Identification and In Silico Characterization of a Genetically Distinct Avian Rotavirus D Capsid Gene, VP7

Figure 1. RT-PCR-amplified products of RV-D. (A) Lane 1: 100-bp DNA ladder (Thermo Scientific); lane 2: 185-bp amplicon of the VP6 gene of RV-D; lane 3: positive-RVD insert plasmid as control; lane 4: non-template control; lane 5: empty well. (B) Lane 1: non-template control; lane 2: 1 kb plus DNA ladder (Thermo Scientific); lane 3: 996-bp amplicon of the VP7 gene of RV-D.

Figure 2. Maximum likelihood phylogenetic reconstruction of rotavirus D (UKD48 strain), based on the 996-bp complete coding sequence of the VP7 gene. The Tamura three-parameter substitution model with the evolutionary invariable method (T3+G+I) was identified using the “find best DNA/protein model tool available” in MEGA6, which was confirmed with the FindModel online tool. Only >50% bootstrap values are shown. Numbers on branches indicate the percentages of bootstrap support from 1000 replicates. The analysis involved 21 nucleotide sequences, including one study strain (UKD48), denoted by the solid dot, and one chicken RV-A sequence as an outgroup. The scale bar indicates nucleotide substitutions per site.

Figure 3. Analysis of hydrophobic domains in rotavirus D and rotavirus A VP7 gene sequences. Depiction of the yellow regions shows the hydrophobic domains as S1 and S2. (A) S1: 15–33 and S2: 37–54 of RV-D, and (B) S1: 14–35 and S2: 42–57 of avian RV-A (GU733451)) within the VP7 gene. The domains were predicted using Phyre2 [9].