1.

Prevention and Control of COVID 19 and the different variants

INTRO

Coronavirus Disease 2019 is an emerging and rapidly evolving global health

concern designated as a Public Health Emergency of International Concern by the
World Health Organization (WHO). Last February 12, 2020, the World Health
Organization (WHO) announced that the novel disease is officially called Coronavirus
Disease 19 or COVID-19, and the virus infecting it is referred to as COVID-19 virus.
Paules, C. (2020) stated that “In the 21st century, 2 highly pathogenic Coronaviruses
namely: Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle
East Respiratory Syndrome Coronavirus (MERS-CoV) emerged from animal reservoirs
that caused global pandemics”. In December 2019, yet another novel coronavirus was
recognized in Wuhan, China which has now spread worldwide. SARS-CoV-2 emerged
in Wuhan, spread all over the world through human to human transmission, and
infected millions of individuals. Currently, each pasing day, the virus is causing deaths
in thousands of COVID-19 infected individuals across the globe.

Causative agent

Coronavirus disease (COVID-19) is caused by SARS-COV2.

Genetic variants of SARS-CoV-2 have been emerging and circulating around the
world throughout the COVID-19 pandemic. Viral mutations and variants are
routinely monitored through sequence-based surveillance, laboratory studies,
and epidemiological investigations.

Under coronaviruses, there are 4 variants namely: Alpha Coronavirus, Beta

Coronavirus, Delta Coronavirus and Gamma Coronavirus

The SARS-CoV-2 virus is a betacoronavirus, as well as the MERS-CoV and SARS-

CoV. All three of these viruses have originated from bats.

However, The virus that causes COVID-19 is constantly changing. A variant has
one or more mutations that differentiate it from other variants in circulation. As
expected, multiple variants of SARS-CoV-2 have been documented in the United
States and globally throughout this pandemic.

Infact, we already have local transmissions of the Delta Variant which causes
more infections and spreads faster than earlier forms of the virus that causes
COVID-19. According to the CDC, this strain might cause more severe illness
than previous strains in unvaccinated people.

Different Variants of SARS-CoV-2

Alpha (B.1.1.7) . In late 2020, experts noted gene mutations in COVID-19 cases
seen in people in southeastern England. This variant has since been reported in
other countries, including the U.S. Scientists estimate that these mutations could
make the virus up to 70% more transmissible, meaning it could spread more easily.
Some research has linked this variant to a higher risk of death, but the evidence
isn't strong.

The mutation on the Alpha variant is on the spike protein, which helps the virus
infect its host. This is what COVID-19 vaccines target. These vaccines make
antibodies against many parts of the spike protein, so it’s unlikely that a single new
mutation in the Alpha variant will make the vaccine less effective.

Beta (B.1.351). Other variants of the virus have been found in other countries,
including South Africa and Nigeria. The Beta variant appears to spread more easily
than the original virus but doesn’t seem to cause worse illness.

Delta (B.1.617.2). This variant was spotted in India in December 2020. It

caused a huge surge in cases in mid-April 2021. This highly contagious
variant is now found in 43 countries including the U.S., the U.K., Australia,
and Singapore. It's the dominant strain in the U.S. and the U.K.

Gamma (P.1). In January 2021, experts spotted this COVID-19 variant in people
from Brazil who’d traveled to Japan. By the end of that month, it was showing up in
the U.S.

The Gamma variant appears to be more contagious than earlier strains of the virus.
And it may be able to infect people who've already had COVID-19. A report from
Brazil confirms that a 29-year-old woman came down with this variant after an
earlier coronavirus infection a few months before.

Some early research suggests that the variant’s changes might help it evade
antibodies (made by your immune system after an infection or a vaccine) that fight
the coronavirus.

Mu (B.1.621). Experts first spotted this COVID-19 variant (pronounced m’yoo) in

Colombia in January 2021. Since then, countries in South America and Europe have
reported outbreaks of Mu.
In the U.S., the CDC says Mu reached a peak in June 2021, when it made up less
than 5% of variants going around the country. As of early September, it had been
steadily declining.

