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

Ouédraogo N, Kaplon J, Bonkoungou IJ, Traoré AS, Pothier P, Barro N, Ambert-Balay K - PLoS ONE (2016)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire de Biologie Moléculaire, d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments, Centre de Recherche en Sciences Biologiques Alimentaires et Nutritionnelles (CRSBAN), Université de Ouagadougou, Ouagadougou, Burkina Faso.

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.

No MeSH data available.


Related in: MedlinePlus

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.
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pone.0153652.g004: 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.

Mentions: Phylogenetic tree based on the partial nucleotide sequences (277 bp) of an area located in the open-reading frame (ORF2) of sapovirus is showed in Fig 4. Eight SaV strains out of 30 were successfully genotyped and fell into two distinct genogroups: GI (1/8; 12.5%) and GII (7/8; 87.5%). GII strains were further classified into genotypes GII.1 (n = 3), GII.2 (n = 2) and GII.3 (n = 1) and in a new cluster of GII (n = 1) represented by the reference strain SaKaeo-15 (AY646855). The GI strain was classified into GI.2. Phylogenetic analysis showed that the GII.1 strains presented 72–89% nucleotides identity (60–98% aa identity) with the reference strain Bristol/98 (AJ249939). The GII.2 presented 93% nucleotide identity (99% aa identity) with the reference strain SLV/Mex340/1990 (AF435812). The new cluster of GII related to the reference strain SaKaeo-15 (AY646855) with 93% nucleotide (99% amino-acids). The GII.3 displayed 94% nucleotides identity (99% aa identity) with the reference strains CruiseShip/00 (AY289804). GI.2 strain shared 93% nucleotide (100% aa) with the reference strain Potsdam/GI.2 (AF294739).


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

Ouédraogo N, Kaplon J, Bonkoungou IJ, Traoré AS, Pothier P, Barro N, Ambert-Balay K - PLoS ONE (2016)

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.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4836733&req=5

pone.0153652.g004: 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.
Mentions: Phylogenetic tree based on the partial nucleotide sequences (277 bp) of an area located in the open-reading frame (ORF2) of sapovirus is showed in Fig 4. Eight SaV strains out of 30 were successfully genotyped and fell into two distinct genogroups: GI (1/8; 12.5%) and GII (7/8; 87.5%). GII strains were further classified into genotypes GII.1 (n = 3), GII.2 (n = 2) and GII.3 (n = 1) and in a new cluster of GII (n = 1) represented by the reference strain SaKaeo-15 (AY646855). The GI strain was classified into GI.2. Phylogenetic analysis showed that the GII.1 strains presented 72–89% nucleotides identity (60–98% aa identity) with the reference strain Bristol/98 (AJ249939). The GII.2 presented 93% nucleotide identity (99% aa identity) with the reference strain SLV/Mex340/1990 (AF435812). The new cluster of GII related to the reference strain SaKaeo-15 (AY646855) with 93% nucleotide (99% amino-acids). The GII.3 displayed 94% nucleotides identity (99% aa identity) with the reference strains CruiseShip/00 (AY289804). GI.2 strain shared 93% nucleotide (100% aa) with the reference strain Potsdam/GI.2 (AF294739).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire de Biologie Moléculaire, d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments, Centre de Recherche en Sciences Biologiques Alimentaires et Nutritionnelles (CRSBAN), Université de Ouagadougou, Ouagadougou, Burkina Faso.

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.

No MeSH data available.


Related in: MedlinePlus