Journal of Immunology Research

Journal of Immunology Research / 2015 / Article
Special Issue

Peptide-Based Immunotherapeutics and Vaccines 2015

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Research Article | Open Access

Volume 2015 |Article ID 541282 | https://doi.org/10.1155/2015/541282

Darja Kanduc, Candida Fasano, Giovanni Capone, Antonella Pesce Delfino, Michele Calabrò, Lorenzo Polimeno, "Applying the Concept of Peptide Uniqueness to Anti-Polio Vaccination", Journal of Immunology Research, vol. 2015, Article ID 541282, 8 pages, 2015. https://doi.org/10.1155/2015/541282

Applying the Concept of Peptide Uniqueness to Anti-Polio Vaccination

Academic Editor: Yoshihiko Hoshino
Received05 Feb 2015
Accepted28 Apr 2015
Published19 Oct 2015

Abstract

Background. Although rare, adverse events may associate with anti-poliovirus vaccination thus possibly hampering global polio eradication worldwide. Objective. To design peptide-based anti-polio vaccines exempt from potential cross-reactivity risks and possibly able to reduce rare potential adverse events such as the postvaccine paralytic poliomyelitis due to the tendency of the poliovirus genome to mutate. Methods. Proteins from poliovirus type 1, strain Mahoney, were analyzed for amino acid sequence identity to the human proteome at the pentapeptide level, searching for sequences that (1) have zero percent of identity to human proteins, (2) are potentially endowed with an immunologic potential, and (3) are highly conserved among poliovirus strains. Results. Sequence analyses produced a set of consensus epitopic peptides potentially able to generate specific anti-polio immune responses exempt from cross-reactivity with the human host. Conclusion. Peptide sequences unique to poliovirus proteins and conserved among polio strains might help formulate a specific and universal anti-polio vaccine able to react with multiple viral strains and exempt from the burden of possible cross-reactions with human proteins. As an additional advantage, using a peptide-based vaccine instead of current anti-polio DNA vaccines would eliminate the rare post-polio poliomyelitis cases and other disabling symptoms that may appear following vaccination.

1. Introduction

Vaccine-associated paralytic poliomyelitis (VAPP) [1] is the consequence of the replication of vaccine-derived polioviruses (VDPVs) that originate by genetic mutations from the strain contained in the oral polio vaccine (OPV). In fact, the poliovirus (PV) genetic mutability [2] appears to be the molecular basis of VAPP, which throws a shadow over the great success represented by vaccination in fighting PV infection [3, 4].

Currently, two new monovalent OPVs [5] and the change of the schedule from OPV to the exclusive use of inactivated polio vaccine (IPV) [6] represent options to interrupt PV transmission. However, it has been observed that reduction of exposure to a live attenuated virus such as that contained in OPV will inevitably lead to a decrease in herd immunity to a live microorganism and to natural boosters [7]. Such considerations, along with recent PV infection outbreaks, further complicate the issue of polio eradication [8].

In this scenario, new vaccine formulations and renewed research efforts might help to specifically fight PV infection. Recently, we analyzed the peptide overlap between PV1, strain Mahoney, and the human proteome and described a high extent of peptide sharing involving human proteins linked to fundamental cellular functions [9]. These data appeared to be of interest also because PV has been studied mainly at the nucleotide level [10], and, in general, there is a lack of knowledge of the interaction(s) between PV and the human host at the peptide/protein level. Actually, phenetic analyses of PV might help define peptide-based therapeutic approaches against PV infection, given that, for example,(i)one single amino acid (aa) change, that is, His to Tyr at aa position 142 of virion protein 2 (VP2) or Val to Ile at aa position 160 of virion protein 1 (VP1), on the capsid surface of PV1 Sabin allows the establishment of persistent infections in HEp-2c cell cultures [11];(ii)replacement of the Ala residue with Asp at aa position 3 is linked to 50% loss of virion protein 4 (VP4) precursor myristoylation and severe reduction in specific infectivity [12];(iii)the 25th aa, Ile, of PV 2C protein interacts with human reticulon 3, a protein involved in viral replication and/or pathogenesis [13].

Moreover, since the 1980s we have known that small aa groupings can play a critical role in neutralizing PV. For example, the discontinuous E4T7T/S8R9 tetrapeptide, which is present in PV VP1, is crucial for neutralizing PV3 by anti-PV3 25-1-14 monoclonal antibody (mAb) [14]. Additional examples of short immune determinants in the immune response against PV are the following ones:(i)A linear heptapeptide (DNNQTSP) is an Ab-binding site mapped to aa residues 164–170 of VP2 [15].(ii)Short synthetic peptides (e.g., DNTVRET, RSRSES, RSRSESSIESF, and STTNKDK) from PV VP1 prime the immune system of rabbits for a long-lasting, virus-neutralizing IgG Ab response following a single inoculation of intact virus [16].(iii)The Immune Epitope Database (IEDB; http://www.immuneepitope.org) [17] includes the continuous linear pentapeptide STTNK (IEDB ID: 61944) [18, 19] and the discontinuous pentapeptide T141E143S312E315P417 (IEDB ID: 91064) [20] as PV-derived epitopes.

