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Scientific Reports logoLink to Scientific Reports
. 2021 Aug 25;11:17199. doi: 10.1038/s41598-021-96233-7

Homology between SARS CoV-2 and human proteins

Vladimir Khavinson 1,3, Alexander Terekhov 1, Dmitry Kormilets 2, Alexander Maryanovich 1,
PMCID: PMC8387358  PMID: 34433832

Abstract

An extremely high contagiousness of SARS CoV-2 indicates that the virus developed the ability to deceive the innate immune system. The virus could have included in its outer protein domains some motifs that are structurally similar to those that the potential victim's immune system has learned to ignore. The similarity of the primary structures of the viral and human proteins can provoke an autoimmune process. Using an open-access protein database Uniprot, we have compared the SARS CoV-2 proteome with those of other organisms. In the SARS CoV-2 spike (S) protein molecule, we have localized more than two dozen hepta- and octamers homologous to human proteins. They are scattered along the entire length of the S protein molecule, while some of them fuse into sequences of considerable length. Except for one, all these n-mers project from the virus particle and therefore can be involved in providing mimicry and misleading the immune system. All hepta- and octamers of the envelope (E) protein, homologous to human proteins, are located in the viral transmembrane domain and form a 28-mer protein E14-41 VNSVLLFLAFVVFLLVTLAILTALRLCA. The involvement of the protein E in provoking an autoimmune response (after the destruction of the virus particle) seems to be highly likely. Some SARS CoV-2 nonstructural proteins may also be involved in this process, namely ORF3a, ORF7a, ORF7b, ORF8, and ORF9b. It is possible that ORF7b is involved in the dysfunction of olfactory receptors, and the S protein in the dysfunction of taste perception.

Subject terms: Infection, Computational biology and bioinformatics, SARS-CoV-2

Introduction

The interaction of SARS CoV-2 with the host immune system is largely determined by the structural similarities between viral and host proteins. The studies of SARS CoV-2 are still focused on the S protein1.

An extremely high contagiousness of the coronavirus SARS CoV-2 indicates that during its evolution the virus developed the ability to deceive the innate immune system. The simplest way to achieve this ability would be to incorporate into its membrane the proteins that share structural similarity with those which the immune system of the potential victim has learnt to ignore. Probably, the virus borrowed some n-mers from bats or other mammals. Any motif of any mammalian protein was suitable for borrowing, if only the immune system considered it to be of its own.

The knowledge of the homology between the SARS CoV-2 and human proteins would help understand the mechanisms of mimicry at the moment of infection. The SARS CoV-2 proteins may simulate human proteins, mislead the immune system, and slow down its response.

However, mimicry is not the only process that is determined by the protein homology between the virus and host organism. After the inevitable destruction of the virus particle, the proteins or their domains, which were inside the virus until then, come into contact with the immune system. With some structural similarity, a part of the immune response will be directed against the proteins of the host organism, i.e., an autoimmune response will arise.

This study aimed to identify the human proteins which share a significant structural homology with the SARS CoV-2 proteins. We hope this information will be useful to the developers of vaccines against coronavirus.

Joshua Lederberg2 believed that "microbes and their human hosts constitute a superorganism." According to this, we considered the concept of "human proteins" as a combination of human own proteome and the proteomes of gut microbiota. We have paid particular attention to the proteins that are involved in the three functions that are almost necessarily affected in this disease, namely digestion, olfaction and taste.

Methods

Using an open-access protein database Uniprot and our original computer program Ouroboros3, we compared the SARS CoV-2 proteome4 with those of other organisms. We also searched for a separate database of 75,777 human proteins5. The algorithm we used compares primary sequences of SARS CoV-2 and human proteins, presented in the form of a one-letter code. We performed a comparison of proteins by a consecutive search for regions of one protein in the others, which is essentially a standard task of finding a substring in a string. This algorithm is implemented in standard methods of many programming languages, including Python, in which the main program was coded. The URL to the source code is provided above3.

When assessing the homology between the viral and human proteins, we took into account the presence of the common 7-/8-mers and especially their fusion into longer sequences. For example, 7-dimensional viruses, one of which is homologous to the human protein A, and the other to the protein B, can "overlap" at the ends, forming regions of 8 to 14 amino acid residues in length.

