Abstract
Rotavirus has been identified as a major cause of gastroenteritis in Nigeria. There is limited information on the intragenotype diversity of Nigerian rotavirus isolates. We therefore investigated the molecular characteristics of some rotavirus gene sequences detected in sewage from Nigeria. Seven sewage samples, out of a total of 68, tested positive for rotavirus RNA (10.3%). Genotype G1P[4] was the most common genotype (5 isolates) and one isolate for genotypes G1P[8] and G3P[6]. Phylogenetic analysis of the partial VP7 gene of 3 G1P[4] isolates analyzed identified them as genotype G1 Lineage 2 along with Chinese strains with 99.1% to 100% amino acid similarity. Amino acid substitutions D-97→E and S-147→D/N were observed within the 7-1a and 7-2 domains of VP7 gene among the study G1P4 isolates in reference to vaccine strain RotaTeq®. Phylogenetic analysis of the G3P[6] study isolate identified it as genotype G3 Lineage 3, forming a monophyletic cluster with 100% bootstrap value with other West African strains G3 isolates. Phylogenetic analysis of GIP[4] VP4 genes identified them as P4 Lineage 5, while 3 NSP4 gene sequences belonged to genotype E1, while 1 belonged to E2. The results from this study represent phylogenetic analysis of partial gene sequences of environmental group A rotavirus (RVA) isolates from Nigeria.
Highlights
Rotavirus is the most important agent of viral gastroenteritis in children [1, 2]
Our current study investigates the molecular characteristics and intragenotype diversity of partial VP7, VP4, and NSP4 genes of Rotavirus A (RVA) isolated from sewage water in Nigeria in 2014
Seven samples tested positive for rotavirus out of 68 tested (10.3%), genotype G1P[4] had the highest number with five
Summary
Rotavirus is the most important agent of viral gastroenteritis in children [1, 2]. The virus is responsible for about 200,000 deaths in children below 5 years of age annually in low income countries [1, 3]. Rotaviruses are members of the virus family Reoviridae, possessing a double stranded (ds) RNA genome segmented into 11 compartments, coding for six structural proteins (VP1 to VP4, VP6, and VP7) and five or six nonstructural proteins (NSP1 to NSP5/6) [4] Based on this structural organization at least 10 distinct species/groups (AI, J) are differentiated based on their VP6 coding sequences [5, 6]. The major proteins capable of eliciting neutralizing antibodies against rotavirus challenge are the 34kDa glycoprotein VP7 and the 88kDa nonglycosylated spike protein VP4 These 2 proteins have been used to form a binary classification scheme for rotaviruses in analogy to that used for influenza virus classification [7]
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