies6,7, whereas B.1.617.2
(Delta) quickly outcompeted all other circulating isolates through the
acquisition of mutations that enhanced transmission and

pathogenicity9,10,11 and eroded the neutralizing activity of antibody
responses9.

The Omicron (B.1.1.529) variant was first detected in November 2021, was
immediately declared to be a VOC by the World Health Organization (WHO)
and quickly rose in frequency worldwide. The Omicron variant is substantially
mutated compared to any previously described SARS-CoV-2 isolates, including
37 substitutions of residues in the spike protein in the predominant haplotype
(Fig. 1a, Extended Data Figs. 1–4). Fifteen of the Omicron mutations are
clustered in the RBD, which is the main target of neutralizing antibodies after
infection or vaccination12,13, suggesting that Omicron might escape infection-
and vaccine-elicited antibodies and therapeutic monoclonal antibodies. Nine of
these mutations map to the receptor-binding motif (RBM), which is the RBD
subdomain that directly interacts with the host receptor, ACE214.

Increased risk of SARS reinfection associated with emergence of the
Omicron.

Link :
https://www.medrxiv.org/content/10.1101/2021.11.11.21266068v2?__cf
_chl_jschl_tk__=s7vuVAdADG0Pc_Af5hZvgL8hj3WzO1K48eVrB1.OgVc-
1639497284-0-gaNycGzNCL0

Objective To examine whether SARS-CoV-2 reinfection risk has changed
through time in South Africa, in the context of the emergence of the Beta, Delta,
and Omicron variants
Design Retrospective analysis of routine epidemiological surveillance data
Setting Line list data on SARS-CoV-2 with specimen receipt dates between 04
March 2020 and 27 November 2021, collected through South Africa’s National
Notifiable Medical Conditions Surveillance System
Participants 2,796,982 individuals with laboratory-confirmed SARS-CoV-2
who had a positive test result at least 90 days prior to 27 November 2021.
Individuals having sequential positive tests at least 90 days apart were
considered to have suspected reinfections.
Main outcome measures Incidence of suspected reinfections through time;
comparison of reinfection rates to the expectation under a null model (approach
1); empirical estimates of the time-varying hazards of infection and reinfection
throughout the epidemic (approach 2)
Results 35,670 suspected reinfections were identified among 2,796,982
individuals with laboratory-confirmed SARS-CoV-2 who had a positive test

result at least 90 days prior to 27 November 2021. The number of reinfections
observed through the end of the third wave was consistent with the null model
of no change in reinfection risk (approach 1). Although increases in the hazard
of primary infection were observed following the introduction of both the Beta
and Delta variants, no corresponding increase was observed in the reinfection
hazard (approach 2). Contrary to expectation, the estimated hazard ratio for
reinfection versus primary infection was lower during waves driven by the Beta
and Delta variants than for the first wave (relative hazard ratio for wave 2
versus wave 1: 0.75 (CI95: 0.59–0.97); for wave 3 versus wave 1: 0.71 (CI95:
0.56–0.92)). In contrast, the recent spread of the Omicron variant has been
associated with a decrease in the hazard coefficient for primary infection and an
increase in reinfection hazard coefficient. The estimated hazard ratio for
reinfection versus primary infection for the period from 1 November 2021 to 27
November 2021 versus wave 1 was 2.39 (CI95: 1.88–3.11).
Conclusion Population-level evidence suggests that the Omicron variant is
associated with substantial ability to evade immunity from prior infection. In
contrast, there is no population-wide epidemiological evidence of immune
escape associated with the Beta or Delta variants. This finding has important
implications for public health planning, particularly in countries like South
Africa with high rates of immunity from prior infection. Urgent questions
remain regarding whether Omicron is also able to evade vaccine-induced
immunity and the potential implications of reduced immunity to infection on
protection against severe disease and death.

