Web-tools for the genomic analysis of the 2022 Monkeypox virus global outbreak.
Herramientas web para el análisis genómico del virus de la viruela símica durante el brote mundial de 2022.
Keywords:
Monkeypox virus, outbreak, genome analysis, web tools, database
Abstract
The resources and platforms available on the internet for collecting and sharing information and performing genomic sequence analysis have made it possible to follow closely the evolution the evolution of SARS-CoV-2. However, the current monkeypox outbreak in the world brings us back to the need to use these resources to appraise the extent of this outbreak. The objective of this work was an analysis of the information presented so far in the genomic database GISAID EpiPox™, using various tools available on the web. The results indicate that the monkeypox outbreak is referred as MPXV clade II B.1 lineage and sub-lineages, isolated from male patients mainly from the European and American continents. In the current scenario, the access to genomic sequences, epidemiological information, and tools available to the scientific community is of great importance for global public health in order to follow the evolution of pathogens.
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References
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Silva NIO, de Oliveira JS, Kroon EG, Trindade G de S, Drumond BP. Here, there, and everywhere: the wide host range and geographic dstribution of zoonotic orthopoxviruses. Viruses 2020;13(1):43. doi:10.3390/V13010043
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Elbe S, Buckland-Merrett G. Data, disease and diplomacy: GISAID’s innovative contribution to global health. Global Challenges 2017;1(1):33-46. doi:10.1002/GCH2.1018
Mauri M, Elli T, Caviglia G, Uboldi G, Azzi RAWGraphs: A visualisation platform to create open outputs. ACM International Conference Proceeding Series. 2017;Part F131371. doi:10.1145/3125571.3125585
Vilsker M, Moosa Y, Nooij S, Fonseca V, Ghysens Y, Dumon K, Pauwels R, Alcantara LC, vanden Eynden E, Vandamme AM, Deforche K, de Oliveira T. Genome Detective: an automated system for virus identification from high-throughput sequencing data. Bioinformatics 2019;35(5):871-873. doi:10.1093/BIOINFORMATICS/BTY695
Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, Sagulenko P, Bedford T, Neher RA. NextStrain: Real-time tracking of pathogen evolution. Bioinformatics 2018;34(23):4121-4123. doi:10.1093/ BIOINFORMATICS/BTY407
Letunic I, Bork P. Interactive tree of life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021;49(W1):W293-W296. doi:10.1093/NAR/GKAB301
Mauri M, Elli T, Caviglia G, Uboldi G, Azzi RAWGraphs: A visualisation platform to create open outputs. ACM International Conference Proceeding Series. 2017;Part F131371. doi:10.1145/3125571.3125585
Lucas-Dominguez R, Alonso-Arroyo A, Vidal- Infer A, Aleixandre-Benavent R. The sharing of research data facing the COVID-19 pandemic. Scientometrics 2021; 126(6):4975. doi:10.1007/S11192-021-03971-6
Adegboye OA, Castellanos ME, Alele FO, Pak A, Ezechukwu HC, Hou K, Emeto TI. Travel-related Monkeypox outbreaks in the era of COVID-19 pandemic: are we prepared? Viruses 2022;14(6):1283. doi:10.3390/V14061283