Following the mathematical quantification of pentapeptide sharing between PV1 and human proteins, we reported that 2,040 out of the 2,204 pentamers composing the PV1 proteome are shared with the human proteome for a total of 18,223 matches, including multiple occurrences [9]. In general, a vast peptide sharing with human proteins is a characteristic of viral proteomes [21]. This peptide commonality suggests the existence of common evolutionary links between entities widely different as viruses and Homo sapiens and, in addition, indicates that potential cross-reactivity may affect antivirus vaccine formulations [22] and serological analyses [23]. Hence, it is reasonable to postulate that vaccines based on peptides unique to a virus and absent in the host proteome would guarantee high specificity and, at the same time, eliminate potential cross-reactivity.

Pursuing the objectives of overcoming the difficulties posed by the PV tendency to mutate and eliminating the viral reactivation-related VAPP in order to contribute to the global eradication of poliomyelitis, here we examine PV1 Mahoney polyprotein primary sequence and describe a set of pentapeptides uniquely owned by PV1, endowed with immunologic potential, and conserved among 43 PV strains. We propose that this set of pentapeptides might be used in preclinical and in vivo protocols with the ultimate aim of formulating effective, safe, and universal anti-PV vaccines.

2. Methods

The primary aa sequence of human PV1 polyproteins, strain Mahoney (NCBI taxonomic identifier: 12081; Swiss-Prot/UniProtKB entry: P03300), consisting of 11 viral proteins, 2,209 aa long [25] (further details at http://www.uniprot.org/uniprot/P03300), was analyzed for aa sequence similarity to the human proteome at the pentapeptide level. In brief, the viral polyprotein was dissected into 5-mers sequentially overlapped by four residues: MGAQV, GAQVS, AQVSS, QVSSQ, VSSQK, and so forth; then, each viral pentapeptide was used as a probe to scan the human proteome for instances of the same pentapeptide, as already described [9]. The similarity analysis used the Protein Information Resource (PIR) peptide match program (http://pir.georgetown.edu/) [26].

PV-derived epitopes were retrieved from the Immune Epitope Database (IEDB; http://www.immuneepitope.org) [17]. Only PV epitopes that had been experimentally validated in the human host were considered in this study.

Consensus peptide sequences were defined by ClustalW multialignment analysis (http://www.uniprot.org/program/?query=clustalw&sort=score) [24] of sequences from 43 PV strains retrieved from UniProt database (http://www.uniprot.org/) on the basis of the following characteristics: (1) described in scientific literature; (2) corresponding to the entire PV polyprotein; (3) derived from PV1 and PV3; (4) derived from PV variants isolated from VAPP or acute flaccid paralysis (AFP) patients or from immunocompromised patients with residual paralysis. Description and references of the 43 PV sequences used for multialignment analysis are reported in detail at http://www.uniprot.org/; the relative Swiss-Prot/UniProtKB entries are P03300, P03301, P03302, P06209, Q9Q281, Q9Q280, Q71AZ9, Q5TLH5, D1YSI9, D1YSJ1, D1YSJ2, D1YSJ3, D1YSJ4, D1YSJ5, D1YSJ6, D1YSJ7, D1YSJ9, D1YSK1, D1YSK2, D1YSK3, D1YSK4, D1YSK5, D1YSK6, D1YSK7, D1YSK8, D1YSK9, D1YSL0, D1YSL1, D1YSL2, D1YSL3, D1YSL4, D1YSL5, D2X673, D8L541, B4YUL3, B4YUL4, Q84792, C5HJY2, C5HJY3, D1GE40, D2E679, D1GE41, and D2XUS9.

3. Results and Discussion

3.1. Identification of Pentapeptides Unique to PV Type 1, Strain Mahoney

Using the procedure described under Section 2, we searched the human PV1, strain Mahoney, primary sequence for pentapeptides not shared with human proteins. We used pentapeptides as probes since a pentapeptide is a minimal functional unit in immunology [27], thus representing an appropriate length unit in measuring the qualitative/quantitative parameters of immunological phenomena [28].

Table 1 reports the pentapeptide platform that characterizes PV1 Mahoney polyprotein when compared to the Homo sapiens proteome. We find that 164 pentapeptides are unique to the viral polyprotein and absent in human proteins. In a few instances, viral 5-mers consecutively overlap (Table 1, pentapeptides in bold), thus forming 6-, 7-, and 8-mer stretches (e.g., PV163–169QNMYYHY, PV446–453NYYTHWAG, PV783–789AYSHFYD, PV1496–1498KGWIVNI, PV1594–1600GIHDNVA, PV1699–1706RTLMYNFP, and PV1750–1756EIQWMRP).


