High-throughput genome-wide sequencing has revealed high genomic variability of HPV16 in different geographic regions which is the most predominant genotype in human papillomavirus (HPV)–associated malignancies. Analysis of the HPV16 by whole-genome sequence (WGS) is an advanced method for the identification of mutations in the genome. There is limited information about HPV16 diversity in Pakistan, especially at the genomic level. Till now, WGS for HPV16 has not been previously reported in Pakistan. The current study has sequenced three HPV16 viral genomes, from two cervical and one oral cavity positive sample of women presented with general gynecological problems without any evidence of precancerous or cancerous lesions using an ion ampliseq customized panel. Sequencing analysis detected 38 variations, including single-nucleotide polymorphisms (SNPs) and two Indels, across three samples with the highest number of SNPs present in E1, E2, and L2, respectively. A total of 20 non-synonymous and 11 synonymous mutations with amino acid substitutions (T1421C, G1515A, T2223C, T1389C, G1483A, and T2191C) were identified. The phylogenetic analysis revealed the genomes of HPV16 are closely associated with those reported from Thailand and the United States. These are the first HPV16 WGS from Pakistan. However, more research is needed with a large sample size from diversified areas to assess the carcinogenic consequences and impact of HPV vaccinations.
BeliakovISeninaMTyulenevYNovoselovaESurovtsevVGuschinA. The prevalence of high carcinogenic risk of HPV genotypes among HIV-positive and HIV-negative MSM from Russia.Can J Infect Dis Med Microbiol2021;2021:6641888
2.
SungHFerlayJSiegelRLLaversanneMSoerjomataramIJemalABrayF. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.CA Cancer J Clin2021;71:209–49
3.
BaigSRubabZArifMMLuckyMH. Chewable risk factors—threatened oral cancer HPV’s looming epidemic in Pakistan.Eur J Biotechnol Biosci2015;3:39–45
4.
BaigSZamanULuckyMH. Human papilloma virus 16/18: fabricator of trouble in oral squamous cell carcinoma.Int J Infect Dis2018;69:115–9
5.
AbdullahAQasimMShafiqMIjazMParveenSMurtazaSJavedQMalikSATararSHMehmoodSSamiANaqviSMHyderMZ. Molecular diagnosis and phylogenetic analysis of human papillomavirus type-16 from suspected patients in Pakistan.Infect Agent Cancer2016;11:1
6.
AzizHIqbalHMahmoodHFatimaSFaheemMSattarAATabassumSNapperSBatoolSRasheedN. Human papillomavirus infection in females with normal cervical cytology: genotyping and phylogenetic analysis among women in Punjab, Pakistan.Int J Infect Dis2018;66:83–9
7.
De VilliersE-MFauquetCBrokerTRBernardH-UZur HausenH. Classification of papillomaviruses.Virol2004;324:17–27
8.
BurdEM. Human papillomavirus and cervical cancer.Clin Microbiol Rev2003;16:1–17
9.
LiuSMinaguchiTLachkarBZhangSXuCTenjimbayashiYShikamaATasakaNAkiyamaASakuraiMNakaoSOchiHOnukiMMatsumotoKYoshikawaHSatohT. Separate analysis of human papillomavirus E6 and E7 messenger RNAs to predict cervical neoplasia progression.PLoS One2018;13:e0193061
10.
MichaudDSLangevinSMEliotMNelsonHHPawlitaMMcCleanMDKelseyKT. High-risk HPV types and head and neck cancer.Int J Cancer Res2014;135:1653–61
11.
LiWQiYCuiXHuoQZhuLZhangATanMHongQYangYZhangHLiuCKongQGengJTianYKongFManD. Characteristic of HPV integration in the genome and transcriptome of cervical cancer tissues.Biomed Res Int2018;2018:6242173
12.
LetianTTianyuZ. Cellular receptor binding and entry of human papillomavirus.Virol J2010;7:2
13.
BernardH-UBurkRDChenZVan DoorslaerKZur HausenHDe VilliersE-M. Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments.Virol2010;401:70–9
14.
Arias-PulidoHPeytonCLTorrez-MartínezNAndersonDNWheelerCM. Human papillomavirus type 18 variant lineages in United States populations characterized by sequence analysis of LCR-E6, E2, and L1regions.Virol2005;338:22–34
15.