World Health Organization (WHO). Multi-country monkeypox outbreak: situation update. Accessed August 1, 2022. https:// www.who.int/emergencies/disease-out-break-news/item/2022-DON393
Mauldin MR, McCollum AM, Nakazawa YJ, Mandra A, Whitehouse ER, Davidson W, Zhao H, Gao J, Li Y, Doty J, Yinka-Ogunleye A, Akinpelu A, Aruna O, Naidoo D, Lewandowski K, Afrough B, Graham V, Aarons E, Hewson R, Vipond R, Dunning J, Chand M, Brown C, Cohen-Gihon I, Erez N, Shifman O, Israeli O, Sharon M, Schwartz E, Beth- Din A, Zvi A, Mak TM, Ng YK, Cui L, Lin RTP, Olson VA, Brooks T, Paran N, Ihekweazu C, Reynolds MG. Exportation of Monkeypox Virus from the African continent. J Infect Dis 2022;225(8):1367-1376.doi:10.1093/ INFDIS/JIAA559
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/ Genome Reports - Virological. Accessed August 2, 2022. https://virological.org/t/two-draft-canadian-monkeypox-virus-mpxv-genomes-june-2022/870
Kumar S, Subramaniam G, Karuppanan K. Human monkeypox outbreak in 2022. J Med Virol Epub 2022 Jun 6. doi:10.1002/ JMV.27894
World Health Organization (WHO). Multi- country monkeypox outbreak: situation update. Accessed August 2, 2022. https://www.who.int/emergencies/disease-out-break-news/item/2022-DON390
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Instituto Nacional de Salud. Peru identifies monkeypox virus B.1.6 lineage - Outbreak News Today. Accessed September 6, 2022. https://web.ins.gob.pe/
O’Toole A, Rambaut A. Initial observations about putative APOBEC3 deamina- se editing driving short-term evolution of MPXV since 2017-Monkeypox / Evolution - Virological. Accessed September 6, 2022. https://virological.org/t/initial-observa- tions-about-putative-apobec3-deaminase- editing-driving-short-term-evolution-of- mpxv-since-2017/830#post_1
Yu Q, König R, Pillai S, Chiles K, Kearney M, Palmer S, Richman D, Coffin JM, Landau NR. Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome. Nat Struct Mol Biol 2004;11(5):435-442. doi:10.1038/NSMB758
Armitage AE, Katzourakis A, de Oliveira T, Welch JJ, Belshaw R, Bishop KN, Kramer B, McMichael AJ, Rambaut A, Iversen AKN. Conserved footprints of APOBEC3G on Hypermutated human immunodeficiency virus type 1 and human endogenous retrovirus HERV-K(HML2) sequences. J Virol 2008;82(17):8743-8761. doi:10.1128/JVI.00584-08
Isidro J, Borges V, Pinto M, Sobral D, Santos JD, Nunes A, Mixão V, Ferreira R, Santos D, Duarte S, Vieira L, Borrego MJ, Núncio S, de Carvalho IL, Pelerito A, Cordeiro R, Gomes JP. Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus. Nat Med 2022;28(8). doi:10.1038/S41591-022- 01907-Y
Abubaker Bagabir S, Ibrahim NK, Abubaker Bagabir H, Hashem Ateeq R. Covid-19 and Artificial Intelligence: Genome sequencing, drug development and vaccine discovery. J Infect Public Health 2022;15(2):289. doi:10.1016/J.JIPH.2022.01.011.
Kharisma VD, Ansori ANM. Construction of epitope-based peptide vaccine against SARS-CoV-2: Immunoinformatics study. J Pure Appl Microbiol 2020;14(Suppl1):999-1005. doi:10.22207/JPAM.14.SPL1.38.
Prier JE, Sauer RM. A Pox Disease of Monkeys. Ann N Y Acad Sci 1960;85(3):951-959. doi:10.1111/J.1749-6632.1960.TB50 015.X.
