Greatest Common Divisor Deciphered SARS-CoV-2 superpandemic

Global cases and deaths showed that COVID-19 and 1918 in�uenza were not normal pandemics, but superpandemics. Was there a common mechanism to push pandemics into superpandemics? This common ground was explored here from a new perspective and approach using the greatest common divisor (GCD). The results showed that superpandemic viruses played tricks like superbugs. One subtlety was that SARS-CoV-2 �ghted antibodies, just as superbugs �ghted antibiotics. The SARS-CoV-2 spike and ORF8 proteins recognized the "Achilles heel" of secretory antibodies, namely J-chains and secretory components, and hijacked them respectively. Another subtlety was that SARS-CoV-2 expanded ORF8 protein as a superpandemic catalyst, just as drug-resistant enzyme facilitated the spread of superbugs. The SARS-CoV-2 ORF8 protein corresponded to the 1918 H1N1 virus neuraminidase. Both functioned as glycosylated-modication enzyme and RNA base-modication enzyme. Tampering with the enzymes was not found in SARS-CoV and pandemic (H1N1) 2009 virus. The synergy of spike and ORF8 proteins acted as the ignition for SARS-CoV-2 superpandemic. Through GCD analysis of clinical and experimental results of different coronaviruses, it was proposed to comprehend the epidemiological traceability and evolutionary from virus sequence up to virus GCD. We sincerely recommend the GCD platform to WHO for early warning.


Main
The number is life.So far, more than 6.6 million deaths of COVID-19 have been con rmed worldwide.The number of deaths was similar to that of the 1918 u 1 .While the two genomes were markedly different, SARS-CoV-2 was as devastating a pandemic as the 1918 u virus 1,2 .The prevalence indicated that neither COVID-19 nor the 1918 u were normal pandemics, but superpandemics.It was known that the transformation of antigen from drift to shift turned virus epidemic into pandemic, so what was the molecular basis for the virus to go further from the pandemic to a superpandemic?At present, viral metagenomics, protein structure and genetic manipulation were the three fundamental approaches for our understanding of viral biology 3 .However, the key issue was the complex relationship between protein structure and function.Although more than 200 million protein structure predictions were available in the AlphaFold database, structure similarity did not necessarily equal function similarity.In particular, the structural and functional information of intrinsically disordered protein extended the traditional structurefunction pattern of protein.Some new strategies were needed to decode SARS-COV-2.In the vast universe, number law showed up in everything, such as from the redshift of cosmic microwave background radiation to the number of C. elegans cells, from the quantum number of particle physics to the life cycle of periodic cicadas 4,5 .These studies revealed that number theory could bridge the three elds of mathematics, physics and biology 6,7 .Since the process of nding the greatest common divisor (GCD) was the process of nding common ground, the protein@integer GCD platform was created here to uncover the common mysteries of superpandemic viruses.Our research showed that superpandemic viruses differed from pandemic viruses in that they expanded a self-modi cation multifunctional enzyme, which acted as a catalyst for virus superpandemic, just as enzyme contributed to the spread of superbugs.Through combined computational analysis with clinical epidemiological experimental research, the superpandemic mechanism is proposed, and the greatest common divisor is raised from the original mathematical term to the epidemiological concept.The GCD platform was not only used to crack the superpandemic mechanism, but also used to capture superpandemic strains of different coronaviruses.

