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. 2016 Apr 19;11(4):e0153652.
doi: 10.1371/journal.pone.0153652. eCollection 2016.

Prevalence and Genetic Diversity of Enteric Viruses in Children with Diarrhea in Ouagadougou, Burkina Faso

Nafissatou Ouédraogo  1 , Jérôme Kaplon  2 , Isidore Juste O Bonkoungou  1   3 , Alfred Sababénédjo Traoré  1 , Pierre Pothier  2 , Nicolas Barro  1 , Katia Ambert-Balay  2
Affiliations

Prevalence and Genetic Diversity of Enteric Viruses in Children with Diarrhea in Ouagadougou, Burkina Faso

Nafissatou Ouédraogo et al. PLoS One. .

Abstract

Enteric viruses are a major cause of diarrhea in children, especially those under five years old. Identifying the viral agents is critical to the development of effective preventive measures. This study aimed to determine the prevalence and genetic diversity of common enteric viruses in children under five years old in Burkina Faso. Stool samples from children with (n = 263) and without (n = 50) diarrhea disorders were collected in Ouagadougou, Burkina Faso from November 2011 to September 2012. Rotavirus, norovirus, sapovirus, astrovirus, adenovirus and Aichivirus A were detected using real-time or end-point (RT-)PCR. Rotavirus strains were G and P genotyped by multiplex RT-PCR and other viral strains were characterized by sequencing of viral subgenomic segements. At least one viral agent was detected in 85.6% and 72% of the symptomatic and asymptomatic patients, respectively. Rotavirus (63.5%), adenovirus (31.2%) and genogroup II norovirus (18.2%) were the most prevalent viruses in symptomatic patients, but only rotavirus and genogroup II norovirus were significantly associated with diarrhea (OR: 7.9, 95%CI: 3.7-17; OR: 3.5, 95%CI: 1-11.7, respectively). Sapovirus (10.3%), astrovirus (4.9%), genogroup I norovirus (2.7%) and Aichivirus A (0.8%) were less prevalent. The predominant genotype of rotavirus was G9P[8] (36.5%), and the predominant norovirus strain was GII.4 variant 2012 (71.4%). Among sapovirus, the genogroup II (87.5%) predominated. Astrovirus type 1 (41.7%) was the most frequent astrovirus identified. Aichivirus A belonged to the three genotypes (A, B and C). Enteric adenoviruses type 40 and 41 were identified in 10.2% and 5.1% respectively. Several cases of co-infections were detected. The results highlight the high prevalence and the high diversity of enteric viruses in Burkinabe children.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Phylogenetic analysis based on the partial nucleotide sequences (842 bp) of the rotavirus VP7 gene detected in Ouagadougou, Burkina Faso, between November 2011 and September 2012.
The tree was constructed using Maximum likelihood clustering. Reference strains of rotavirus were selected from the GenBank database.
Fig 2
Fig 2. Phylogenetic analysis based on the partial nucleotide sequences (285 bp) of the RNA-dependent RNA polymerase coding gene of the norovirus strains detected in Ouagadougou, Burkina Faso, between November 2011 and September 2012.
The tree was constructed using Maximum Likelihood method. Reference strains of norovirus were selected from the GenBank database.
Fig 3
Fig 3. Phylogenetic analysis based on the partial nucleotide sequences (302 bp) of the capsid coding gene of NoV strains detected in Ouagadougou, Burkina Faso, between November 2011 and September 2012.
The tree was constructed using Maximum Likelihood method. Reference strains of norovirus were selected from the GenBank database.
Fig 4
Fig 4. Phylogenetic analysis based on the partial nucleotide sequences (277 bp) of an area located in the open-reading frame (ORF2) of sapovirus strains detected in Ouagadougou, Burkina Faso, between November 2011 and September 2012.
The tree was constructed using Maximum Likelihood method. Reference strains of sapovirus were selected from the GenBank database.
Fig 5
Fig 5. Phylogenetic analysis based on hexon protein gene of AdV 40/41 of human adenovirus strains detected in Ouagadougou, Burkina Faso, between November 2011 and September 2012.
The tree was constructed using Maximum Likelihood method. Reference strains of adenovirus type 40 and type 41 were selected from the GenBank database.
Fig 6
Fig 6. Phylogenetic analysis based on the partial nucleotide sequences (373 bp) of an area located in the open-reading frame (ORF2) of Astrovirus detected in Ouagadougou, Burkina Faso, between November 2011 and September 2012.
The tree was constructed using Maximum Likelihood method. Reference strains of astrovirus were selected from the GenBank database.
Fig 7
Fig 7. Phylogenetic analysis based on the partial nucleotide sequence (477 bp) of the 3CD-encoding gene of the Aichivirus A detected in Ouagadougou, Burkina Faso, between November 2011 and September 2012.
The tree was constructed using Maximum Likelihood method. Reference strains of Aichivirus A were selected from the GenBank database.
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