Final Assignment

MCB 210: Departmental Seminar in Health, Biotechnology and Development

1. Provide a brief note on the research background of the invited speaker?

Our invited speaker DR Mohammad Rubayet Hasan who is well-known as a clinical molecular
biologist at the department of pathology of Sidra medication and he joined Sidra in 2014. Dr. Hasan
could be a specialist of the American Board of Medical Microbiology (DABMM) and a Fellow of the
Canadian College of Microbiology (FCCM). He obtained his Ph.D. in Cell and biology from Kyushu
Institute of Technology, Japan in 2006 and worked as a postdoctoral scientist in many North American
educational institutes, as well as the University of the American state, Berkeley, USA, and thus the
University of the Canadian province, Canada. He is conjointly Associate in Nursing academic of
Clinical Pathology and Laboratory medication in Kurt Weill Cornell Medical Faculty in Qatar
(WCMC-Q).
He wrote a bunch of research papers. ⅰ) One of his paper on the SARS-CoV-2 vaccine that is the
mRNA-1273(Moderna) vaccine shows the effectiveness of up to 94.1% at preventing symptomatic
COVID-19 as a result of infection with variants like B.1.1.7(alpha) and B.1.351(beta) in Qatar. ⅱ) He
wrote another paper on coronavirus that supported the mutation among the N cistron of SARS-CoV-2
that affected the detection of the virus by Reverse Transcription-Quantitative PCR. ⅲ) Besides writing
an analysis paper on the coronavirus issue he conjointly wrote on topics like immune management of B
cells by invariant natural killer T cells, ⅳ) cancer metabolism and drug resistance, ⅴ) infective agent
detection by next-generation sequencing and plenty of additional.

2) According to you, what is the objective of the seminar course?

MCB210: Departmental Seminar in Health, Biotechnology, and Development. This is a 1 credit course
based on acquired knowledge and maintains an interest in the study of microbiology and other aspects.
The main objective of the seminar course is to develop and perpetuate critical thinking in the biological
sciences basically in the research field. Also in this course, there is always a very intellectual and
highly professional researcher to share their experiences, research work and also inspire the students
about that seminar topics. From this course, we can also get a good idea of papers and practical
laboratory skills. As a microbiology student, I think it is a course that can cover my ideas not only in
microbiology but also in other areas like molecular design, vaccines, and working in pandemics.
Another thing is, in the last phase of the seminar there was a time where students were invited to talk
with the speaker for an informal discussion, and in that discussion, they could ask additional questions
about the seminar. In the Summer 2021 seminar, the objective is to talk about the most burning issue in
the world which we are all facing right now SARS-CoV-2. In this seminar, I learned about the COVID-
19 current situation in the whole world and the vaccination process.

3) In your own words, explain what you learned from attending this seminar. Mention the things
that you found interesting.

The attending speaker from Sidra, Qatar first told us the short note about the coronavirus specifically
about SARS-CoV-2 and therefore the pandemic cases. He started talking about the initiation of
COVID-19, how it came, where it came from, how it spread globally, became a pandemic. In his
presentation, he mentioned, on March 11, 2020, WHO declared COVID-19 as a severe acute
respiratory syndrome. He conjointly added the first vaccine approved in December 2020 that is
approved by FDA. Globally 20 August 2021, there are 209,876,613 confirmed cases of COVID-19, as
well as 4,400,284 deaths, reportable to UN agency WHO. As of 19 August 2021, a complete of
4,562,256,778 vaccine doses are administered. Later, he started talking about the traditional symptoms
of COVID-19 symptoms. As he's from Qatar, so then he discussed the case of Qatar. How Qatar first
detected their first COVID-19 case and besides he worked during a hospital lab, so how his hospital
detected the primary case so the entire procedure. After detecting the primary case of COVID-19, they
use the RNA extraction process which was used for that point for testing. But our invited speaker DR.
Md Rubayet Hasan and his team then developed another simplified and rapid method that uses a pre-
treatment of the specimen (swab sample) to interchange the RNA extraction process. The new method
they made that's faster and budget-friendly than the first method. the explanation for creating this new
method is because within the first stage of COVID-19 there is a scarcity of viral RNA extraction cause
the world’s largest country couldn't supply enough of them. there's another thing he told about egene
primary target for covid testing and TAT. He also talked about B.1.1.7, the alpha variant, and B.1.351,
the beta variant. After the FDA approved the mRNA-1273 (Moderna) they also learned about the
effectiveness against the alpha and beta variant and severe COVID-19 cases in Qatar and therefore the
efficacy around 94.1% in preventing symptomatic COVID-19 cases. Another interesting thing he added
is when the majority of the cases were negative it was very costly to test everybody individually, so that
they came up with a plan which is termed pool idea. During this pool idea, they combine like 100 test
samples together and try to identify results together. As a result, the test contains less cost. The
foremost eye-catching concept of this seminar is that the Sidra medicine laboratory team identified a
replacement novel mutation within the SARS-CoV-2 genome that will be tormented by an FDA
approved test. This mutation relies on to avoid potential false-negative results. Ultimately he talked
about the mRNA vaccine and its efficiency and so on.

