Prevalence and Genetic Diversity of Enteric Viruses in Children with Diarrhea in 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.

Epidemiology of enteric viruses in children with gastroenteritis in Ogun State, Nigeria

“…This disparity amongst studies may be due to the number of viruses analyzed, viral detection methods, season of sampling, and sample size. The most common coinfections were between RVA and HAstV which is in contrast with reports of Biscaro et al, Ferreira et al, and Ouédraogo et al who had RVA and HAdV as the most prevalent. Pang and Vesikari previously reported the rate of HAstV and RVA coinfections among gastroenteritis in children to be extremely low (10 of 1528 or 0.006%).…”

“…A relatively low frequency of coinfection (9.7%) was observed in this study, which is lower than previously reported in Burkina Faso (35.7%) and Brazil (14%), but higher compared with studies from China (5.2%), Northern Italy (2.3%), and Nigeria (7.1%) . This disparity amongst studies may be due to the number of viruses analyzed, viral detection methods, season of sampling, and sample size.…”

“…Worldwide, the prevalence of enteric viruses (EVs) in children with acute gastroenteritis has been reported to range from 29.6% to 85.6% . Previous studies in Nigeria showed the different prevalence of EVs infection .…”

Temporal distribution of gastroenteritis viruses in Ouagadougou, Burkina Faso: seasonality of rotavirus

“…AdV all types were detected using a commercial real-time PCR assay designed to detect all types of human AdV (Adenovirus R-gene™, Argène, Verniolle, France) and AiV were detected by end-point RT-PCR using the Qiagen One-Step RT-PCR kit (Qiagen, Hilden, Germany) and the primer set Ai6261/Ai6779 [20]. …”

Emergence of new recombinant noroviruses GII.p16-GII.4 and GII.p16-GII.2, France, winter 2016 to 2017

“…NoV detection was performed by real-time RT-PCR as previously described [1]. A total of 222 stool samples, corresponding to 87 outbreaks (76%), were positive for norovirus.…”