Emergence of Equine-like G3P[8] Rotavirus Strains Infecting Children in Venezuela

Figures

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  Figure 1. Multiple alignments of the VP7 rotavirus nucleotide sequences reveal mismatches at the primer-binding region (in gray) used in the G-typing assay [56]. (A) The G3 primer sequence was compared to G3 reference strains (SPN/115Madrid and equine-like/THA/SKT-289), and Venezuelan strains: VEN/VCE18950/2003 (old G3), and VEN/3-CLC/2023 (novel equine-like G3). (B) The G9 primer sequence was compared to G9 reference strains (IND/ISO-3, and the ancestral USA/WI61), equine-like strain THA/SKT-289, and the novel Venezuelan equine-like G3 VEN/3-CLC/2023.

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  Figure 2. Phylogenetic tree of VP7 gene nucleotide sequences of Venezuelan human rotaviruses circulating from 2003 to 2024. The tree was generated by the neighbor-joining method and the Kimura two-parameter model as the substitution method. Bootstrap values above 70%, estimated with 1000 pseudo-replicate data sets, are indicated at each node. Venezuelan human G3 RVA isolated between 2003 and 2008 (old strains) [marked with a black down-pointing triangle (⯆)], equine-like G3 (novel G3) strains circulating in 2023–2024 [marked with a filled dot (●) symbol], and one wastewater G3 strain [VEN/80-IZET/2022, OR626614, marked by a white up-pointing triangle (Δ)], from Caracas, were compared to reference sequences from the GenBank database of the most common G1-4, -9, and -12 human and animal rotaviruses, and the RotaTeq® vaccine G3 strain [marked with a white diamond (◊)]. VP7 non-G3 genotype clades were collapsed. Each taxon was named according to the proposed nomenclature of the Rotavirus Classification Working Group [57], and the rotavirus group, species isolated from, country of strain isolation, common name, year of isolation, and genotypes for genome segments 9 and 4 are indicated. The…

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  Figure 3. Phylogenetic trees constructed after full-genome analysis of one representative human equine-like G3P[8] rotavirus isolated in Venezuela in 2023. The nucleotide sequences obtained from all the rotavirus gene segments, VP4 (A), VP6 (B), VP1 (C), VP2 (D), VP3 (E), NSP1 (F), NSP2 (G), NSP3 (H), NSP4 (I), and NSP5 (J), from one human equine-like Venezuelan G3 collected in 2023, marked with a filled dot (●) symbol, were compared with reference strains available in GenBank. Gene sequences from RotaTeq™ and Rotarix® vaccine strains, marked with a white diamond (◊), were included. Bootstrap values above 70%, estimated with 1000 pseudo-replicate data sets, are indicated at each node. The scale bar at the bottom of the tree represents genetic distance expressed as nucleotide substitutions/site.

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  Figure 4. Alignment of the antigenic residues from deduced amino acid sequences defining the neutralization domains on the VP7 protein of the rotaviruses analyzed: Neutralization domains of VP7 are designated as 7-1a, 7-1b, and 7-2 [60]. Deduced amino acid sequences ranging from 180 to 284 residues obtained from Venezuelan G3P[8] strains were compared with the WI78-8-RotaTeq® vaccine strain (GU565079) of lineage G3-I, and the reference human equine-like SKT-289 (LC086730) from Thailand of lineage IX (both in italics). For each strain, host species, country of origin, year of isolation, and genotypes G-P are shown. Numbering is based on the open reading frame of WI78-8-RotaTeq® vaccine strain. The sites not included in the analysis are indicated with a hyphen (-). In each isolate, identical amino acids with the RotaTeq™ vaccine strain are identified by dots. Amino acid changes that have been shown to escape neutralization with monoclonal antibodies [60] are indicated with a filled triangle (▲).