Multiple variant-to-variant recombination events identified by Omicron subvariants

Since the onset of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), several new variants have emerged due to multiple genomic mutations. .. These mutants are classified by the World Health Organization (WHO) as Variant of Concern (VOC) and Variant of Concern (VOI).

Currently, SARS-CoV-2 omicron variants are the predominant circulating strains in many countries around the world as a result of their high contagiousness and ability to circumvent immune protection induced by both natural infections and vaccination. It has become.

study: Identify multiple intervariant recombination events by tracking diverse spike gene mutations in SARS-CoV-2 Omicron. Image Credit: CROCOTHERY / Shutterstock.com

SARS-CoV-2 Omicron variant

The SARS-CoV-2 Omicron variant (B.1.1.529) was first identified in South Africa in November 2021 and was quickly detected in many countries around the world. Researchers have classified Omicron variants into three subspecies, including BA.1, BA.2, and BA.3.

Over 30 mutations have been identified in the spike (S) protein of the Omicron strain compared to the original SARS-CoV-2 strain. These mutations have been shown to alter the immunogenicity and binding efficiency of Omicron variants.

Earlier VOCs, including alpha (B.1.1.7) and delta (B.1.617.2) variants, as well as the Omicron variant, also contributed to improved transfer rates for these strains of SARS-CoV-. It is composed of spike gene mutations. 2.2.

SARS-CoV-2 recombination

One of the major concerns about the evolution of SARS-CoV-2 is the potential to develop recombinants often called “decmicrons” or “deltacrons” that arise from various mutants that replicate simultaneously in the host. Scientists often argue whether the new variant is true, recombinant, or the result of a sequence error.

The process of recombination promotes the evolution of the virus via genes. Recombinations can cause phenotypic changes and pathogenic profile changes, host species pathogenicity, zoonotic and zoonotic transmission, and host adaptation.

Other related recombination events coronavirus Recombinations of the SARS-CoV-2 variant due to its high similarity to SARS-CoV-2, as well documented for SARS-CoV-1 and the Middle East Respiratory Syndrome coronavirus (MERS-CoV). It was difficult to identify the signature. Separate

About research

In a new study published in bioRxiv * Preprint servers, researchers have shown that the newly emerging and circulating Omicron subvariants were partially generated by recombination with other variants.For this purpose, researchers Spike protein Omicron variants, as well as spike mutations shared between Omicrons and other VOCs and VOIs.

In summary, a total of 52,563 high quality omicron spike amino acid sequences were obtained from the GISAID database, including both BA.1 and BA.2 sequences. Researchers analyzed sequences using a variety of computational tools such as Pymol 2.0, TBTools, BioEdit, BioAider, and jvenn, while NextClade was used to develop and annotate whole-genome phylogenetic trees.

Comparison of peplomer amino acid mutations in the Omicron subvariants (BA.1 and BA.2) with mutations in the other four variant of concern (VOCs). (A) Venn diagram showing mutations in Omicron (BA.1) and VOC. (B) Venn diagram of Omicron (BA.2) mutation compared to that of VOC. (C) Venn diagram of the mutation between Omicron (BA.1) and Omicron (BA.2). (D) Spike protein amino acid mutation counts of Omicron (BA.1 and BA.2) subvariants compared to VOC mutations.

Survey results

Of the two Omicron variants, BA.2 is rapidly replacing BA.1 and becoming the major epidemic variant in many countries. In this study, researchers identified mutations common to BA.1 and BA.2 mutants and other SARS-CoV-2 VOCs. In summary, the BA.1 and BA.2 subvariants are one in the N-terminal domain (NTD), twelve in the receptor binding domain (RBD), and subdomains (SD).

BA.1 subvariants share 6, 3, 3, and two common amino acid mutations with alpha, beta, gamma, and delta VOCs, respectively. The sharing of this mutation indicates the possible origin of the Omicron mutants from these VOCs. Scientists have also identified eight novel mutations in BA.1 isolates present in other VOCs and VOIs. By comparison, BA.2 shares only 6 amino acid mutations with most VOCs.

Studies of the spike protein haplotypes of the Omicron subvariants revealed that the spike genes in these subvariants are composed of 49 representative haplotypes. Numerous nucleotide mutations were also identified in haplotypes compared to BA.1 and BA.2.

Researchers have also studied phylogenetic networks to detect possible recombination events between very similar Omicron or submutants. Some models reveal that pathogenicity can increase as a result of viral coinfection and recombination. In fact, one previous study revealed that Orf1ab and spike gene recombination occurred in patients who were co-infected with both beta and delta mutants in a 1: 9 ratio after 14 days of infection. rice field. These events may not be uncommon because multiple variants circulate at specific times.

Conclusion

The authors of this study revealed that some recombination events occurred between the two omicron subvariants and some VOCs and VOIs. This finding indicates that both co-infection and subsequent genomic recombination play important roles in the evolution of SARS-CoV-2. Continuous genomic surveillance is essential to determine SARS-CoV-2 mutations and their effects on humans.

*Important Notices

bioRxiv Publish preliminary scientific reports that should not be considered definitive as they have not been peer-reviewed, guide clinical practice / health-related behaviors, and should not be treated as established information.