PosaSequenceb,cPosaSequenceb,cPosaSequenceb,cPosaSequenceb,cPosaSequenceb,cPosaSequenceb,c

11GAHEN393MIPLN746PAKWD969YYPAR1399CHQPA1750EIQWM
29TINYY403KNTMD748KWDDY974YQSHI1403ANFKR1751IQWMR
72NIEAC404NTMDM749WDDYT996CHHGV1413CGKAI1752QWMRP
73IEACG408MYRVQ752YTWQT1014FADIR1418QLMDK1762YPIIN
104YGRWP414NDNPH763FYTYG1021YAYEE1437IVNER1810YVGNK
106RWPEY436LSHTM783AYSHF1084ITRNY1458PIQYK1840TEQMC
107WPEYL446NYYTH784YSHFY1105VSPWQ1475ECIND1849MYGTD
130CRFYT447YYTHW785SHFYD1136TEACN1489VRNYC1933VAMRM
145RGWWW448YTHWA835KIRVY1139CNAAK1490RNYCE1935MRMAF
146GWWWK449THWAG841KPKHI1188STIHQ1496KGWIV1946FHKNP
148WWKLP464SMMAT847VWCPR1190IHQSC1497GWIVN1947HKNPG
149WKLPD465MMATG857AYYGP1204FNNVR1498WIVNI1966WSKIP
163QNMYY494HVIWD863VDYKD1205NNVRW1513NRAMT1979AFDYT
164NMYYH495VIWDI880TYGFG1209WLSIQ1532VYVMY1983TGYDA
165MYYHY497WDIGL881YGFGH1231LEHTI1534VMYKL1993WFEAL
179VQCNA507MVVPW883FGHQN1291FDGYK1536YKLFA2028YCVKG
199MCLAG510PWISN884GHQNK1311GADMK1588GEFTM2070KMIAY
242RFCPV518RQTTN894GYKIC1314MKLFC1592MLGIH2073AYGDD
244CPVDY534FYQTR895YKICN1326FIPPM1594GIHDN2115TWENV
271TNNCA556SACND897ICNYH1340FTSNY1595IHDNV2131KYPFL
292KHNNW557ACNDF912VSTMW1341TSNYV1596HDNVA2148SIRWT
293HNNWG558CNDFS914TMWDR1368RFAFD1660TETND2158TQDHV
295NWGIA568DTTHI934ARCNC1369FAFDM1677MFVPV2168LAWHN
323PMCC569TTHIG942VYYCE1371FDMDI1699RTLMY2201LYRRW
324PMCCE588MIDNT948RRKYY1388DMTMA1700TLMYN
326CCEFN665CVSII959PTFQY1389MTMAT1701LMYNF
327CEFNG708RFDME961FQYME1394EMCKN1702MYNFP
391DTMIP735QIMYV962QYMEA1398NCHQP1742SYFTQ

aa position along the human PV type 1, strain Mahoney, primary sequence.
baa sequences given in one-letter code.
cConsecutively overlapping pentapeptides forming 7- and 8-mer stretches unique to PV are given in bold.
3.2. Analysis of the Immunologic Potential of Peptides Unique to PV

Next, the pentapeptides described in Table 1 were analyzed for their immunologic potential as follows. PV-derived epitopes were retrieved from IEDB, and the epitopes that had been experimentally validated in the human host were analyzed for the presence of pentapeptides unique to PV1 (see Table 1).

As reported in Table 2, the search through IEDB produced a final list of 78 viral epitopes derived from PV1 Mahoney, PV3 Sabin, and PV3 (P3/LEON/37 and P3/LEON 12A (1)B). Epitopes derived from PV2 strains were not considered since only data from immunoassays in mice, rats, and/or rabbits were available in IEDB for PV2 strains at the time of this study. Following sequence analysis, it was found that 20 of the 78 epitopes (i.e., IEDB IDs: 31814, 48785, 58511, 59797, 71769, 79272, 79480, 99910, 100138, 100244, 100349, 100382, 100536, 100576, 100631, 100667, 100672, 146181, 146248, and 146390; see IEDB IDs in bold in Table 2) have a total of 12 viral pentapeptides that are absent in the human proteome (pentapeptides in capital letters in Table 2). That is, a first conclusion from Table 2 is that 12 out of the 164 pentapeptides unique to PV1, strain Mahoney, are part of 20 PV epitopic sequences endowed with an immunologic potential in the human host.