Population immunity and covid 19 severity with omicron variant in south
Africa.
Link : https://www.nejm.org/doi/full/10.1056/NEJMoa2119658

The B.1.1.529 (omicron) variant of severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) was first identified on November 25, 2021, in
Gauteng province, South Africa. Data regarding the seroprevalence of SARS-
CoV-2 IgG in Gauteng before the fourth wave of coronavirus disease 2019
(Covid-19), in which the omicron variant was dominant, are needed.

METHODS

We conducted a seroepidemiologic survey from October 22 to December 9,
2021, in Gauteng to determine the seroprevalence of SARS-CoV-2 IgG.
Households included in a previous seroepidemiologic survey (conducted from
November 2020 to January 2021) were contacted; to account for changes in the
survey population, there was a 10% increase in the households contacted, with
the use of the same sampling framework. Dried-blood-spot samples were tested
for IgG against SARS-CoV-2 spike protein and nucleocapsid protein with the
use of quantitative assays. We also evaluated Covid-19 epidemiologic trends in
Gauteng, including cases, hospitalizations, recorded deaths, and excess deaths
from the start of the pandemic through January 12, 2022.

RESULTS
Samples were obtained from 7010 participants, of whom 1319 (18.8%) had
received a Covid-19 vaccine. The seroprevalence of SARS-CoV-2 IgG ranged
from 56.2% (95% confidence interval [CI], 52.6 to 59.7) among children
younger than 12 years of age to 79.7% (95% CI, 77.6 to 81.5) among adults
older than 50 years of age. Vaccinated participants were more likely to be
seropositive for SARS-CoV-2 than unvaccinated participants (93.1% vs.
68.4%). Epidemiologic data showed that the incidence of SARS-CoV-2
infection increased and subsequently declined more rapidly during the fourth
wave than it had during the three previous waves. The incidence of infection
was decoupled from the incidences of hospitalization, recorded death, and
excess death during the fourth wave, as compared with the proportions seen
during previous waves.

CONCLUSIONS
Widespread underlying SARS-CoV-2 seropositivity was observed in Gauteng
before the omicron-dominant wave of Covid-19. Epidemiologic data showed a
decoupling of hospitalizations and deaths from infections while omicron was
circulating. (Funded by the Bill and Melinda Gates Foundation.)

Newspaper online

Link : https://www.malaysiakini.com/news/609192

Malaysia is better prepared to deal with Omicron surge – Khairy

Bernama
Published: Feb 1, 2022 4:19 PM
⋅
Updated: 5:18 PM

Malaysia is seen as better prepared to deal with the surge in
Covid-19 cases due to the Omicron variant and know how to
protect the most vulnerable, said Health Minister Khairy
Jamaluddin.
In his tweet today, Khairy said the situation was not the same as
seen in June to September last year because the country is better
protected now...

Omicron sweeps Malaysia

Link: https://www.malaysiakini.com/newsletter/609680

Health Minister Khairy Jamaluddin acknowledged that the country is now
facing a full-blown spread of the Omicron Covid-19 variant.

The infectivity rate stands at 1.20, the highest level since May last year that
preceded the deadly Covid-19 wave involving the Delta variant.

Khairy said the Health Ministry expected daily cases to rise to 15,000 soon
while Health Ministry director-general Dr Noor Hisham Abdullah said if the
infectivity rate remained at 1.20, daily cases will hit 22,000 by late March.

The daily Covid-19 cases in recent days have increased steeply, breaking
more than five digits yesterday, the first time since October last year.

In Sarawak, surveillance data showed that the Omicron has replaced Delta as
the dominant variant.

Khairy urged the most vulnerable groups, particularly the elderly, to get their
Covid-19 vaccine booster shot.

Minister urges booster shot as country now facing full Omicron
wave

Link : https://www.malaysiakini.com/news/609667

Published: Feb 6, 2022 6:05 PM
⋅
Updated: Feb 8, 2022 9:59 AM

The country recorded new Covid-19 cases in the five digits for the first time in
four months but Health Minister Khairy Jamaluddin cautioned that the worst is
yet to come due to the spread of the Omicron variant.

