MICROBIOLOGY & PARASITOLOGY LECTURE 0900-1200 Tue

REVIEW PAPER MICROORGANISM: COVID-19

Section: N102
ABUTIN, MARIDEE;
BERNANCIO, KYLA MAE;
PROF. RICHARD LAGRIMAS
PUERTE, DANICA SHANE;
RAÑOLA, ANDREY MARY; &
RIVERA ROMER

CHEMICAL PROPERTIES AND COMPOSITION by Rañola, Andrey Mary C.

Severe Acute Respiratory Syndrome Corona Virus 2 which is also known as SARS-CoV-2 actually
causes the COVID-19 disease belongs to the beta coronavirus, it is one of the seven coronaviruses to be
known as a type of coronavirus that infects the humans. Symptoms of common cold are manifested slightly
in Four (4) of this coronaviruses. A much more severe symptoms and can even cause fatality belongs to
the 3 remaining types of coronavirus which are known as SARS-CoV, MERS-CoV, and now COVID-19 or
SARS-CoV-2.

The shape of SARS-CoV-2 is round or elliptical and often pleomorphic with a diameter depending
approximately between 60 to 140 nm. (Scheller et al. 2020) SARS-CoV-2 is known to be an enveloped
virus, mostly shapes of enveloped viruses is different from one single virus to the other because their
lipophilic envelope. Which can integrate different types and amounts of proteins that allows its malleability
or moldability. According to Zhu (2020), generally SARS-CoV-2 particles look spherical but in his presented
electron micrographs it is shown that there are some pleomorphism. It has distinctive spikes that are about
9-12 nm long protruding from the particle's main surface which looks like a solar corona. This cannot only
be seen in SARS-CoV-2 but also to other Coronaviridae family.

According to Shi (2020), SARS-CoV-2 is a linear, single-stranded, positive RNA virus. While it's viral
genome structure is approximately 29903nt (GenBank, MN908947.3) in length. The genome of SARS-
CoV-2 contains two (2) flanking untranslated regions (UTRs) and a long Open Reading Frame (ORF). The
arrangement for which is 5’-replicase (ORF1ab)-structural proteins [Spike (S)-Envelope (E)-Membrane
(M)-Nucleocapsid (N)]−3’ (9,). It shares both the genome sequence identity of MERS-CoV and SARS-
CoV. 79% genome sequence identity matched with SARS-CoV while with MERS-CoV only 50%. With a
higher match with SARS-CoV, most of the proteins in SARS-CoV-2 have a similar length to the accessory
proteins that interspersed with the structural genes of SARS-CoV. Except for the S gene or protein that
diverges, SARS-CoV-2 shares more than 90% amino acid identity with SARS-CoV. The S gene of SARS-
CoV-2 has a full size of 1,273 amino acids which are longer than SARS-CoV that has 1,255 amino acids.
SARS-CoV-2 is also known that has an insertion of four (4) amino acid residues(PRRA) which are V483A,
L4551, F456V, and G476S that are located at the junction of subunits S1 and S2 of the S protein near the
binding interface in the RBD. Which differentiates it with other known coronaviruses or related viruses
because with this insertion it generates a polybasic cleavage site that enables effective cleavage by furin
and other proteases.

According to Hu (2020), the other additional distinction of SARS-CoV-2 are the accessory gene orf8.
It shows that SARS-CoV-2 contains a novel protein that has a 40% amino acid identity with the orf8 of
SARS-CoV. SARS-CoV's orf8 protein has a motif that triggers intracellular stress pathways while the
findings do not show that SARS-CoV-2's new protein have it. And the other distinction is the marker
mutation for SARS-CoV-2 evolution is the amino acid substitution of Ser for Lys with a residue of 84 of the
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orf8 protein that was made because of the single-nucleotide polymorphism at the nucleotide position
28,144.

