Next-Generation Sequencing (NGS) Based Detection of Viral Pathogens

Abid Qureshi, Vaqar Gani Tantray, Altaf Rehman Kirmani, Abdul Ghani Ahangar

Abstract


Viral diseases are some of the most widespread causes of human death worldwide. Diagnosis of the pathogenic viruses using next-generation sequencing (NGS) technologies can play a vital task in dealing with the global viral epidemics. NGS based diagnostic approaches are more sensitive and efficient compared to traditional methods. NGS technology has the capability to screen multiple pathogens simultaneously as well as identify quasispecies and new or previously unknown viruses. Bioinformatics analysis and interpretation of high throughput sequencing datasets can help in screening different samples or products for viral contamination. Besides, it also allows an in-depth phylogenetic analysis which can predict the pathogenicity and potential host range of the virus. Dedicated bioinformatics analysis pipelines are now available for automated identification of viruses and their integration sites in the host genome from clinical samples using NGS data. This review will focus on the different applications of NGS to viral diagnosis.

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References


Anthony SJ, Epstein JH, Murray KA, Navarrete-Macias I, Zambrana-Torrelio CM, Solovyov A, Ojeda-Flores R, Arrigo NC, Islam A, Ali Khan S, Hosseini P, Bogich TL, Olival KJ, Sanchez-Leon MD, Karesh WB, Goldstein T, Luby SP, Morse SS, Mazet JA, Daszak P, Lipkin WI (2013) A strategy to estimate unknown viral diversity in mammals. MBio 4: e00598-00513.

Artenstein AW (2012) The discovery of viruses: advancing science and medicine by challenging dogma. Int J Infect Dis 16: e470-473.

Bai H, Wang Y, Li X, Mao H, Li Y, Han S, Shi Z, Chen X (2011) Isolation and characterization of a novel alphanodavirus. Virol J 8: 311.

Barzon L, Lavezzo E, Costanzi G, Franchin E, Toppo S, Palù G (2013) Next-generation sequencing technologies in diagnostic virology. J Clin Virol 58: 346-350.

Barzon L, Lavezzo E, Militello V, Toppo S, Palù G (2011) Applications of next-generation sequencing technologies to diagnostic virology. Int J Mol Sci 12: 7861-7884.

Bull RA, Luciani F, McElroy K, Gaudieri S, Pham ST, Chopra A, Cameron B, Maher L, Dore GJ, White PA, Lloyd AR (2011) Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection. PLoS Pathog 7: e1002243.

Capobianchi MR, Giombini E, Rozera G (2013) Next-generation sequencing technology in clinical virology. Clin Microbiol Infect 19: 15-22.

Chandriani S1, Skewes-Cox P, Zhong W, Ganem DE, Divers TJ, Van Blaricum AJ, Tennant BC, Kistler AL (2013) Identification of a previously undescribed divergent virus from the Flaviviridae family in an outbreak of equine serum hepatitis. Proc Natl Acad Sci USA 110: E1407-1415.

Chen Y, Yao H, Thompson EJ, Tannir NM, Weinstein JN, Su X. VirusSeq (2013) VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue. Bioinformatics 29: 266-267.

Chiu C Y (2013) Viral pathogen discovery. Curr Opin Microbiol 16: 468-478.

Culley AI, Lang AS, Suttle CA (2006) Metagenomic analysis of coastal RNA virus communities. Science 312: 1795-1798.

Daly GM, Bexfield N, Heaney J, Stubbs S, Mayer AP, Palser A, Kellam P, Drou N, Caccamo M, Tiley L, Alexander GJ, Bernal W, Heeney JL (2011) A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing. PLoS One 6: e28879.

de Vries M, Deijs M, Canuti M, van Schaik BD, Faria NR, van de Garde MD, Jachimowski LC, Jebbink MF, Jakobs M, Luyf AC, Coenjaerts FE, Claas EC, Molenkamp R, Koekkoek SM, Lammens C, Leus F, Goossens H, Ieven M, Baas F, van der Hoek L (2011) A sensitive assay for virus discovery in respiratory clinical samples. PLoS One 6: e16118.

Dean FB, Nelson JR, Giesler TL, Lasken RS (2001) Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res 11: 1095-1099.

Delang L, Vliegen I, Froeyen M, Neyts J (2011) Comparative study of the genetic barriers and pathways towards resistance of selective inhibitors of hepatitis C virus replication. Antimicrob Agents Chemother 55: 4103-4113.

