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

ABSTRACT: BACKGROUND:Human enteroviruses (EV) have been associated with severe acute respiratory illness (SARI) in South Africa. OBJECTIVES:We aimed to describe the molecular epidemiology of EV serotypes among patients hospitalized with SARI during 2009-2011. PATIENTS/METHODS:Study samples from patients were tested for the presence of enterovirus using a polymerase chain reaction assay. RESULTS:8.2% (842/10 260) of SARI cases tested positive for enterovirus; 16% (7/45) were species EV-A, 44% (20/45) EV-B, 18% (8/45) EV-C and 22% (10/45) EV-D. Seventeen different EV serotypes were identified within EV-A to EV-D, of which EV-D68 (22%; 10/45) and Echovirus 3 (11%; 5/45) were the most prevalent. CONCLUSIONS:EV-D68 should be monitored in South Africa to assess the emergence of highly pathogenic strains.

SUBMITTER: Hellferscee O

PROVIDER: S-EPMC5410726 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

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

Hellferscee Orienka O Treurnicht Florette K FK Tempia Stefano S Variava Ebrahim E Dawood Halima H Kahn Kathleen K Cohen Adam L AL Pretorius Marthi M Cohen Cheryl C Madhi Shabir A SA Venter Marietjie M

Influenza and other respiratory viruses 20170226 3

<h4>Background</h4>Human enteroviruses (EV) have been associated with severe acute respiratory illness (SARI) in South Africa.<h4>Objectives</h4>We aimed to describe the molecular epidemiology of EV serotypes among patients hospitalized with SARI during 2009-2011.<h4>Patients/methods</h4>Study samples from patients were tested for the presence of enterovirus using a polymerase chain reaction assay.<h4>Results</h4>8.2% (842/10 260) of SARI cases tested positive for enterovirus; 16% (7/45) were sp ...[more]

PMID: 28122175

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Project description:BackgroundSince 1962, enterovirus D68 (EV-D68) has been implicated in multiple outbreaks and sporadic cases of respiratory infection worldwide, but especially in the USA and Europe with an increasing frequency between 2010 and 2014. We describe the detection, associated clinical features and molecular characterization of EV-D68 in central and southern Viet Nam between 2009 and 2015.MethodsEnterovirus/rhinovirus PCR positive respiratory or CSF samples taken from children and adults with respiratory/central nervous system infections in Viet Nam were tested by an EV-D68 specific PCR. The included samples were derived from 3 different observational studies conducted at referral hospitals across central and southern Viet Nam between 2009 and 2015. Whole-genome sequencing was carried out using a MiSeq based approach. Phylogenetic reconstruction and estimation of evolutionary rate and recombination were carried out in BEAST and Recombination Detection Program, respectively.ResultsEV-D68 was detected in 21/625 (3.4%) enterovirus/rhinovirus PCR positive respiratory samples but in none of the 15 CSF. All the EV-D68 patients were young children (age range: 11.8 - 24.5 months) and had moderate respiratory infections. Phylogenetic analysis suggested that the Vietnamese sequences clustered with those from Asian countries, of which 9 fell in the B1 clade, and the remaining sequence was identified within the A2 clade. One intra sub-clade recombination event was detected, representing the second reported recombination within EV-D68. The evolutionary rate of EV-D68 was estimated to be 5.12E -3 substitutions/site/year. Phylogenetic analysis indicated that the virus was imported into Viet Nam in 2008.ConclusionsWe have demonstrated for the first time EV-D68 has been circulating at low levels in Viet Nam since 2008, associated with moderate acute respiratory infection in children. EV-D68 in Viet Nam is most closely related to Asian viruses, and clusters separately from recent US and European viruses that were suggested to be associated with acute flaccid paralysis.

Dataset Information

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

Publications

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

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