LABORATORY PREPARATION by Abutin, Maridee

For laboratory safety due to SARS-CoV-2 the viruse that causes COVID-19, National guidelines on
laboratory biosafety should be followed in all circumstances for appropriate practices especially when
clinical specimen of the clients that are in suspected case are in checking, it should be performed by the
staff that are trained in relevant technical and safety procedures in appropriately equipped laboratories.

Recommendations addressing essential working conditions associated with specific manipulations in

laboratory setting:
1.Risk Assessment
In this step it is evaluating the impact of exposure to release workplace hazard and
determining appropriate risk control to reduce risk. It is recommended to conduct local
risk assessment for each process step to ensure its competent to safely perform.
Specific Hazards such as:
-Aerosol exposure (during sample processing)
-Eye splash
-Infectious culture spill
-Leaking sample receptors
2.Routine Laboratory Procedures including Non-progparative Diagnostic Work and PCR Analysis
Non cultural based diagnostic laboratory work and PCR analysis on clinical specimens
from patients who are suspected or confirmed to Covid-19 should conduct adopting
practices and procedures. All infectious materials should be performed in appropriate
maintained and validate primary containment devices by personnel with demonstrated
capability. Core Requirements and GMPP should be followed.
Routine Laboratory Procedures:
-Diagnostic testing of serum, blood, respiratory specimens such as
nasopharyngeal and oropharyngeal swabs.
-Routine examination of mycotic and bacterial cultures developed from
respiratory tract specimens.
3.Point of care (POC) or Near POC Assay
This was recently release for Covid-19 testing samples. Each POC molecular platform
uses different procedures to process samples because there are still chances of spill
especially when the staff are not well trained and pressure to deliver rapid results.
-Performed on a diaper or large paper towel in a well-ventilated area free of
clutter, where there are no documents, computers or personal stuff.
-Appropriate PPE
-Risk assessment should inform the use of respiratory protection as a
supplementary precaution.
-Staff well trained in GMPP
- Increased pressure for test turnaround time
- Validated infectious waste process including excess specimens
If similar platform of tuberculosis programme is to be temporarily shared for Covid-19
testing the equipment should be already installed in a suitable area with ventilation it is
important before starting the test for Covid-19.
4.Use of Appropriate Disinfectant
Appropriate disinfectant with proven activity should be use. Attention should not be only
focus to the selection of disinfectant but also in:
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 -contact time
-correct dilution
-shelf life and within expiry date after working solution is prepared.
Covid-19 is known persistent on inmate surfaces such as metal, plastic and glass for 7-9
days.
5.Viral Isolation
Viral isolation in clinical specimens from patient who are suspected or confirmed to be
infected in Covid-19 must be performed only in laboratories that are capable in:
-Controlled ventilation system maintain inward directional air flow into laboratory
room.
-Exhausted air from laboratory is not reticulated to other area within the building.
Air must be HEPA (high efficiency particular air) filtered.
- Hand-wash sink is available in the laboratory.
-All manipulations of potentially infectious materials must be performed in
appropriately maintained and validated BSC.
-Laboratory workers should wear protective equipment:
disposable gloves
wraparound gowns
scrub suits
coveralls with sleeves that fully cover the forearm
head coverings
shoe covers
eye protection (goggles or face shield).
-Risk assessment should inform the use of respiratory protection
-Centrifugation of specimens should be performed using sealed centrifuge rotors
or sample cups.
6.Additional Risk Associated with Virus Isolation Studies
Specific risk assessment should be conducted and specific risk reduction should be
adopted before any of the following procedures is to be conducted:
-Coinfection of cell cultures with different coronaviruses, or any procedures that
may result in a coinfection and in turn recombination.
-Culture of viruses in the presence of antiviral drugs
-Deliberate genetic modification of viruses.
Because experimental procedures may carry additional risk viruses that are possible to
increased pathogenicity.
7.Work with Animals Infected with the Virus Responsible for Covid-19.
Following activities require an animal facility and work practices:
-Inoculation of animals for potential recovery of the virus responsible for COVID-
19
-Any protocol involving animal inoculation for confirmation and characterization
of the COVID19 virus.
8. Referral of Specimens to Laboratories with Appropriate Risk Control Measures in Place
-Laboratories that are not able to meet the biosafety recommendations should consider
transferring specimens to national, regional, or international referral laboratories with
COVID-19-detection capacity that can meet the biosafety requirements.