Results and discussion

Structural proteins

Spike glycoprotein

S protein, 1273 aa

graphic file with name 41598_2021_96233_Figa_HTML.jpg

Hereinafter, regions homologous to human proteins are highlighted in red. Transmembrane tail TM1214-1237 is underlined.

In the S protein molecule, we localized more than two dozen of 7-/8-mers homologous to human proteins (Table 1).

Table 1.

Localization of homologous 7-/8-mers in the S protein and human proteins.

Subunit SARS CoV-2 S protein domain In S protein In human proteins
S1 Signal peptide (N-terminus)1–13 None
N-terminus domain NTD14-305 DKVFRSS40-46 Zinc finger protein 528275–281
FLPFFSN55-61 OTU domain-containing protein 6A185-191
VSGTNGT70-76 Lysosome-associated membrane glycoprotein 1171–177
SLLIVNN116-122 ATP-binding cassette sub-family A member 10825–831
FKNLREF186-192 Isovaleryl-CoA dehydrogenase, mitochondrial77-83
TRFQTLL236-242 Disheveled-associated activator of morphogenesis 2251–257
KIYSKHT202-208 Uncharacterized protein C1orf1057-13
SSSGWTA254-260 Uncharacterized protein KIAA1109 (Fragment)610–616
Uncharacterized fragment306-318 None
Receptor-binding domain RBD319-541 KLNDLCF386-392 Interleukin-7149–155
DEVRQIA405-411 Histone-lysine N-methyltransferase 2C4530-4536
Uncharacterized fragment542-787 VYSTGSN635-641 Neural cell adhesion molecule L1-like protein341-347
IGAGICA666-672 Hepatitis A virus cellular receptor 2205–211
SPRRARS680-686 Hermansky-Pudlak syndrome 1 protein258-264
RRARSVAS682-689 Amiloride-sensitive sodium channel subunit alpha201-208
S2 Fusion peptide FP788-806 None
Uncharacterized fragment807-911 VTLADAG826-832 Non-receptor tyrosine-protein kinase TNK1440-446
GLTVLPP857-863 FH1/FH2 domain-containing protein 3972–978
LPPLLTD861-867 Maestro heat-like repeat-containing protein family member 9250–256
Heptapeptide repeat sequence 1 HR1912-984 SSTASAL939-945 40S ribosomal protein S13143-149
LVKQLSS962-968 E3 SUMO-protein ligase PIAS1284-290
Uncharacterized fragment985-1162 KVEAEVQ986-974 Emilin-3625–631
TGRLQSL998-1004 Neuron navigator 31610–1616
LIRAAEI1012-1018 Unconventional myosin-XVIIIa1352-1358
LDKYFKN1152-1158 Follistatin-related protein 1149–155
Heptapeptide repeat sequence 2 HR21163-1213 NASVVNI1173-1179 Thyroid adenoma-associated protein1022-1028
EIDRLNE1182-1188 Protein SETSIP64-70; Protein SET54-60
Transmembrane tail TM1214-1237 None
Cytoplasm tail CT1238-1273 DEDDSEPV1257-1264 Unconventional myosin-XVI1404-1421

Fragments homologous to human proteins are scattered along the entire length of the S protein molecule, and some of them fuse in sequences of considerable length, namely 10-mers SPRRARSVAS680-689, 11-mers GLTVLPPLLTD857-867 and two closely spaced 7-mers NASVVNI1173-1179 and EIDRLNE1182-1188. Octamer RRARSVAS682-689 is located at the junction of the S1 and S2 subunits. All these n-mers stand out from the virus particles and may be involved in the effect of mimicry.

SARS CoV-2 can cause smell and taste dysfunction, as well as muscle injury6.

The 8-mer DEDDSEPV1257-1264, located in the cytoplasmic tail, can be released during the destruction of the virus particle and get involved in orchestrating the immune system’s response, directing a part of it to the homologous 8-mer in human unconventional myosin-XVI1404-1421. The role of this mechanism in muscle dysfunction in coronavirus infection deserves a special investigation.

The 8-mer RRARSVAS682-689 is homologous to the amiloride-sensitive sodium channel subunit alpha201-208, which is involved in salt taste perception7.

