bioRxiv: Zhang Qiwei/Wu Jianguo of Jinan University found that Omicron has undergone multiple genetic recombinations

The current COVID-19 pandemic around the world is primarily caused by the more contagious Omicron variant
.

Scientists have been continuously paying attention to the possible emergence of new recombination variants, because genetic recombination is an important evolutionary mechanism for the production of new and re-emerging human viral pathogens, and an important way of evolutionary adaptation of coronaviruses

Recently, Professor Zhang Qiwei and Professor Wu Jianguo from the pathogenic microorganism research team of Jinan University published a research paper titled: Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events in the preprint bioRxiv .

bioRxiv Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events

The study carried out a fine analysis of the whole genome sequence of the new coronavirus Omicron variant and its spike gene sequence, and found for the first time that the spike protein gene of the Omicron variant is related to Alpha (Alpha).

Reliable evidence of multiple cross-variant recombination between mutant strains such as , Beta, Delta, etc.

The spike protein (Spike) of the new coronavirus is mainly responsible for receptor recognition and mediating the invasion of the coronavirus into host cells
.

The mutation of the amino acid sequence of the viral S protein can change the binding efficiency of the S protein to the host cell receptor, thereby affecting the viral infection and infectivity

The research team first conducted a comprehensive and detailed comparison of the 52,563 gene sequences of the S protein of the new coronavirus Omikron variant that was prevalent before January 15, 2022, and found that the early Omikron variant itself had carried many more genes.
The characteristic amino acid mutation of a previous VOC epidemic strain suggests that the S protein gene of the Omicron variant has undergone multiple gene recombination events (Fig.
1)
.

Further identification revealed 18 core mutations (>99% frequency) of BA.

Figure 1.
The BA.
1 subvariant of the omicron strain shares 6 mutations with the alpha variant (del69-70, delY144, N501Y, D614G and P681H) and 3 mutations with the beta strain (K417N, N501Y and D614G) ), shared 3 mutations (N501Y, D614G and H655Y) with the gamma strain and 2 mutations (T478K and D614G) with the delta strain
.

Figure 1.
The BA.
1 subvariant of the omicron strain shares 6 mutations with the alpha variant (del69-70, delY144, N501Y, D614G and P681H) and 3 mutations with the beta strain (K417N, N501Y and D614G) ), shared 3 mutations (N501Y, D614G and H655Y) with the gamma strain and 2 mutations (T478K and D614G) with the delta strain
.

Figure 1.

Figure 2.
Amino acid mutations from other mutants were newly added to each region of the spike protein of some Omicron mutants
.

Figure 2.
Amino acid mutations from other mutants were newly added to each region of the spike protein of some Omicron mutants
.

Figure 2.

Figure 3.
(A) The S gene of the Omicron variant strain exhibits certain genetic polymorphisms and forms multiple subgroups
.

(B) Some regions of the S gene of some subsets show atavism

Figure 3.

Figure 4.
(A) Global distribution of the BA.
1 subvariety of Omicron carrying the L452R mutation
.

(B) The genome-wide phylogenetic tree of the Omicron BA.
1 subvariety carrying the L452R mutation exhibits sequence polymorphisms
.

Figure 4.
(A) Global distribution of the BA.
1 subvariety of Omicron carrying the L452R mutation
.
(B) The genome-wide phylogenetic tree of the Omicron BA.
1 subvariety carrying the L452R mutation exhibits sequence polymorphisms
.
Figure 4.
(A) Global distribution of the BA.
1 subvariety of Omicron carrying the L452R mutation
.
(B) The genome-wide phylogenetic tree of the Omicron BA.
1 subvariety carrying the L452R mutation exhibits sequence polymorphisms
.

In addition to the Omicron BA.
1 subvariant, the research team also found a small number of delta mutations suspected of recombination in the S gene of some Omicron BA.
2 subvariants
.
Through the analysis of the S gene sequence of a large number of Omicron strains, the study found that there are multiple cross-variant recombination events in the S gene of Omicron and other strains, indicating that co-infection and subsequent genome recombination promote the continuous evolution of the new coronavirus
.
Some recombination events may lead to changes in viral infectivity and immune evasion capabilities
.
Therefore, continuous monitoring of mutations in the 2019-nCoV genome is crucial for understanding the evolution and origin of the virus.
At the same time, the design of anti-2019-nCoV drugs and new vaccines also needs to consider the impact of recombination on the formation of virus targeting sites
.

Professor Zhang Qiwei and Professor Wu Jianguo from the Institute of Pathogenic Microbiology of Jinan University/Guangdong Provincial Key Laboratory of Virology are the corresponding authors of the paper, and doctoral student Ou Junxian is the first author of the paper.
Research provides guidance and assistance
.

Original source:

Original source:

Junxian Ou, Wendong Lan, Xiaowei Wu, et al.
Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events .
bioRxiv, 2022.

Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events