Citation: Yuda Chen, Changcheng Wu, Ruhan A, Li Zhao, Zhongxian Zhang, Wenjie Tan. Perspective on the application of genome sequencing for monkeypox virus surveillance .VIROLOGICA SINICA, 2023, 38(2) : 327-333.

Perspective on the application of genome sequencing for monkeypox virus surveillance

  • Corresponding author: Wenjie Tan,
  • Received Date: 27 September 2022
    Accepted Date: 21 March 2023
    Available online: 25 March 2023
  • Highlights
    1. Whole genome sequencing of MPXV is crucial for monitoring emerging variants and assessing their potential pathogenicity.
    2. The critical steps of mNGS, encompassing nucleic acid extraction, library preparation, sequencing, and data analysis, are concisely explained.
    3. Optimization strategies for sample pre-processing, virus enrichment, and sequencing platform selection are deliberated.
    4. Conducting next-generation sequencing and third-generation sequencing concurrently is highly recommended.

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    1. Aksamentov I, Roemer C, Hodcroft EB, Neher RA. (2021). Nextclade:Clade assignment, mutation calling and quality control for viral genomes. Journal of Open Source Software, 6:3773.

    2. Alakunle E, Moens U, Nchinda G, Okeke MI. (2020). Monkeypox virus in nigeria:Infection biology, epidemiology, and evolution. Viruses, 12, 1257.

    3. Alcoba-Florez J, Muñoz-Barrera A, Ciuffreda L, Rodríguez-Pérez H, Rubio-Rodríguez LA, Gil-Campesino H, Artola DG-Md, Íñigo-Campos A, Díez-Gil O, González-Montelongo R, Valenzuela-Fernández A, Lorenzo-Salazar JM, Flores C. (2022). A draft of the first genome sequence of monkeypox virus associated with the multi-country outbreak in may 2022 from the canary islands, spain.[] (Accessed 16 June 2022)

    4. Bronner IF, Quail MA. (2019). Best practices for illumina library preparation. Curr Protoc Hum Genet, 102:e86.

    5. Buenestado-Serrano S, Palomino-Cabrera R, Peñas-Utrilla D, Herranz-Martín M, Cobos A, Ventimilla C, Catalán P, Alonso R, Muñoz P, Pérez-Lago L, Viedma DGd. (2022). Second draft genome from spain of the monkeypox virus 2022 outbreak.[] (Accessed 8 June 2022)

    6. Chen N, Li G, Liszewski MK, Atkinson JP, Jahrling PB, Feng Z, Schriewer J, Buck C, Wang C, Lefkowitz EJ, Esposito JJ, Harms T, Damon IK, Roper RL, Upton C, Buller RM. (2005). Virulence differences between monkeypox virus isolates from west africa and the congo basin. Virology, 340:46-63.

    7. Chen NFG, Chaguza C, Gagne L, Doucette M, Smole S, Buzby E, Hall J, Ash S, Harrington R, Cofsky S, Clancy S, Kapsak CJ, Sevinsky J, Libuit K, Park DJ, Hemarajata P, Garrigues JM, Green NM, Sierra-Patev S, Carpenter-Azevedo K, Huard RC, Pearson C, Incekara K, Nishimura C, Huang JP, Gagnon E, Reever E, Razeq J, Muyombwe A, Borges V, Ferreira R, Sobral D, Duarte S, Santos D, Vieira L, Gomes JP, Aquino C, Savino IM, Felton K, Bajwa M, Hayward N, Miller H, Naumann A, Allman R, Greer N, Fall A, Mostafa HH, McHugh MP, Maloney DM, Dewar R, Kenicer J, Parker A, Mathers K, Wild J, Cotton S, Templeton KE, Churchwell G, Lee PA, Pedrosa M, McGruder B, Schmedes S, Plumb MR, Wang X, Barcellos RB, Godinho FMS, Salvato RS, Ceniseros A, Breban MI, Grubaugh ND, Gallagher GR, Vogels CBF. (2023). Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus. medRxiv. 10.1101/2022.10.14.22280783.