Results
The GCD decoded virus superpandemic.
We sought to determine whether different superpandemic pathogens shared an identical or similar mechanism.In order to nd the common mechanism, we developed the GCD platform to search for the molecular basis from different pandemic viruses and superbugs (Fig. 1a).The key to the molecular basis was to identify the common function of different antigens.Through GCD analysis of the SARS-CoV-2 proteome versus pandemic in uenza virus and superbug antigens, we identi ed the S and ORF8 proteins as key antigens causing the SARS-CoV-2 superpandemic (supplementary table 1-2).The GCD results showed that the key antigens of SARS-CoV-2 had the dual properties of immune and enzyme.On the one hand, the SARS-CoV-2 S protein shared the GCD with the clumping factor A (ClfA) of methicillin-resistant Staphylococcus aureus (MRSA) and hijacked the SIg J chain (SIg-JC); the SARS-CoV-2 ORF8 protein shared the GCD with the SpsA or PspA of methicillin-resistant Streptococcus pneumoniae (MRSP) and hijacked the SIg secretory component (SIg-SC) (Fig. 1b and Supplementary Tables 1 and 3).On the other hand, the ORF8 protein of SARS-CoV-2 corresponded to the neuraminidase of the 1918 H1N1 virus (Supplementary Table 1).The ORF8 protein and the neuraminidase shared the GCD not only with the human glycosylation-modi ed enzymes GlcNAcase and HexNAcase, but also with the human RNA editing enzymes ADAR1 and ADAR2.Both might function as glycosylation-modi ed enzymes and RNA base-modi ed enzymes.In contrast, tampering with the enzymes was not found in SARS-CoV and the pandemic 2009 H1N1 virus (Supplementary Table 4).These GCD results explained why SARS-CoV-2 possessed the superpandemic characteristcs of the 1918 u virus.
Next, we further investigated how SARS-CoV-2 exerted a synergistic effect of immunohijacking and enzyme modi cation.The key to synergy was to identify common molecular pathways.We used the GCD to detect whether there was a common molecular pathway between SIg/ SC hijacking and enzyme modi cation, and found that SARS-CoV-2 worked together to destroy CD4 cells through two different pathways, namely ORF8-SIg/SC-CD4 and ORF8-ADAR1-CD4.Since ADAR was also RNA base-modi ed enzyme, we used the GCD to analyze SARS-CoV-2 accessory proteins and nonstructural proteins.The GCD results showed that the accessory protein ORF8 shared the GCD with the nonstructural proteins nsp1, 11, 13 (Supplementary Tables 5-6).This result indicated that the synergistic interaction of modi cation enzyme ORF8 and helicase nsp13.The SARS-CoV-2 ORF8-based synergistic effects told us that although superpandemic viruses still lacked protein translation system, they had evolved a uni ed mechanism of replication, immunity, and modi cation through the expansion of single-functional enzymes to multifunctional enzymes.
Finally, we used the uni ed mechanism to decode the emergence of SARS-CoV-2 variants of concern.
Why was Omicron, the SARS CoV-2 variant, so subtle?In supplementary Table 7-8, Omicron , such as OQ151515, showed that it had special properties similar to the original strain but distinct from the other variants.Omicron S and ORF8 proteins had synergistic immune and modi cation effects.
The GCD capturing superpandemic virus.
Table 1 took SARS-CoV-2 and the 1918 H1N1 virus as standard superpandemic viruses and compared them with human, bat and synthetic coronaviruses.The S and ORF8 proteins of SARS-CoV-2 or the hemagglutinin and neuraminidase of the 1918 H1N1 virus were used as reference antigens.In human coronaviruses, the GCD results showed that HCoV-OC43 and SARS-CoV-2 S protein had the GCD, indicating that HCoV-OC43 and SARS-CoV-2 S protein had similar functions.In bat coronaviruses, the BtCoV-HKU3-1 ORF8 protein and SARS-CoV-2 ORF8 protein had the GCD, indicating that the BtCoV-HKU3-1 ORF8 protein and SARS-CoV-2 ORF8 protein had similar functions.The S and ORF8 proteins of both RaTG13 (MN996532.2) and RpYN06 (MZ081381.1)did not have signi cant GCD with the SARS-CoV-2 S and ORF8 proteins or the 1918 H1N1 viral hemagglutinin and neuraminidase.However, the synthetic CoV (Bat-SRBD) S protein and ORF8 protein possessed the GCD with SARS-CoV-2 S protein and ORF8 protein, respectively.Therefore, although RaTG13 and RpYN06 are closer to SARS-CoV-2 than Bat-SRBD in sequence similarity, Bat-SRBD is more likely to become a superpandemic strain than RaTG13 and RpYN06 due to the funtion similarity.Discussion protein @ integer.It is a new model for studying proteins.By upgrading protein sequences to protein integers, we strove to decode virus superpandemic and capture superpandemic virus from a new perspective-GCD, unveiling the epidemic evolutionary mechanism.