IEDB IDaEpitope sequenceb,cPV antigenPV strainImmune context

30661kevpaltavetgatVP1PV3 SabinB
31814klefftysRFDMEltfvvtanVP1PV1 MahoneyT
46859paltavetgatnplVP1PV1 MahoneyB-T
48785ppgapvpeKWDDYTWQTssnpVP1PV1 MahoneyT
55952rsrsessiesfVP1PV1 MahoneyB
58511siFYTYGtaparisvpyvgiVP1PV1 MahoneyT
59797snAYSHFYDgfskvplkdqsVP1PV1 MahoneyT
66978tvdnsasttnkdklfavwkPolyproteinPV1 MahoneyT
71769vvndhnptkvtsKIRVYlkpPolyproteinPV1 MahoneyT
79155altlslpkqqdslpdtkaPolyproteinPV3 (P3/LEON/37 and P3/LEON 12A (1)B)T
79160atnplapsdtvqtrhvvqPolyproteinPV3 (P3/LEON/37 and P3/LEON 12A (1)B)T
79186dneqpttraqklfamPolyproteinPV3 (P3/LEON/37 and P3/LEON 12A (1)B)T
79269kevpaltavetgatnplaPolyproteinPV3 (P3/LEON/37 and P3/LEON 12A (1)B)T
79272khvrVWCPRppravpyygPolyproteinPV3 (P3/LEON/37 and P3/LEON 12A (1)B)T
79318nghalnqvyqimyippgaPolyproteinPV3 (P3/LEON/37 and P3/LEON 12A (1)B)T
79350qklfamwritykdtvPolyproteinPV3 (P3/LEON/37 and P3/LEON 12A (1)B)T
79354qpttraqklfamwriPolyproteinPV3 (P3/LEON/37 and P3/LEON 12A (1)B)T
79433traqklfamwritykPolyproteinPV3 (P3/LEON/37 and P3/LEON 12A (1)B)T
79434traqklfamwritykdtvPolyproteinPV3 (P3/LEON/37 and P3/LEON 12A (1)B)T
79435trhvvqrrsrsestiesfPolyproteinPV3 (P3/LEON/37 and P3/LEON 12A (1)B)T
79436tskvriymkpkhvrvwPolyproteinPV3 (P3/LEON/37 and P3/LEON 12A (1)B)T
79443vaiievdneqpttraqklPolyproteinPV3 (P3/LEON/37 and P3/LEON 12A (1)B)T
79461vrvvndhnptkvtskvriPolyproteinPV3 (P3/LEON/37 and P3/LEON 12A (1)B)T
79480yippgaptpksWDDYTwqPolyproteinPV3 (P3/LEON/37 and P3/LEON 12A (1)B)T
80446argacvtimtvdnpaVP1PV1 MahoneyB
81394easgpthskeipaltVP1PV1 MahoneyB
82831gpthskeipaltaveVP1PV1 MahoneyB
83234hskeipaltavetgaVP1PV1 MahoneyB
88446sdtvqtrhvvqhrsrVP1PV1 MahoneyB
88495sessiesffargacvVP1PV1 MahoneyB
99863aaparisvpyvglaPolyproteinPV3 SabinB
99886ahskevpaltavetPolyproteinPV3 SabinB
99901arisvpyvglanayPolyproteinPV3 SabinB
99910AYSHFYDgfakvplPolyproteinPV3 SabinB
99933dfgvlavrvvndhnPolyproteinPV3 SabinB
99963dtvqlrrklefftyPolyproteinPV3 SabinB
100029famwritykdtvqlPolyproteinPV3 SabinB
100101hfydgfakvplktdPolyproteinPV3 SabinB
100117hnptkvtskvriymPolyproteinPV3 SabinB
100138iFYTYGaaparisvPolyproteinPV3 SabinB
100244lanAYSHFYDgfakPolyproteinPV3 SabinB
100349npsiFYTYGaaparPolyproteinPV3 SabinB
100382pkhvrVWCPRppraPolyproteinPV3 SabinB
100391psdtvqtrhvvqrrPolyproteinPV3 SabinB
100425qklfamwritykdtPolyproteinPV3 SabinB
100430qlrrklefftysrfPolyproteinPV3 SabinB
100439qpttraqklfamwrPolyproteinPV3 SabinB
100482rppravpyygpgvdPolyproteinPV3 SabinB
100492samtvddfgvlavrPolyproteinPV3 SabinB
100504sevaqgaltlslpkPolyproteinPV3 SabinB
100536svpyvglanAYSHFPolyproteinPV3 SabinB
100559tkvtskvriymkpkPolyproteinPV3 SabinB
100573traqklfamwrityPolyproteinPV3 SabinB
100575tskvriymkpkhvrPolyproteinPV3 SabinB
100576tssnpsiFYTYGaaPolyproteinPV3 SabinB
100580tvddfgvlavrvvnPolyproteinPV3 SabinB
100583tvqtrhvvqrrsrsPolyproteinPV3 SabinB
100585twqtssnpsifytyPolyproteinPV3 SabinB
100586tygaaparisvpyvPolyproteinPV3 SabinB
100587tykdtvqlrrklefPolyproteinPV3 SabinB
100613vlavrvvndhnptkPolyproteinPV3 SabinB
100619vndhnptkvtskvrPolyproteinPV3 SabinB
100628vriymkpkhvrvwcPolyproteinPV3 SabinB
100630vrvvndhnptkvtsPolyproteinPV3 SabinB
100631vrVWCPRppravpyPolyproteinPV3 SabinB
100638wcprppravpyygpPolyproteinPV3 SabinB
100644writykdtvqlrrkPolyproteinPV3 SabinB
100667ymkpkhvrVWCPRpPolyproteinPV3 SabinB
100672yvglanAYSHFYDgPolyproteinPV3 SabinB
146178ayappgaqpptsrkPolyproteinPV3 SabinB
146181cgSMMATGkilvayPolyproteinPV3 SabinB
146248flfcgSMMATGkilPolyproteinPV3 SabinB
146311hqgalgvfaipeycPolyproteinPV3 SabinB
146333ilvayappgaqpptPolyproteinPV3 SabinB
146390kftflfcgSMMATGPolyproteinPV3 SabinB
146494phqiinlrtnnsatPolyproteinPV3 SabinB
146496ppgaqpptsrkeamPolyproteinPV3 SabinB
146516ravpyygpgvdyrnPolyproteinPV3 SabinB