    8. Chen S, Zhou Y, Chen Y, Gu J. (2018). Fastp:An ultra-fast all-in-one fastq preprocessor. Bioinformatics, 34:i884-i890.

    9. Chiu CY, Miller SA. (2019). Clinical metagenomics. Nat Rev Genet, 20:341-355.

    10. Claro IM, Lima ELd, Romano CM, Candido DdS, Lindoso JAL, Barra LAC, Borges LMS, Medeiros LA, Tomishige MYS, Ramundo MS, Moutinho T, Silva AJDd, Rodrigues CCM, Azevedo LCFd, Villas-Boas LS, Silva CAMd, Coletti TM, O'Toole Á, Quick J, Loman N, Rambaut A, Faria NR, Figueiredo-Mello C, Sabino EC. (2022). First monkeypox virus genome sequence from brazil.[] (Accessed 10 June 2022)

    11. Croville G, Walch M, Guérin J-L, Mansuy J-M, Pasquier C, Izopet J. (2022). First french draft genome sequence of monkeypox virus, may 2022.[] (Accessed 26 May 2022)

    12. 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.

    13. Di Giulio DB, Eckburg PB. (2004). Human monkeypox:An emerging zoonosis. Lancet Infect Dis, 4:15-25.

    14. EPI2ME. (2022). Monkeypox workflow.[] (Accessed 1 June 2022)

    15. Erez N, Achdout H, Milrot E, Schwartz Y, Wiener-Well Y, Paran N, Politi B, Tamir H, Israely T, Weiss S, Beth-Din A, Shifman O, Israeli O, Yitzhaki S, Shapira SC, Melamed S, Schwartz E. (2019). Diagnosis of imported monkeypox, israel, 2018. Emerg Infect Dis, 25:980-983.

    16. Filipe AdS, Tong L, Sreenu VB, Maclean A, Gunson R, Holden MT, Barr D, Ho A, Palmarini M, Rambaut A, Robertson DL, Thomson EC. (2022). Monkeypox virus genome sequences from multiple lesions indicates co-infection of a uk returning traveller.[] (Accessed 23 June 2022)

    17. Fuchs J, Nekrutenko A, Kohl A-K, Technau-Hafsi K, Hornuß D, Rieg S, Jaki L, Huzly D, Maier W, Grüning B, Gutbrod L, Falcone V, Hengel H, Panning M. (2022). Travel-associated monkeypox virus genomes from two german patients and of a derived virus isolate all closely related to a us sequence, 2022.[] (Accessed 03 June 2022)

    18. Galán-Huerta KA, Paz-Infanzon M, Nuzzolo-Shihadeh L, Ruiz-Higareda AF, Bocanegra-Ibarias P, Zacarias-Villarea D, Yamallel-Ortega LA, Guerrero-Putz MD, Ocampo-Candiani J, Rivas-Estilla AM, Camacho-Ortiz A. (2022). First monkeypox virus sequence from northern mexico.[] (Accessed 8 July 2022)

    19. Gigante CM, Korber B, Seabolt MH, Wilkins K, Davidson W, Rao AK, Zhao H, Smith TG, Hughes CM, Minhaj F, Waltenburg MA, Theiler J, Smole S, Gallagher GR, Blythe D, Myers R, Schulte J, Stringer J, Lee P, Mendoza RM, Griffin-Thomas LA, Crain J, Murray J, Atkinson A, Gonzalez AH, Nash J, Batra D, Damon I, McQuiston J, Hutson CL, McCollum AM, Li Y. (2022). Multiple lineages of monkeypox virus detected in the united states, 2021-2022. Science, 378:560-565.