R.1. Scientists first detected R.1 in a number of countries, including Japan. There
was an outbreak at a Kentucky nursing home in March 2021, when an unvaccinated
health care worker passed it to about 45 other staff and residents.
Variants being monitored:
WHO Label Pango Lineage Date of Designation

Alpha B.1.1.7 and Q lineages VOC: December 29, VBM: September 21,
2020 2021

Beta B.1.351 and descendent VOC: December 29, VBM: September 21,
lineages 2020 2021

Gamma P.1and descendent lineages VOC: December 29, VBM: September 21,
2020 2021

Epsilon B.1.427 VOC: March 19, 2021 VOI: February 26, VBM: September 21,
B.1.429 2021 2021
VOI: June 29, 2021

Eta B.1.525 VOI: February 26, VBM: September 21,

2021 2021

Iota B.1.526 VOI: February 26, VBM: September 21,

2021 2021

Kappa B.1.617.1 VOI: May 7, 2021 VBM: September 21,

2021

N/A B.1.617.3 VOI: May 7, 2021 VBM: September 21,

2021

Zeta P.2 VOI: February 26, VBM: September 21,

2021 2021

Mu B.1.621, B.1.621.1 VBM: September 21,

2021

Variant of Concern:

Pango GISAID Nextstrain Additional Earliest Date of

WHO
lineage* clade clade amino acid documented designation
label changes samples
monitored°
 United
+S:484K
Kingdom,
Alpha B.1.1.7 # GRY 20I (V1) 18-Dec-2020
+S:452R
Sep-2020

GH/ 20H (V2) +S:L18F 18-Dec-2020

B.1.351 South Africa,
Beta 501Y.V2 May-2020

Gamma GR/ 20J (V3) +S:681H Brazil, 11-Jan-2021

P.1 Nov-2020
501Y.V3

Delta G/ 21A +S:417N India, VOI: 4-Apr-

B.1.617. Oct-2020 2021
478K.V1
2§ VOC: 11-
May-2021

Variants of Interest:

Currently designated Variants of Interest:

Pango GISAID Nextstrain Earliest Date of
WHO label lineage* clade clade documented designation
samples

Lambda C.37 GR/ 21G Peru, Dec-

14-Jun-2021
452Q.V1 2020

Colombia,
Mu B.1.621 GH 21H 30-Aug-2021
Jan-2021

Mode of transmission

SARS-CoV-2 spreads from person to person via droplets, contact, and fomites.
Direct transmission
- When persons with COVID-19 coughs, sneezes, speaks, sings or
breathes small droplets containing the virus are expelled.
Aerosol’s or droplets containing the virus are inhaled which then
enters the mucous membranes of the nose and mouth and of the
eyes.
- COVID-19 is usually transmitted through close contact with another
person. Close contact is within around 6 feet therefore it is important to
maintain a distance of more than 1 meter away from anyone.

Indirect transmission
- Virus-carrying droplets can potentially fall onto nearby surfaces or objects.
By contacting these surfaces or objects, other people can become
infected with the virus. If the person then touches their nose, eyes, or
mouth, they are likely to become infected.
https://doh.gov.ph/COVID-19/FAQs

Incubation period
According to the CDC, COVID-19 is thought to have a 14-day incubation
period, with a median time of 4-5 days from exposure to symptom manifestation.
According to one study, 97.5 percent of patients infected with COVID-19 who
develop symptoms do so within 11.5 days of contracting SARS-CoV-2.
Rarely, symptoms appear as soon as 2 days after exposure.
https://www.webmd.com/lung/coronavirus-incubation-period#1

