This document discusses serological approaches for detecting COVID-19 through immune-based detection of antibodies. It provides an overview of the SARS-CoV-2 virus, current diagnostic methods including RT-PCR and immunoassays, considerations around specificity and sensitivity of different viral targets for immunoassays, applications of immunoassays for surveillance and developing treatments, and the need for point-of-care tests. Moving forward, it emphasizes that collating immunoassay data and developing rapid decentralized tests can help address testing shortages, while ensuring rigorous evaluation of new tests.
SARS Corona-virus 2: Genome Sequencing And Its ApplicationSarbajitRay2
This presentation encompasses the details of genomic sequencing of SARS CoV-2 and the applications of genomic sequencing.
Prepared By:
Adyasha Nayak
Sarbajit Ray
Sugata Lahiri
Badri Prasad Sarangi
SARS Corona-virus 2: Genome Sequencing And Its ApplicationSarbajitRay2
This presentation encompasses the details of genomic sequencing of SARS CoV-2 and the applications of genomic sequencing.
Prepared By:
Adyasha Nayak
Sarbajit Ray
Sugata Lahiri
Badri Prasad Sarangi
This video lecture is in continuation to the previous lecture: "Introduction to Coronaviruses (SARS, MERS, COVID-19): Hosts, Symptoms & History" uploaded on 16/04/2020. This lecture gives a detailed description of the difference between SARS-CoV-2 and COVID-19, relationship between the two, mode of infection used by the virus, different testing methods employed and description of the genome of this virus and related databases.
1. Genome of corona viruses
2. Comparative analysis of emergence and spreading
3. Entry Mechanism
4. COVID-19 Case Study
5. Face mask Case Study
6. Pharmacologic Treatments for Coronavirus Disease
7. BCG vaccine
Unusual Features of the SARS-CoV-2 Genome Suggesting Sophisticated Laboratory Modification Rather Than Natural Evolution and Delineation of Its Probable Synthetic Route
https://zenodo.org/record/4028830#.X2EiXWhKiUn
ABO Blood Groups and SARS-CoV-2 Infection by Fumiichiro Yamamoto, Ph.D.FumiichiroYamamoto
Scientific knowledge is depicted on the association between A and B glycan antigens of the ABO blood group system important in blood transfusion and cell/tissue/organ transplantation and infection of the SARS-CoV-2 virus responsible for the ongoing epidemic of coronavirus disease COVID-19.
Creative Biolabs has extensive experience in coronavirus research. Provide comprehensive high-quality coronavirus (SARS-CoV-2, SARS-CoV, MERS-CoV, etc.) related services and products.
This slide provides a brief introduction to SARS-CoV-2. If you need more knowledge, products and services related to SARS-CoV-2, please follow us.
Introduction to SARS-CoV-2-Creative BiolabsCandySwift_NY
An ongoing outbreak of a novel coronavirus (SARS-CoV-2) has raised global concerns. It is identified as the cause of pneumonia with unknown etiology. Since the early outbreak in Wuhan, China, it has subsequently spread to all provinces of China and many other countries. The urgent epidemic situation has spurred the development of antiviral drugs and vaccines. As a leading service provider in the field of biological research and drug discovery, Creative Biolabs provides fast & elaborate therapeutic antibody discovery, drug candidates screening and vaccine development services to help combat this outbreak.
https://sars-cov-2.creative-biolabs.com/novel-coronavirus-sars-cov2.htm
The severity and emergency of SARS-CoV-2 infection spurs an urgent need for antiviral drug and vaccine discovery. Creative Biolabs has spent considerable efforts to provide scientific support and comprehensive services to promote the success of this combat.
Equipped with cutting-edge techniques and vast experience, Creative Biolabs is keeping up with current research hotspots and integrating all resources to guarantee high-quality services (including but not limiting to): Antiviral Drug Discovery, Vaccine Discovery, Evaluation Platforms, In Vitro Diagnostic (IVD) Immunoassays.
https://sars-cov-2.creative-biolabs.com/novel-coronavirus-sars-cov2.htm
An ongoing outbreak of a novel coronavirus (SARS-CoV-2) has raised global concerns. It is identified as the cause of pneumonia with unknown etiology. Since the early outbreak in Wuhan, China, it has subsequently spread to all provinces of China and many other countries. The urgent epidemic situation has spurred the development of antiviral drugs and vaccines. As a leading service provider in the field of biological research and drug discovery, Creative Biolabs provides fast & elaborate therapeutic antibody discovery, drug candidates screening and vaccine development services to help combat this outbreak.
https://sars-cov-2.creative-biolabs.com/novel-coronavirus-sars-cov2.htm
This video lecture is in continuation to the previous lecture: "Introduction to Coronaviruses (SARS, MERS, COVID-19): Hosts, Symptoms & History" uploaded on 16/04/2020. This lecture gives a detailed description of the difference between SARS-CoV-2 and COVID-19, relationship between the two, mode of infection used by the virus, different testing methods employed and description of the genome of this virus and related databases.