MORPHOLOGICAL FEATURES by Bernancio, Kyla Mae

The Coronaviruses (CoVs) called the attention of the world in causing outbreaks worldwide in acute
respiratory syndrome (SARS-CoV). This new virus is highly transmissible and goes quickly spread around

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the people in China and other countries. As the outcome, by the World Health Organisation (WHO) raised
the status of an outbreak of COVID-19 from an emergency of international significance to a pandemic on
11 March 2020. COVID-19 was first reported in Wuhan, Hubei Province, Republic of China, on 1 December
2019, but the original findings were released only on 31 December of the same year. On 30 January 2020
the WHO proclaimed COVID-19 to be the sixth public health emergency of international significance and
on 11 March 2020 the declaration of SARS-CoV-2 to be a pandemic. At the time of the WHO declaration,
more than 118,000 people have already been affected in 114 countries.

SARS-CoV-2 is an enveloped, positive-sense RNA virus that belongs to the Betacoronavirus genus.
SARS-CoV-2 virions (infectious particles) are about 50 to 200 nm in diameter. Like other coronaviruses,
the SARS-CoV-2 lipid envelope comprises spike protein (S), membrane protein (M), and envelope protein
(M) (E). S protein mediates viral binding to host cell 68 membranes by interacting with the angiotensin-
converting enzyme (ACE2) receptor. The nucleocapsid protein (N) forms the virion core, which encases
the 70 viral RNA genomes. There are currently no specific antiviral medicines or vaccines for the treatment
and prevention of COVID-19.

Nuclear detachment with elongated nucleoplasty and ring-shaped nucleus with platelet surface
attachment was observed. C-shaped, the fetus-like nucleus was noted with aberrant nuclear projections,
which we called COVID nucleus. As shown in Figure 1.

Figure 1: COVID nucleus Figure 2: Lymphocytes

Most lymphocytes were seen as large granular lymphocytes (LGLs) with circular to the indented
nucleus, condensed chromatin, prominent nucleoli in a couple, together with abundant light blue cytoplasm
with distinctly variable azurophilic granules. As shown on Figure 2.
Cytoplasmic pod forming and apoptosis have also been observed in a few lymphocytes. They can
represent natural killer cells or cytotoxic T lymphocytes. Enabled monocytes showed pronounced
nanisocytosis with prominent cytoplasmic vacuolation and few granules. Nuclei were big, with fine
chromatin and nuclear blebbing in a few. Nuclear overlapping of vacuoles has been found in some cells.
As shown in Figure 3.

Figure 3: Cytoplasmic pod forming

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 These results specifically suggested that original neutrophilia, lymphocytopenia, and monocytopenia
were eventually followed by monocytosis in COVID-19. During the hospital stay, the patient was provided
with oral hydroxychloroquine, azithromycin, and antipyretics along with intravenous fluids, bronchodilators,
and compassionate treatment. The patient discharged after two negative tests on 8 April 2020.
Inflammatory reaction and viral effects on leukocytes can be responsible for these changes, which can be
easily detected on PBF and can be easily and serially tracked. Monocytosis can be linked with a positive
result, as seen in our patient.

Understanding the hematological manifestations of SARS-CoV-2 is also at an emerging level. To draw

a definitive conclusion on the specificity and durability of these viral cytopathic effects in the peripheral
smear, more COVID-19-positive patients need to be tested in larger trials. We aim to explain the peculiar
morphological findings of the infected leukocytes, which will make doctors suspect a diagnosis in the
absence of a negative RT-PCR or antibody result. If confirmed in larger trials, these morphological
characteristics along with blood counts will be helpful in the screening, detection, and treatment of these
patients at all stages of health care.