4. What are the common detection tools available for COVID-19 testing? In Bangladesh which
technique is being widely followed? Explain this principle using SARS-COV2 as an example.

A robust and responsive testing infrastructure is important to stop the spread of SARS-CoV-2, the virus
that causes COVID-19. To treat the patients of COVID-19 a range of molecular and immunoassay-
based techniques, also nanomaterial-based tools are needed for the diagnosis. So, now I am going to
describe the common detection tools which are available for COVID-19 testing.

1. Nucleic acid-based/RT-PCR: Nucleic acid-based testing is also called PCR testing. This is the most
common and widely used test for COVID-19 detection. Real-time RT–PCR could be a nuclear-derived
technique for detecting the presence of specific genetic material in any infectious agent, together with a
virus. The reverse transcription-polymerase chain reaction(RT-PCR)can be run in a singleplex format
which contains 3 individual assays for each of the three SARA-CoV-2 targets and amplification set up.
For this test, some tools are used like three primers and probe sets to detect human RNase P (RP).

2. Nucleic acid amplification test (NAAT): It is used for a viral diagnostic test for SARA-CoV-2 and
specifically detects RNA sequences of the genetic material of the virus. NAAT procedure works are
amplifying or making many copies of the virus’s genetic materials. Amplifying those nucleic acids
allows NAATs to observe very little amounts of SARS-CoV-2 RNA during a specimen, creating these
tests sensitive for designation COVID-19. In alternative words, NAATs will dependably observe little
amounts of SARS-CoV-2 and are unlikely to return false-negative results of SARS-CoV-2.

3. Protein-based detection: Viral macromolecules which are protein antigens and antibodies that are
created in response to a SARS-CoV-2 infection that may be used for diagnosis COVID-19. For protein-
based detection, many systems are used like ELISA, chromogenic-based or fluorescence-based
detection using dye, lateral flow-based detection.

ⅰ) Antigen-based testing: Antigen can easily detect if anyone is infected with SARS-CoV-2. These
detecting tools mostly detect proteins such as spike proteins found on the surface of the virus.

ⅱ) Antibody-based testing: From all of the major classes of the antibody IgG has been the first line of
defense of the immune system when infected by an infectious agent and creates immunologic memory
to any fight the infection is generally targeted in the detection of COVID-19. Conjointly reportable is
that IgM appears at intervals in the blood of the patient once infected by respiratory disorder once 3 to
6 days and IgM are going to be detected 8 days once the infection occurred.

4. Rapid diagnostic test based on antigen: It detects the presence of infectious agent proteins which is
known as antigen demonstrated by the COVID-19 virus in an exceeding sample from the tract of an
individual. Once the target substance is present in an exceedingly adequate concentration in the sample
then it'll bind to specific antibodies that are fixed to a paper strip and embedded in a plastic casing and
generate a visually detectable signal. When the virus is actively replicating and detecting infection,
wherever substances detected are expressed. Materials for the test are extraction buffer, extraction
tubes, tips, test cassettes.

5. Rapid diagnostic test based on antibody: With this test, COVID-19 detects the presence of the
antibodies in the blood of the infected people. This can be used once the body's immune reaction seems
to eradicate the virus within the body. An antibody assembles after the infection with a virus. The
strength of antibody response depends on many factors, as well as age, nutritionary standing. They can
not quickly diagnose acute infection to tell actions required for treatment. Some clinical have used
these tests for antibody response to form a presumptive diagnosing to resent COVID-19 illness in cases
wherever molecular testing was negative but wherever there was a robust medical specialty link to
COVID-19 infection and paired blood samples showing rising protein levels.

