“Hunter” for SARS-CoV-2 variants

Introduction to SARS-CoV-2 variants

Since the outbreak of the COVID-19, SARS-CoV-2 has continued to undergo mutations. According to reports, SARS-CoV-2 usually accumulates mutations at a rate of 1-2 mutations per month. This means that many of the SARS-CoV-2 genomes measured now are about 20 sites different from the SARS-CoV-2 genomes measured at the beginning. On December 31, 2020, the World Health Organization officially notified the main SARS-CoV-2 variants, including the following three variants:

On December 14, 2020, the United Kingdom reported a new SARS-CoV-2 variant B.1.1.7 (also known as 501Y.V1) to the World Health Organization. Except for the United Kingdom, SARS-CoV-2 variant B.1.1.7 has been detected in more than 30 countries. Sequence analysis showed that the SARS-CoV-2 variant B.1.1.7 has a large number of site mutations at the same time, of which 9 mutations occur on the spike protein on the surface of the virus. The most important mutation is the N501Y mutation in the spike protein, which enhanced the binding affinity between SARS-CoV-2 and the human receptor angiotensin converting enzyme 2 (ACE2), and affected the spread of the virus. Scientists believe that this new variant is 40-70% more transmissible than the original strain.

On December 18, 2020, South Africa reported a new SARS-CoV-2 variant, which also has the N501Y mutation, and South Africa named it 501Y.V2. Although both the 501Y.V2 South African mutant and the 501Y.V1 mutant have N501Y mutations, phylogenetic analysis shows that 501Y.V2 and 501Y.V1 are two different mutants. The South African 501Y.V2 mutant belongs to the B.1.351 evolutionary branch. There are three important mutation sites in the receptor binding region of the spike protein: K417N, E484K and N501Y. These mutations may cause the variant to have a stronger transmission power and a higher viral load. According to CNN reports, scientists have confirmed that the E484K mutation can make SARS-CoV-2 escape certain antibodies produced by the vaccine and may invalidate existing vaccines.

Japan announced on January 10, 2021 that four passengers who had flown from Brazil to Japan and were judged to be infected with SARS-CoV-2 in the airport quarantine had detected a new SARS-CoV-2 variant, which is different from the British and South African mutant strains, named It is P.1 (also known as 501Y.V3). The genome of SARS-CoV-2 variant P.1 also has a large number of mutations, including 3 mutations of important biological significance, namely N501Y, K417T and E484K mutations. Although they share common mutation sites with the British and South African mutant strains, they belong to different variants. The transmission characteristics and pathogenicity of this variant are still under further study.

 

Variant designation

First identification

Characteristic mutations (protein: mutation)

Location

Date

B.1.1.7 (20I/501Y.V1)

United Kingdom

Sep 2020

ORF1ab: T1001I, A1708D, I2230T, del3675-3677 SGF

S: del69–70 HV, del144 Y, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H

ORF8: Q27stop, R52I, Y73C

N: D3L, S235F

B.1.351 (20H/501Y.V2)

South Africa

Oct 2020

ORF1ab: K1655N

E: P71L

N: T205I

S: K417N, E484K, N501Y, D614G, A701V

P.1

(20J/501Y.V3)

Brazil and Japan

Jan 2021

ORF1ab: F681L, I760T, S1188L, K1795Q, del3675–3677 SGF, E5662D

S: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, T1027I

ORF3a: C174G

ORF8: E92K

ORF9: Q77E

ORF14: V49L

N: P80R

Table 1. Characteristics of major SARS-CoV-2 variants from September 2020 to January 2021

Note: del = deletion; E = envelope protein; N = nucleocapsid protein; ORF = open reading frame; S = spike protein.

Form source: https://www.cdc.gov/mmwr/volumes/70/wr/mm7003e2.htm?s_cid=mm7003e2_w#T1_down

SARS-CoV-2 variants identification program provided by Zeesan Biotech

Xiamen Zeesan Biotech Co., Ltd. and the Engineering Research Center for Molecular Diagnostics of the Ministry of Education of Xiamen University have used the “Multicolor Melting Curve Analysis” (MMCA®) technology (Figure 1) with independent intellectual property rights to develop ” SARS-CoV-2 Variant B.1.1.7 Identification Kit (Real-time PCR Melting Curve Analysis)”, ” SARS-CoV-2 Variant B.1.351 Identification Kit (Real-time PCR Melting Curve Analysis)” and ” SARS-CoV-2 Variant P.1 Identification Kit (Real-time PCR Melting Curve Analysis)” for the mutant strains first found in United Kingdom, South Africa and Brazil. The “Multicolor Melting Curve Analysis” (MMCA®) technology is like a “hunter” who specializes in catching SARS-CoV-2 variants. It can accurately identify the SARS-CoV-2 variants based on the characteristic mutation sites of SARS-CoV-2, through clever probe design, and melting point combinations. Based on this, we can carry out customized service and develop a specific SARS-CoV-2 variant identification kit for any new SARS-CoV-2 variant.

Figure1. Principle of “Multicolor Melting Curve Analysis” (MMCA®) technology

Product Name

Features

Progress of CE certificate

SARS-CoV-2 Variant B.1.1.7 Identification Kit(Real-time PCR Melting Curve Analysis)

Detection of 4 mutation sites that can represent the mutant strain B.1.1.7 COVID-19 first found in the UK: N501Y, HV69-70del, Y144del, D614G

Obtained CE certificate on February 8, 2021

SARS-CoV-2 Variant B.1.351 Identification Kit(Real-time PCR Melting Curve Analysis)

Detection of 3 mutation sites that can represent the mutant strain B.1.351 COVID-19 first found in South Africa: N501Y, E484K, K417N

CE certificate is being applied for

SARS-CoV-2 Variant P.1 Identification Kit(Real-time PCR Melting Curve Analysis)

Detection of 3 mutation sites that can represent the mutant strain P.1 COVID-19 first found in Brazil: N501Y, E484K, K417T

CE certificate is being applied for

……

……

……

Table 2. SARS-CoV-2 variants identification kit launched by Zeesan Biotech

 

Reference

1. https://www.cogconsortium.uk/data/

2. https://www.who.int/csr/don/31-december-2020-sars-cov2-variants/en/

3. https://www.cdc.gov/mmwr/volumes/70/wr/mm7003e2.htm?s_cid=mm7003e2_w

4. Greaney, A.J., et al., Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies. bioRxiv, 2021: p. 2020.12.31.425021.

5. https://edition.cnn.com/2021/01/12/health/coronavirus-mutation-south-africa-variant/index.html


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