Kmiec D, Kirchhoff F. Monkeypox: A new treat? Int J Mol Sci 2022;23(14):7866. doi:10.3390/IJMS23147866
Alakunle E, Moens U, Nchinda G, Okeke MI. Monkeypox Virus in Nigeria: infection biology, epidemiology, and evolution. Viruses 2020;12(11):1257. doi:10.3390/V12111257
Alakunle EF, Okeke MI. Monkeypox virus: a neglected zoonotic pathogen spreads globally. Nat Rev Microbiol Published online July 20, 2022:1. doi:10.1038/S41579-022- 00776-Z
Silva NIO, de Oliveira JS, Kroon EG, Trindade G de S, Drumond BP. Here, there, and everywhere: the wide host range and geographic dstribution of zoonotic orthopoxviruses. Viruses 2020;13(1):43. doi:10.3390/V13010043
Yurchenko V, Riccò M, Ferraro P, Camisa V, Satta E, Zaniboni A, Ranzieri S, Baldassarre A, Zaffina S, Marchesi F. When a neglected tropical disease goes global: knowledge, attitudes and practices of Italian pysicians towards monkeypox, preliminary results. Trop Med Infect Dis 2022;7(7):135. doi:10.3390/TROPICALMED7070135
Nolen LD, Osadebe L, Katomba J, Likofata J, Mukadi D, Monroe B, Doty J, Hughes CM, Kabamba J, Malekani J, Bomponda PL, Lokota JI, Balilo MP, Likafi T, Shongo Lushima R, Kebela Ilunga B, Nkawa F, Pukuta E, Karhemere S, Muyembe Tamfum JJ, Nguete B, Okitolonda Wemakoy E, McCollum AM, Reynolds MG. Extended human-to- human transmission during a Monkeypox outbreak in the Democratic Republic of the Congo. Emerg Infect Dis 2016;22(6):1014. doi:10.3201/EID2206.150579
Rodriguez-Morales AJ, Lopardo G. Monkey-pox: another sexually transmitted infection? Pathogens 2022;11(7):713. doi:10.3390/ PATHOGENS11070713
Luna N, Ramírez AL, Muñoz M, Ballesteros N, Patiño LH, Castañeda SA, Bonilla- Aldana DK, Paniz-Mondolfi A, Ramírez JD. Phylogenomic analysis of the monkeypox virus (MPXV) 2022 outbreak: Emergence of a novel viral lineage? Travel Med Infect Dis 2022;49:102402. doi:10.1016/J. TMAID.2022.102402
World Health Organization (WHO). Monke-ypox: experts give virus variants new names. Accessed September 5, 2022. https://www. who.int/news/item/12-08-2022-monkey- pox--experts-give-virus-variants-new-names
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 A, 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, de Oliveira T. Urgent need for a non-discriminatory and non-stigma- tizing nomenclature for monkeypox virus - Monkeypox - Virological. Accessed Sept- ember 5, 2022. https://virological.org/t/ urgent-need-for-a-non-discriminatory-and- non-stigmatizing-nomenclature-for-monke- ypox-virus/853
Wang L, Shang J, Weng S, Aliyari SR, Chen-gyang Ji, Cheng G, Wu A. Genomic annotation and molecular evolution of monkeypox virus outbreak in 2022. J Med Virol Published online July 29, 2022. doi:10.1002/ JMV.28036
Saravanan KA, Panigrahi M, Kumar H, Rajawat D, Nayak SS, Bhushan B, Dutt T. Role of genomics in combating COVID-19 pandemic. Gene 2022;823:146387. doi:10.1016/J. GENE.2022.146387
Elbe S, Buckland-Merrett G. Data, disease and diplomacy: GISAID’s innovative contribution to global health. Global Challenges 2017;1(1):33-46. doi:10.1002/GCH2.1018
Mauri M, Elli T, Caviglia G, Uboldi G, Azzi RAWGraphs: A visualisation platform to create open outputs. ACM International Conference Proceeding Series. 2017;Part F131371. doi:10.1145/3125571.3125585