1. Genome of corona viruses
2. Comparative analysis of emergence and spreading
3. Entry Mechanism
4. COVID-19 Case Study
5. Face mask Case Study
6. Pharmacologic Treatments for Coronavirus Disease
7. BCG vaccine
Unusual Features of the SARS-CoV-2 Genome Suggesting Sophisticated Laboratory Modification Rather Than Natural Evolution and Delineation of Its Probable Synthetic Route
https://zenodo.org/record/4028830#.X2EiXWhKiUn
ABO Blood Groups and SARS-CoV-2 Infection by Fumiichiro Yamamoto, Ph.D.FumiichiroYamamoto
Scientific knowledge is depicted on the association between A and B glycan antigens of the ABO blood group system important in blood transfusion and cell/tissue/organ transplantation and infection of the SARS-CoV-2 virus responsible for the ongoing epidemic of coronavirus disease COVID-19.
Creative Biolabs has extensive experience in coronavirus research. Provide comprehensive high-quality coronavirus (SARS-CoV-2, SARS-CoV, MERS-CoV, etc.) related services and products.
This slide provides a brief introduction to SARS-CoV-2. If you need more knowledge, products and services related to SARS-CoV-2, please follow us.
Introduction to SARS-CoV-2-Creative BiolabsCandySwift_NY
An ongoing outbreak of a novel coronavirus (SARS-CoV-2) has raised global concerns. It is identified as the cause of pneumonia with unknown etiology. Since the early outbreak in Wuhan, China, it has subsequently spread to all provinces of China and many other countries. The urgent epidemic situation has spurred the development of antiviral drugs and vaccines. As a leading service provider in the field of biological research and drug discovery, Creative Biolabs provides fast & elaborate therapeutic antibody discovery, drug candidates screening and vaccine development services to help combat this outbreak.
https://sars-cov-2.creative-biolabs.com/novel-coronavirus-sars-cov2.htm
The severity and emergency of SARS-CoV-2 infection spurs an urgent need for antiviral drug and vaccine discovery. Creative Biolabs has spent considerable efforts to provide scientific support and comprehensive services to promote the success of this combat.
Equipped with cutting-edge techniques and vast experience, Creative Biolabs is keeping up with current research hotspots and integrating all resources to guarantee high-quality services (including but not limiting to): Antiviral Drug Discovery, Vaccine Discovery, Evaluation Platforms, In Vitro Diagnostic (IVD) Immunoassays.
https://sars-cov-2.creative-biolabs.com/novel-coronavirus-sars-cov2.htm
An ongoing outbreak of a novel coronavirus (SARS-CoV-2) has raised global concerns. It is identified as the cause of pneumonia with unknown etiology. Since the early outbreak in Wuhan, China, it has subsequently spread to all provinces of China and many other countries. The urgent epidemic situation has spurred the development of antiviral drugs and vaccines. As a leading service provider in the field of biological research and drug discovery, Creative Biolabs provides fast & elaborate therapeutic antibody discovery, drug candidates screening and vaccine development services to help combat this outbreak.
https://sars-cov-2.creative-biolabs.com/novel-coronavirus-sars-cov2.htm
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Unveiling the Energy Potential of Marshmallow Deposits.pdf
COVID-19.pptx
1. Serological Approaches for COVID-19: Epidemiologic Perspective on Surveillance
and Control
By Mesele Tilahun Belete
University of Science and Technology,
Korean Research Institute of Bioscience and Biotechnology (KRIBB) Campus
Dec 21, 2022
KRISS
Course Instructor: 최 준혁 (Ph.D.)
2.
3. Contents
1. Introduction to the Virus
2. Diagnosis SARSCoV-2
3. Current immune-based detection approaches against sars-cov-2
4. Specificity and Sensitivity of Immunoassays Against SARS-CoV-2
5. Identification of B-Cell Epitopes Against SARS-CoV-2 on Immunogenic Proteins
6. Applications of immunoassays to control sars-cov-2 transmission
7. Drawbacks of Serological Studies
8. The Way Forward
9. Conclusion
4. 1. Introduction to the Virus
Ongoing pandemic and the most serious new health threats
In March 2020, the WHO declared COVID-19 as pandemic,
- issued guidelines about clinical and epidemiological findings
caused by SARS-CoV-2, a Beta-coronavirus closely related to the SARS virus.
There after, 2019-nCOV was named SARS-CoV-2.
COVID-19
family / genus Coronaviridae , Betacoronavirus,
Enveloped, spherical, Monopartite, linear ssRNA(+) genome
Capped, and polyadenylated (guanosine nucleotide @5'-end of mRNAs and then, methylating the guanosine).