ANTIMICROBIAL RESISTANCE by Rivera, Romer

One of the fundamental approaches to battle the virus through the use of antibiotics by guaranteeing
accurate antibiotic use with the proper amount of dose in a way that ensures the best result and administers
the reaction and the antimicrobial resistance. But according to World Health Organization, they stated that
antibiotics didn’t cure or eliminate the virus, it only works against the bacterial infections. In any case, since
the start of the COVID-19 pandemic, there has been developing worry for a possible ascent in AMR
optional to expanded anti-infection remedy for COVID-19 patients. The points of this review paper are to
portray how this viral pandemic has caused expanded antibiotics use furthermore the danger of expanding
AMR, especially in low and center-pay countries, AMR is a grave and squeezing general medical condition.
An examination directed in January 2020 of every grown-up irresistible illness unit in China, discovered
that 71% of the patients hospitalized for COVID-19 had gotten anti-toxins not withstanding an affirmed
bacterial co-disease pace of just 1%. Another examination in two medical clinics in China announced that
95% of COVID-19 patients had been put on antibiotics regimens even though an auxiliary bacterial disease
was just found in 15% of the patients. It shows up, in this manner, that the commonness of bacterial
contamination may change contingent upon the country being referred to furthermore on the time after the
beginning of indications at which the examples are acquired. This proposes a distinction in the co-
contaminating microorganisms of COVID-19 patients from those ordinarily seen in co-tainted patients with
flu (Example, Streptococcus pneumoniae, S.aureus, and Streptococcus pyogenes). Be that as it may,
despite this developing pandemic, exercises can be drawn from past extreme episodes of Covid-19 to
advise antimicrobial administration regarding auxiliary co-diseases in COVID-19 patients, just as
contamination anticipation control estimates dependent on AMR. On account of COVID-19, it has been
exhibited that 80% of contamination are identified with 20% of subjects. Regardless, this is a significant
perception to remember to decrease the danger of AMR diseases and emergency clinic transmission,
especially in LMIC where medical clinic contamination anticipation and control measures are frequently
imperfect.

If the utilization of antibiotics to treat nosocomial bacterial co-contamination is advocated by the danger
of requiring obtrusive mechanical ventilation, the lack of ventilators in LMIC limits this danger and ought to
along these lines incredibly lessen pointless antimicrobial use. Nonetheless, even as transient fringe
venous catheters can be related to higher paces of circulatory system contamination in LMIC than in HIC,
there is a danger that the expanding number of hospitalized patients with COVID-19 may prompt expanded
dependence on anti-infection agents to battle nosocomial catheter-related diseases. The usage of
contamination counteraction and control measures could help intercede this danger, just as antimicrobial

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utilization. It is uncovering to direct investigations on bacterial co-diseases in COVID-19 patients in LMIC,
since past examinations have uncovered that, for similar bacterial microorganisms, contrasts exist among
HIC and LMIC concerning populaces in danger, clinical indications, recurrence of microbe appropriation,
and anti-microbial helplessness. The danger of COVID-19 may, truth be told, offer open doors in LMIC to
execute antimicrobial stewardship programs following the WHO rules: instruction and preparing of an
antimicrobial stewardship group, improvement of clinical rules, reconnaissance of obstruction, and
antibiotics use.

There are various potential procedures to diminish extreme antimicrobial use and the resultant anti-
infection opposition. The direct technique advanced by most services of well being could restrict anti-
infection use, if you have a fever or manifestations like influenza, stay at home, drink fluids, and take
paracetamol. Besides the undeniable general medical advantage of this methodology, such conduct could
lessen anti-toxin utilization, since patients looking for care for intense respiratory diseases may get
superfluous anti-infection agents in 41% of cases. Quick popular testing could likewise additionally
decrease the outlandish solution of antimicrobial in LMIC, as it has been shown that the individuals who
test positive for flu are half more averse to get anti-toxins. As bacterial co-disease in COVID-19 patients
might be under 15%, it is reasonable to hold antimicrobial for patients with suspected or serious COVID-
19 signs. Testing for COVID-19 in respiratory patients may accordingly be a viable method to restrict anti-
infection use during the pandemic.