Eisenstein M (2012) Oxford Nanopore announcement sets sequencing sector abuzz. Nat Biotechnol 30: 295-296.

Feng H, Shuda M, Chang Y, Moore PS (2008) Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 319: 1096-1100.

Finotello F, Lavezzo E, Fontana P, Peruzzo D, Albiero A, Barzon L, Falda M, Di Camillo B, Toppo S (2012) Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data. Brief Bioinform 13: 269-280.

Fischer, W., V. V. Ganusov, et al. (2010). "Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing." PLoS One 5(8): e12303.

Fischer W, Ganusov VV, Giorgi EE, Hraber PT, Keele BF, Leitner T, Han CS, Gleasner CD, Green L, Lo CC, Nag A, Wallstrom TC, Wang S, McMichael AJ, Haynes BF, Hahn BH, Perelson AS, Borrow P, Shaw GM, Bhattacharya T, Korber BT (2014) Ebola virus disease: a review on epidemiology, symptoms, treatment and pathogenesis. Neth J Med 72: 442-448.

Grard G, Fair JN, Lee D, Slikas E, Steffen I, Muyembe JJ, Sittler T, Veeraraghavan N, Ruby JG, Wang C, Makuwa M, Mulembakani P, Tesh RB, Mazet J, Rimoin AW, Taylor T, Schneider BS, Simmons G, Delwart E, Wolfe ND, Chiu CY, Leroy EM (2012) A novel rhabdovirus associated with acute hemorrhagic fever in central Africa. PLoS Pathog 8: e1002924.

Hall N (2007) Advanced sequencing technologies and their wider impact in microbiology. J Exp Biol 210: 1518-1525.

Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, Frazer KA (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 10: R32.

Kapoor A, Simmonds P, Gerold G, Qaisar N, Jain K, Henriquez JA, Firth C, Hirschberg DL, Rice CM, Shields S, Lipkin WI (2011) Characterization of a canine homolog of hepatitis C virus. Proc Natl Acad Sci USA 108: 11608-11613.

Kuroda M, Katano H, Nakajima N, Tobiume M, Ainai A, Sekizuka T, Hasegawa H, Tashiro M, Sasaki Y, Arakawa Y, Hata S, Watanabe M, Sata T (2010) Characterization of quasispecies of pandemic 2009 influenza A virus (A/H1N1/2009) by de novo sequencing using a next-generation DNA sequencer. PLoS One 5: e10256.

Lauring AS, Andino R (2010) Quasispecies theory and the behavior of RNA viruses. PLoS Pathog 6: e1001005.

Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589-595.

Li JW, Wan R, Yu CS, Co NN, Wong N, Chan TF (2013) ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution. Bioinformatics 29: 649-651.

Lipkin WI, Firth C (2013) Viral surveillance and discovery. Curr Opin Virol 3: 199-204.

Liu S, Vijayendran D, Bonning BC (2011) Next generation sequencing technologies for insect virus discovery. Viruses 3: 1849-1869.

Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ (2010) Target-enrichment strategies for next-generation sequencing. Nat Methods 7: 111-118.

Margeridon-Thermet S, Shulman NS, Ahmed A, Shahriar R, Liu T, Wang C, Holmes SP, Babrzadeh F, Gharizadeh B, Hanczaruk B, Simen BB, Egholm M, Shafer RW (2009) Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients. J Infect Dis 199: 1275-1285.

Moore RA1, Warren RL, Freeman JD, Gustavsen JA, Chénard C, Friedman JM, Suttle CA, Zhao Y, Holt RA (2011). The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue" PLoS One 6: e19838.

Mundry M, Bornberg-Bauer E, Sammeth M, Feulner PG (2012) Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach. PLoS One 7: e31410.

Neverov A, Chumakov K (2010). "Massively parallel sequencing for monitoring genetic consistency and quality control of live viral vaccines." Proc Natl Acad Sci U S A 107(46): 20063-20068.

Nichol ST, Arikawa J, Kawaoka Y (2000). Emerging viral diseases. Proc Natl Acad Sci USA 97: 12411-12412.

Quan PL, Firth C, Street C, Henriquez JA, Petrosov A, Tashmukhamedova A, Hutchison SK, Egholm M, Osinubi MO, Niezgoda M, Ogunkoya AB, Briese T, Rupprecht CE, Lipkin WI(2010). Identification of a severe acute respiratory syndrome coronavirus-like virus in a leaf-nosed bat in Nigeria. MBio 1 .pii: e00208-10

Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12: 38.

