Omicron: a chimera of two early SARS-CoV-2 lineages

doi:10.21203/rs.3.rs-1302993/v1

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Omicron: a chimera of two early SARS-CoV-2 lineages

https://doi.org/10.21203/rs.3.rs-1302993/v1

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The current global epidemiology of COVID-19 is now characterized by the emergence and rapid spread of the SARS-CoV-2 Omicron variant on a global scale^1,2. Despite the variant’s prompt predominance, there remain knowledge gaps in its origin and evolution history^3–6. Here, we show that Omicron lineage SARS-CoV-2 is characterized by the feature of chimera. It was generated by genomic recombination of two early PANGO lineages of SARS-CoV-2. In the recombination event, strains with medium or high circulating intensity like SARS-CoV-2/human/USA/COR-21-434196/2021 belonging to PANGO lineage BA.1 provided the fundamental genome and served as the major parents, while the rare lineage strains like SARS-CoV-2/human/IRN/Ir-3/2019 belonging to B.35, as the minor parents, hybridized their genomic fractions into the major genomes at position 21593-23118nt. This recombination event results in 22 amino acid residue substitutions for the variant of Omicron, including 16 in the pivotal RBD of the spike protein. These substitutions have led to some subtle variations in the spatial structure and the affinity to hACE2 receptor of the spike protein^7,8, thereby raising concerns about the effectiveness of available vaccines and antibody therapeutics^9–12. The global spread and explosive growth of the SARS-CoV-2 in human population increase opportunities for future recombination^13–15.

The outbreak of the current coronavirus disease (COVID-19) occurred in late 2019 and quickly spread globally. It has posed a remarkable threat to public health around the world^16,17. This pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which belongs to the Betacoronavirus genus and is characterized by an unsegmented, positive-sense, single-stranded RNA genome^18,19. It is known that SARS-CoV-2 is a genetically diverse group that mutates continuously leading to the emergence of multiple variants^9,10,15.

As new variants become more widespread, additional genetic markers emerge^12,14. By determining the phyletic lineages of the SARS-CoV-2 genomic variants and those of the conserved regions in the accessory and spike proteins of all the SARS-related coronaviruses, research in the evolution of molecular pathways involved in emergence of pandemic is critical for the development of therapeutics and vaccines as well as the prevention of future zoonosis^9,10,13. One tool for this purpose is the PANGO (Pangolin lineage) nomenclature by Rambaut et al which takes a granular approach to classify and describe viral evolution with detailed lineages; as evidence becomes available, classifications of variants will be revised to reflect the continuous evolution of circulating variants and their changing epidemiology^20,21. Potential variants of concern (VOCs), variants of interest (VOIs) or variants under monitoring (VUMs) are regularly assessed based on the risk posed to global public health²².

Following the identification of a novel variant in South Africa on 24 November 2021, WHO designated Omicron (clade GRA, PANGO lineage B.1.1.529 and descendants BA.1 and BA.2) as the fifth SARS-CoV-2 VOC two days later due to its large number of substitutions^2,4. The variant has since spread to most countries. The current global epidemiology of SARS-CoV-2 is now characterized by the emergence and rapid spread of the Omicron variant on a global scale, continued decline in the prevalence of the previous Delta and other variants¹. Despite its prompt predominance, there remain knowledge gaps in its origin and evolution, which has attracted people's interests and speculations^3–6. Here, we propose that Omicron variant may be derived from recombination of two early PANGO lineages of SARS-CoV-2.

We retrieved a total of 4,192 whole-length genomes of SARS-CoV-2 from EpiCoV^TM database of Global Initiative on Sharing All Infuenza Data (GISAID) and SARS-CoV-2 data (NCBI). These genome sequences belong to 1,263 PANGO lineages, including 29 lineages of VOCs, VOIs, VUMs and formerly monitored variants (FMVs) according WHO’s Tracking SARS-CoV-2 variants (https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/, accessed December 18, 2021), and are those with the earliest collection times within each PANGO lineage (Extended Data 1 and 2: Tab. S1 and S2). After quality control which is mainly assessed by the extent of sequencing completion, 2609 whole-length genomes of SARS-CoV-2 were used for the first round rapid screen (Extended Data 3, Genome sequence matrix 1), while the genome sequences involved in all putative recombination events identified by the first round screen were picked out for further verification (Extended Data 4, Genome sequence matrix 2). Taking SARS-CoV-2/human/USA/UT-UPHL-211211887190/2021 (Accession, OL920485) as the query genome sequence, recombination events were detected and verified by Recombination Detection Program (RDP) v4.101^23,24 and the SimPlot Program package²⁵.