The leader RNA (65-89 bp) at the 5' end of the genome is also present at the end of each subgenomic RNAs.
• 10 or more nonstructural proteins (nsp proteins)
• structural proteins spike (S)
• envelope (E)
• membrane (M) and
• nucleocapsid(N)
Genome size of ~30kb,
encodes for multiple structural proteins comprising
5. GENE EXPRESSION
gRNA encodes ORF1a, as for ORF1b, it is translated
by ribosomal frameshifting. Resulting polyproteins pp1a and
pp1ab are processed into the viral polymerase (RdRp) and
other non-structural proteins involved in RNA synthesis.
Structural proteins are expressed as subgenomic RNAs.
https://viralzone.expasy.org/764
Genome and proteins
-two-third of 5’genome occupied by the NS proteins
-one-third of 3’genome occupied by major structural proteins (S,E,M and N)
-Spike glycoprotein (S) key protein
-S-protein composed of two subunits, S1 and S2
-S1 much more variable while the S2 conserved
others
-lipid bilayer envelop, membrane proteins, and nucleocapsid protect the virus when it is outside the host cell
-lipid bilayer in which the M,E, and S structural proteins are anchored
-M protein crucial during the assembly, budding, envelop formation, and pathogenesis stages of the virus lifecycle.
6. The clinical manifestations of COVID-19 form a spectrum, from being asymptomatic to fever with mild respiratory illness,
to acute respiratory distress syndrome, and death from respiratory failure or associated complications.
2. Diagnosis SARSCoV-2
Incubation period varies among different patient cohorts,
Difficult to ascertain the actual day of onset,
Asymptomatic (pre-symptomatic) may go undetected
Early detection: crucial interventions to control virus transmission
With the discovery of the virus, numerous diagnostic assays were developed.
qRT-PCR: gold standard, high sensitivity & accuracy in the acute phase.
viral RNA has been detected in both throat and nasal swabs
which becomes almost undetectable by 14 days post-illness onset (pio)
(symptom onset)
Costly and time consuming to perform,
False negative results due to
-improper handling of nucleic acid samples,
-inadequate & variable sampling insufficient viral genetic material
biological variation
With the limitations of qRT-PCR, immunoassays may
offer another avenue to reduce undiagnosed cases,
with the advantage that rapid test formats may deliver
results in a relatively shorter time and lower cost
7. SARS-CoV-2 viral RNA (pink) in throat or nasal
swab of patients are typically undetectable by 14 day
post illness onset (pio).
IgM
-detectable as early as 3 days pio, and
-peaks between 2 and 3 weeks pio.
-it’s response was still detectable after >1 month pio
Both IgA and IgG are
-present as early as 4 days pio, and
-peaks after 2 weeks pio in serum samples
No reports on the presence of SARS-CoV-2-specific
antibodies in the later phase pio, indicated dotted lines.
This depicts the importance of serological studies to
identify individuals with current or prior exposure
to SARS-CoV-2 that went undetected, by testing for
either IgM, IgG, or IgA antibodies against SARS-
CoV-2.
Fig.2 Schematic illustration on the window period of detection for either
viral RNA or antibodies in SARS-CoV-2-infected individuals.
SARS-CoV-2-specific antibodies (blue):
8. Immunoassays: alternative diagnostic approach,
-provide information on active viral infections and past exposures (Fig. 2).
To date, many serological assays have developed to detect SARSCoV-2 AB from patient serum/plasma samples.
3. Current immune-based detection approaches against sars-cov-2
• S protein: the most exposed viral protein, and
• N protein: abundantly expressed during infection.
• Receptor-binding domain (RBD): located along the S protein, is also
a target of interest to detect the presence of SARS-CoV-2-specific
antibodies
Main target immunogenic coronavirus proteins:
• Molecular targets with in their positive sense , ss RNA genome
• Include structural proteins: S, E, M, Hel, N,
• RdRp, HE (hemagglutinin-esterase), ORF1 and ORF1b
• CDC recommends two nucleocapsid targets (N1 and N2)
• WHO recommends initial screening with E followed by confirmation using the RdRp
• Ideal design would include at least one conserved region and
• one specific region to mitigate against the effect of genetic drift.
9. 4. Specificity and Sensitivity of Immunoassays Against SARS-CoV-2
Human population has prior exposure to endemic coronavirus infections including
alphacoronaviruses (229E and NL63),
betacoronaviruses (OC42 and HKU1),
Sever acute respiratory syndrome-related coronavirus (SARCOV) identified in 2003)
Middle East Respiratory Syndrome coronavirus (MERS-CoV) identified in 2012
Sever acute respiratory syndrome-related coronavirus (SARCOV-2) identified in 2019)
S protein antigen: cross-reactivity was observed with MERS-CoV protein when samples tested against SARS-CoV-S
Interestingly, there was no cross-reactivity with the S1 subunit of MERS-CoV.
