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Research Paper

Viral metagenomics of the gut virome of diarrheal children with Rotavirus A infection

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Article: 2234653 | Received 24 Apr 2023, Accepted 05 Jul 2023, Published online: 13 Jul 2023

References

  • Cohen AL, Platts-Mills JA, Nakamura T, Operario DJ, Antoni S, Mwenda JM, Weldegebriel G, Rey-Benito G, de Oliveira LH, Ortiz C, et al. Aetiology and incidence of diarrhoea requiring hospitalisation in children under 5 years of age in 28 low-income and middle-income countries: findings from the global pediatric diarrhea surveillance network. BMJ Glob Health. 2022 Sep;7(9):e009548. doi:10.1136/bmjgh-2022-009548.
  • Collaborators GBDDD. Estimates of the global, regional, and national morbidity, mortality, and aetiologies of diarrhoea in 195 countries: a systematic analysis for the global burden of disease study 2016. Lancet Infect Dis. 2018 Nov;18(11):1211–15. doi:10.1016/S1473-3099(18)30362-1.
  • Reiner RC, Wiens KE, Deshpande A, Baumann MM, Lindstedt PA, Blacker BF, Troeger CE, Earl L, Munro SB, Abate D, et al. Mapping geographical inequalities in childhood diarrhoeal morbidity and mortality in low-income and middle-income countries, 2000–17: analysis for the global burden of disease study 2017. Lancet. 2020 Jun 6;395(10239):1779–1801. doi:10.1016/S0140-6736(20)30114-8.
  • Platts-Mills JA, Babji S, Bodhidatta L, Gratz J, Haque R, Havt A, McCormick BJ, McGrath M, Olortegui MP, Samie A, et al. Pathogen-specific burdens of community diarrhoea in developing countries: a multisite birth cohort study (MAL-ED). Lancet Glob Health. 2015 Sep;3(9):e564–75. doi:10.1016/S2214-109X(15)00151-5.
  • Guerrant RL, DeBoer MD, Moore SR, Scharf RJ, Lima AA. The impoverished gut–a triple burden of diarrhoea, stunting and chronic disease. Nat Rev Gastroenterol Hepatol. 2013 Apr;10(4):220–229. doi:10.1038/nrgastro.2012.239.
  • Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, Hossain M, Oundo J, Tamboura B, Mai V, Astrovskaya I, et al. Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. Genome Biol. 2014 Jun 27;15(6):R76. doi:10.1186/gb-2014-15-6-r76.
  • Troeger C, Khalil IA, Rao PC, Cao S, Blacker BF, Ahmed T, Armah G, Bines JE, Brewer TG, Colombara DV, et al. Rotavirus vaccination and the global burden of rotavirus diarrhea among children younger than 5 years. JAMA Pediatr. 2018 Oct 1;172(10):958–965. doi:10.1001/jamapediatrics.2018.1960.
  • Crawford SE, Ramani S, Tate JE, Parashar UD, Svensson L, Hagbom M, Franco MA, Greenberg HB, O’Ryan M, Kang G, et al. Rotavirus infection. Nat Rev Dis Primers. 2017 Nov 9;3(1):17083. doi:10.1038/nrdp.2017.83.
  • Sadiq A, Bostan N, Yinda KC, Naseem S, Sattar S. Rotavirus: genetics, pathogenesis and vaccine advances. Rev Med Virol. 2018 Nov;28(6):e2003. doi:10.1002/rmv.2003.
  • Naghavi M, Abajobir AA, Abbafati C, Abbas KM, Abd-Allah F, Abera SF, Aboyans V, Adetokunboh O, Afshin A, Agrawal A, et al. Global, regional, and national age-sex specific mortality for 264 causes of death, 1980–2016: a systematic analysis for the global burden of disease study 2016. The Lancet. 2017 Sep 16;390(10100):1151–1210. doi:10.1016/S0140-6736(17)32152-9.
  • Patel MM, Pitzer VE, Alonso WJ, Vera D, Lopman B, Tate J, Viboud C, Parashar UD. Global seasonality of rotavirus disease. Pediatr Infect Dis J. 2013 Apr;32(4):e134–47. doi:10.1097/INF.0b013e31827d3b68.
  • Adak A, Khan MR. An insight into gut microbiota and its functionalities. Cell Mol Life Sci. 2019 Feb;76(3):473–493. doi:10.1007/s00018-018-2943-4.
  • Heintz-Buschart A, Wilmes P. Human gut microbiome: function matters. Trends Microbiol. 2018 Jul;26(7):563–574. doi:10.1016/j.tim.2017.11.002.
  • Weiss GA, Hennet T. Mechanisms and consequences of intestinal dysbiosis. Cell Mol Life Sci. 2017 Aug;74(16):2959–2977. doi:10.1007/s00018-017-2509-x.
  • The HC, Florez de Sessions P, Jie S, Pham Thanh D, Thompson CN, Nguyen Ngoc Minh C, Chu CW, Tran TA, Thomson NR, Thwaites GE, et al. Assessing gut microbiota perturbations during the early phase of infectious diarrhea in Vietnamese children. Gut Microbes. 2018 Jan 2;9(1):38–54. doi:10.1080/19490976.2017.1361093.
  • Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, et al. Population-level analysis of gut microbiome variation. Science. 2016 Apr 29;352(6285):560–564. doi:10.1126/science.aad3503.
  • Norman JM, Handley SA, Virgin HW. Kingdom-agnostic metagenomics and the importance of complete characterization of enteric microbial communities. Gastroenterol. 2014 May;146(6):1459–1469. doi:10.1053/j.gastro.2014.02.001.
  • Virgin HW. The virome in mammalian physiology and disease. Cell. 2014 Mar 27;157(1):142–150. doi:10.1016/j.cell.2014.02.032.
  • Norman JM, Handley SA, Baldridge MT, Droit L, Liu C, Keller B, Kambal A, Monaco C, Zhao G, Fleshner P, et al. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell. 2015 Jan 29;160(3):447–460. doi:10.1016/j.cell.2015.01.002.
  • Parks DH, Tyson GW, Hugenholtz P, Beiko RG. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformat. 2014 Nov 1;30(21):3123–3124. doi:10.1093/bioinformatics/btu494.
  • Lu J, Yang S, Zhang X, Tang X, Zhang J, Wang X, Wang H, Shen Q, Zhang W. Metagenomic analysis of viral community in the Yangtze river expands known eukaryotic and prokaryotic virus diversity in freshwater. Virol Sin. 2022 Feb;37(1):60–69. doi:10.1016/j.virs.2022.01.003.
  • Jalanka J, Gunn D, Singh G, Krishnasamy S, Lingaya M, Crispie F, Finnegan L, Cotter P, James L, Nowak A, et al. Postinfective bowel dysfunction following campylobacter enteritis is characterised by reduced microbiota diversity and impaired microbiota recovery. Gut. 2023 Mar;72(3):451–459. doi:10.1136/gutjnl-2021-326828.
  • Bao S, Wang H, Li W, Ji L, Wang X, Shen Q, Yang S, Zhou C, Zhang W. Dynamic alterations of the mice gut virome after coxsackievirus B3 infection. J Med Virol. 2022 Oct;94(10):4959–4969. doi:10.1002/jmv.27946.
  • Lu X, Hua X, Wang Y, Zhang D, Jiang S, Yang S, Wang X, Shen Q, Zhou T, Lin Z, et al. Comparison of gut viral communities in diarrhoea and healthy dairy calves. J Gen Virol. 2021 Oct;102(10). doi:10.1099/jgv.0.001663.
  • Becerra A, Iša P, Gutiérrez-Escolano AL, Velázquez, FR, Torres, J., Arias, CF, Estrada-Garcia, T. Differential virome composition and richness between children’s diarrheagenic stools kept at ultra-low temperatures for long-term. J Infect Dev Ctries. 2023;17(1):93–101. doi:10.3855/jidc.17572.
  • Chung the H, Le SH. Dynamic of the human gut microbiome under infectious diarrhea. Curr Opin Microbiol. 2022 Apr;66:79–85. doi:10.1016/j.mib.2022.01.006.
  • Taboada B, Moran P, Serrano-Vazquez A, Iša P, Rojas-Velázquez L, Pérez-Juárez H, López S, Torres J, Ximenez C, Arias CF, et al. The gut virome of healthy children during the first year of life is diverse and dynamic. PLoS One. 2021;16(4):e0240958. doi:10.1371/journal.pone.0240958.
  • Yan Q, Wang Y, Chen X, Jin H, Wang G, Guan K, Zhang Y, Zhang P, Ayaz T, Liang Y, et al. Characterization of the gut DNA and RNA viromes in a cohort of Chinese residents and visiting Pakistanis. Virus Evol. 2021 Jan;7(1):veab022. doi:10.1093/ve/veab022.
  • Zhang T, Breitbart M, Lee WH, Run JQ, Wei CL, Soh SWL, Hibberd ML, Liu ET, Rohwer F, Ruan Y, et al. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol. 2006 Jan;4(1):e3. doi:10.1371/journal.pbio.0040003.
  • Li H, Wang H, Ju H, Lv J, Yang S, Zhang W, Lu H. Comparison of gut viral communities in children under 5 years old and newborns. Virol J. 2023 Mar 27;20(1):52. doi:10.1186/s12985-023-02013-2.
  • Kennedy EA, Holtz LR. Gut virome in early life: origins and implications. Curr Opin Virol. 2022 Aug;55:101233. doi:10.1016/j.coviro.2022.101233.
  • Mihindukulasuriya KA, Mars RAT, Johnson AJ, Ward T, Priya S, Lekatz HR, Kalari KR, Droit L, Zheng T, Blekhman R, et al. Multi-omics analyses show disease, diet, and transcriptome interactions with the virome. Gastroenterol. 2021 Oct;161(4):1194–1207. doi:10.1053/j.gastro.2021.06.077.
