Rotavirus in diarrheal children in rural Burkina Faso: High prevalence of genotype G6P[6] Johan Nordgren a,⇑,1 , Isidore Juste O. Bonkoungou b,c,1 , Leon W. Nitiema d,e , Sumit Sharma a , Djeneba Ouermi d , Jacques Simpore d , Nicolas Barro c , Lennart Svensson a a Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, SE-58185 Linköping, Sweden b Laboratoire National de Santé Publique du Burkina Faso, 09 BP 24 Ouagadougou, Burkina Faso c Laboratoire de Biologie Moléculaire, d’Epidémiologie et Surveillance des Bactéries et Virus Transmissibles par les Aliments, CRSBAN/UFR-SVT, Université de Ouagadougou, 03 BP 7021 Ouagadougou 03, Burkina Faso d Centre de Recherche Biomoléculaire Pietro Annigoni, Saint Camille CERBA/LABIOGENE, Université de Ouagadougou, 01 BP 364 Ouagadougou, Burkina Faso e Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN), Université de Ouagadougou, 03 BP 7021 Ouagadougou 03, Burkina Faso article info Article history: Received 12 June 2012 Received in revised form 9 August 2012 Accepted 14 August 2012 Available online 3 September 2012 Keywords: Rotavirus Genotypes G6P[6] Rural areas Gastroenteritis Children abstract Group A rotavirus (RVA) is the most common cause of severe gastroenteritis in young children globally, and responsible for a significant number of deaths in African countries. While vaccines are available, trials have shown a lesser efficacy in Africa. One of the reasons could be the prevalence and/or emergence of unusual or novel RVA strains, as many strains detected in African countries remain uncharacterized. In this study, we characterized RVA positive specimens from two remote rural areas in Burkina Faso, West Africa. In total 56 RVA positive specimens were subgrouped by their VP6 gene, and G-and P typed by PCR and/or sequencing of the VP7 and VP4 genes, respectively. Notably, we found a high prevalence of the unusual G6P[6]SGI strains (23%). It was the second most common constellation after G9P[8]SGII (32%); and followed by G1P[8]SGII (20%) and G2P[4]SGI (9%). We also detected a G8P[6]SGI strain, for the first time in Burkina Faso. The intra-genetic diversity was high for the VP4 gene with two subclusters within the P[8] genotype and three subclusters within the P[6] genotype which were each associated with a specific G-type, thereby suggesting a genetic linkage. The G6P[6]SGI and other SGI RVA strains infected younger children as compared to SGII strains (p < 0.05). To conclude, in this study we observed the emergence of unusual RVA strains and high genetic diversity of RVA in remote rural areas of Burkina Faso. The results highlight the complexity of RVA epidemiology which may have implication for the introduction of rotavirus vaccines currently being evaluated in many African countries. Ó 2012 Elsevier B.V. All rights reserved. 1. Introduction Group A rotavirus (RVA) is the leading cause of severe acute gastroenteritis in infants and young children, responsible for approximately 453,000 deaths annually (Tate et al., 2011), with more than 230,000 of the deaths occurring in sub-Saharan Africa. Five of 10 countries with the highest mortality due to RVA diarrhea are located in Africa (Tate et al., 2011). The high burden of RVA disease in children has accelerated the development of vaccines (Parashar et al., 2006; Patel et al., 2008), and the World Health Organization (WHO) now recommends the inclusion of RVA vaccines in the national immunization program in countries highly affected by RVA. Currently, two vaccines, Rotarix and RotaTeq, are licensed and available in many countries. Although the vaccines have demonstrated high efficacy in industri- alized countries, vaccine trials from African countries have shown a lesser efficacy (Madhi et al., 2010; Sow et al., 2012). The reasons for this are yet unknown, but a different and more diverse genetic set- up of RVA strains could be one of the reasons. The RVA strain diver- sity in Africa is higher than from industrialized countries and also have a high degree of animal or animal derived genes (Nordgren et al., 2012; Todd et al., 2010). Some other major differences include the relatively high prevalence of the P[6] genotype as well as a high detection rate of G8 in certain countries (Armah et al., 2010; Nordgren et al., 2012; Page et al., 2010b; Todd et al., 2010). This highlights the need for understanding of the molecular epidemio- logical patterns of human and animal RVA strains in the continent in order to assess factors that could be important for vaccine effi- cacy. Few studies regarding the molecular epidemiology of RVA in rural areas in Africa have been performed (Armah et al., 2003), 1567-1348/$ - see front matter Ó 2012 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.meegid.2012.08.014 ⇑ Corresponding author. Address: Division of Molecular Virology, Department of Clinical and Experimental Medicine, Medical Faculty, Linköping University, SE-581 85 Linköping, Sweden. Tel.: +46 70 2239323; fax: +46 10 31375. E-mail address: johan.nordgren@liu.se (J. Nordgren). 1 These authors are contributed equally to this study. Infection, Genetics and Evolution 12 (2012) 1892–1898 Contents lists available at SciVerse ScienceDirect Infection, Genetics and Evolution journal homepage: www.elsevier.com/locate/meegid