Pathophysiology including signs & symptoms

VIRAL LIFE CYCLE AND HOST CELL INVASION

The virus is transmitted via respiratory droplets and aerosols from person to
person. Once inside the body, the virus binds to host receptors and enters host
cells through endocytosis or membrane fusion. The coronaviruses are made up
of four structural proteins, namely, the spike (S), membrane (M), envelop (E) and
nucleocapsid (N) proteins.The S protein is seen to be protruding from the viral
surface and is the most important one for host attachment and penetration. This
protein is composed of two functional subunits (S1 and S2), among which S1 is
responsible for binding to the host cell receptor and S2 subunit plays a role in the
fusion of viral and host cellular membranes.
1. ACE-2 has been identified as a functional receptor for SARS-CoV and is
highly expressed on the pulmonary epithelial cells.It is through this host
receptor that the S protein binds initially to start the host cell invasion by
the virus.
2. After binding of SARS-CoV-2 to the ACE-2, the S protein undergoes
activation via a two-step protease cleavage: the first one for priming at the
S1/S2 cleavage site and the second cleavage for activation at a position
adjacent to a fusion peptide within the S2 subunit.
3. The initial cleavage stabilises the S2 subunit at the attachment site and
the subsequent cleavage presumably activates the S protein causing
conformational changes
4. leading to viral and host cell membrane fusion via s2 subunit of spike
protein
5. Postmembrane fusion, the virus enters the pulmonary alveolar epithelial
cells and the viral contents are released inside.
6. Now since the viral contents are inside the host cell, the virus undergoes
replication and formation of a negative strand RNA by the pre-existing
single-strand positive RNA through RNA polymerase activity
(transcription). This newly formed negative strand RNA serves to produce
new strands of positive RNAs which then go on to synthesise new proteins
in the cell cytoplasm (translation).
7. The viral N protein binds the new genomic RNA and the M protein
facilitates integration to the cellular endoplasmic reticulum.
8. These newly formed Nucleocapsids are then enclosed in the ER
membrane and transported to the lumen, from where they are transported
via golgi vesicles to the cell membrane and then via exocytosis to the
extracellular space.
9. The new viral particles are now ready to invade the adjacent epithelial
cells as well as for providing fresh infective material for community
transmission via respiratory droplets. An overview of the viral life cycle is
shown in
Signs and Symptoms

People with COVID-19 have had a wide range of symptoms reported – ranging
from mild symptoms to severe illness. Symptoms may appear 2-14 days after
exposure to the virus. Anyone can have mild to severe symptoms. People with
these symptoms may have COVID-19:

● Fever or chills
● Cough
● Shortness of breath or difficulty breathing
● Fatigue
● Muscle or body aches
● Headache
● New loss of taste or smell
● Sore throat
 ● Congestion or runny nose
● Nausea or vomiting
● Diarrhea
●

When to seek emergency medical attention

● Trouble breathing
● Persistent pain or pressure in the chest
● sudden confusion
● Inability to wake or stay awake
● Pale, gray, or blue-colored skin, lips, or nail beds, depending on skin tone

DELTA VARIANT S/S

The symptoms of the Delta variant appear to be the same as the original version of
COVID-19. However, physicians are seeing people getting sicker quicker, especially for
younger people. Recent research found that the Delta variant grows more rapidly – and
to much greater levels – in the respiratory tract.

Typically, vaccinated people are either asymptomatic or have very mild symptoms if
they contract the Delta variant. Their symptoms are more like those of a common cold,
such as cough, fever or headache, with the addition of significant loss of smell.

Management in the community setting

Methods of Prevention

Government Programs in controlling the spread

The Philippine government mounted a multi-sectoral response to the
COVID-19, through the Interagency Task Force (IATF) on Emerging Infectious
Diseases chaired by the Department of Health (DOH).

The Philippines implemented various actions including a community quarantine

in Metro Manila which expanded to Luzon as well as other parts of the country;
expanded its testing capacity from one national reference laboratory with the
Research Institute of Tropical Medicine (RITM) to 23 licensed testing labs across
the country; worked towards ensuring that its health care system can handle
surge capacity, including for financing of services and management of cases
needing isolation, quarantine and hospitalization; and addressed the social and
economic impact to the community including by providing social amelioration to
low income families.

STRATEGIES

Surveillance

Surveillance is a critical component and is used to detect cases of COVID-

19 as well as to understand the disease dynamics and trends and identify
hotspots of disease transmission. The Department of Health included COVID-19
in the list of nationally notifiable diseases early in the outbreak to ensure that
information was being collected to guide appropriate response actions. Existing
surveillance systems were capitalized upon to speed up identification of cases as
well as identify unusual clusters. Laboratory confirmation is a critical component
of the surveillance system but cannot be the only sources of information. The
non-specific symptoms and the novel nature of the disease means that the DOH,
with support from WHO, are looking at all available information sources to guide
response decision making. WHO also provided technical assistance to selected
local government units to strengthen field surveillance for timely data for action at
the local level.

Contact tracing

Contact tracing is crucial to the response. It is a system to detect and

isolate cases and identify close contacts who will be advised for quarantine. It
allows the investigation of the system to track the chain of infections as well as
the settings, places, events or other avenues where transmission have occurred
or may have been amplified. A major bottleneck to doing this is the availability of
timely and complete information from the hospitals for suspected, probable and
confirmed COVID-19 cases. WHO assisted the DOH Epidemiology Bureau in
developing COVID KAYA, a case and contact tracing reporting system for
epidemiology and surveillance officers, health care providers and laboratory-
based users, expanding the capacity of the previous COVID-19 information
system. WHO also continued to support the government to establish the system
and improve capacity for contact tracing at the city and municipal levels.

