1887

Abstract

Viral nucleic acids present in the plasma of 498 Kenyan adults with unexplained fever were characterized by metagenomics analysis of 51 sample pools. The highest to lowest fraction of plasma pools was positive for parvovirus B19 (75 %), pegivirus C (GBV-C) (67 %), alpha anellovirus (59 %), gamma anellovirus (55 %), beta anellovirus (41 %), dengue virus genotype 2 (DENV-2) (16 %), human immunodeficiency virus type 1 (6 %), human herpesvirus 6 (6 %), HBV (4 %), rotavirus (4 %), hepatitis B virus (4 %), rhinovirus C (2 %), Merkel cell polyomavirus (MCPyV; 2 %) and Kadipiro virus (2 %). Ranking by overall percentage of viral reads yielded similar results. Characterization of viral nucleic acids in the plasma of a febrile East African population showed a high frequency of parvovirus B19 and DENV infections and detected a reovirus (Kadipiro virus) previously reported only in Asian mosquitoes, providing a baseline to compare with future virome studies to detect emerging viruses in this region.

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2016-12-16
2021-07-27
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References

  1. Allander T., Emerson S. U., Engle R. E., Purcell R. H., Bukh J. 2001; A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species. Proc Natl Acad Sci U S A 98:11609–11614 [View Article][PubMed]
    [Google Scholar]
  2. Attoui H., Billoir F., Biagini P., de Micco P., de Lamballerie X. 2000; Complete sequence determination and genetic analysis of Banna virus and Kadipiro virus: proposal for assignment to a new genus (Seadornavirus) within the family Reoviridae . J Gen Virol 81:1507–1515 [View Article][PubMed]
    [Google Scholar]
  3. Attoui H., Mohd Jaafar F., Belhouchet M., Tao S., Chen B., Liang G., Tesh R. B., de Micco P., de Lamballerie X. 2006; Liao ning virus, a new Chinese seadornavirus that replicates in transformed and embryonic mammalian cells. J Gen Virol 87:199–208 [View Article][PubMed]
    [Google Scholar]
  4. Attoui H., Mohd Jaafar F., de Micco P., de Lamballerie X. 2005; Coltiviruses and seadornaviruses in North America, Europe, and Asia. Emerg Infect Dis 11:1673–1679 [View Article][PubMed]
    [Google Scholar]
  5. Baba M., Villinger J., Masiga D. K. 2016; Repetitive dengue outbreaks in East Africa: a proposed phased mitigation approach may reduce its impact. Rev Med Virol 26:183–196 [View Article][PubMed]
    [Google Scholar]
  6. Bernardin F., Operskalski E., Busch M., Delwart E. 2010; Transfusion transmission of highly prevalent commensal human viruses. Transfusion 50:2474–2483 [View Article][PubMed]
    [Google Scholar]
  7. Breitbart M., Salamon P., Andresen B., Mahaffy J. M., Segall A. M., Mead D., Azam F., Rohwer F. 2002; Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A 99:14250–14255 [View Article][PubMed]
    [Google Scholar]
  8. Brown S. E., Gorman B. M., Tesh R. B., Knudson D. L. 1993; Coltiviruses isolated from mosquitoes collected in Indonesia. Virology 196:363–367 [View Article][PubMed]
    [Google Scholar]
  9. Chen B., Tao S. 1996; Arbovirus survey in China in recent ten years. Chin Med J 109:13–15[PubMed]
    [Google Scholar]
  10. De Vlaminck I., Khush K. K., Strehl C., Kohli B., Luikart H., Neff N. F., Okamoto J., Snyder T. M., Cornfield D. N. et al. 2013; Temporal response of the human virome to immunosuppression and antiviral therapy. Cell 155:1178–1187 [View Article][PubMed]
    [Google Scholar]