    20. Gorgé O, Jarjaval F, Nolent, F., Criqui A, Lourenco, J., Badaoui A, Khoury, R., Burrel SL, O., Chapus C, Simon-Loriere E, Tournier JN, Ferraris O. (2022). Minion-produced illumina-confirmed genomes of the two first isolated cases from france.[] (Accessed 17 June 2022)

    21. Happi C, Adetifa I, Mbala P, Njouom R, Nakoune E, Happi A, Ndodo N, Ayansola O, Mboowa G, Bedford T, Neher RA, Roemer C, Hodcroft E, Tegally H, O'Toole Á, Rambaut A, Pybus O, Kraemer MUG, Wilkinson E, Isidro J, Borges V, Pinto M, Gomes JP, Baxter C, Lessells R, Ogwell AE, Kebede Y, Tessema SK, Oliveira Td. (2022). Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus.[] (Accessed 10 June 2022)

    22. Hoz-Sánchez Bdl, López-Ortiz M, Gutiérrez-Arroyo A, Roces-Álvarez P, Lázaro-Perona F, Dahdouh E, Bloise I, García-Rodríguez J, Mingorance J. (2022). Whole genome sequences of monkey pox virus from two cases in madrid, spain, may-june 2022.[] (Accessed 23 June 2022)

    23. Huo S, Chen Y, Lu R, Zhang Z, Zhang G, Zhao L, Deng Y, Wu C, Tan W. (2022). Development of two multiplex real-time pcr assays for simultaneous detection and differentiation of monkeypox virus iia, iib, and i clades and the b.1 lineage. Biosaf Health, 4:392-398.

    24. Isidro J, Borges V, Pinto M, Ferreira R, Sobral D, Nunes A, Santos JD, Borrego MJ, Núncio S, Pelerito A, Cordeiro R, Gomes JP. (2022a). First draft genome sequence of monkeypox virus associated with the suspected multi-country outbreak, may 2022 (confirmed case in portugal).[] (Accessed 20 May 2022)

    25. Isidro J, Borges V, Pinto M, Ferreira R, Sobral D, Nunes A, Santos JD, Mixão V, Santos D, Duarte S, Vieira L, Borrego MJ, Núncio S, Pelerito A, Cordeiro R, Gomes JP. (2022b). Multi-country outbreak of monkeypox virus:Genetic divergence and first signs of microevolution.[] (Accessed 23 May 2022)

    26. Israeli O, Guedj-Dana Y, Lazar S, Shifman O, Erez N, Weiss S, Paran N, Israely T, Schuster O, Zvi A, Beth-Din A, Gihon IC. (2022). First israeli whole-genome sequence of monkeypox virus associated with the may 2022 multi country outbreak.[] (Accessed 2 June 2022)

    27. Kabuga AI, El Zowalaty ME. (2019). A review of the monkeypox virus and a recent outbreak of skin rash disease in nigeria. J Med Virol, 91:533-540.

    28. Katoh K, Standley DM. (2013). Mafft multiple sequence alignment software version 7:Improvements in performance and usability. Mol Biol Evol, 30:772-780.

    29. Kulesh DA, Loveless BM, Norwood D, Garrison J, Whitehouse CA, Hartmann C, Mucker E, Miller D, Wasieloski LP, Jr., Huggins J, Huhn G, Miser LL, Imig C, Martinez M, Larsen T, Rossi CA, Ludwig GV. (2004). Monkeypox virus detection in rodents using real-time 3'-minor groove binder taqman assays on the roche lightcycler. Lab Invest, 84:1200-1208.

    30. Ladnyj ID, Ziegler P, Kima E. (1972). A human infection caused by monkeypox virus in basankusu territory, democratic republic of the congo. Bull World Health Organ, 46:593-597.

    31. Lefkowitz EJ, Wang C, Upton C. (2006). Poxviruses:Past, present and future. Virus Res, 117:105-118.

    32. Li H. (2011). A statistical framework for snp calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics, 27:2987-2993.

    33. Li H, Durbin R. (2009a). Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics, 25:1754-1760.

    34. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S. (2009b). The sequence alignment/map format and samtools. Bioinformatics, 25:2078-2079.

    35. Li N, Jin K, Bai Y, Fu H, Liu L, Liu B. (2020). Tn5 transposase applied in genomics research. Int J Mol Sci, 21, 8329.

    36. Li Y, Olson VA, Laue T, Laker MT, Damon IK. (2006). Detection of monkeypox virus with real-time pcr assays. J Clin Virol, 36:194-203.

    37. Li Y, Zhao H, Wilkins K, Hughes C, Damon IK. (2010). Real-time pcr assays for the specific detection of monkeypox virus west african and congo basin strain DNA. J Virol Methods, 169:223-227.