We confirmed that at least one recombination event occurred in the origin and evolution history of Omicron variant of SARS-CoV-2. In this event, strains like SARS-CoV-2/human/USA/COR-21-434196/2021 (Accession, OL849989) belonging to PANGO lineage BA.1 provided the fundamental genome for VOC Omicron and served as its major parents, while strains like SARS-CoV-2/human/IRN/Ir-3/2019 (Accession, MW737421) belonging to PANGO lineage B.35, as the minor parents, hybridized the genomic fractions into the major genome at the position of 21593-23118 nt (Fig. 1, Extended Data 5: Fig. S1). From the perspective of encoding protein by the recombination fraction, it may have a profound impact on the pathogenicity and transmission potential of the novel variant, i.e., Omicron lineage of SARS-CoV-2. This fraction encodes 144-505 amino acid residues of SARS-CoV-2’s spike protein (S). As a result of the recombination, VOC Omicron did derived the substitutions of N211I, L212V, V213R, R214E, deletion215P, deletion216E, R346K, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, from the minor parent of SARS-CoV-2/human/IRN/Ir-3/2019-like strains, while the substitution of G/D339D may come from a back mutation after recombination. All these substitutions locate in the NTD (N-terminal domain, residues 18~330) and RBD (receptor-binding domain, residues 331~528) of the S1 subunit of spike protein^7,26,27, and even up to 16 in RBD (Tab. 1). The consistency of amino acid residues encoded by VOC Omicron and its minor parent in the corresponding fraction, as well as the difference between it and the major parent, proved at the level of amino acids that the recombination event may have actually happened. It is known that SARS-CoV-2 Omicron variant encodes 37 amino acid substitutions (including insertions and deletions) in the spike protein^7,8, and then the recombination event alone leads to 22 of them.

By checking the isolation frequency of BA.1 in the databases, it is a lineage with medium or high circulating intensity. There are 292,755 and 82,610 isolates in GISAID’s EpiCoV^TM database and SARS-CoV-2 data of NCBI (both accessed January 13, 2022), accounting for 4.17% (292755/7022141) and 2.57% (82610/3218586) of the total isolates in the two databases, respectively, while B.35 is obviously a rare lineage, accounting for 0.0019% (130/7022141) and 0.0018% (59/3218586) respectively in the two databases, and its striking area is more limited to several countries such as United Kingdom, Iceland, Australia, USA, Jordan, Timor-Leste and New Zealand. Fig. 2 shows the temporal order and isolation frequency of the PANGO lineages involved in the recombination event and the VOCs, VOIs, VUMs and FMVs then.

Interestingly, both major parent BA.1 and minor parent B.35 are lineages that emerged in the early outbreak of COVID-19. Considering the rapid transmission potential of lineage BA.1, which accounted for 71.9% of the isolating proportion in less than two months after the emergence, BA.1 cannot be the descendant but the parent of VOC Omicron. In fact, when investigating 5,100 genomes of BA.1 PANGO lineage SARS-CoV-2, we found these viruses were different from the major parent of recombination only at 346 amino acid residue (R vs. K) but fundamentally different from the index Omicron variants (Accessions, OL920485, OL901845, and OL902308), which indicated that BA.1 lineage should be the recombination parent of VOC Omicron rather than the descendant of it (Tab. 1). However, the recombination event for VOC Omicron did not occurred until recently. The reason may be that the circulating frequency of the lineage B.35 is too low and its striking area is too limited, which reduces the chance of recombination between it and other lineages of SARS-CoV-2. After all, the prerequisite for recombination is that no less than two lineages of viruses co-infect an individual simultaneously^28,29, but the isolation frequency of the minor parent lineage B.35 is so rare that it hardly has the opportunity to infect an individual with a prior SARS-CoV-2 infection, and vice versa.