Vilsker M, Moosa Y, Nooij S, Fonseca V, Ghysens Y, Dumon K, Pauwels R, Alcantara LC, vanden Eynden E, Vandamme AM, Deforche K, de Oliveira T. Genome Detective: an automated system for virus identification from high-throughput sequencing data. Bioinformatics 2019;35(5):871-873. doi:10.1093/BIOINFORMATICS/BTY695
Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, Sagulenko P, Bedford T, Neher RA. NextStrain: Real-time tracking of pathogen evolution. Bioinformatics 2018;34(23):4121-4123. doi:10.1093/ BIOINFORMATICS/BTY407
Letunic I, Bork P. Interactive tree of life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021;49(W1):W293-W296. doi:10.1093/NAR/GKAB301
Mauri M, Elli T, Caviglia G, Uboldi G, Azzi RAWGraphs: A visualisation platform to create open outputs. ACM International Conference Proceeding Series. 2017;Part F131371. doi:10.1145/3125571.3125585
Lucas-Dominguez R, Alonso-Arroyo A, Vidal- Infer A, Aleixandre-Benavent R. The sharing of research data facing the COVID-19 pandemic. Scientometrics 2021; 126(6):4975. doi:10.1007/S11192-021-03971-6
Adegboye OA, Castellanos ME, Alele FO, Pak A, Ezechukwu HC, Hou K, Emeto TI. Travel-related Monkeypox outbreaks in the era of COVID-19 pandemic: are we prepared? Viruses 2022;14(6):1283. doi:10.3390/V14061283
World Health Organization (WHO). Multi-country monkeypox outbreak: situation update. Accessed August 1, 2022. https:// www.who.int/emergencies/disease-out-break-news/item/2022-DON393
Mauldin MR, McCollum AM, Nakazawa YJ, Mandra A, Whitehouse ER, Davidson W, Zhao H, Gao J, Li Y, Doty J, Yinka-Ogunleye A, Akinpelu A, Aruna O, Naidoo D, Lewandowski K, Afrough B, Graham V, Aarons E, Hewson R, Vipond R, Dunning J, Chand M, Brown C, Cohen-Gihon I, Erez N, Shifman O, Israeli O, Sharon M, Schwartz E, Beth- Din A, Zvi A, Mak TM, Ng YK, Cui L, Lin RTP, Olson VA, Brooks T, Paran N, Ihekweazu C, Reynolds MG. Exportation of Monkeypox Virus from the African continent. J Infect Dis 2022;225(8):1367-1376.doi:10.1093/ INFDIS/JIAA559
Selhorst P, Rezende AM, de Block T, Coppens S, Smet H, Mariën J, Hauner A, Brosius I, Liesenborghs L, Bottieau E, Florence E, Bangwen E, Ariën K, Van Esbroeck M, Kenyon C, Vercauteren K. Belgian case of Monkeypox virus linked to outbreak in Portugal - Monkeypox / Genome Reports - Virological. Accessed August 2, 2022. https://virological.org/t/belgian-case-of-monkeypox-virus-linked-to-outbreak-in-por-tugal/801
Isidro J, Borges V, Pinto M, Ferreira R, Sobral D, Nunes A, Santos JD, Borrego MJ, Núncio S, Pelerito A, Cordeiro R, Gomes JP. First draft genome sequence of Monkeypox virus associated with the suspected multi-country outbreak, May 2022 (confirmed case in Portugal) - Monkeypox / Genome Reports - Virological. Accessed August 2, 2022. https://virological.org/t/first-draft-genome-sequence-of-monkeypox-virus-associated-with-the-suspected-multi-country-outbreak-may-2022-confirmed-ca- se-in-portugal/799
Laiton-Donato K, Álvarez-Díaz DA, Franco-Muñoz C, Ruiz-Moreno HA, Rojas-Estevez P, Prada A, Rosales A, Ospina ML, Mercado- Reyes M. Monkeypox virus genome sequence from an imported case in Colombia - Monkeypox / Genome Reports - Virological. Acces- sed August 2, 2022. https://virological.org/t/ monkeypox-virus-genome-sequence-from-an-imported-case-in-colombia/880
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. First Monkeypox virus sequence from northern Mexico - Monkeypox /Genome Reports - Virological. Accessed August 2, 2022. https://virological.org/t/ first-monkeypox-virus-sequence-from-nor-thern-mexico/882