PV-derived epitopes are listed according to increasing IEDB ID number. Further details and reference(s) on each IEDB ID are reported at http://www.immuneepitope.org [17].
bOnly PV-derived epitopes that had been experimentally validated in the human host are reported.
cThe twenty PV-derived epitopes (and related IDs) containing PV-pentapeptide(s) absent in the human proteome are in bold, with the pentapeptide(s) absent in the human proteome given in capital.

Moreover, it can be seen that the 12 unique PV1 pentapeptides are not distributed at random among the PV-derived epitopes. For example, three unique pentapeptides (KWDDY, WDDYT, and YTWQT) overlap each other in the epitope IEDB ID 48785, sequence ppgapvpeKWDDYTWQTssnp (with unique overlapping pentapeptides in capital); the heptapeptide AYSHFYD, formed by three overlapping unique pentapeptides shifted by one residue, characterizes four PV-derived epitopes (IEDB IDs: 59797, 99910, 100244, and 100672); the hexapeptide SMMATG formed by two overlapped 5-mers is present in three epitopes (IEDB IDs: 146181, 146248, and 146390).

Theoretically, vaccines based on such PV epitopic peptides (i.e., KWDDYTWQT, AYSHFYD, and SMMATG) might evoke highly specific anti-PV immune responses exempt of possible collateral cross-reactions in the human host.

3.3. Identification of Consensus Pentapeptides Unique to PVs and Endowed with Immunologic Potential

We reasoned that using epitopic peptides unique to the virus and conserved among PV strains might help develop a global anti-PV peptide-based vaccination protocol. Such an approach would be of special importance in providing an effective and wide coverage to the human population worldwide, thus allowing reaching the goal of PV eradication [29, 30]. To this aim, we searched for unique conserved sequences by analysing a set of 43 PV polyproteins selected as described under Section 2 and comprehending also PV variants isolated from faeces of VAPP or AFP or from immunocompromised patient(s) with residual paralysis. The 43 PV polyprotein sequences were aligned using multialignment ClustalW program [24] and the peptide sequences present in PV-derived epitopes (see Table 2) and absent in the human proteome were localized.

Table 3 shows that seven potentially immunogenic peptides (in the order PV465–469MMATG, PV708–712RFDME, PV752–756DYTWQT, PV763–767FYTYG, PV783–789AYSHFYD, PV835–839KIRVY, and PV847–851VWCPR), derived from epitopes corresponding to (or formed of) pentapeptides unique to PV1 (see Tables 1 and 2), have 100% conservation among the 43 PV strains/variants under analysis. The seven potentially immunogenic unique peptide sequences had the same level of conservativeness in PV2 derived strains (data not shown).


PV strainUniProt/Swiss-Prot entry aa Pos 464aa Pos 708aa Pos 748aa Pos 763aa Pos
783
aa Pos 835aa Pos 847