The WHO has implemented rules for the clinical regulation of COVID-19 that don't support the solution
of antimicrobial for patients with suspected or affirmed gentle COVID-19 with a low doubt of a bacterial
disease. At last, even though there isn't yet an ideal technique for fighting worldwide COVID-19, suppliers
in LMIC should attempt to set up or potentially fortify antimicrobial stewardship just as contamination
counteraction and control projects to diminish the rise and dispersal of AMR. The sort of antimicrobial
stewardship program that will work will be very setting explicit, yet could incorporate instruction about
AMR, the advancement of rules, contamination avoidance and control rules, commitments from an
irresistible sickness expert at the emergency clinic level, intravenous to oral switch treatment, rules and
guidelines for anti-infection quality control, redesigned microbiology research center limit, the improvement
of a public activity plan, and the usage of a disease counteraction control program. The consequences of
these examinations could assist with characterizing the best techniques to use in settings with restricted
research facility limits to pick reasonable empiric antimicrobial treatment.

TAXONOMIC CLASSIFICATION by Rañola, Andrey Mary

The overall the Coronaviradae family is known for a type of virus that's the main surface area of the
virus has ring projections. Seen under the electron microscope, coronaviradae viruses are notable to have
a solar crown or corona. From the latin meaning of crown is where the Corona of Coronaviradae came
from. They are large, enveloped, icosahedral symmetric particles that are about 80-220 nm in diameter.
They also have a positive-sense RNA genome that have a size about 26-32 kb which is the largest known
RNA virus.

Coronaviradae family is one of the largest groups of viruses that are categorized to the order
Nidovirales, and to the suborder Coridovirineae. This family is classified between two subfamilies that are
named Torovirinae and Coronavirinae. Coronavirinae is subdivided into alpha(α) coronavirus, beta(β)
coronavirus, delta(δ) coronavirus, and gamma(γ) coronavirus. The members of the main subfamily,
coronavirinae are common among mammals and are often showing symptoms of only mild respiratory or
enteric infections. According to Woo (2012), For coronavirus their ideal hosts are mostly bats for alpha(α)
and beta(β) coronavirus. As for delta(δ) and gamma(γ) coronavirus' ideal hosts are birds. Beta coronavirus
have five (5) subgenera which are Embecovirus (previously known as lineage A), Sarbecovirus (previously

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known as lineage B), Merbecovirus (previously known as lineage C), Nobecovirus (previously known as
lineage D), and Hibecovirus. As shown in Figure 4.

Figure 4: Taxonomy of SARS-CoV-2

Coronaviridae Study Group (CSG) developed the said taxonomy and family classification with
International Committee on Taxonomy of Viruses (ICTV). They assess the place of the new viruses by
using their relation to other known viruses in the established taxa and that includes the placements relating
to the species related to SARS-CoV. Assigning and naming of individual living organisms requires
specialized knowledge and tools to assess the individual differences that are required. With the use of
computational framework of comparative genomics, CSG along with ICTV are the ones in charge for the
categorization and naming of the order.