Croxen M, Deo A, Dieu P, Dong X, Ferrato C, Gill K, Granger D, Ikkurti V, Kanji J, Koleva P, Li V, Lloyd C, Lynch T, Ma R, Pabbaraju K, Rotich S, Sergeant H, Shideler S, Skitsko T, Shokoples S, Tipples G, Thayer J, Wong A. Two draft Canadian monkeypox virus (MPXV) genomes, June 2022 - Monkeypox
/ Genome Reports - Virological. Accessed August 2, 2022. https://virological.org/t/two-draft-canadian-monkeypox-virus-mpxv-genomes-june-2022/870
Kumar S, Subramaniam G, Karuppanan K. Human monkeypox outbreak in 2022. J Med Virol Epub 2022 Jun 6. doi:10.1002/ JMV.27894
World Health Organization (WHO). Multi- country monkeypox outbreak: situation update. Accessed August 2, 2022. https://www.who.int/emergencies/disease-out-break-news/item/2022-DON390
Centers for Disease Control and Prevention (CDC). 2022 Monkeypox Outbreak Global Map | Monkeypox | Poxvirus | CDC. Accessed September 6, 2022. https:// www.cdc.gov/poxvirus/monkeypox/response/2022/world-map.html
Instituto Nacional de Salud. Peru identifies monkeypox virus B.1.6 lineage - Outbreak News Today. Accessed September 6, 2022. https://web.ins.gob.pe/
O’Toole A, Rambaut A. Initial observations about putative APOBEC3 deamina- se editing driving short-term evolution of MPXV since 2017-Monkeypox / Evolution - Virological. Accessed September 6, 2022. https://virological.org/t/initial-observa- tions-about-putative-apobec3-deaminase- editing-driving-short-term-evolution-of- mpxv-since-2017/830#post_1
Yu Q, König R, Pillai S, Chiles K, Kearney M, Palmer S, Richman D, Coffin JM, Landau NR. Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome. Nat Struct Mol Biol 2004;11(5):435-442. doi:10.1038/NSMB758
Armitage AE, Katzourakis A, de Oliveira T, Welch JJ, Belshaw R, Bishop KN, Kramer B, McMichael AJ, Rambaut A, Iversen AKN. Conserved footprints of APOBEC3G on Hypermutated human immunodeficiency virus type 1 and human endogenous retrovirus HERV-K(HML2) sequences. J Virol 2008;82(17):8743-8761. doi:10.1128/JVI.00584-08
Isidro J, Borges V, Pinto M, Sobral D, Santos JD, Nunes A, Mixão V, Ferreira R, Santos D, Duarte S, Vieira L, Borrego MJ, Núncio S, de Carvalho IL, Pelerito A, Cordeiro R, Gomes JP. Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus. Nat Med 2022;28(8). doi:10.1038/S41591-022- 01907-Y
Abubaker Bagabir S, Ibrahim NK, Abubaker Bagabir H, Hashem Ateeq R. Covid-19 and Artificial Intelligence: Genome sequencing, drug development and vaccine discovery. J Infect Public Health 2022;15(2):289. doi:10.1016/J.JIPH.2022.01.011.
Kharisma VD, Ansori ANM. Construction of epitope-based peptide vaccine against SARS-CoV-2: Immunoinformatics study. J Pure Appl Microbiol 2020;14(Suppl1):999-1005. doi:10.22207/JPAM.14.SPL1.38.
Published
2023-03-02
How to Cite
Moros , Z. C., Loureiro, C. L., Jaspe, R. C., Sulbarán, Y., Delgado, M., Aristimuño, O. C., Franco, C., Garzaro, D. J., Rodríguez, M., Rangel , H. R., Liprandi, F., Pujol, F. H., & Zambrano, J. L. (2023). Web-tools for the genomic analysis of the 2022 Monkeypox virus global outbreak.: Herramientas web para el análisis genómico del virus de la viruela símica durante el brote mundial de 2022. Investigación Clínica, 64(1), 68-80. https://doi.org/10.54817/IC.v64n1a06
Section
Original Works