PV1 MahoneyP03300FMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1 SabinP03301SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV3 P3/Leon/37P03302SMMATGRFDMEsWDDYTWQTFYTYGAYSHFYDKvRiYVWCPR
PV3 23127P06209SMMATGRFDMEsWDDYTWQTFYTYGAYSHFYDKvRvYVWCPR
PV1 isolatedQ9Q281SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKvRVYVWCPR
PV1 isolatedQ9Q280SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1 isolatedQ71AZ9SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1 isolatedQ5TLH5SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-HAI01008C2D1YSI9SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-HAI01009D1YSJ1SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-HAI01008D1YSJ2SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-HAI01002D1YSJ3SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-HAI01001D1YSJ4SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-DOR01012D1YSJ5SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-DOR01002CD1YSJ6SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-DOR01002D1YSJ7SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-DOR01001C1D1YSJ9SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-DOR00042C2D1YSK1SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-DOR00042C1D1YSK2SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-DOR00042D1YSK3SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-DOR00041C3D1YSK4SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-DOR00041C2D1YSK5SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-DOR00044D1YSK6SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-DOR00028CD1YSK7SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-DOR00028D1YSK8SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-DOR00023CD1YSK9SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-DOR00025D1YSL0SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-DOOR24D1YSL1SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-DOR00015D1YSL2SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-DOR00016D1YSL3SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-HAI01013allD1YSL4SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-HAI01015D1YSL5SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV1-S302D2X673SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
CHN8184/GZ/CHN/2004D8L541SMMATGRFDMEKWDDYTWQTFYTYGAYSHFYDKIRVYVWCPR
PV3 isolatedB4YUL3SMMATGRFDMEsWDDYTWQTFYTYGAYSHFYDKvRVYVWCPR
PV3 isolatedB4YUL4SMMATGRFDMEsWDDYTWQTFYTYGAYSHFYDKvRVYVWCPR
PV3 (vacc.StrainSabin3
(Leon 12a1b))
Q84792SMMATGRFDMEsWDDYTWQTFYTYGAYSHFYDKvRiYVWCPR
PV3-33239C5HJY2SMMATGRFDMEsWDDYTWQTFYTYGAYSHFYDKvRiYVWCPR
PV3-31974C5HJY3SMMATGRFDMEsWDDYTWQTFYTYGAYSHFYDKvRiYVWCPR
PV3-FIN84-60212D1GE40SMMATGRFDMEsWDDYTWQTFYTYGAYSHFYDKvRiYVWCPR
PV3-SWI10947D2E679SMMATGRFDMEsWDDYTWQTFYTYGAYSHFYDKvRiYVWCPR
PV3-FIN84-2493D1GE41SMMATGRFDMEsWDDYTWQTFYTYGAYSHFYDKvRiYVWCPR
PV3-P3/Jinan/1/09D2XUS9SMMATGRFDMEsWDDYTWQTFYTYGAYSHFYDKvRiYVWCPR

The 43 PV sequences were aligned using ClustalW multialignment program (http://www.uniprot.org/align/) [24]. The analyzed PV sequences and related references are described at http://www.uniprot.org/ and reported by Swiss-Prot/UniProtKB accession number. Peptide sequences present in PV-derived epitopes (see Table 2) and absent in the human proteome were localized along the 43 aligned PV sequences and analyzed for conservativeness. Peptide sequences are indicated by their position along the PV polyprotein. Mutated aa residues are in lower case.

4. Conclusion

Anti-PV immunization has been one of the major public health measures of the last century. International campaigns to eliminate polio reduced the incidence of this disease in the world. However, problematic issues remain, such as the tendency of the PV genome to mutate, the potential risk to develop postvaccine paralytic poliomyelitis, and the difficulty to completely eradicate PV infection in the world. In fact, according to the World Health Organization, in 2012, still three countries in the world remain polio-endemic: Nigeria, Pakistan, and Afghanistan [31].

The present data propose the concept of sequence uniqueness as a tool to define specific immunotherapies exempt of collateral effects [22] and describe a methodology to identify PV peptides that have zero percent identity to human proteins, are endowed with an immunologic potential, and are highly conserved among PV strains (e.g., PV465–469MMATG, PV708–712RFDME, PV752–756DYTWQT, PV763–767FYTYG, PV783–789AYSHFYD, PV835–839KIRVY, and PV847–851VWCPR; see Table 3). Importantly, polio peptide sequences alternate through the human proteome with a frequency versus rarity pattern that characterizes other pathogens too [3235].

Theoretically, such viral consensus epitopic peptides appear to be ideal tools to generate anti-PV immune responses promising of high specificity, thus avoiding serological cross-reactivity between human polyomaviruses [23], as well as possible cross-reactions with the human host [22]. As an example, a construct composed of the coding frames corresponding to the immunogenic consensus sequences described above (Table 2) might determine a specific anti-PV immune response and, at the same time, by being based on peptides, might eliminate the issues inherent to the tendency of the PV genome to mutate (i.e., VAPP). Such viral peptide sequences might also be used in passive anti-PV immunotherapies, that is, to produce specific antibodies capable of reacting with intact viral protein antigens.

Actually, the present report is intended to represent a first approach to preclinical and animal studies. As a matter of fact, the solidity of a large body of theoretical and in silico data is the mandatory basis to design in vivo experimentation and validation protocols especially when considering that (i) although monkeys can be experimentally infected, humans are the only known natural hosts of poliovirus; (ii) small animal models for testing polio pathogenesis mainly relate to transgenic mice to express a human receptor to poliovirus [36]; and, moreover, (iii) current laws on in vivo experimentation are increasingly restrictive.

Conflict of Interests

The authors declare that this paper is based on research that was not funded entirely or partially by an outside source.

Authors’ Contribution

Darja Kanduc proposed the original idea, supervised the work, interpreted the data, and wrote the paper. All authors contributed to the computational analyses; Giovanni Capone also contributed to the project definition. All authors discussed and approved the paper.

