Whole Genome characterization of G9P[4] and G9P[8] Rotaviruses strains identified in Lebanon

Abstract

Rotavirus is considered globally the leading cause of severe diarrheal infections among children under the age of 5 years and is responsible for about 215 000 deaths annually. Rotaviruses are classified based on their outermost shell proteins, VP7 (G-genotype) and VP4 (P-genotype) with at least 36 G genotypes and 51 P genotypes identified up-to-date. Although there are common globally circulating genotypes (G1P[8],G3P[8], G9P[8],G2P[4]), the segmented genome of the virus and possible vaccine pressure might explain the emergence of unique genotypes such as G9P[4]. In Lebanon, a hospital-based study conducted between 2011-2013 revealed that 30.3percent of gastroenteritis-hospitalizations were attributed to rotavirus A (RVA), with major genotypes being G1P[8] (36percent) and G9P[8] (26.4percent). Newly emerging, unique genotypes such as G9P[4] constituted 1percent. In this study we performed full genome characterization these unique G9P[4] strains and one G9P[8] strain in Lebanon by using virome capture technology and phylogenetic analysis. Our goal was to elucidate their origin and genetic relatedness compared to globally circulating G9P[4] and G9P[8] specimens as well as their genetic vaccine matching. One G9P[4] specimen was of pure DS-1 like origin and the remaining two were of mixed and diverse Wa-like-DS-1-like genotypes: RVA-Human-LEB-A095-2011-G9P[4] (G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2), RVA-Human-LEB-H017-2011-G9P[4] (G9-P[4]-I2-R2-C2-M2-A2-N1-T2-E2-H2), RVA-Human-LEB-H199-2011-G9P[4] (G9-P[4]-I1-R1-C1-M1-A2-N1-T1-E1-H1). The RVA-Human-LEB-NG184-2011-G9P[8] was of pure Wa-like origin (G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1). Phylogenetic analysis revealed that the G9P[4] strains with mixed genomic constellation emerged from a reassortment events between G2P[4] and G9P[8] stains. Overall, unlike the G9P[8] strains’ pure genomic backbone, multiple lineages of G9P[4] seemed to have emerged globally. The analysis indicated that Lebanese G9P[4] strains seemed to have emerged through multiple introductions or reassortment event