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.

Keywords: EV-D68; South Africa; enterovirus; pneumonia.

Figure 1

Molecular characterization of enterovirus clinical samples based on phylogenetic analysis of nucleotide sequences of the partial VP1 genomic region. Trees were constructed using neighbour‐joining methods as implemented in MEGA 5 software (http://www.megasoftware.net). Bootstrap values from 1000 replicates are shown on the nodes. Black dots=South African samples 2009‐2011

Figure 2

Epidemiologic graphs showing: (A) Distribution of enterovirus in South Africa during 2009‐2011 and (B) Distribution of enterovirus species detected in South Africa during 2009‐2011

Figure 3

Molecular characterization of EV‐D68 clinical samples based on phylogenetic analysis of nucleotide sequences of the partial VP1 genomic region. Trees were constructed using neighbour‐joining methods as implicated in mega 5 software (http://www.megasoftware.net). Bootstrap values from 1000 replicates are shown on the nodes. Scale bar indicates number of nucleotide substitutions per site. Black dots=South African strains 2009‐2011; Open dots=South African strains 2000‐2001. Clades B1, B3, C A1 and partial B2 and A2 have been compressed to show comparison of South African strains to strains from other countries (country and year in blocks). Total number of sequences=312 (representative strains from 2000 to 2016)