LavezzoEMasiGToppoSFranchinEGazzolaVSinigagliaAMasieroSTrevisanMPagniSPalùG. Characterization of intra-type variants of oncogenic human papillomaviruses by next-generation deep sequencing of the E6/E7 region.Viruses2016;8:79
16.
CornetIGheitTIannaconeMRVignatJSyllaBSDel MistroAFranceschiSTommasinoMCliffordGM. HPV16 genetic variation and the development of cervical cancer worldwide.Br J Cancer2013;108:240–4
17.
LeeSHVigliottiVSPappuS. Signature sequence validation of human papillomavirus type 16 (HPV-16) in clinical specimens.J Clin Pathol2010;63:235–9
18.
MinhasSKashifMRehmanZPashaMBIdreesMAnsariF. Distribution of high-risk human papillomavirus genotypes in cervical secretions in Punjab.J Coll Physicians Surg Pak2021;30:786–91
19.
MohammedRLeigh CambellJCooper-WhiteJDimeskiGPunyadeeraC. The impact of saliva collection and processing methods on Crp, Ige, and myoglobin immunoassays.Clin Transl Med2012;1:19
20.
AndrewsSKruegerFSegonds-PichonABigginsLKruegerCWingettS. FastQC: a quality control tool for high throughput sequence data.Babraham Bioinformatics, Cambridge, 2010
21.
LiHDurbinR. Fast and accurate short read alignment with Burrows–Wheeler transform.Bioinformatics2009;25:1754–60
22.
ZerbinoDRBirneyE. Velvet: algorithms for de novo short read assembly using de Bruijn graphs.Genome Res2008;18:821–9
23.
BegunDJHollowayAKStevensKHillierLWPohY-PHahnMWNistaPMJonesCDKernADDeweyCN. Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.PLoS Biol2007;5:e310
24.
NguyenLTSchmidtHAVon HaeselerAMinhBQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.Mol Biol Evol2015;32:268–74
25.
Da SilvaRLDa Silva BatistaZBastosGRCunhaAPAFigueiredoFVDe CastroLODos Anjos PereiraLDa SilvaMACNVidalFCBBarrosMC. Role of HPV 16 variants among cervical carcinoma samples from Northeastern Brazil.BMC Women’s Health2020;20:162
26.
DaiM-ZQiuYDiX-HShiW-WXuH-H. Association of cervical carcinogenesis risk with HPV16 E6 and E7 variants in the Taizhou area, China.BMC Cancer2021;21:769
27.
BarnabasRVLaukkanenPKoskelaPKontulaOLehtinenMGarnettGP. Epidemiology of HPV 16 and cervical cancer in Finland and the potential impact of vaccination: mathematical modelling analyses.PLoS Med2006;3:e138
28.
CornetIGheitTCliffordGMCombesJ-DDalsteinVFranceschiSTommasinoMClavelC. Human papillomavirus type 16 E6 variants in France and risk of viral persistence.Infect Agents Cancer2013;8:4
29.
Nicolás-PárragaSAlemanyLDe SanjoséSBoschFXBravoIG, RIS HPV TT and HPV VVAP study groups. Differential HPV16 variant distribution in squamous cell carcinoma, adenocarcinoma and adenosquamous cell carcinoma.Int J Cancer Res2017;140:2092–100
30.
CornetIGheitTFranceschiSVignatJBurkRDSyllaBSTommasinoMCliffordGM, IARC HPV Variant Study Group. Human papillomavirus type 16 genetic variants: phylogeny and classification based on E6 and LCR.J Virol2012;86:6855–61
31.
HoLChanSYChowVChongTTaySKVillaLLBernardHU. Sequence variants of human papillomavirus type 16 in clinical samples permit verification and extension of epidemiological studies and construction of a phylogenetic tree.J Clin Microbiol1991;29:1765–72
32.
YamadaTManosMMPetoJGreerCEMunozNBoschFXWheelerCM. Human papillomavirus type 16 sequence variation in cervical cancers: a worldwide perspective.J Virol1997;71:2463–72
33.
PimenoffVNDe OliveiraCMBravoIG. Transmission between archaic and modern human ancestors during the evolution of the oncogenic human papillomavirus 16.Mol Biol Evol2017;34:4–19
34.
ChenZDeSalleRSchiffmanMHerreroRWoodCERuizJCCliffordGMChanPKSBurkRD. Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans.PLoS Pathog2018;14:e1007352
35.
