Enterovirus D68 and other enterovirus serotypes identified in South African patients with severe acute respiratory illness, 2009–2011

Influenza and other Respiratory Viruses

Volumn 11, Issue 3, 2017, Pages 211-219

  Hellferscee, Orienka ^a,b   Treurnicht, Florette K ^a   Tempia, Stefano ^a,c   Variava, Ebrahim ^b,d   Dawood, Halima ^d,e   Kahn, Kathleen ^b   Cohen, Adam L ^c   Pretorius, Marthi ^f   Cohen, Cheryl ^a,b   Madhi, Shabir A ^a,b   Venter, Marietjie ^c,f  

^a NATIONAL INSTITUTE FOR COMMUNICABLE DISEASES   (South Africa)

^b UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^c CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^d Pietermaritzburg Metropolitan Hosp   (South Africa)

^e UNIVERSITY OF KWAZULU NATAL   (South Africa)

^f UNIVERSITY OF PRETORIA   (South Africa)

Author keywords

enterovirus; EV D68; pneumonia; South Africa

Indexed keywords

ANTIBIOTIC AGENT;

ACUTE RESPIRATORY TRACT DISEASE; ARTICLE; CASE FATALITY RATE; CHILD; ECHOVIRUS 3; ENTEROVIRUS A; ENTEROVIRUS B; ENTEROVIRUS C; ENTEROVIRUS D; ENTEROVIRUS D68; FEMALE; FEVER; GENE AMPLIFICATION; GENOTYPE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MAJOR CLINICAL STUDY; MALE; MIXED INFECTION; MOLECULAR EPIDEMIOLOGY; PHYLOGENY; POLYMERASE CHAIN REACTION; PRESCHOOL CHILD; PREVALENCE; PRIORITY JOURNAL; RETROSPECTIVE STUDY; RISK FACTOR; SEROTYPE; SOUTH AFRICAN; ADOLESCENT; CLASSIFICATION; ENTEROVIRUS; ENTEROVIRUS INFECTIONS; GENETICS; INFANT; ISOLATION AND PURIFICATION; RESPIRATORY TRACT INFECTIONS; SOUTH AFRICA; VIROLOGY;

ADOLESCENT; CHILD; CHILD, PRESCHOOL; ENTEROVIRUS; ENTEROVIRUS D, HUMAN; ENTEROVIRUS INFECTIONS; FEMALE; HUMANS; INFANT; MALE; PHYLOGENY; RESPIRATORY TRACT INFECTIONS; SEROGROUP; SOUTH AFRICA;

EID: 85013831945     PISSN: 17502640     EISSN: 17502659     Source Type: Journal    
DOI: 10.1111/irv.12444     Document Type: Article

References (28)

