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Examine proposes Omicron variant could also be derived from recombination of two early SARS-CoV-2 PANGO lineages

A current research posted to the Analysis Sq.* preprint platform confirmed that the extreme acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Omicron variant is a chimera of two earlier PANGO lineages of SARS-CoV-2.

Examine: Omicron: a chimera of two early SARS-CoV-2 lineages. Picture Credit score: anushkaniroshan/Shutterstock

The coronavirus illness 2019 (COVID-19) pandemic continues to threaten world public well being with the emergence of latest SARS-CoV-2 variants over time. SARS-CoV-2 Omicron is the most recent variant of concern (VOC) first detected in November 2021.

SARS-CoV-2 is a genetically numerous, single-stranded, unsegmented, positive-sense ribonucleic acid (RNA) virus and evolves frequently, buying enhanced traits. The spike (S) protein of SARS-CoV-2 is essential for viral attachment and entry into host cells and can also be the prime goal of antibodies, vaccines, and entry inhibitor medication.

Earlier research involving coronaviruses (CoVs) carefully associated to SARS-CoV-2 confirmed that it gained the power to contaminate people as a result of recombination throughout the S protein sequence, indicating that recombination occasions needs to be surveilled to determine variants earlier than they trigger widespread infections.

The research

Within the current research, researchers investigated whether or not the Omicron variant resulted from recombination between two early SARS-CoV-2 PANGO lineages (BA.1 and B.35). The staff obtained a set of almost 4200 whole-genome sequences of SARS-CoV-2 from the worldwide initiative on sharing all Influenza information (GISAID) repository and Nationwide Heart for Biotechnology Info (NCBI) that fall beneath 1263 PANGO lineages, together with 29 lineages of SARS-CoV-2 variants of curiosity (VOIs), variants beneath monitoring (VUMs), and VOCs.

Initially, the sequences have been filtered primarily based on the extent of completion of sequencing that yielded about 2609 sequences. The authors screened these sequences to determine these with putative recombination occasions and chosen them for additional evaluation. Utilizing SARS-CoV-2/human/USA/UT-UPHL-211211887190/2021 as a question sequence, the researchers appeared for recombination occasions with the recombination detection program (RDP) and verified them with the SimPlot Program bundle.


The authors noticed that within the origin and evolution of the SARS-CoV-2 Omicron variant, at the least one recombination occasion had occurred. The SARS-CoV-2/human/USA/COR-21-434196/2021 pressure from the BA.1 PANGO lineage was recognized as the most important dad or mum/supply of the chimera, whereas the SARS-CoV-2/human/IRN/Ir-3/2019 pressure (of the B.35 lineage) served as a minor supply. Sequences from the minor dad or mum hybridized into Omicron variant between the nucleotide websites 21593-23118.

This chimeric sequence encodes 144-505 amino acids of the S protein and harbors many mutations similar to N211I, L212V, V213R, R214E, deletion215P, deletion216E, R346K, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, and Y505H. It has been noticed that these substitutions are seen throughout the N-terminal area (NTD) of the receptor-binding area (RBD) of the S protein.

Based mostly on the frequency of isolation from the GISAID and NCBI databases, the BA.1 lineage is taken into account as a medium or excessive circulating lineage forming round 4.17% of complete SARS-CoV-2 sequences on the GISAID repository. In distinction, B.35 lineage is uncommon, constituting simply 0.0019% of GISAID sequences.

Furthermore, the researchers report that the BA.1 lineage just isn’t the descendent or sub-lineage of the Omicron variant however the dad or mum lineage that recombined with the B.35 lineage to type the current Omicron VOC. It has been proposed that regardless of the emergence of each BA.1 and B.35 lineages within the early part of the COVID-19 outbreak, the chimera of the 2 lineages didn’t happen till after the frequency of B.35 lineage in circulation was excessive sufficient to allow the recombination occasion.


The current research findings revealed that the looks of the SARS-CoV-2 Omicron variant is a consequence of recombination between BA.1 and B.35 PANGO lineages, which emerged within the early phases of the COVID-19 outbreak. It was noticed that recombination alone resulted in 22 amino acid substitutions of the Omicron VOC, together with 16 mutations inside the important thing RBD of the S protein.

The excessive variety of mutations in Omicron is regarding as these impart enhanced transmissibility and binding affinity to the human angiotensin-converting enzyme 2 (hACE2) and immune escape traits. Moreover, diminished effectivity of accessible vaccines and therapeutic antibodies has additionally been reported for Omicron-driven infections.

To summarize, the recombination occasion is pivotal for the evolution and variety of coronaviruses because it permits the viruses to adapt to new host environments and overcome choice stress. Subsequently, analysis and public well being measures ought to deal with these findings and goal the recombination occasions to forestall the emergence of newer SARS-CoV-2 strains sooner or later.

*Essential discover

Analysis Sq. publishes preliminary scientific stories that aren’t peer-reviewed and, subsequently, shouldn’t be thought to be conclusive, information medical follow/health-related conduct, or handled as established info

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