Firstly, the GCD results explained why SARS-CoV-2 possessed the superpandemic characteristcs of the 1918 u virus.The enigma was that SARS-CoV-2 ORF8 protein was not only the key antigen, but also a multifunctional modi cation enzyme, which corresponded to the neuraminidase of the 1918 H1N1 virus 8, 9 .Both functioned as glycosylation-modi ed enzymes and RNA base-modi ed enzymes.Tampering with the enzymes was not found in SARS-CoV and the pandemic 2009 H1N1 virus.Second, for SARS-CoV-2, the key antigens S and ORF8 had the adhesin function like the multidrug-resistant S. aureus ClfA antigen and the S. pneumoniae PspA antigen, respectively 10,11,12,13 .These adhesin antigens hijacked SIg-JC or SC to enhance immune invasion.This mechanism could explain the T-cell pathology in COVID-19.
Although T cells lacked ACE2 and AQP1 (Supplementary Table 6), T cells might be destroyed by the SARS-CoV-2 hijacked ORF8-SIg/SC-CD4 and ORF8-ADAR1-CD4 pathway 14 , which was similar to that S. pneumoniae hijacked SIg SC to result in functional impairment of CD4+ cells.
But how did the SARS-CoV-2 ORF8 protein became a multifunctional modi cation enzyme?The versatility of proteins was related to the self-assembly of proteins.The crystal structure showed that SARS-CoV-2 ORF8 protein had the same self-assembled dimer as GlcNAcase and HexNAcase 15,16,17 .These structures revealed why dimerization was crucial for catalytic activity.The dimeric form of ORF8 protein had been observed in the tobacco BY2 cell expression system 18 .ORF8 protein from single molecule to functional architecture showed the relationship between protein function evolution and selfassembly.The evolution of ORF8 protein self-assembly further expanded its versatility.Just as gene evolution from scratch had expanded protein diversity 19 .It will be a new antiviral strategy to regulate the functional evolution of viral protein by controlling its self-assembly.However, the enzymatic transitionstate of ORF8 oligomer remained to be elucidated by further experiments.
The GCD results revealed a uni ed relationship for superpandemic virus replication, immunity and modi cation.Why was SARS-CoV-2 mutation and evasion so fast?Based on the GCD results, on the one hand, the intrinsic interaction between the accessory protein ORF8 and the nonstructural proteins nsp1, 11, 13 promoted SARS-CoV-2 replication.On the other hand, the accessory protein ORF8 and the nonstructural proteins nsp1, 11, and 13 participated in the dual-cycle of SARS-CoV-2 life cycle and glycan cycle by hijacking SIg-SC and modi cation enzyme.The SIg SC-hijacked and IgG Fc-glycan hydrolysis reduced antibody-mediated neutralization and opsonization, facilitating the synergistic effect of the accessory protein ORF8 and the nonstructural proteins nsp1, 11, and 13 to enhance virus replication, generate mutations and evasion 20 .The clinical observation of SARS-CoV-2 con rmed that the deletion of ORF8 gene broke this epidemiological evolution and returned the SARS-CoV-2 superpandemic to a normal pandemic, similar to the deletion of neuraminidase in in uenza C virus.
In terms of prediction and early warning, the GCD platform enabled us from virus sequence up to virus GCD to comprehend epidemic principle.Although RaTG13 and RpYN06 are closer to SARS-CoV-2 than Bat-SRBD in sequence similarity, the GCD results support that Bat-SRBD is more likely to be a superpandemic virus than RaTG13 and RpYN06.Previous experiments had also shown that Bat-SRBD was infectious in cultured cells and in mice 21 .According to the GCD analysis in Table 1, among human CoVs, the results showed that human OC43 CoV S protein and SARS-CoV-2 S protein have signi cant GCD.Although human OC43 CoV and SARS-CoV-2 S proteins share 29% sequence similarity, the GCD effect re ects the common function of human OC43 CoV and SARS-CoV-2 S proteins 22 . Similarly, bat HKU3-1 CoV ORF8 and SARS-CoV-2 ORF8 proteins have signi cant GCD, re ecting the common function of bat HKU3-1 CoV and SARS-CoV-2 ORF8 proteins.These GCD results, on the one hand, were supported by existing experimental studies, and on the other hand, further indicated that recombinant bat HKU3-1 CoV (OC43 CoV S protein + HKU3-1 CoV) or recombinant human OC43 CoV (OC43 CoV + SARS-CoV-2 ORF8 protein) would become a new superpandemic virus.

Figures
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Figure 1 Protein
Figure 1

Table Table 1
The GCD capturing superpandemic virus Bat-SRBD is more likely to be a superpandemic virus; The recombinant bat HKU3-1 CoV (human OC43 CoV S protein instead of bat HKU3-1 CoV S protein) will become a new superpandemic virus.