With a high degree of probability, it can be argued that the S protein is involved in the process of mimicry. It may also take some part in provoking an autoimmune response.

We have checked the S protein homology across10 species, specifically primates, bats and some other mammals. The results are presented in Table entitled Similarity of SARS CoV-2 spike glycoprotein structure with some mammalian proteins in the electronic attachement. Probably, attention should be paid to the homologous regions common to SARS CoV-2, humans, and bats. The data presented so far do not allow us to derive a more general rule.

Envelope small membrane protein

E protein, 75 aa (transmembrane domain8-38 is underlined)

graphic file with name 41598_2021_96233_Figb_HTML.jpg

In the E protein molecule, we localized seven 7-mers and one 8-mer homologous to human proteins (Table 2).

Table 2.

Localization of homologous 7-/8-mers in the E protein and human proteins.

E protein domainsa In E protein In human proteins
Signal peptide (N-terminus domain)1–7 None
Transmembrane domain8-38 VNSVLLF14-20 Heterogeneous nuclear ribonucleoprotein L191-197
VNSVLLFL14-21 Ran-binding protein 6409–416
NSVLLFL15-21 Lysosomal amino acid transporter 1 homolog133-139
SVLLFLA16-22 Cytochrome P450 2B64-10 ; Cytochrome P450 2B74-10; GPI ethanolamine phosphate transferase 35–11
LAFVVFL21-27 Solute carrier family 15 member 4235–241
VFLLVTL25-31 Alpha-(1,3)-fucosyltransferase 1020–26
LAILTAL31-37 Transient receptor potential cation channel subfamily M member 6394–400 ; Transient receptor potential cation channel subfamily M member 3465–471
TALRLCA35-41b Protein disulfide-isomerase TMX38-14
Internal domain39-75 None

aDomain boundaries see in8.

bHeptamer TALRLCA35-41 is located at the junction of the transmembrane domain8-38 and internal domain39-75.

A fragment of the E8-38 protein transmembrane domain can be represented as follows:graphic file with name 41598_2021_96233_Figc_HTML.jpg

The size of the letters (point size) corresponds to the frequency of the viral 7-/8-mers in the human proteome.

The protein E transmembrane domain contains 7-/8-mers, homologous to the proteins of some gut bacteria and even cereals, for example, corn, sorghum, wheat, and barley (Table 3).

Table 3.

Localization of some of homologous 7-/8-mers in the E protein and human gut proteome.

In E protein In bacterial and plant proteins
AFVVFLLV22-29

Lpp126 large-conductance mechanosensitive channel:

Lactobacillus casei80-87; L. paracasei80-87; L. florum80-87

TLAILTA30-36

Uncharacterized proteins:

Zea mays90-164; Sorghum bicolor97-127; Triticum aestivum116-190; Hordeum vulgare87-161

The simulation targets may have been the proteins synthesized by a macroorganism itself or by its normal gut microbiota.

All protein E 7-/8-mers, homologous to proteins of humans, gut bacteria and cereals, are located in the transmembrane domain of the virus and form the 28-mer protein E14-41. A random selection of 28 amino acid residues in a row would require an astronomical number of iterations: 2028 = 2.7 ∙ 1036.

The involvement of the E protein in mimicry is hardly possible, but its implication in provoking an autoimmune response (after the destruction of the virus particle) seems very likely.

As a major target, the viral E protein has usually been used for the development of vaccines, specifically against HIV-19, Dengue virus10, hepatitis B virus11, SARS CoV-212 and many other viruses. A deletion of the SARS-CoV E protein reduces pathogenicity and mortality in laboratory animals13. In the transmembrane domain of the SARS-CoV E protein, specific critical virulence-determining features have been identified14.

Membrane protein

Membrane protein, 222 aa

graphic file with name 41598_2021_96233_Figd_HTML.jpg

In the M protein molecule, we localized six 7-mers homologous to human proteins (Table 4).

Table 4.

Localization of homologous 7-mers in the M protein and human proteins.