  11. Deng X., Naccache S. N., Ng T., Federman S., Li L., Chiu C. Y., Delwart E. L. 2015; An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data. Nucleic Acids Res 43:e46 [View Article]
    [Google Scholar]
  12. Ellis E. M., Neatherlin J. C., Delorey M., Ochieng M., Mohamed A. H., Mogeni D. O., Hunsperger E., Patta S., Gikunju S. et al. 2015; A household serosurvey to estimate the magnitude of a dengue outbreak in Mombasa, Kenya, 2013. PLoS Negl Trop Dis 9:e0003733 [View Article][PubMed]
    [Google Scholar]
  13. Esposito S., Daleno C., Scala A., Castellazzi L., Terranova L., Sferrazza Papa S., Longo M. R., Pelucchi C., Principi N. 2014; Impact of rhinovirus nasopharyngeal viral load and viremia on severity of respiratory infections in children. Eur J Clin Microbiol Infect Dis 33:41–48 [View Article][PubMed]
    [Google Scholar]
  14. Franco M. A., Greenberg H. B. 2013; Rotavirus. Microbiol Spectr 1: [View Article][PubMed]
    [Google Scholar]
  15. Frange P., Touzot F., Debré M., Héritier S., Leruez-Ville M., Cros G., Rouzioux C., Blanche S., Fischer A., Avettand-Fenoël V. 2012; Prevalence and clinical impact of norovirus fecal shedding in children with inherited immune deficiencies. J Infect Dis 206:1269–1274 [View Article][PubMed]
    [Google Scholar]
  16. Fuji N., Suzuki A., Lupisan S., Sombrero L., Galang H., Kamigaki T., Tamaki R., Saito M., Aniceto R. et al. 2011; Detection of human rhinovirus C viral genome in blood among children with severe respiratory infections in the Philippines. PLoS One 6:e27247 [View Article][PubMed]
    [Google Scholar]
  17. Fukumoto H., Sato Y., Hasegawa H., Katano H. 2013; Frequent detection of Merkel cell polyomavirus DNA in sera of HIV-1-positive patients. Virol J 10:84 [View Article][PubMed]
    [Google Scholar]
  18. Fumian T. M., Justino M. C., D'Arc Pereira Mascarenhas J., Reymão T. K., Abreu E., Soares L., Linhares A. C., Gabbay Y. B. 2013; Quantitative and molecular analysis of noroviruses RNA in blood from children hospitalized for acute gastroenteritis in Belém, Brazil. J Clin Virol 58:31–35 [View Article][PubMed]
    [Google Scholar]
  19. Graf E. H., Simmon K. E., Tardif K. D., Hymas W., Flygare S., Eilbeck K., Yandell M., Schlaberg R. 2016; Unbiased detection of respiratory viruses by use of RNA sequencing-based metagenomics: a systematic comparison to a commercial PCR panel. J Clin Microbiol 54:1000–1007 [View Article][PubMed]
    [Google Scholar]
  20. Greninger A. L., Naccache S. N., Messacar K., Clayton A., Yu G., Somasekar S., Federman S., Stryke D., Anderson C. et al. 2015; A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012-14): a retrospective cohort study. Lancet Infect Dis 15:671–682 [View Article][PubMed]
    [Google Scholar]
  21. Hayakawa H., Tara M., Niina K., Osame M. 2002; A clinical study of adult human parvovirus B19 infection. Intern Med 41:295–299 [View Article][PubMed]
    [Google Scholar]
  22. Johnson B. K., Ocheng D., Gichogo A., Okiro M., Libondo D., Kinyanjui P., Tukei P. M. 1982; Epidemic dengue fever caused by dengue type 2 virus in Kenya: preliminary results of human virological and serological studies. East Afr Med J 59:781–784[PubMed]
    [Google Scholar]
  23. Li L., Deng X., Linsuwanon P., Bangsberg D., Bwana M. B., Hunt P., Martin J. N., Deeks S. G., Delwart E. 2013; AIDS alters the commensal plasma virome. J Virol 87:10912–10915 [View Article][PubMed]
    [Google Scholar]