  • Rasmussen TS, Mentzel CMJ, Kot W, Castro-Mejía JL, Zuffa S, Swann JR, Hansen LH, Vogensen FK, Hansen AK, Nielsen DS, et al. Faecal virome transplantation decreases symptoms of type 2 diabetes and obesity in a murine model. Gut. 2020 Dec;69(12):2122–2130. doi:10.1136/gutjnl-2019-320005.
  • Ott SJ, Waetzig GH, Rehman A, Moltzau-Anderson J, Bharti R, Grasis JA, Cassidy L, Tholey A, Fickenscher H, Seegert D, et al. Efficacy of sterile fecal filtrate transfer for treating patients with clostridium difficile infection. Gastroenterol. 2017 Mar;152(4):799–811 e7. doi:10.1053/j.gastro.2016.11.010.
  • Mogotsi MT, Mwangi PN, Bester PA, Mphahlele MJ, Seheri ML, O’Neill HG, Nyaga MM. Metagenomic analysis of the enteric RNA virome of infants from the oukasie clinic, North West province, South Africa, reveals diverse eukaryotic viruses. Viruses. 2020 Nov 5;12(11):1260. doi:10.3390/v12111260.
  • Rivera-Gutierrez X, Moran P, Taboada B, Serrano-Vázquez A, Iša P, Rojas-Velázquez L, Pérez-Juárez H, López S, Torres J, Ximénez C, et al. High prevalence and diversity of caliciviruses in a community setting determined by a metagenomic approach. Microbiol Spectr. 2022 Feb 23;10(1):e0185321. doi:10.1128/spectrum.01853-21.
  • Zhang W, Yang S, Shan T, Hou R, Liu Z, Li W, Guo L, Wang Y, Chen P, Wang X, et al. Virome comparisons in wild-diseased and healthy captive giant pandas. Microbiome. 2017 Aug 7;5(1):90. doi:10.1186/s40168-017-0308-0.
  • Xu H, Ling Y, Xi Y, Ma H, Wang H, Hu HM, Liu Q, Li YM, Deng XT, Yang SX, et al. Viral metagenomics updated the prevalence of human papillomavirus types in anogenital warts. Emerg Microbes Infect. 2019;8(1):1291–1299. doi:10.1080/22221751.2019.1661757.
  • Wang H, Ling Y, Shan T, Yang S, Xu H, Deng X, Delwart E, Zhang W. Gut virome of mammals and birds reveals high genetic diversity of the family microviridae. Virus Evol. 2019 Jan;5(1):vez013. doi:10.1093/ve/vez013.
  • Conceicao-Neto N, Zeller M, Lefrere H, De Bruyn P, Beller L, Deboutte W, Yinda CK, Lavigne R, Maes P, Ranst MV, et al. Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis. Sci Rep. 2015 Nov 12;5(1):16532. doi:10.1038/srep16532.
  • Hoyles L, McCartney AL, Neve H, Gibson GR, Sanderson JD, Heller KJ, van Sinderen D. Characterization of virus-like particles associated with the human faecal and caecal microbiota. Res Microbiol. 2014 Dec;165(10):803–812. doi:10.1016/j.resmic.2014.10.006.
  • Zhang W, Li L, Deng X, Blümel J, Nübling CM, Hunfeld A, Baylis SA, Delwart E. Viral nucleic acids in human plasma pools. Transfus. 2016 Sep;56(9):2248–2255. doi:10.1111/trf.13692.
  • Zhang W, Li L, Deng X, Kapusinszky B, Pesavento PA, Delwart E. Faecal virome of cats in an animal shelter. J Gen Virol. 2014 Nov;95(Pt 11):2553–2564. doi:10.1099/vir.0.069674-0.
  • Liu Z, Yang S, Wang Y, Shen Q, Yang Y, Deng X, Zhang W, Delwart E. Identification of a novel human papillomavirus by metagenomic analysis of vaginal swab samples from pregnant women. Virol J. 2016 Jul 4;13(1):122. doi:10.1186/s12985-016-0583-6.
  • Mao Q, Sun G, Qian Y, Qian Y, Li W, Wang X, Shen Q, Yang S, Zhou C, Wang H, et al. Viral metagenomics of pharyngeal secretions from children with acute respiratory diseases with unknown etiology revealed diverse viruses. Virus Res. 2022 Nov;321:198912. doi:10.1016/j.virusres.2022.198912.
  • Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformat. 2012 Jun 15;28(12):1647–1649. doi:10.1093/bioinformatics/bts199.
  • Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL, Tse H. Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PLoS One. 2014;9(8):e105067. doi:10.1371/journal.pone.0105067.
  • Deng X, Naccache SN, Ng T, Federman S, Li L, Chiu CY, Delwart EL. An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data. Nucleic Acids Res. 2015 Apr 20;43(7):e46. doi:10.1093/nar/gkv002.
  • Kumar S, Stecher G, Li M, Knyaz C, Tamura KMX, Battistuzzi FU. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018 Jun 1;35(6):1547–1549. doi:10.1093/molbev/msy096.
  • Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformat. 2001 Aug;17(8):754–755. doi:10.1093/bioinformatics/17.8.754.
  • Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res. 2007 Mar;17(3):377–386. doi:10.1101/gr.5969107.