1. Black RE, Cousens S, Johnson HL, et al. Global, regional, and national causes of child mortality in 2008: a systematic analysis. Lancet. 2010;375:1969–1987.
2. Pretorius MA, Tempia S, Walaza S, et al. The role of influenza, RSV and other common respiratory viruses in severe acute respiratory infections and influenza-like illness in a population with a high HIV sero-prevalence, South Africa 2012-2015. J Clin Virol. 2016;75:21–26.
3. Smura T, Ylipaasto P, Klemola P, et al. Cellular tropism of human enterovirus D species serotypes EV-94, EV-70, and EV-68 in vitro: implications for pathogenesis. J Med Virol. 2010;82:1940–1949.
4. Pallansch MA, Roos R. Enteroviruses. Polioviruses, Coxsackieviruses, Echoviruses and newer enteroviruses. 5th edn. Virology F, editor. Philadelphia, PA: Lippincott Williams & Wilkin; 2007.
5. Knowles HJ, Hovi T, Hyypia T, King AMQ, Lindberg AM, Pallansch MA. Virus taxonomy: Classification and nomenclature of viruses: Ninth Report of the International Committee on Taxonomy of Viruses. San Diego: Elsevier; 2012.
6. Hu L, Zhang Y, Hong M, et al. Phylogenetic evidence for multiple intertypic recombinations in enterovirus B81 strains isolated in Tibet, China. Sci Rep. 2014;4:6035.
7. Tokarz R, Firth C, Madhi SA, et al. Worldwide emergence of multiple clades of enterovirus 68. J Gen Virol. 2012;93(Pt 9):1952–1958.
8. Owens B. Rare enterovirus continues to circulate in North America. Lancet. 2014;384:1250.
9. Bottcher S, Prifert C, Weissbrich B, et al. Detection of enterovirus D68 in patients hospitalised in three tertiary university hospitals in Germany, 2013 to 2014. Euro Surveill. 2016;21.
10. Gong YN, Yang SL, Shih SR, et al. Molecular evolution and the global reemergence of enterovirus D68 by genome-wide analysis. Medicine. 2016;95:e4416.
11. Linsuwanon P, Puenpa J, Suwannakarn K, et al. Molecular epidemiology and evolution of human enterovirus serotype 68 in Thailand, 2006-2011. PLoS One. 2012;7:e35190.
12. Lauinger IL, Bible JM, Halligan EP, Aarons EJ, MacMahon E, Tong CY. Lineages, sub-lineages and variants of enterovirus 68 in recent outbreaks. PLoS One. 2012;7:e36005.
13. Imamura T, Fuji N, Suzuki A, et al. Enterovirus 68 among children with severe acute respiratory infection, the Philippines. Emerg Infect Dis. 2011;17:1430–1435.
14. Pretorius MA, Madhi SA, Cohen C, et al. Respiratory viral coinfections identified by a 10-plex real-time reverse-transcription polymerase chain reaction assay in patients hospitalized with severe acute respiratory illness–South Africa, 2009-2010. J Infect Dis. 2012;206(Suppl 1):S159–S165.
15. Cohen C, Moyes J, Tempia S, et al. Severe influenza-associated respiratory infection in high HIV prevalence setting, South Africa, 2009-2011. Emerg Infect Dis. 2013;19:1766–1774.
16. Nix WA, Oberste MS, Pallansch MA. Sensitive, seminested PCR amplification of VP1 sequences for direct identification of all enterovirus serotypes from original clinical specimens. J Clin Microbiol. 2006;44:2698–2704.
17. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–780.
18. Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 2012;9:772.
19. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52:696–704.
20. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28:2731–2739.
21. Du J, Zheng B, Zheng W, et al. Analysis of Enterovirus 68 Strains from the 2014 North American Outbreak Reveals a New Clade, Indicating Viral Evolution. PLoS One. 2015;10:e0144208.
22. Meijer A, van der Sanden S, Snijders BE, et al. Emergence and epidemic occurrence of enterovirus 68 respiratory infections in The Netherlands in 2010. Virology. 2012;423:49–57.
23. Khetsuriani N, Lamonte-Fowlkes A, Oberst S, Pallansch MA. Enterovirus surveillance–United States, 1970-2005. MMWR Surveill Summ. 2006;55:1–20.
24. Renois F, Leveque N, Deliege PG, et al. Enteroviruses as major cause of microbiologically unexplained acute respiratory tract infections in hospitalized pediatric patients. J Infect. 2013;66:494–502.
25. Meijer A, Benschop KS, Donker GA, van der Avoort HG. Continued seasonal circulation of enterovirus D68 in the Netherlands, 2011-2014. Euro Surveill. 2014;19.
26. Reiche J, Bottcher S, Diedrich S, et al. Low-level Circulation of Enterovirus D68-Associated Acute Respiratory Infections, Germany, 2014. Emerg Infect Dis. 2015;21:837–841.
27. Todd AK, Hall RJ, Wang J, et al. Detection and whole genome sequence analysis of an enterovirus 68 cluster. Virol J. 2013;10:103.
28. Schuster JE, Miller JO, Selvarangan R, et al. Severe enterovirus 68 respiratory illness in children requiring intensive care management. J Clin Virol. 2015;70:77–82.