  24. Li L., Deng X., Mee E. T., Collot-Teixeira S., Anderson R., Schepelmann S., Minor P. D., Delwart E. 2015; Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent. J Virol Methods 213:139–146 [View Article][PubMed]
    [Google Scholar]
  25. Liu H., Li M. H., Zhai Y. G., Meng W. S., Sun X. H., Cao Y., Fu S. H., Wang H. Y., Xu L. H. et al. 2010; Banna virus, China, 1987-2007. Emerg Infect Dis 16:514–517 [View Article][PubMed]
    [Google Scholar]
  26. Lupo J., Schuffenecker I., Morel-Baccard C., Bardet J., Payen V., Kaiser L., Constant S., Lobrinus J. A., Lin-Marq N. et al. 2015; Disseminated rhinovirus C8 infection with infectious virus in blood and fatal outcome in a child with repeated episodes of bronchiolitis. J Clin Microbiol 53:1775–1777 [View Article][PubMed]
    [Google Scholar]
  27. Lv X., Mohd Jaafar F., Sun X., Belhouchet M., Fu S., Zhang S., Tong S., Lv Z., Mertens P. P. et al. 2012; Isolates of Liao ning virus from wild-caught mosquitoes in the Xinjiang province of China in 2005. PLoS One 7:e37732 [View Article][PubMed]
    [Google Scholar]
  28. Mease L. E., Coldren R. L., Musila L. A., Prosser T., Ogolla F., Ofula V. O., Schoepp R. J., Rossi C. A., Adungo N. 2011; Seroprevalence and distribution of arboviral infections among rural Kenyan adults: a cross-sectional study. Virol J 8:371 [View Article][PubMed]
    [Google Scholar]
  29. Monaco C. L., Gootenberg D. B., Zhao G., Handley S. A., Ghebremichael M. S., Lim E. S., Lankowski A., Baldridge M. T., Wilen C. B. et al. 2016; Altered virome and bacterial microbiome in human immunodeficiency virus-associated acquired immunodeficiency syndrome. Cell Host Microbe 19:311–322 [View Article][PubMed]
    [Google Scholar]
  30. Naccache S. N., Greninger A. L., Lee D., Coffey L. L., Phan T., Rein-Weston A., Aronsohn A., Hackett J., Delwart E. L., Chiu C. Y. 2013; The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns. J Virol 87:11966–11977 [View Article][PubMed]
    [Google Scholar]
  31. Naccache S. N., Hackett J., Delwart E. L., Chiu C. Y. 2014; Concerns over the origin of NIH-CQV, a novel virus discovered in Chinese patients with seronegative hepatitis. Proc Natl Acad Sci U S A 111:E976 [View Article][PubMed]
    [Google Scholar]
  32. Newman K. L., Marsh Z., Kirby A. E., Moe C. L., Leon J. S. 2015; Immunocompetent adults from human norovirus challenge studies do not exhibit norovirus viremia. J Virol 89:6968–6969 [View Article][PubMed]
    [Google Scholar]
  33. Oiwa H., Shimada T., Hashimoto M., Kawaguchi A., Ueda T., Sugiyama E., Kamiya T. 2011; Clinical findings in parvovirus B19 infection in 30 adult patients in Kyoto. Mod Rheumatol 21:24–31 [View Article][PubMed]
    [Google Scholar]
  34. Okamoto H. 2009; History of discoveries and pathogenicity of TT viruses. Curr Top Microbiol Immunol 331:1–20[PubMed]
    [Google Scholar]
  35. Quail M. A., Smith M., Jackson D., Leonard S., Skelly T., Swerdlow H. P., Gu Y., Ellis P. 2014; SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing. BMC Genomics 15:110 [View Article][PubMed]
    [Google Scholar]
  36. Reuter G., Boros A., Delwart E., Pankovics P. 2013; Novel seadornavirus (family Reoviridae) related to Banna virus in Europe. Arch Virol 158:2163–2167 [View Article][PubMed]
    [Google Scholar]
  37. Rogo L. D., Mokhtari-Azad T., Kabir M. H., Rezaei F. 2014; Human parvovirus B19: a review. Acta Virol 58:199–213 [View Article][PubMed]
    [Google Scholar]