Quiñones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA (2014) Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 61: 9-19.

Radford AD, Chapman D, Dixon L, Chantrey J, Darby AC, Hall N (2012). Application of next-generation sequencing technologies in virology. J Gen Virol 93: 1853-1868.

Rector A, Tachezy R, Van Ranst M (2004) A sequence-independent strategy for detection and cloning of circular DNA virus genomes by using multiply primed rolling-circle amplification. J Virol 78: 4993-4998.

Schelhorn SE, Fischer M, Tolosi L, Altmüller J, Nürnberg P, Pfister H, Lengauer T, Berthold F (2013) Sensitive detection of viral transcripts in human tumor transcriptomes. PLoS Comput Biol 9: e1003228.

Sedlazeck FJ, Rescheneder P, von Haeseler A (2013) NextGenMap: fast and accurate read mapping in highly polymorphic genomes. Bioinformatics 29: 2790-2791.

Simen BB1, Simons JF, Hullsiek KH, Novak RM, Macarthur RD, Baxter JD, Huang C, Lubeski C, Turenchalk GS, Braverman MS, Desany B, Rothberg JM, Egholm M, Kozal MJ (2009) Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J Infect Dis 199: 693-701.

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I (2009). ABySS: a parallel assembler for short read sequence data. Genome Res 19: 1117-1123.

Stenglein MD, Sanders C, Kistler AL, Ruby JG, Franco JY, Reavill DR, Dunker F, Derisi JL (2012) Identification, characterization, and in vitro culture of highly divergent arenaviruses from boa constrictors and annulated tree boas: candidate etiological agents for snake inclusion body disease. MBio 3: e00180-00112.

Swenson LC, Mo T, Dong WW, Zhong X, Woods CK, Jensen MA, Thielen A, Chapman D, Lewis M, James I, Heera J, Valdez H, Harrigan PR (2011). Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients. J Infect Dis 203: 237-245.

Tapparel C1, Cordey S, Junier T, Farinelli L, Van Belle S, Soccal PM, Aubert JD, Zdobnov E, Kaiser L (2011) Rhinovirus genome variation during chronic upper and lower respiratory tract infections. PLoS One 6: e21163.

Tebit DM, Arts EJ (2011) Tracking a century of global expansion and evolution of HIV to drive understanding and to combat disease. Lancet Infect Dis 11: 45-56.

van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C (2014) Ten years of next-generation sequencing technology. Trends Genet 30: 418-426.

Victoria JG, Wang C, Jones MS, Jaing C, McLoughlin K, Gardner S, Delwart EL (2010). Viral nucleic acids in live-attenuated vaccines: detection of minority variants and an adventitious virus. J Virol 84: 6033-6040.

Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW (2007) Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res 17: 1195-1201.

Wang GP, Ciuffi A, Leipzig J, Berry CC, Bushman FD (2007) HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Res 17: 1186-1194.

Wang Q, Jia P, Zhao Z (2013) VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data. PLoS One 8: e64465.

Wang Q, Jia P2, Zhao Z (2015) VERSE: a novel approach to detect virus integration in host genomes through reference genome customization. Genome Med 7: 2.

Wu Q, Luo Y, Lu R, Lau N, Lai EC, Li WX, Ding SW (2010) Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc Natl Acad Sci USA 107: 1606-1611.

Wu X, Zhou T, Zhu J, Zhang B, Georgiev I, Wang C, Chen X, Longo NS, Louder M, McKee K, O'Dell S, Perfetto S, Schmidt SD, Shi W, Wu L, Yang Y, Yang ZY, Yang Z, Zhang Z, Bonsignori M, Crump JA, Kapiga SH, Sam NE, Haynes BF, Simek M, Burton DR, Koff WC, Doria-Rose NA, Connors M; NISC Comparative Sequencing Program, Mullikin JC, Nabel GJ, Roederer M, Shapiro L, Kwong PD, Mascola JR (2011) Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing. Science 333: 1593-1602.

Yin L, Liu L, Sun Y, Hou W, Lowe AC, Gardner BP, Salemi M, Williams WB, Farmerie WG, Sleasman JW, Goodenow MM (2012) High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems. Retrovirology 9: 108.

Zagordi O, Geyrhofer L, Roth V, Beerenwinkel N (2010) Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction. J Comput Biol 17: 417-428.

Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.




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