SicheroLFerreiraSTrottierHDuarte-FrancoEFerenczyAFrancoELVillaLL. High grade cervical lesions are caused preferentially by non-European variants of HPVs 16 and 18.Int J Cancer2007;120:1763–8
36.
HildesheimASchiffmanMBromleyCWacholderSHerreroRRodriguezABrattiMCShermanMEScarpidisULinQQTeraiMBromleyRLBuetowKAppleRJBurkRD. Human papillomavirus type 16 variants and risk of cervical cancer.J Natl Cancer Inst2001;93:315–8
37.
RomanczukHHowleyPM. Disruption of either the E1 or the E2 regulatory gene of human papillomavirus type 16 increases viral immortalization capacity.Proc Natl Acad Sci U S A1992;89:3159–63
38.
BerumenJOrdoñezRMLazcanoESalmeronJGalvanSCEstradaRAYunesEGarcia-CarrancaAGonzalez-LiraGMadrigal-DeLaCampaA. Asian-American variants of human papillomavirus 16 and risk for cervical cancer: a case–control study.J Natl Cancer Inst2001;93:1325–30
39.
HangDGaoLSunMLiuYKeY. Functional effects of sequence variations in the E6 and E2 genes of human papillomavirus 16 European and Asian variants.J Med Virol2014;86:618–26
40.
SchiffmanMHerreroRDeSalleRHildesheimAWacholderSRodriguezACBrattiMCShermanMEMoralesJGuillenD. The carcinogenicity of human papillomavirus types reflects viral evolution.Virol2005;337:76–84
41.
LinDKouzyRAbi JaoudeJNoticewalaSSDelgado MedranoAYKloppAHTaniguchiCMColbertLE. Microbiome factors in HPV-driven carcinogenesis and cancers.PLoS Pathog2020;16:e1008524
42.
MitraAMacIntyreDALeeYSSmithAMarchesiJRLehneBBhatiaRLyonsDParaskevaidisELiJV. Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity.Sci Rep2015;5:16865
43.
Guerrero-PrestonRGodoy-VitorinoFJedlickaARodríguez-HilarioAGonzálezHBondyJLawsonFFolawiyoOMichailidiCDziedzicA. 16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment.Oncotarget2016;7:51320–34
44.
YaoYYanZDaiSLiCYangLLiuSZhangXShiLYaoY. Human papillomavirus type 16 E1 mutations associated with cervical cancer in a Han Chinese population.Int J Med Sci2019;16:1042–9
45.
BergvallMMelendyTArchambaultJ. The E1 proteins.Virol2013;445:35–56
46.
TsakogiannisDDarmisFGortsilasPRuetherIGKyriakopoulouZDimitriouTGAmoutziasGMarkoulatosP. Nucleotide polymorphisms of the human papillomavirus 16 E1 gene.Arch Virol2014;159:51–63
47.
BreamGLOhmstedeCAPhelpsWC. Characterization of human papillomavirus type 11 E1 and E2 proteins expressed in insect cells.J Virol1993;67:2655–63
48.
GudlevičienėŽStumbrytėAJuknėGSimanavičienėVŽvirblienėA. Distribution of human papillomavirus type 16 variants in Lithuanian women with cervical cancer.Medicina2015;51:328–35
49.
HuaCZhuJZhangBSunSSongYVan Der VeenSChengH. Digital RNA sequencing of human epidermal keratinocytes carrying human papillomavirus type 16 E7.Front Genet2020;11:819
50.
LiuHXuJYangYWangXWuEMajerciakVZhangTSteenbergenRDMWangH-KBanerjeeNSLiYLuWMeyersCZhuJXieXChowLTZhengZ-M. Oncogenic HPV promotes the expression of the long noncoding RNA lnc-FANCI-2 through E7 and YY1.Proc Natl Acad Sci U S A2021;118:e2014195118
51.
AalijahanHGhorbianS. Long non-coding RNAs and cervical cancer.Exp Mol Pathol2019;106:7–16
52.
DongJSuMChangWZhangKWuSXuT. Long non-coding RNAs on the stage of cervical cancer.Oncol Rep2017;38:1923–31
53.
HardenMEPrasadNGriffithsAMungerK. Modulation of microRNA-mRNA target pairs by human papillomavirus 16 oncoproteins.mBio2017;8:e02170–16
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