The first known coronavirus case was from poultry with respiratory disease, infectious bronchitis was
dated back in the 1930s and still a worldwide problem in the poultry production industry. According to
Helmy (2020), The first isolated case of humans which were infected with coronavirus was dated back
1960s which was named B814, most of them where hospitalized who are having a common cold
symptoms. Last 2019 there had been a new emerging virus closely related to SARS-CoV from bats and
MERS-CoV, from the Sarbecovirus also known as lineage B of Beta coronavirus, which in now known to
be SARS-CoV-2. It was officialy named by the International Committee on Taxonomy of Viruses, severe
acute respiratory syndrome coronavirus 2 (SARS-CoV-2), based on the phylogenetic analysis. According
to Liu (2020), SARS-CoV-2 is a spill over from an animal coronavirus then it adapted to a human-to-human
transmission. It is easily transmissible and continue to evolve in different countries and places. According
to the World Health Organization, since last December 2019 COVID-19 pandemic had spread globally and
resulted with 2,527,891 deaths and 113,820,168 confirmed cases as of 1 March 2021.

HISTORICAL PERSPECTIVE by Puerte, Danica Shane

Thousands of people died each day facing the new virus, because knowing this kind of virus is life-
threatening to people and need to necessarily follow the rules and regulation for the people not to get
infected. The emergence of viruses and it spread faster unexpectedly is considerably known as the
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deadliest part of history. SARS-CoV-2 came in 2003, SFTS came in 2010 and the novel coronavirus known
as Covid-19 came in 2019, all of the said viruses have the same origin place which is in China. In March,
the covid-19 considered as the pandemic of the World Health Organization because of the overall fatality
rate of a number of cases internationally. Novel coronavirus or the designated name now is Covid-19 is
rapidly spreading all over the world. World Health Organization state that Covid-19 is the worst pandemic
in human history.

Half the percentage total of patients inside the country of China had a history in China Seafood Market
wherein the people sell illegal meat like snakes, birds, bats, and others. In December 2019, reportedly
people with pneumonia in Wuhan, China, the percentage of infections leads more than a million and
declared the virus as a novel coronavirus because this is related to the sequence of SARS which is the
causative agent of Covid-19. In January 2020, the world health organization takes lead to conquer the new
virus, in order to settle first the outbreak the organization investigates and visit China to have in-depth
knowledge and research about the virus. China takes the hotspot of increasing rate number of cases in
provinces and later on, the government manages to announce the lockdown. Scientists and other
professionals suggested animals may transmit the virus to humans, but during the covid-19 outbreak, the
transmission mode has this evidence the earlier transmission came from the animals to human yet some
believed that the transmission is human to human.

On the other hand, the organization declared Covid-19 a public health emergency internationally. And
because of that, the outbreak made a huge impact wherein some of the countries cancelled the flights,
limiting the transaction across the world, corresponding the guidelines and protocols, protecting the health
workers, and in April 2020, the organization regularly updated publications on journals and articles
regarding the information relevant to Covid-19 at the time of a global public health crisis. Unfortunately,
the number of cases is ringing and increasingly faster each month, slow rate recovery, and also the death
cases. The accuracy of getting a cure is complex and worst; all the professionals gathered around to
identify the causative agent, characterization of these outbreak, and develop a specific diagnostic. World
Health Organization takes place in leading the outbreak to make a possible way to conquer the crisis as
early in January, the Incident Management Support Team set for dealing the outbreak, and in March, the
launching solidarity triad came for working on the treatment because of the showing data source of an
increasing number of cases globally. The fatality rate of cases is alarming to the point that some of the
countries make a decision to lockdown and most importantly limiting the entering of people outside the
country because the scientists and other professionals said those people entering from the outside are the
most dangerous and threat because it may transmit quickly whoever came in. Generally, after months of
studying of collecting data gathering about the virus, some professional thought of this virus is human to
human airborne transmission because of the selected countries showing the finding measures; Wuhan,
China, Italy, and New York City. Additionally, the start of a pandemic is the start of getting isolated to their
houses, before leaving the house needs to wear a mask and face shield and most importantly, sanitation
and social distancing.

Recently, the organization tries everything to make a vaccine just to end the covid-19 pandemic. Until
now, we still conquering the virus, the news is showing the details of a number of cases even though the
progress is slow yet still believing of hope that someday, the accuracy of getting intervention might end the
pandemic outbreak.

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REFERENCES

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