    38. Martínez-Puchol S, Coello A, Bordoy AE, Soler L, Panisello D, González-Gómez S, Clarà G, León APd, Not A, Hernández Á, Bofill-Mas S, Saludes V, Martró E, Cardona PJ. (2022). Spanish draft genome sequence of monkeypox virus related to multi-country outbreak (may 2022).[] (Accessed 27 May 2022)

    39. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. (2010). The genome analysis toolkit:A mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res, 20:1297-1303.

    40. Nakazawa Y, Mauldin MR, Emerson GL, Reynolds MG, Lash RR, Gao J, Zhao H, Li Y, Muyembe JJ, Kingebeni PM, Wemakoy O, Malekani J, Karem KL, Damon IK, Carroll DS. (2015). A phylogeographic investigation of african monkeypox. Viruses, 7:2168-2184.

    41. Ng OT, Lee V, Marimuthu K, Vasoo S, Chan G, Lin RTP, Leo YS. (2019). A case of imported monkeypox in singapore. Lancet Infect Dis, 19:1166.

    42. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. (2015). Iq-tree:A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol, 32:268-274.

    43. Orba Y, Sasaki M, Yamaguchi H, Ishii A, Thomas Y, Ogawa H, Hang'ombe BM, Mweene AS, Morikawa S, Saijo M, Sawa H. (2015). Orthopoxvirus infection among wildlife in zambia. J Gen Virol, 96:390-394.

    44. Palich R, Burrel S, Monsel G, Nouchi A, Bleibtreu A, Seang S, Berot V, Brin C, Gavaud A, Wakim Y, Godefroy N, Faycal A, Tamzali Y, Grunemwald T, Ohayon M, Todesco E, Leducq V, Marot S, Calvez V, Marcelin AG, Pourcher V. (2023). Viral loads in clinical samples of men with monkeypox virus infection:A french case series. Lancet Infect Dis, 23:74-80.

    45. Peng Q, Xie Y, Kuai L, Wang H, Qi J, Gao GF, Shi Y. (2023). Structure of monkeypox virus DNA polymerase holoenzyme. Science, 379:100-105.

    46. Pop M, Salzberg SL. (2008). Bioinformatics challenges of new sequencing technology. Trends Genet, 24:142-149.

    47. Saud Z, Hitchings MD, Butt TM. (2021). Nanopore sequencing and de novo assembly of a misidentified camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides. Sci Rep, 11:17758.

    48. Shchelkunov SN, Shcherbakov DN, Maksyutov RA, Gavrilova EV. (2011). Species-specific identification of variola, monkeypox, cowpox, and vaccinia viruses by multiplex real-time pcr assay. J Virol Methods, 175:163-169.

    49. Shchelkunov SN, Totmenin AV, Babkin IV, Safronov PF, Ryazankina OI, Petrov NA, Gutorov VV, Uvarova EA, Mikheev MV, Sisler JR, Esposito JJ, Jahrling PB, Moss B, Sandakhchiev LS. (2001). Human monkeypox and smallpox viruses:Genomic comparison. FEBS Lett, 509:66-70.

    50. Suner C, Ubals M, Tarin-Vicente EJ, Mendoza A, Alemany A, Hernandez-Rodriguez A, Casan C, Descalzo V, Ouchi D, Marc A, Rivero A, Coll P, Oller X, Miguel Cabrera J, Vall-Mayans M, Dolores Folgueira M, Angeles Melendez M, Agud-Dios M, Gil-Cruz E, Paris de Leon A, Ramirez Marinero A, Buhiichyk V, Galvan-Casas C, Paredes R, Prat N, Sala Farre MR, Bonet-Simo JM, Farre M, Ortiz-Romero PL, Clotet B, Garcia-Patos V, Casabona J, Guedj J, Cardona PJ, Blanco I, Movie G, Marks M, Mitja O. (2022). Viral dynamics in patients with monkeypox infection:A prospective cohort study in spain. Lancet Infect Dis. doi:10.1016/S1473-3099(22)00794-0

    51. Tan W, Gao GF. (2022). Neglected zoonotic monkeypox in africa but now back in the spotlight worldwide. China CDC Weekly, 4, 847-848.