As such, he said those who have yet to receive their Covid-19 vaccine booster
dose, particularly the elderly who are more vulnerable, should do so.

Magazine online

Link : https://www.the-scientist.com/news-opinion/scientists-investigate-omicron-
subvariant-ba-2-69657

Scientists Investigate Omicron Subvariant
BA.2

Researchers are monitoring the behavior of BA.2, a subvariant of SARS-CoV-2
that is responsible for a number of outbreaks ongoing in Europe and some parts
of Asia. First described in November, the strain is a subtype of the Omicron
variant, and preliminary data hint that it might spread slightly faster than the
better-studied BA.1, the subtype responsible for most Omicron outbreaks to
date.

“Among all the lineages of Omicron, this is the one showing a higher increase
of cases,” Ramon Lorenzo-Redondo, assistant professor of medicine for
infectious diseases at Northwestern University Feinberg School of Medicine in
Chicago, tells CNN. “But we have to be careful in interpreting that, because
higher increases from a very low number are easier to observe.”

The BA.1 version of Omicron has been the dominant strain in many countries
for weeks, and nearly all Omicron infections in the US at the moment are due to
this subtype, according to the Centers for Disease Control and Prevention
(CDC). However, BA.2 has been spreading rapidly in European countries such
as Denmark—where almost half of all COVID-19 cases reported in mid-
January were attributed to this subtype—and has recently been detected in
several US states, including California and Texas.

Scientists already have documented some of the differences between the
variants. At the end of last year, researchers in India reported that BA.1 and
BA.2 showed divergence in sequences coding for the spike protein, for
example, although overall the two strains were still too similar to be classed as
different variants.

How mild is omicron really?

Link : https://www.the-scientist.com/news-opinion/how-mild-is-omicron-really-69610

When the Omicron variant of SARS-CoV-2 first began to spread rapidly and
outcompete other variants in late 2021, it quickly became apparent that the
variant was quite different than those that came before it.

Unlike Delta, which emerged in December 2020 and was linked to a massive
surge in hospitalizations and deaths last year, Omicron didn’t seem to be as
dangerous on the scale of individual infected people. Yet hospitals, clinics, and
intensive care units have still filled up with patients as the tally of new cases
and hospitalizations, currently at more than 145,000 in the United States,
shattered records day after day, in no small part because a series of mutations in
the virus’s spike protein render vaccines far less effective at stopping infection
than they have been with previous variants. The parallel spike in deaths that
lagged shortly behind case numbers in other surges is now starting to emerge.

Meanwhile, record numbers of children are being hospitalized with COVID-19,
according to The New York Times, and the number of new infections reported
per day continues to skyrocket. On Wednesday (January 12), the 14-day
average tally of new daily cases in the US surpassed 780,000.

As Omicron continues to spread, several questions remain about how and why it
differs from other variants in terms of both disease outcomes and
transmissibility. Some findings, such as clinical reports indicating that Omicron
patients fare better than those with other variants and research suggesting that
Omicron doesn’t target tissues associated with worse disease outcomes, offer
encouraging signs. But whether that makes Omicron “mild” is, experts say, less
clear.

“I think it’s pretty clear Omicron causes less severe disease than the Delta
variant, but that’s not saying much,” University of Western Australia
epidemiologist and biostatistician Zoë Hyde writes in an email to The Scientist.
“We know that Delta was more than twice as severe as the original strain, and if
Imperial College is right to say that Omicron is about 40-45% less likely to put
people in hospital [than Delta was], we’re back to 2020 but with a more
contagious strain.”

Copies of related book

1.Understanding omicron variant

2. omicron covid-19 variant.

3 covid 19 omicron variant by Dr Bright Owen.