In Bangladesh basically, the RT-PCR technique is used for COVID-19 detection. In March 2020 the
Government of Bangladesh started testing and detecting COVID-19 cases, using only 1 Real-Time
Reverse transcription-polymerase Chain Reaction (RT-PCR) laboratory, which detects unique
sequences of virus Ribonucleic Acid (RNA) by Nucleic Acid Application Test (NAAT), at the Institute
of Epidemiology Disease Control and Research (IEDCR). After that, only 7 months later, in December
2020 Bangladesh created a total of 118 labs for COVID-19 testing, and from 103 are rRT-PCR labs.
The Directorate General of Health Services (DGHS) of Bangladesh requested WHO and then they
provided 240000 Antigen-based Rapid Diagnostic Tests (Ag. RDT) for 1159125 US dollars to ensure a
better-distributed testing coverage throughout the country. So in short, from the starting of the COVID-
19 case of Bangladesh RT-PCR is widely used though later they used rapid antigen tests also.
5. Which are the four vaccine types that are being administered to vaccinate the population in
Bangladesh? For each, mention the following: production background
(country/lab/organization), storage conditions, type of vaccine, mode of action.

To end a pandemic, we need an effective vaccine against the virus. For the SARS-CoV-2 situation, till
now only vaccination can not change the whole situation. To be approved, the efficacy rate of the
vaccine is 50% and above. A vaccine’s effectuality is measured during a controlled clinical test and
relies on what number of folks that got immunized developed the ‘outcome of interest’ (usually
disease) compared with what number of folks that got the placebo (a dummy vaccine) developed a
similar outcome. So there are still chances to get infected and transmitted by the virus. So we need to
be more careful like continuing to wear masks, cleaning our hands, physically distancing ourselves, and
avoiding the crowd. Bangladesh administration began the journey of COVID-19 vaccination on 27
January 2021 and the mass vaccination started on 7 February 2021. There are four vaccines that are
being administered to the mass population in Bangladesh.

Name of vaccine Country/Organi Storage Type of Mode of action

zation conditions vaccine
Pfizer–BioNTech Country: ⅰ. -70°C±10°C for mRNA mRNA vaccine contains
Germany & up to 10 days nucleic acids which are the
United States. unopened. building blocks of our cells.
Organization: ⅱ. With POU The mRNA carries directions
BioNTech receives thermal within a lipid coating or fat
shippers, bubble that instruct the cells to
commercially supply harmless “spikes”
available vaccines proteins which is one of the
have to be stored structural proteins of SARS-
in ultra-low- CoV-2. The vaccine immune
temperature process starts, creating
freezers for up to antibodies that will attach to
6 months. the virus, and these virus
ⅲ. In the hospital, shields from obtaining
the vaccine can be COVID-19 and build T & B
stored in lymphocytes that will
refrigeration 2- remember how to fight with
8°C for 5 days. the virus. Also after the work
done by the mRNA vaccine,
the mRNA exits the body.

Moderna Country: United ⅰ. For multiple- mRNA mRNA vaccine contains

States dose vials are nucleic acids which are the
Lab: stored between(- building blocks of our cells.
Organization: 50º to -15ºC) and The mRNA carries directions
Moderna their shelf life is 6 within a lipid coating or fat
months. bubble that instruct the cells to
ⅱ. It is inhibited to supply harmless “spikes”
stored below proteins which is one of the
-50ºC structural proteins of SARS-
 ⅲ. Stored CoV-2. The vaccine immune
between -25°C process starts, creating
and -15degree C antibodies that will attach to
up to expiration the virus, and these virus
date. shields from obtaining
ⅳ. It can be stored COVID-19 and build T & B
refrigerated lymphocytes that will
between 2° to 8°C remember how to fight with
for up to 30 days the virus. Also after the work
to first use. done by the mRNA vaccine,
ⅴ. Unpunctured the mRNA exits the body.
vials may be
stored between 8°
to 25°C for up to
24 hours but they
can not be
refrozen.
ⅵ. If the first dose
has been
withdrawn, the
vaccine should be
held between 2°
to 25°C.