In M protein In human proteins
VEELKKL10-16 Glutaredoxin-related protein 5, mitochondrial135-141
EELKKLL11-17 GDP-fucose protein O-fucosyltransferase 2340–346
ELKKLLE12-18 Cullin-1335–341
LKKLLEQ13-19 Filamin-A-interacting protein 1211–217
LLESELV133-139 Leucine-rich repeat-containing protein 71439–445
AGDSGFA188-194 Myosin-14359–365

A N-terminus fragment1-19 of the M protein can be represented as follows:graphic file with name 41598_2021_96233_Fige_HTML.jpg

In the protein M, four 7-dimensional homologues of human proteins are fused into 10-mer VEELKKLLEQ10-19, the hydrophilic composition of which indicates a possible contact with the external environment, i.e., with the host's immune system, and the involvement in mimicry.

Outside of the 10-mer, we found only two homologous 7-mers. It is unlikely that the M protein is involved in provoking an autoimmune response (after the destruction of the virus particle).

Nucleoprotein

Nucleoprotein, 419 aa

graphic file with name 41598_2021_96233_Figf_HTML.jpg

In the N protein molecule, we localized eleven 7-mers homologous to human proteins (Table 5).

Table 5.

Localization of homologous 7-mers in the N protein and human proteins.

In N protein In human proteins
RPQGLPN41-47 GATOR complex protein WDR59757-763
RGQGVPI68-74 Putative uncharacterized protein encoded by LINC00346154-160
NSSPDDQ77-83 NEDD4-binding protein 2154–160
GKMKDLS99-105 Chromodomain-helicase-DNA-binding protein 1-like770-776
VLQLPQG157-163 Prestin92-98
AEGSRGG173-179 snRNA-activating protein complex subunit32-8
SRGGSQA176-182 Ras-associating and dilute domain-containing protein886-892
KADETQA375-381 Myopalladin90-96
LLPAADL394-400 Probable E3 ubiquitin-protein ligase HERC11098-1104
SKQLQQS404-410 Codanin-1259–265
SMSSADS410-416 Protein PRRC2B416-422

The N protein is located completely inside the virus particle and cannot be involved in mimicry. All heptamers homologous to human proteins form several rather long fragments, including the 13-mer SKQLQQSMSSADS404-416 and 10-mer AEGSRGGSQA173-182, which increases the likelihood of the protein involvement in provoking an autoimmune response.

Nonstructural proteins

All non-structural proteins of SARS CoV-2 are located completely inside the virus particle and, by definition, cannot be involved in the process of mimicry. It remains to consider the possibility of their implication in provoking an autoimmune process.

ORF3a protein

ORF3a protein, 275 aa

graphic file with name 41598_2021_96233_Figg_HTML.jpg

In the ORF3a protein molecule, we localized five 7-mers homologous to human proteins (Table 6).

Table 6.

Localization of homologous 7-mers in the ORF3a protein and human proteins.

In ORF3a protein In human proteins
VGVALLA48-54 Manganese-transporting ATPase 13A1876-882
LLVAAGL95-101 Glycerophosphoinositol inositolphosphodiesterase GDPD2129-135
KCRSKNP132-138 Vacuolar protein sorting-associated protein 13A2066-2972
SVTSSIV162-168 Protein piccolo2779-2785
TQLSTDT217-223 Septin-14418–424

The 7-mers scattered along the entire length of its molecule do not form long n-mers anywhere else. ORF3a does not appear to be involved in provoking an autoimmune response.

ORF7a protein

ORF7a 121 aa

graphic file with name 41598_2021_96233_Figh_HTML.jpg

In the ORF7a protein molecule, we found two 7-mers homologous to human proteins and located in close proximity to each other (Table 7).

Table 7.

Localization of homologous 7-mers in the ORF7a protein and human proteins.

In ORF7a protein In human proteins
VAAIVFI104-110 Transmembrane protein 255B86-92
FTLKRKT114-120 Cytosolic 5'-nucleotidase 3A36-42

It is possible that ORF7a is involved in provoking an autoimmune response.

ORF7b protein

ORF7b protein, 43 aa

graphic file with name 41598_2021_96233_Figi_HTML.jpg

In this polypeptide, we found only one 7-mer homologous to the human protein (Table 8).

Table 8.

Localization of the homologous 7-mer in ORF7b and a human protein.