  38. Sanders E. J., Mugo P., Prins H. A., Wahome E., Thiong'o A. N., Mwashigadi G., van der Elst E. M., Omar A., Smith A. D., Graham S. M. 2014; Acute HIV-1 infection is as common as malaria in young febrile adults seeking care in coastal Kenya. AIDS 28:1357–1363 [View Article][PubMed]
    [Google Scholar]
  39. Santiago G. A., Vergne E., Quiles Y., Cosme J., Vazquez J., Medina J. F., Medina F., Colón C., Margolis H., Muñoz-Jordán J. L. 2013; Analytical and clinical performance of the CDC real time RT-PCR assay for detection and typing of dengue virus. PLoS Negl Trop Dis 7:e2311 [View Article][PubMed]
    [Google Scholar]
  40. Slavov S. N., Kashima S., Pinto A. C., Covas D. T. 2011; Human parvovirus B19: general considerations and impact on patients with sickle-cell disease and thalassemia and on blood transfusions. FEMS Immunol Med Microbiol 62:247–262 [View Article][PubMed]
    [Google Scholar]
  41. Smuts H., Kew M., Khan A., Korsman S. 2014; Novel hybrid parvovirus-like virus, NIH-CQV/PHV, contaminants in silica column-based nucleic acid extraction kits. J Virol 88:1398 [View Article][PubMed]
    [Google Scholar]
  42. Spandole S., Cimponeriu D., Berca L. M., Mihăescu G. 2015; Human anelloviruses: an update of molecular, epidemiological and clinical aspects. Arch Virol 160:893–908 [View Article][PubMed]
    [Google Scholar]
  43. Stegmann B. J., Carey J. C. 2002; TORCH infections. Toxoplasmosis, other (syphilis, varicella-zoster, parvovirus B19), Rubella, Cytomegalovirus (CMV), and Herpes infections. Curr Womens Health Rep 2:253–258[PubMed]
    [Google Scholar]
  44. Stremlau M. H., Andersen K. G., Folarin O. A., Grove J. N., Odia I., Ehiane P. E., Omoniwa O., Omoregie O., Jiang P. P. et al. 2015; Discovery of novel rhabdoviruses in the blood of healthy individuals from West Africa. PLoS Negl Trop Dis 9:e0003631 [View Article][PubMed]
    [Google Scholar]
  45. Sun X. H., Meng W. S., Fu S. H., Feng Y., Zhai Y. G., Wang J. L., Wang H. Q., Lv X. J., Liang G. D. 2009; [The first report of Kadipiro virus isolation in China]. Bing Du Xue Bao = Chinese Journal of Virology/ [Bian Ji, Bing Du Xue Bao Bian Ji Wei Yuan Hui] 25:173–177
    [Google Scholar]
  46. Takanashi S., Hashira S., Matsunaga T., Yoshida A., Shiota T., Tung P. G., Khamrin P., Okitsu S., Mizuguchi M. et al. 2009; Detection, genetic characterization, and quantification of norovirus RNA from sera of children with gastroenteritis. J Clin Virol 44:161–163 [View Article][PubMed]
    [Google Scholar]
  47. Thom K., Petrik J. 2007; Progression towards AIDS leads to increased Torque teno virus and Torque teno minivirus titers in tissues of HIV infected individuals. J Med Virol 79:1–7 [View Article][PubMed]
    [Google Scholar]
  48. Wang J., Li H., He Y., Zhou Y., Meng J., Zhu W., Chen H., Liao D., Man Y. 2015; Isolation and genetic characterization of Mangshi virus: a newly discovered Seadornavirus of the Reoviridae family found in Yunnan Province, China. PLoS One 10:e0143601 [View Article][PubMed]
    [Google Scholar]
  49. Young J. C., Chehoud C., Bittinger K., Bailey A., Diamond J. M., Cantu E., Haas A. R., Abbas A., Frye L. et al. 2015; Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients. Am J Transplant 15:200–209 [View Article][PubMed]
    [Google Scholar]
  50. Yozwiak N. L., Skewes-Cox P., Stenglein M. D., Balmaseda A., Harris E., DeRisi J. L. 2012; Virus identification in unknown tropical febrile illness cases using deep sequencing. PLoS Negl Trop Dis 6:e1485 [View Article][PubMed]
    [Google Scholar]
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