Our study suggested that Omicron PANGO lineage SARS-CoV-2 is characterized by the feature of chimera. It was generated by genomic recombination of two early SARS-CoV-2 lineages in the coding sequence (CDS) of spike protein, and the recombination event results in 22 amino acid residue substitutions for the variant of Omicron, including 16 in the pivotal RBD. Spike protein is the most critical structural protein of SARS-CoVs, which is responsible for recognizing and binding to the surface receptors of host cells^26,27,30. The recently emerged SARS-CoV-2 Omicron variant encodes 37 amino acid substitutions in the spike protein, thereby raising concerns about the effectiveness of available vaccines and antibody therapeutics^9–12. Unfortunately, these concerns do not seem unreasonable. It has been reported that these substitutions have led to some subtle variations in the spatial structure and the affinity to hACE2 receptor of the spike protein^3,8,31. More importantly, it has caused the immune escape of Omicron variant to the available vaccines and antibody therapeutics^11,32−34.

Recombination is proposed to be critical for coronavirus diversity and emergence of SARS-CoV-2, MERS-CoV, SARS-CoV (2002), and other zoonotic CoVs. It allows viruses to overcome selective pressure and adapt to new hosts and environments^35–37. Viral recombination between different CoVs within animal populations may lead to the emergence of novel zoonotic CoVs that are lethal to humans³⁸. Spike proteins are type I membrane glycoproteins with signal peptides used for receptor binding and play a crucial role in viral attachment, fusion and entry, being a target for development of antibodies, entry inhibitors and vaccines^39,40. Recombination events in the evolutionary history of the spike protein have particular significance for the current pandemic. Studies comparing coronavirus strains that are closely related to SARS-CoV-2 have proposed that SARS-CoV-2 acquired the ability to infect human cells through recombination within the spike protein sequence^37,41,42. The enrichment for recombination found at spike protein is in agreement with many other recently published works as well^37,41,43,44.

Undoubtedly, recombination may be occurring during infections in humans^36,45. The global spread and explosive growth of the SARS-CoV-2 in human population has contributed additional mutational variability into this genome, increasing opportunities for future recombination. It has been reported that recombination among SARS-CoV-2 is associated with increased spread and severe disease, and has resulted in vaccine failure^41,46. Thus, targeting the ability of the virus to recombine is a critical consideration for vaccine development in the ongoing SARS-CoV-2 pandemic as well as future animal and zoonotic CoVs.

Acknowledgements

This research was funded by the National Natural Science Foundation of China (Grant No. 81872673), the Three-Year Action Plan of Shanghai Public Health System Construction-Key Discipline Construction (2020-2022, No. GWV-10.1-XK03), and the Three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai (2020-2022, GWV-10.1-XK23). The funders had no role in study design, data collection, data analysis, data interpretation, or writing of the report. We acknowledge the contributions of scientists and researchers from all over the world for depositing the genomes of SARS-CoV-2 in SARS-CoV-2 data (NCBI) and EpiCoV^TM database of Global Initiative on Sharing All Infuenza Data (GISAID).

Author contributions

Conceived research and designed study: C.X., Q.J., Q.Z., Y.F., and M.C. Bioinformatic analyses: X.L., J.X., Z.S., J.H., and Y.W. Epidemiology analyses: J.X., W.H., and K.L. Interpreted Data: C.X., K.T., Q.J., Q.Z., and Y.F. First draft: C.X., X.L, and J.X. Revision: C.X., X.L, J.X., Z.S., W.H., J.H., Y.W., K.L., K.T., M.C., Q.Z., Y.F., and Q.J. Supervision: M.C., and Q.J.

Competing interests

The authors declare no competing interests.

Additional information

Correspondence and requests for materials should be addressed to Chenglong Xiong ([email protected]), Yi Feng ([email protected]), or Qi Zhao ([email protected]). The corresponding authors had full access to all the data in the study and had final responsibility for the decision to submit for publication, but GISAID data access, if needed, requires registration.

Peer review information

We thanks the reviewers for their contribution to the peer review of this work.

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Table 1 is available in the supplementary files section.

There is NO Competing Interest.

ExtendedData1Tab.S1.xlsx
(xlsx): Information of VOCs, VOIs, VUMs and FMVs of SARS-CoV-2 retrieval form GISAID
ExtendedData2Tab.S2.xlsx
(xlsx): Information of PANGO lineages of SARS-CoV-2 retrieval form NCBI
ExtendedData4Genomesequencematrix238SQ.txt
(fasta): Genome sequence matrix 2
ExtendedData5Fig.S1.tif
(tiff): Recombination event verified by SimPlot 3.5.1 program package
ExtendedData3Genomesequencematrix12609SQ.rar
(rar): Genome sequence matrix 1
Tab.1Aminoacidsubstitutionscorrespondingtotherecombinationfraction.docx

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Omicron: a chimera of two early SARS-CoV-2 lineages

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