The high level of cross reactivity b/n SARS-CoV and SARS-CoV-2 (attributed to high degree of genetic homology).
S2 subunit domain: cross-reactivity observed with only the S protein of MERS-CoV, and not with the S1 subunit.
These data suggest that using an S1 subunit-based immunoassay may be more specific than the entire S antigen
The RBD: lies along the S protein is usually the target of many neutralizing antibodies against SARS-CoV.
Due to high level of similarity (90%) bn SARSCoV & SARS-CoV-2 N proteins, the N antigen of SARS-CoV was
also used for serological detection of SARS-CoV-2-specific antibodies.
These N-based assays were reported to be more sensitive than S1 subunit-based tests.
11. conformational B-cell epitopes mapped onto the S1 subunit in few identical residues within SARS-CoV & SARS-
CoV-2.
These indicate that SARS-CoV-specific AB targeting these discontinuous regions may not be able to cross-react with
SARS-CoV-2.
To identify other SARS-CoV AB that may recognize the conformational epitopes of SARS-CoV-2 S protein, which can
greatly reduce the amount of time needed to develop novel neutralizing antibodies.
5. Identification of B-Cell Epitopes Against SARS-CoV-2 on Immunogenic Proteins
Apart from immunoassays early detection of SARSCoV-2, is critical to determine the regions where SARS-CoV-2-
specific AB bind to help guide vaccine designs.
Using SARS-CoV-derived B-cell epitopes that have been experimentally identified from positive B-cell assays,
49 out of 298 linear B-cell epitopes have an identical match with SARS-CoV-2 protein sequences without any mutations.
• Majority of these matches were located at both S & N viral antigens,
• Only 4 from the M protein, and
• None in the E protein
6 conformational B-cell epitopes identified from the same database were located on the S antigen.
However, unlike the linear epitopes, none of these mapped identically to the SARS-CoV-2 protein.
12. 6. Applications of immunoassays to control sars-cov-2 transmission
To support diagnosis, treatment, and prevention of SARS-CoV-2 infections.
Determining the optimal time points to collect serum or plasma samples for immunoassay screening
Generation of therapeutic MoAB from peripheral blood B cells
• CR3022 recognizes an epitope along the RBD of SARS-CoV-2
• MoAB 47D11: enabling cross-neutralization against SARS-CoV-2 infection.
• Reports on antibodies against the coronavirus E protein are scarce, possibly due to it being the smallest protein
Todate, two human SARS-CoV-specific antibodies (CR3022 & 47D11), have been shown to recognize SARS-CoV-2
Able to detect mildly infected cases, which is important to ascertain the extent of community spread.
13. Inability to detect early stage infection
-antibodies take several days to be generated after exposure to foreign material.
-A recent infection may provide false negative results.
instead, RT-PCR may be more suitable to diagnose an early acute SARS-CoV-2 infection.
Inherent variability of the antibody response
-due to the unique genetic makeup of each individual.
-This could possibly explain the d/ce in AB profiles elicited among individuals infected with SARS-CoV-2 .
Cross-reactivity could potentially be a limitation of immunoassays as
-it severely impacts the specificity and sensitivity of the test.
7. Drawbacks of Serological Studies
While it is fast, robust and easy to perform, there are several limitations to serological assays.
14. Rapid development of diagnostic tools & immune-based assays are important against the ongoing pandemic.
Serological assays: that target a diverse range of viral antigen has no doubt assisted in accurate diagnosis.
data generated through serological studies can greatly aid in supplementing the results from qRT-PCR,
Contribute to sero-epidemiology, which has been shown to help in the design of virus elimination programs.
Moving forward, extensive collation of the current immunoassays against SARS-CoV-2 will provide insights toward
MoAB discovery & characterization for dev’t of a SARS-CoV-2 vaccine.
Rapid increase in number of confirmed COVID-19 cases coupled with the shortage in test kits to meet rising demands,
Decentralized point-of-care tests (POCT): alternative to facilitate SARS-CoV-2 diagnosis.
lateral flow assay (LFA): a paper-based platform for detection & quantification of analytes in complex mixtures.
designed to be rapid, sensitive, highly accessible, and easily performed, requiring small amount of sample.
However, POCTs can't replace RT-PCR, it is crucial that these developing tests are rigorously assessed prior to use.
wrong use and interpretation could lead to disastrous public health consequences.
9. Conclusions
8. The Way Forward
Editor's Notes
Most serological assays are based on the SARS-CoV-2 nucleocapsid protein (N), transmembrane spike protein (S), or S receptor-binding domain (RBD) because of their high antigenicity.