Sinopharm Country: China ⅰ. Stored between Inactivated This vaccine makes antibodies
Lab: +2 to +8 °C in a against the SARA-CoV-2
Organization: refrigerator, not in coronavirus which attach to the
Beijing Institute freezers. spike proteins. A chemical
of Biological ⅱ. Its shelf life is called beta-propiolactone
Products (BBIBP 3 years. disabled the coronavirus by
or BIBP) bonding with their genes and
then this inactivated virus
could not replicated but their
protein remain intact. So when
the coronavirus is dead , it can
be injected to the patients
without causing COVID-19. It
then activated in the body by
some helper cell called T and
B cells and can help recruit
other immune cells to respond
to the vaccine. After get
vaccinated, B cells produce
antibodies that target spike
protein which can prevent the
virus from entering.
Oxford– Country: UK ⅰ. It has to be Adenovirus This virus is made based on
AstraZeneca Organization: stored in a vector the virus’s genetic instruction
AstraZeneca, refrigerator for building the spike protein
University of between 2 to 8°C. while it uses double-stranded
Oxford but in ⅱ. The maximum DNA to store the information.
Bangladesh the shelf life is 6 They put the spike protein
vaccine come months. gene of coronavirus into the
from India. So ⅲ. Once removed adenovirus. When the vaccine
the organization from the fridge, it is injected into a person’s body
is Serum may be stored the adenovirus encounters the
Institute. between 2 to cells and latch onto the protein
25°C for up 6 surface. The cells engulf the
hours. bubble and enter the nucleus to
store the DNA. Because the
adenovirus is genetically
engineered so it can’t make
copies but the spike protein of
coronavirus is read by the cell
and copied mRNA. Then these
mRNA builds spike proteins
and spot the intruder. When a
vaccinated cell dies the debris
of a dead cell, spike protein is
taken by an immune cell called
an antigen-presenting cell
which is called helper T cells
to detect and fight. After that B
and T cells make antibodies.
The coronavirus will latch the
destruction and prevent
infection by block the spikes
from attaching to different
cells.

6) The following graph shows the trend in number of confirmed COVID-19 cases in Bangladesh
from end of March 2021 to 23 August 2021. Study the graph and answer the following
questions:
a) Explain the trend observed in the cases in Bangladesh in the period shown in the graph.
b) Identify the number of major waves seen in Bangladesh in this given period. Discuss
your answer with relevant data.

a)
The given graph is the confirmed graph of COVID-19 cases in Bangladesh at a certain time. In this
graph, we can see that from the period of the end of March 2021 to the beginning of April, the average
number of daily new cases was a little more than 5000 which gradually decreased till the mid of May.
After that from the first quarter of June, the case gradually increased and this rate was increasing
continuously till July 7th to 12th which crossed more than 10000 and assumed the number could be
11000-12000. After a little time went by, downfall at the mid and late of July but from the starting of
the new month August, the daily new cases increased suddenly which crossed 15000 at some point and
then a drastic downfall is observed to 5000 per day by the end of August 2021.

b)
There are three major waves observed from the data of March 2021 to 23 August 2021. Here these
waves denote the highest number of cases for that specific time for COVID-19 cases. The first wave hit
exactly after the end of March and exceeded the number of 10,000 daily cases. After a progressive
downfall, a gradual rise of the new cases was observed which made the second wave at the first quarter
of July. During the second wave, the average number of cases daily was more than 10,000. At the end
of July, a steep rise was observed to 15000, which can be considered the third as well as the major
wave during this period and by 23 August, a dramatic decrease was followed. From these three major
waves, the summarization would be each wave has a different number of cases and that crossed before
a major wave.

7) The table provides cumulative data on COVID-19 testing, detection, death, and recovery
cases in Bangladesh from March to August 2021(source WHO).

Using the table answer the following questions:

a) Calculate the recovery rate in each of the four phases.
b) Calculate the death rate for each of the phases.
c) Calculate the positivity rate for each of the phases.
d) Combining your answers from question 6 and question 7, explain which has been
the worst phase in the pandemic to date.

a)
Recovery rate for every phase is= (Cumulative recovery÷Cumulative positive cases)×100%

➔ For phase A (29/03/21): Here, Cumulative positive cases= 595714 &

Cumulative recovery= 535941
So, the recovery rate for phase A is = (535941÷595714)×100%
= 89.97%
➔ For phase B (26/04/21): Here, Cumulative positive cases= 745322 &
Cumulative recovery= 657452
So, the recovery rate for phase B is = (657452÷745322)×100%
= 88.21%
➔ For phase C (28/06/21): Here, Cumulative positive cases= 888,406 &
Cumulative recovery= 804103
So, the recovery rate for phase C is = (804103÷888406)×100%
= 90.51%
➔ For phase D (22/08/21): Here, Cumulative positive cases= 1,461,998 &
 Cumulative recovery= 1363874
So, the recovery rate for phase D is= (1363874÷1461998)×100%
= 93.29%

b)
Death rate for each phases is= (Cumulative deaths÷Cumulative positive cases)×100%

