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. 2014 Sep;8(5):567-73.
doi: 10.1111/irv.12264. Epub 2014 Jul 3.

Genetic diversity and molecular epidemiology of human rhinoviruses in South Africa

Marthi A Pretorius  1 , Stefano Tempia, Florette K Treurnicht, Sibongile Walaza, Adam L Cohen, Jocelyn Moyes, Orienka Hellferscee, Ebrahim Variava, Halima Dawood, Meera Chhagan, Sumayya Haffjee, Shabir A Madhi, Cheryl Cohen, Marietjie Venter
Affiliations

Genetic diversity and molecular epidemiology of human rhinoviruses in South Africa

Marthi A Pretorius et al. Influenza Other Respir Viruses. 2014 Sep.

Abstract

Background: Rhinoviruses (RV) are a well-established cause of respiratory illness. RV-C has been associated with more severe illness. We aimed to characterize and compare the clinical presentations and disease severity of different RV type circulating in South Africa.

Method: We performed two analyses of RV-positive specimens identified through surveillance in South Africa across all age groups. First, RV-positive specimens identified through severe acute respiratory illness (SARI) surveillance in four provinces was randomly selected from 2009 to 2010 for molecular characterization. Second, RV-positive specimens identified through SARI, influenza-like illness (ILI) and control surveillance at hospitals and outpatient clinics in during 2012-2013 were used to determine the association of RV type with severe disease. Selected specimens were sequenced, and phylogenetic analysis was performed.

Results: Among the 599 sequenced specimens from 2009 to 2010 and 2012 to 2013, RV-A (285, 48%) and RV-C (247, 41%) were more commonly identified than RV-B (67, 11%), with no seasonality and a high genetic diversity. A higher prevalence of RV infection was identified in cases with SARI [515/962 (26%); aRRR = 1.6; 95% CI 1.21; 2.2] and ILI [356/962 (28%); aRRR = 1.9; 95% CI 1.37; 2.6] compared with asymptomatic controls (91/962, 22%). There was no difference in disease severity between the different type when comparing SARI, ILI and controls.

Conclusion: All three type of RV were identified in South Africa, although RV-A and RV-C were more common than RV-B. RV was associated with symptomatic respiratory illness; however, there was no association between RV type and disease severity.

Keywords: Disease association; South Africa; genetic diversity; rhinovirus.

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Figures

Figure 1
Figure 1
Phylogenetic analysis of RV type by maximum-likelihood method of the VP4/VP2 region, South Africa, 2009–2010 and 2012–2013. Phylogenetic analysis of Rhinovirus sequences from South Africa and reference sequences from Genbank using maximum-likelihood method of the VP4/VP2 region. Sequences with closed circle denotes type identified in SARI patients, those with open squares denotes type identified in ILI patients, while those with open circles denotes type identified in control patients, those without denotation are the reference sequences. Bootstrap values (100 replicates) shown on the branches, with values <70% omitted from the tree.
Figure 2
Figure 2
Number of positive cases and detection rate of Rhinovirus by month in South Africa, 2009–2010 SARI (A) and 2012–2013 SARI, ILI and control cases (B).
See this image and copyright information in PMC

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