References

  1. T. J. John, “A developing country perspective on vaccine-associated paralytic poliomyelitis,” Bulletin of the World Health Organization, vol. 82, no. 1, pp. 53–57, 2004. View at: Google Scholar
  2. C. Runckel, O. Westesson, R. Andino, and J. L. DeRisi, “Identification and manipulation of the molecular determinants influencing poliovirus recombination,” PLoS Pathogens, vol. 9, no. 2, Article ID e1003164, 2013. View at: Publisher Site | Google Scholar
  3. R. J. D. Tebbens, M. A. Pallansch, J.-H. Kim et al., “Oral poliovirus vaccine evolution and insights relevant to modeling the risks of circulating vaccine-derived polioviruses (cVDPVs),” Risk Analysis, vol. 33, no. 4, pp. 680–702, 2013. View at: Publisher Site | Google Scholar
  4. W. R. Dowdle, E. De Gourville, O. M. Kew, M. A. Pallansch, and D. J. Wood, “Polio eradication: the OPV paradox,” Reviews in Medical Virology, vol. 13, no. 5, pp. 277–291, 2003. View at: Publisher Site | Google Scholar
  5. R. B. Aylward and C. Maher, “Interrupting poliovirus transmission—new solutions to an old problem,” Biologicals, vol. 34, no. 2, pp. 133–139, 2006. View at: Publisher Site | Google Scholar
  6. S. C. Arya and N. Agarwal, “Re: world wide experience with inactivated poliovirus vaccine,” Vaccine, vol. 27, no. 1, p. 1, 2009. View at: Publisher Site | Google Scholar
  7. M.-C. Bonnet and A. Dutta, “World wide experience with inactivated poliovirus vaccine,” Vaccine, vol. 26, no. 39, pp. 4978–4983, 2008. View at: Publisher Site | Google Scholar
  8. B. T. Mayer, J. N. S. Eisenberg, C. J. Henry, M. G. M. Gomes, E. L. Ionides, and J. S. Koopman, “Successes and shortcomings of polio eradication: a transmission modeling analysis,” American Journal of Epidemiology, vol. 177, no. 11, pp. 1236–1245, 2013. View at: Publisher Site | Google Scholar
  9. G. Novello, G. Capone, C. Fasano, S. L. Bavaro, A. N. Polito, and D. Kanduc, “A quantitative description of the peptide sharing between poliovirus and Homo sapiens,” Immunopharmacology and Immunotoxicology, vol. 34, no. 3, pp. 373–378, 2012. View at: Publisher Site | Google Scholar
  10. E. Cherkasova, M. Laassri, V. Chizhikov et al., “Microarray analysis of evolution of RNA viruses: evidence of circulation of virulent highly divergent vaccine-derived polioviruses,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 16, pp. 9398–9403, 2003. View at: Publisher Site | Google Scholar
  11. I. Pelletier, G. Duncan, and F. Colbère-Garapin, “One amino acid change on the capsid surface of poliovirus sabin 1 allows the establishment of persistent infections in HEp-2c cell cultures,” Virology, vol. 241, no. 1, pp. 1–13, 1998. View at: Publisher Site | Google Scholar
  12. N. Moscufo, J. Simons, and M. Chow, “Myristoylation is important at multiple stages in poliovirus assembly,” Journal of Virology, vol. 65, no. 5, pp. 2372–2380, 1991. View at: Google Scholar
  13. W.-F. Tang, S.-Y. Yang, B.-W. Wu et al., “Reticulon 3 binds the 2C protein of enterovirus 71 and is required for viral replication,” The Journal of Biological Chemistry, vol. 282, no. 8, pp. 5888–5898, 2007. View at: Publisher Site | Google Scholar
  14. D. M. A. Evans, P. D. Minor, G. S. Schild, and J. W. Almond, “Critical role of an eight-amino acid sequence of VP1 in neutralization of poliovirus type 3,” Nature, vol. 304, no. 5925, pp. 459–462, 1983. View at: Publisher Site | Google Scholar
  15. K. J. Wiegers, K. Wetz, and R. Dernick, “Molecular basis for linkage of a continuous and discontinuous neutralization epitope on the structural polypeptide VP2 of poliovirus type 1,” Journal of Virology, vol. 64, no. 3, pp. 1283–1289, 1990. View at: Google Scholar
  16. E. A. Emini, B. A. Jameson, and E. Wimmer, “Priming for and induction of anti-poliovirus neutralizing antibodies by synthetic peptides,” Nature, vol. 304, no. 5928, pp. 699–703, 1983. View at: Publisher Site | Google Scholar
  17. R. Vita, L. Zarebski, J. A. Greenbaum et al., “The immune epitope database 2.0,” Nucleic Acids Research, vol. 38, supplement 1, pp. D854–D862, 2010. View at: Publisher Site | Google Scholar
  18. K. Wiegers, H. Uhlig, and R. Dernick, “N-AgIB of poliovirus type 1: a discontinuous epitope formed by two loops of VP1 comprising residues 96-104 and 141-152,” Virology, vol. 170, no. 2, pp. 583–586, 1989. View at: Publisher Site | Google Scholar