In ORF7b protein In human protein
IIFWFSL26-32 Olfactory receptor 7D4151-157

ORF7b may be involved in provoking an autoimmune response, contributing to olfactory dysfunction.

ORF8 protein

ORF8 protein, 121 aa

graphic file with name 41598_2021_96233_Figj_HTML.jpg

The primary structure of SARS-CoV-2 ORF8 is close to that of bat RaTG13-CoV15. In this polypeptide, there are three 7-mers homologous to human proteins (Table 9).

Table 9.

Localization of homologous 7-mers in the ORF8 protein and human proteins.

In ORF8 protein In human proteins
LVFLGII4-10 Zinc finger protein 48649–55
LGIITTV7-13 D-2-hydroxyglutarate dehydrogenase, mitochondrial262-268
KLGSLVV94-100 Sodium leak channel non-selective protein505-511

Due to the fusion of two 7-mers into 10-mer LVFLGIITTV4-13, the ORF8 protein can be involved in provoking an autoimmune response.

ORF9b protein

ORF9b protein, 97 aa

graphic file with name 41598_2021_96233_Figk_HTML.jpg

In the ORF9b protein molecule, we localized six 7-/8-mers, homologous to human proteins (Table 10).

Table 10.

Localization some of homologous 7-/8-mers in ORF9b protein and human proteins.

In ORF9b protein In human proteins
LVDPQIQL14-21 Valine—tRNA ligase, mitochondrial996-1002
MENAVGR26-32 Neprilysin419-425
LGSPLSL48-54 Stress-responsive DNAJB4-interacting membrane protein 137–43
GSPLSLN49-55 E3 ubiquitin-protein ligase HERC24533-4539
TEELPDE84-90 KH homology domain-containing protein 4465–471
ELPDEFVV86-93 Maestro heat-like repeat-containing protein family member 2B103-110

Some of these 7-/8-mers merge into larger n-mers TEELPDEFVV84-93 and LGSPLSLN48-55.

Octamer ELPDEFVV86-93 is homologous to the Maestro heat-like repeat-containing protein family member 2B (Fig. 1), which may play a role in the sperm capacitation16. Male reproductive dysfunction was proposed as a likely consequence of COVID-1917.

Figure 1.

Figure 1

The SARS CoV-2 S, E and ORF9b protein molecules contain hepta/octamers that are homologous to proteins in the human body, including some nutrients and intestinal commensal bacteria.

After the destruction of the virus particle, ORF9b can take part in provoking an autoimmune response.

Replicase polyprotein RPP 1a

Replicase polyprotein RPP 1a, 4405 aa

graphic file with name 41598_2021_96233_Figl_HTML.jpg

The longest n-mers are underlined.

In the RPP 1a molecule, we localized eleven 8-mers (Table 11) and more than a hundred 7-mers homologous to human proteins.

Table 11.

Localization of homologous 8-mers in RPP 1a and human proteins.

In Replicase polyprotein 1a In human proteins
EVEKGVLP55-62 Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1214–221
ESGLKTIL390-397 Annexin A7404-411
REETGLLM724-731 Estrogen-related receptor gamma30-37
GGSCVLSG1100-1107 Sorting nexin-27112–119
DIQLLKSA1127-1134 Echinoderm microtubule-associated protein-like 138–45
RRSFYVYA2431-2438 Transmembrane protein adipocyte-associated 1225–232
AKKNNLPF2733-2740 Acyl-CoA:lysophosphatidylglycerol acyltransferase 1199–206
YNYEPLTQ3500-3507 DNA helicase199-206
SLKELLQN3530-3537 Centromere protein I496-503
DTSLSGFK3671-3678 Solute carrier family 12 member 7995–1002
PEANMDQE4312-4319 Arachidonate 5-lipoxygenase-activating protein54-61

Some of the 8-mers are found in more than one human protein, some fold into long n-mers, for example EDIQLLKSAYENFNQH1126-1141, EVEKGVLPQLEQPY55-68 and SVEEVLSEARQHL34-46.

In the RPP 1a molecule, 7-mers SCGNFKV505-511 and AIFYLIT2785-2791 are homologous to human olfactory receptor proteins 52N2190-196 and 2W132-38, respectively. A heptamer LKTLLSL1556-1562 is homologous to the human bitter taste receptor T2R55181-187 (Fig. 2).

