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PCL Omicron

PCL Inc. declares that in silico analysis of their PCL COVID-19 Ag detection kits shows the kits can detect SARS-CoV-2 variants listed in Table 1. The analysis found mutations in the variants' nucleocapsid protein fall in domains that do not interfere with binding to the kits' detection antibodies. Epitope positions targeted by the kits also were not affected by amino acid variations in the listed variants. Therefore, PCL concludes their COVID-19 antigen test kits will correctly detect the listed SARS-CoV-2 variants of concern and interest.

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0% found this document useful (0 votes)
41 views

PCL Omicron

PCL Inc. declares that in silico analysis of their PCL COVID-19 Ag detection kits shows the kits can detect SARS-CoV-2 variants listed in Table 1. The analysis found mutations in the variants' nucleocapsid protein fall in domains that do not interfere with binding to the kits' detection antibodies. Epitope positions targeted by the kits also were not affected by amino acid variations in the listed variants. Therefore, PCL concludes their COVID-19 antigen test kits will correctly detect the listed SARS-CoV-2 variants of concern and interest.

Uploaded by

Ardeleanu Dragos
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Declaration

Date : December 1st, 2021

Dear Sir or Madam


RE: In Silico Analysis Result regarding PCL COVID-19 Ag detection kits against Variants

We, PCL Inc., located at 701 Star Valley 99 Digital-ro 9-gil, Geumcheon-gu Seoul 08510,
Rep. of Korea, as the legal manufacturer of the PCL COVID-19 Ag detection kits1, hereby declare
as follows;

In Silico Analysis2 Results:

As PCL COVID-19 Ag detection kits are designed to detect the nucleocapsid (N) protein of SARS-
COV-2, in-silico analysis was performed to confirm that SARS-COV-2 variants recited in Table 1
as below have no effect on the diagnostic performance of our product.

[Table 1]

SARS-COV-2 variants
Alpha B.1.1.7 Epsilon B.1.427, B.1.429
Beta B.1.351 Eta B.1.525
Gamma P.1 Iota B.1.526
Delta B.1.617.2 , B.1.617.3 Theta P.3
Kappa B.1.617.1 Zeta P.2
Delta Plus AY.1, AY.2, AY.3 Lambda – C.37
Omicron B.1.1.529

Nucleocapsid (N) protein of SARS-CoV-2 consists a total of 5 domains: N-terminal domain (NTD),
RNA-binding domain (RBD), disordered central linker (LINK), dimerization domain, and C-
terminal domain (CTD) as shown in the figure below.

1
PCL COVID-19 Ag detection kits are referred to either [COV04S] PCL COVID19 Ag Gold or [COV05] PCL COVID19 Ag
Rapid FIA in herewith.

2
NCBI database (https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/), GenBank (http://www.ncbi.nlm.nih.gov/genbank/), PANGO
Lineages: Latest epidemiological lineages of SARS-CoV-2 (https://cov-lineages.org/index.html), Outbreak.info
(https://outbreak.info/) are refereed to investigate.

Rm701, Star Valley, 99 Digital-ro 9-gil, Geumcheon-gu, Seoul, 08510, Republic of Korea
PCL Inc. TEL : +82-2-2144-3960 FAX : +82-2-2144-3910 URL : www.pclchip.com
The following is the SARS-CoV-2 isolate information (reference isolate Wuhan-Hu-1; Accession
number: NC_045512.2) acquired from the NCBI database and GenBank, which includes the SARS-
Cov-2 variants of Table 1. Mutation sites were compared with multi-alignment of the N protein
sequences of each variant, and the variations are recited specifically.

Rm701, Star Valley, 99 Digital-ro 9-gil, Geumcheon-gu, Seoul, 08510, Republic of Korea
PCL Inc. TEL : +82-2-2144-3960 FAX : +82-2-2144-3910 URL : www.pclchip.com
The following reference is an analysis of N protein tertiary structure, confirming that amino acid
mutations from N protein falls under the N-terminal domain (NTD) or linker region, which does not
interfere the binding with ACE2 (Angiotensin-converting enzyme 2) and do not affect its tertiary
structural changes.

S protein mutations in the variants are known to affect the receptor-binding domain (RBD) of SARS-
CoV-2 binding with ACE2 (Angiotensin-converting engine2). Meanwhile, N protein mutations does
not affect with ACE2 binding of SARS-CoV-2, because the mutations primarily occur in the N-
terminal domain (NTD) or linker region.

It is known that the N antigen remains conserved among these variants. Our in-silico analysis
confirms that N protein mutations of the SARS-Cov-2 variants of Table 1 do not affect detecting the
nucleocapsid (N) protein of SARS-CoV-2 by PCL COVID-19 Ag detection kits.

Furthermore, Epitope Position & it’s Amino Acid Sequence of PCL COVID-19 Ag detection kits are
recited in Table 2 as below, which verifies that any SARS-Cov-2 variants of Table 1 does not relate
to the Epitope Position of Table 2.

[Table 2]

Ref. No Test Kit Name Target Epitope Position Amino Acid Sequence
COV04S PCL COVID19 SARS- 44-54, 44-54 ; G L P N N T A S W F
Ag Gold CoV-2 149-178 T
COV05 PCL COVID19 149-178 : R N P A N N A A I
Ag Rapid FIA VLQLPQGTTLPKG
FYAEGSRG

Rm701, Star Valley, 99 Digital-ro 9-gil, Geumcheon-gu, Seoul, 08510, Republic of Korea
PCL Inc. TEL : +82-2-2144-3960 FAX : +82-2-2144-3910 URL : www.pclchip.com
References:

1. https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-
info.html?CDC_AA_refVal=https%3A%2F%2Fptop.only.wip.la%3A443%2Fhttps%2Fwww.cdc.gov%2Fcoronavirus%2F2019-
ncov%2Fcases-updates%2Fvariant-surveillance%2Fvariant-info.html
2. Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary
genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549.
https://doi.org/10.1093/molbev/msy096 (2018).
3. HALL, T. Biological sequence alignment editor (BioEdit), version 7.2. 5. 2013.
4. CUBUK, Jasmine, et al. The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and
phase separates with RNA. Nature communications, 2021, 12.1: 1-17.
5. NARAYANAN, Sai, et al. SARS-CoV-2 Genomes From Oklahoma, United States. Frontiers in
Genetics, 2021, 11: 1867.
6. ELASWAD, A., et al. Mutational spectra of SARS-CoV-2 isolated from animals PeerJ. 8:
e10609. Published online, 2020.
7. SINGH, Jasdeep, et al. Structure-Function Analyses of New SARS-CoV-2 Variants B. 1.1. 7, B.
1.351 and B. 1.1. 28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. Viruses,
2021, 13.3: 439.
8. https://www.path.org/articles/new-variants-will-covid-19-tests-still-
work/?gclid=Cj0KCQjwwLKFBhDPARIsAPzPi-I4MfaGMIy2-Q8i_V1RClKguTDtJtVU-
GbR6bg6SqhyViMGhJeJD8saAnn6EALw_wcB

Sincerely,

Mr. Seung Ji Kim [Patent Attorney]


Head of External Affairs, PCL Inc.
Tel : +82-10-8899-3070
Email : [email protected]
PCL Inc.

Rm701, Star Valley, 99 Digital-ro 9-gil, Geumcheon-gu, Seoul, 08510, Republic of Korea
PCL Inc. TEL : +82-2-2144-3960 FAX : +82-2-2144-3910 URL : www.pclchip.com

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