Infection prevention and control

Patients and health workers must be protected from the possible

transmission of COVID-19 inside health facilities. Infection prevention and control
(IPC) is vital in minimizing the harm caused by the spread of infection in these
facilities. In the early part of the response, WHO supported the DOH with the
provision of personal protective equipment (PPE) for health workers. To
strengthen IPC, WHO and DOH developed modules and conducted online IPC
training of trainers for frontline health workers in health care and community
settings. The training has since been rolled out more widely by partners USAID-
MTaPS and UNICEF to cover over 5,500 health workers to date.

Laboratory and therapeutics access

Laboratory testing for COVID-19 is critical to be able to rapidly identify,

treat and isolate the positive patients, and be able to see the bigger picture of
how many people are infected and ultimately stop the transmission of the virus.
Since the beginning of the response, WHO provided support to the DOH’s
Research Institute for Tropical Medicine with laboratory supplies and extraction
kits. WHO also assisted the DOH in the accreditation of COVID-19 testing
laboratories. To date, 23 real-time reverse transcription polymerase chain
reaction (rRT-PCR) laboratories nationwide are now conducting COVID-19
diagnostic tests. The Philippines has also recently joined the WHO Solidarity trial
to find effective COVID-19 treatment.

Clinical care

With a new disease, there are a lot of unknowns regarding the proper
clinical management of suspect and confirmed cases. But when clinicians are
armed with the necessary knowledge and skills to care for sick patients, the more
the patients are likely to recover. WHO supported the frontline health workers
through a webinar series on clinical management, providing up-to-date WHO
clinical perspectives. At the same time, WHO also supported the DOH and the
Department of Interior and Local Government in preparing policies to form health
care provider networks for COVID-19, from primary care that includes
telemedicine and community management, to tertiary care linking to referral
hospitals.

Mass Vaccination

The government is giving out free Covid vaccines for all the citizens in the
country. The healthcare workers in the community are tasked to facilitate the
distribution of these vaccines in their respective community. Infact, there are
several safe and effective vaccines that prevent people from getting seriously ill
or dying from COVID-19. This is one part of managing COVID-19, in addition to
the main preventive measures of staying at least 1 metre away from others,
covering a cough or sneeze in your elbow, frequently cleaning your hands,
wearing a mask and avoiding poorly ventilated rooms or opening a window.

Vaccines work by training and preparing the body’s natural defences – the
immune system – to recognize and fight off the viruses and bacteria they target.
After vaccination, if the body is later exposed to those disease-causing germs,
the body is immediately ready to destroy them, preventing illness.

· Goals & objectives

Through the National Action Plan (NAP) on COVID-19, the government aims to
contain the spread of COVID-19 and mitigate its socioeconomic impacts.
Difference between COVID-19 & Flu
Influenza (Flu) and COVID-19 are both contagious respiratory illnesses, but they
are caused by different viruses. COVID-19 is caused by infection with a new
coronavirus (called SARS-CoV-2), and flu is caused by infection with influenza
viruses.

COVID-19 seems to spread more easily than flu and causes more serious
illnesses in some people. It can also take longer before people show symptoms
and people can be contagious for longer. More information about differences
between flu and COVID-19 is available in the different sections below.

Because some of the symptoms of flu and COVID-19 are similar, it may be hard
to tell the difference between them based on symptoms alone, and testing may
be needed to help confirm a diagnosis.

(TBC)
https://pmj.bmj.com/content/97/1147/312

https://www.who.int/docs/default-source/coronaviruse/covid19-rcce-guidance-final-
brand
https://pmj.bmj.com/content/97/1147/312
https://www.cdc.gov/coronavirus/2019-ncov/hcp/clinical-guidance-management-
patients.html
https://www.who.int/emergencies/diseases/novel-coronavirus-2019/advice-for-public
https://www.who.int/emergencies/diseases/novel-coronavirus-2019/covid-19-vaccines/
advice
https://www.medicalnewstoday.com/articles/coronavirus-causes#transmission
https://health.ucdavis.edu/coronavirus/covid-19-information/delta-variant.html

https://www.webmd.com/lung/coronavirus-strains#4

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

https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/