Figure 2.

Figure 2

Some SARS CoV-2 hepta/octamers are homologous to human olfactory and taste receptor proteins. Homology to some proteins of commensal gut bacteria is also shown.

Replicase polyprotein RPP 1ab

This huge (7096 aa; the primary structure see in18) molecule contains 210 hepta- and octamers homologous to human proteins. Some of them fold into long (more than 15 aa) n-mers.

The possibility of the involvement of replicases in provoking an autoimmune response is debatable. Enzymes in general, and cell cycle enzymes in particular, are evolutionarily highly conserved. Fragments homologous to human proteins must be thrown in huge quantities into the gut lumen during the decay of any microorganism that dies there. It is possible that the interaction of replicases with the host's immune system obeys the laws other than for shorter proteins.

ORF6, ORF10, and ORF14

In these polypeptides (61, 38, and 73 aa, respectively), we did not find 7-/8-mers homologous to human proteins. When assessing the role of SARS CoV-2 proteins in mimicry and provoking an autoimmune response in humans, we considered the following parameters: (i) the number of homologous n-mers; (ii) the compactness of their arrangement in the SARS CoV-2 protein molecules; (iii) intradomain localization (external, transmembrane, internal) of the SARS CoV-2 proteins, and (iv) physiological functions that involve the homologous human proteins (Table 12).

Table 12.

Qualitative assessment of the possibility for the SARS CoV-2 proteins to be involved in the processes of mimicry and provoking an autoimmune response.

Goup of proteins Protein Mimicry Autoimmune response Comment
Structural S +++ +

Taste?—Amiloride-sensitive sodium channel subunit alpha201–208

Muscle contraction?—Unconventional myosin-XVI1404–1421

E +++

Gut microbiota?—Lactobacillus paracasei

Digestion?—Cereals’ proteins

M ++
N ++
Nonstructural ORF3a +
ORF6 No homology
ORF7a +
ORF7b +

Smell?—Olfactory receptor 7D4

Gut microbiota?—Lactobacillus curvatus

ORF8 ++
ORF9b ++ Sperm capacitation?—Maestro heat-like repeat-containing protein family member 2B103–110
ORF10 No homology
ORF14 No homology
RPP1a ?

Taste?—T2R55 receptor

Smell?—Olfactory receptors 2W1 and 52N2

Gut microbiota?—Eubacterium sp.

RPP1ab ?

Conclusions

Analysis of homology between the SARS CoV-2 and human proteins led us to the following conclusions. Some of the SARS CoV-2 proteins can be implicated in mimicry that can delay the response of innate immunity to the invasion of virus particles into a macroorganism, and in provoking an autoimmune process that directs a part of the immune response to the proteins of a macroorganism (after the destruction of virus particles). Mimicry is probably more characteristic of the spike (S) protein, and the provocation of an autoimmune response seems to be a distinctive feature of the envelope (E) protein. The ORF7b protein may be involved in the impairment of olfactory receptors, and the S protein may be involved in taste perception dysfunction.

Drugs aimed at destructing or blocking these and alike regions in proteins of SARS CoV-2 and other viruses can enable the human immune system not to succumb to viral deception and destroy the invader shortly after its penetration into a macroorganism. It should also be borne in mind that drugs affecting such imitation regions can damage native proteins present of the human body. Destroying or blocking such regions can weaken the autoimmune response.

Author contributions

A.M. and V.K. wrote the main manuscript text. A.T. and D.K. prepared data analysis. All authors reviewed the manuscript.

Funding

This research is an authors’ initiative project funded exclusively from their personal sources.

Data availability

The highest.

Code availability

Source code of Ouroboros (v. 0.5) is fully available at github. URL: https://github.com/liquidbrainisstrain/ouroboros. Artwork: We used GIMP (Version 2.10.22) to create our artwork. The figures are completely original and have not been published anywhere.

Competing interests

The authors declare no competing interests.

Footnotes

Publisher's note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The highest.

Source code of Ouroboros (v. 0.5) is fully available at github. URL: https://github.com/liquidbrainisstrain/ouroboros. Artwork: We used GIMP (Version 2.10.22) to create our artwork. The figures are completely original and have not been published anywhere.


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