    52. Telenius H, Carter NP, Bebb CE, Nordenskjold M, Ponder BA, Tunnacliffe A. (1992). Degenerate oligonucleotide-primed pcr:General amplification of target DNA by a single degenerate primer. Genomics, 13:718-725.

    53. Vandenbogaert M, Kwasiborski A, Gonofio E, Descorps-Declere S, Selekon B, Nkili Meyong AA, Ouilibona RS, Gessain A, Manuguerra JC, Caro V, Nakoune E, Berthet N. (2022). Nanopore sequencing of a monkeypox virus strain isolated from a pustular lesion in the central african republic. Sci Rep, 12:10768.

    54. Vaughan A, Aarons E, Astbury J, Balasegaram S, Beadsworth M, Beck CR, Chand M, O'Connor C, Dunning J, Ghebrehewet S, Harper N, Howlett-Shipley R, Ihekweazu C, Jacobs M, Kaindama L, Katwa P, Khoo S, Lamb L, Mawdsley S, Morgan D, Palmer R, Phin N, Russell K, Said B, Simpson A, Vivancos R, Wade M, Walsh A, Wilburn J. (2018). Two cases of monkeypox imported to the united kingdom, september 2018. Euro Surveill, 23, 1800509.

    55. WHO. (2022a). Who director-general's statement at the press conference following ihr emergency committee regarding the multi-country outbreak of monkeypox-23 july 2022.[] (Accessed 23 July 2022)

    56. WHO. (2022b). Second meeting of the international health regulations (2005) (ihr) emergency committee regarding the multi-country outbreak of monkeypox.[] (Accessed 23 July 2022)

    57. WHO. (2023). 2022-23 mpox (monkeypox) outbreak:Global trends.[](Accessed 5 March 2023)

    58. Yang G, Pevear DC, Davies MH, Collett MS, Bailey T, Rippen S, Barone L, Burns C, Rhodes G, Tohan S, Huggins JW, Baker RO, Buller RL, Touchette E, Waller K, Schriewer J, Neyts J, DeClercq E, Jones K, Hruby D, Jordan R. (2005). An orally bioavailable antipoxvirus compound (st-246) inhibits extracellular virus formation and protects mice from lethal orthopoxvirus challenge. J Virol, 79:13139-13149.

    59. Yang L, Chen Y, Li S, Zhou Y, Zhang Y, Pei R, Chen X, Wang Y. (2022). Immunization of mice with vaccinia virus tiantan strain yields antibodies cross-reactive with protective antigens of monkeypox virus. Virol Sin, 38, 162-164.

    60. Zhao H, Wang W, Zhao L, Ye S, Song J, Lu R, Zong H, Wu C, Huang W, Huang B, Deng Y, A. R, Xie W, Qi L, Xu W, Ling H, Tan W. (2022). The first imported case of monkeypox in the mainland of china-chongqing municipality, china, september 16, 2022. CCDC Weekly, 4, 853-854.

    61. Zhou W, Tan W, Zheng N, Zhang L, Wan H, Ruan L. (2006). Rapid detection and differentiation of smallpox or monkeypox virus infection by real-time pcr assay. Letters in Biotechnology, 17:703-706.

    62. Zong C, Lu S, Chapman AR, Xie XS. (2012). Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science, 338:1622-1626.

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    Perspective on the application of genome sequencing for monkeypox virus surveillance

      Corresponding author: Wenjie Tan,
    • a. School of Public Health, Baotou Medical College, Baotou, 014040, China;
    • b. NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China

    Abstract: Highlights
    1. Whole genome sequencing of MPXV is crucial for monitoring emerging variants and assessing their potential pathogenicity.
    2. The critical steps of mNGS, encompassing nucleic acid extraction, library preparation, sequencing, and data analysis, are concisely explained.
    3. Optimization strategies for sample pre-processing, virus enrichment, and sequencing platform selection are deliberated.
    4. Conducting next-generation sequencing and third-generation sequencing concurrently is highly recommended.

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