  19. R. Ketterlinus and K. Wiegers, “Mapping of antigenic domains in poliovirus VP1 involved in structural rearrangements during virus morphogenesis and antigenic alterations of the virion,” Virology, vol. 204, no. 1, pp. 27–37, 1994. View at: Publisher Site | Google Scholar
  20. C. Reynolds, G. Page, H. Zhou, and M. Chow, “Identification of residues in VP2 that contribute to poliovirus neutralization antigenic site 3B,” Virology, vol. 184, no. 1, pp. 391–396, 1991. View at: Publisher Site | Google Scholar
  21. D. Kanduc, A. Stufano, G. Lucchese, and A. Kusalik, “Massive peptide sharing between viral and human proteomes,” Peptides, vol. 29, no. 10, pp. 1755–1766, 2008. View at: Publisher Site | Google Scholar
  22. D. Kanduc, “Peptide cross-reactivity: the original sin of vaccines,” Frontiers in Bioscience, vol. 4, no. 4, pp. 1393–1401, 2012. View at: Google Scholar
  23. U. Moens, M. van Ghelue, X. Song, and B. Ehlers, “Serological cross-reactivity between human polyomaviruses,” Reviews in Medical Virology, vol. 23, no. 4, pp. 250–264, 2013. View at: Publisher Site | Google Scholar
  24. J. D. Thompson, D. G. Higgins, and T. J. Gibson, “CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research, vol. 22, no. 22, pp. 4673–4680, 1994. View at: Publisher Site | Google Scholar
  25. V. R. Racaniello and D. Baltimore, “Molecular cloning of poliovirus cDNA and determination of the complete nucleotide sequence of the viral genome,” Proceedings of the National Academy of Sciences of the United States of America, vol. 78, no. 8, pp. 4887–4891, 1981. View at: Publisher Site | Google Scholar
  26. C. H. Wu, L.-S. Yeh, H. Huang et al., “The protein information resource,” Nucleic Acids Research, vol. 31, no. 1, pp. 345–347, 2003. View at: Publisher Site | Google Scholar
  27. D. Kanduc, “Homology, similarity, and identity in peptide epitope immunodefinition,” Journal of Peptide Science, vol. 18, no. 8, pp. 487–494, 2012. View at: Publisher Site | Google Scholar
  28. D. Kanduc, “Pentapeptides as minimal functional units in cell biology and immunology,” Current Protein & Peptide Science, vol. 14, no. 2, pp. 111–120, 2013. View at: Publisher Site | Google Scholar
  29. N. C. Grassly, “The final stages of the global eradication of poliomyelitis,” Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences, vol. 368, no. 1623, Article ID 20120140, 2013. View at: Publisher Site | Google Scholar
  30. P. Minor, “The polio endgame,” Human Vaccines & Immunotherapeutics, vol. 10, no. 7, pp. 2106–2108, 2014. View at: Publisher Site | Google Scholar
  31. Z. A. Bhutta, “Conflict and polio: winning the polio wars,” Journal of the American Medical Association, vol. 310, no. 9, pp. 905–906, 2013. View at: Publisher Site | Google Scholar
  32. D. Kanduc, L. Tessitore, G. Lucchese, A. Kusalik, E. Farber, and F. M. Marincola, “Sequence uniqueness and sequence variability as modulating factors of human anti-HCV humoral immune response,” Cancer Immunology, Immunotherapy, vol. 57, no. 8, pp. 1215–1223, 2008. View at: Publisher Site | Google Scholar
  33. G. Lucchese, A. Stufano, and D. Kanduc, “Proposing low-similarity peptide vaccines against Mycobacterium tuberculosis,” Journal of Biomedicine and Biotechnology, vol. 2010, Article ID 832341, 8 pages, 2010. View at: Publisher Site | Google Scholar
  34. G. Capone, G. Lucchese, M. Calabrò, and D. Kanduc, “West Nile virus diagnosis and vaccination: using unique viral peptide sequences to evoke specific immune responses,” Immunopharmacology and Immunotoxicology, vol. 35, no. 1, pp. 64–70, 2013. View at: Publisher Site | Google Scholar
  35. A. Lucchese, A. Guida, G. Capone, M. Petruzzi, D. Lauritano, and R. Serpico, “Designing a peptide-based vaccine against Porphyromonas gingivalis,” Frontiers in Bioscience, vol. 5, no. 2, pp. 631–637, 2013. View at: Google Scholar
  36. S. Khan, H. Toyoda, M. Linehan et al., “Poliomyelitis in transgenic mice expressing CD155 under the control of the Tage4 promoter after oral and parenteral poliovirus inoculation,” Journal of General Virology, vol. 95, part 8, pp. 1668–1676, 2014. View at: Publisher Site | Google Scholar

Copyright © 2015 Darja Kanduc et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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