➔ For phase A: Here, Cumulative positive cases= 595714 &

Cumulative deaths= 8,904
So, the death rate for phase A is= (8904÷595714)×100%
=1.49%
➔ For phase B: Here, Cumulative positive cases = 745322 &
Cumulative deaths = 11,053
So, the death rate for phase B is = (11053÷745322)×100%
= 1.48%
➔ For phase C: Here, Cumulative positive cases = 888,406 &
Cumulative deaths = 14,172
So, the death rate for phase C is = (14172÷888406)×100%
= 1.60%
➔ For phase D: Here, Cumulative positive cases= 1,461,998 &
Cumulative deaths= 25,282
So, the death rate for phase D is = (25282÷1461998)×100%
= 1.73%

c)
Positivity rate for each phase is= (Cumulative positive cases÷Tests done)×100%

➔ For phase A: Here, Cumulative positive cases= 595714 &

Tests done= 4,588,830
So, the positivity rate for phase A is= (595714÷4588830)×100%
= 12.98%
➔ For phase B: Here, Cumulative positive cases = 745322 &
Tests done= 5,345,501
So, the positivity rate for phase B is= (745322÷5345501)×100%
= 13.94%
➔ For phase C: Here, Cumulative positive cases = 888,406 &
Tests done= 6,506,781
So, the positivity rate for phase C is=(888406÷6506781)×100%
= 13.65%
➔ For phase D: Here, Cumulative positive cases= 1,461,998 &
Tests done= 8,649,517
So, the positivity rate for phase D is= (1461998÷8649517)×100%
= 16.90%

d)
First, if I summarize question 6 answer for the worst cases of the pandemic for COVID-19 cases then it
should be the major third wave of the graph. The third wave happened at the end of July approximately
27th July to the starting of August and the number of confirmed cases was 15000. From graph 6, 15000
cases were the highest from the end of March 2021 to 23 August 2021.

Again, in question 7 if I summarize the table and all of the rates like positivity rate, deaths rate, and
recovery rate, according to me the worst case would be phase D which is 22nd August 2021. On that
particular day, people came to test most of all of the days and the cumulative positive cases number
was 1,461,998 while the deaths were 25,282. So, the positivity rate was 16.90% and the death rate was
1.73% but if analysis of other phases positivity rate and death rate that was comparatively lower than
phase D.

So, after combining the answers 6 and 7 the worst phase in the pandemic happened in August 2021. In
August 2021 the confirmed cases were high and from all of the major waves, the dramatic increase
happened in August which we can see in phase D in question 7 and the third major wave of the
question 6 graph.
 References:

For question 4:
1. Verma, N., Patel, D., & Pandya, A. (2020). Emerging diagnostic tools for detection of COVID-19
and perspective. Biomedical microdevices, 22(4), 83. https://doi.org/10.1007/s10544-020-00534-z
2. Get tested! WHO supports the Government of Bangladesh in establishing a broad testing lab network
throughout the country. (2021, March 30). World Health Organization.
https://www.who.int/bangladesh/news/detail/30-03-2021-get-tested!-who-supports-the-government-of-
bangladesh-in-establishing-a-broad-testing-lab-network-throughout-the-country
3. Overview of Testing for SARS-CoV-2 (COVID-19). (2021, August 2). CDC.
https://tools.cdc.gov/api/v2/resources/media/407982/html?mediatype%3Dhtml&mediaid
%3D407982&cssclasses%3Dsyndicate%2C!no-syndicate&stripscripts%3Dtrue&stripanchors
%3Dtrue&stripimages%3Dtrue&stripcomments%3Dtrue&stripstyles%3Dtrue&imagefloat
%3Dnone&oe%3Dutf-8&of%3Dxhtml&ns%3Dcdc&nw%3Dtrue&font%3DHelvetica&showattr%3D1

For question 5:
1. Jonathan, Carl, C. Z. (2021, May 7). How the Pfizer-BioNTech Vaccine Works. The New York Times.
https://www.nytimes.com/interactive/2020/health/pfizer-biontech-covid-19-vaccine.html
2.Jonathan, Carl, C. Z. (2021a, May 7). How Moderna’s Vaccine Works. The New York Times.
https://www.nytimes.com/interactive/2020/health/moderna-covid-19-vaccine.html
3.Jonathan, Carl, C. Z. (2021b, May 7). How the Oxford-AstraZeneca Vccine Works. The New York
Times. https://www.nytimes.com/interactive/2020/health/oxford-astrazeneca-covid-19-vaccine.html
4. COVID-19 data. (n.d.). VIEW-Hub by IVAC. https://view-hub.org/covid-19/characteristics/