Characterization of a triple-recombinant, reassortant rotavirus strain from the Dominican Republic

Abstract

We report the genome of a novel human triple-recombinant G4P[6–8_R] mono-reassortant strain identified in a stool sample from the Dominican Republic during routine facility-based rotavirus strain surveillance. The strain was designated as RVA/Human-wt/DOM/2013840364/2013/G4P[6–8_R], with a genomic constellation of G4-P[6–8_R]-I1-R1-C1-M1-(A1-A8_R)-N1-(T1-T7_R)-E1-H1. Recombinant gene segments NSP1 and NSP3 were generated as a result of recombination between genogroup 1 rotavirus A1 human strain and a genotype A8 porcine strain and between genogroup 1 rotavirus T1 human strain and a genotype T7 bovine strain, respectively. Analyses of the RNA secondary structures of gene segment VP4, NSP1 and NSP3 showed that all the recombinant regions appear to start in a loop (single-stranded) region and terminate in a stem (double-stranded) structure. Also, the VP7 gene occupied lineage VII within the G4 genotypes consisting of mostly porcine or porcine-like G4 strains, suggesting the occurrence of reassortment. The remaining gene segments clustered phylogenetically with genogroup 1 strains. This exchange of whole or partial genetic materials between rotaviruses by recombination and reassortment contributes directly to their diversification, adaptation and evolution.

A G3P[13] porcine group A rotavirus emerging in China is a reassortant and a natural recombinant in the VP4 gene

“…Reassortment events between humans and animal strains have been found previously (Banyai et al., ; Doan et al., ; Esona et al., , ; Ghosh et al., ; He et al., , ; Jere, Mlera, O'Neill, Peenze, & van Dijk, ; Malik et al., ; Masuda et al., ; Matthijnssens et al., ; Mullick et al., ; Steyer, Sagadin, Kolenc, & Poljsak‐Prijatelj, ). Of the 11 segments of the RVA/Pig/China/LNCY/2016/G3P[13] strain, nine gene segments (VP1, VP2, VP3, VP4, VP6, NSP1, NSP2, NSP3 and NPS5) possessed sequences nearly identical with those of the porcine strains, suggesting that RVA/Pig/China/LNCY/2016/G3P[13] was possibly of porcine origin.…”

“…Recombination is considered a potential mechanism for antigenic diversity and a possible mechanism to escape from vaccine‐imposed selective pressure but may not contribute to the long‐term evolution of RVAs (Woods, ). Several reports have identified sequences with recombination in VP4 (Esona et al., ), VP6 (Jere, Mlera, Page, van Dijk, & O'Neill, ; Marthaler et al., ), VP7 (Martinez‐Laso et al., ; Parra, Bok, Martinez, & Gomez, ; Phan et al., , ; Suzuki, Gojobori, & Nakagomi, ), NSP1 (Esona et al., ), NSP2 (Jere et al., ), NSP3 and NSP4 (Donker, Boniface, & Kirkwood, ) (Table S4). Intramolecular recombination could contribute to the development of new RVs phenotypes (Ramig, ).…”

“…Concurrent infection of a single host cell line by different RVs strains is a prerequisite for the occurrence of recombination events in nature (Esona et al., ). In developing countries, animal husbandry (i.e., cattle, sheep and pigs) is closely related to human populations, which provides potential possibilities for reassortment and recombination events.…”

“…Hypotheses have suggested that there may be a direct link between recombination and the formation of the secondary RNA structure, because these RNA structures induce stops, stalls or delays that favour strand invasion (Perez‐Losada, Arenas, Galan, Palero, & Gonzalez‐Candelas, ). The secondary structures in recombinant gene segments and in short stretches of AU‐rich sequence might be associated with recombination events in RVs (Esona et al., ). However, copy choice plays an important role in RNA virus recombination (Kirkegaard & Baltimore, ).…”

“…The classification and nomenclature of RVA genes is Gx‐P[x]‐Ix‐Rx‐Cx‐Mx‐Ax‐Nx‐Tx‐Ex‐Hx, where x indicates the corresponding number of genotypes (Matthijnssens et al., ). To date, 32 G, 47 P, 24 I, 18 R, 17 C, 17 M, 28 A, 18 N, 19 T, 24 E and 19 H genotypes have been identified among RVAs from humans and animals (Esona et al., ), as described at the 7th RCWG meeting (https://rega.kuleuven.be/cev/viralmetagenomics/virus-classification/7th-RCWG-meeting) at Rega Instituut, KU Leuven (Belgium). In pigs, 12 G genotypes (G1 to G6, G8 to G12 and G26) and 16 P genotypes (P[1] to P[8], P[13], P[19], P[23], P[26], P[27], P[28], P[32] and P[34]) of RVA have been identified, and G3, G4, G5, G9 and G11 usually occur in combination with P[5], P[6], P[7], P[13] and P[28], respectively (Vlasova et al., ).…”