Genetic Variability, N-Glycosylation Sites, and Recombination Events in the ORF5 (GP5) Gene of Lineage 1A (NADC34) Betaarterivirus americense Strains from Lima, Peru Molecular Variability of the GP5 Glycoprotein in Betaarterivirus americense

Abstract

Lima is a major swine production hub in Peru; therefore, these data provide an initial overview of GP5 variability in a high-risk epidemiological setting. This study aimed to characterize the genetic variability, N-glycosylation sites, and recombination events in the ORF5 (GP5) gene of lineage 1A (NADC34) Betaarterivirus americense strains circulating in Lima, Peru. Bioinformatics servers and software were employed, including Nextclade v3, NetNGlyc 1.0, RDP v4.1, DnaSP v6, and MEGA6. Nextclade v3 supported the classification of 24 strains within lineage 1, sublineage 1A (NADC34), which exhibited high divergence based on GP5 phylogenetic analysis. Significant amino acid substitutions were identified in the hypervariable regions HVR1 and HVR2, which are associated with the induction of neutralizing and non-neutralizing antibodies: 16/24 at N32 (S/G/R/E), 3/24 at S34 (N/T), 6/24 at S35 (N/I), 7/24 at L39 (F), 6/24 at Q40 (L/R), 3/24 at L41 (Y/V), 15/24 at K58 (E/V/R), and 8/24 at S59 (H/R/N), located within GP5 epitopes A, B, and C. Nine N-glycosylation patterns (A-I) were identified across the 24 strains, comprising nine putative sites at N30, N32, N33, N34, N35, N44, N50, N51, and N57. Patterns A, B, E, and G exhibited five to six glycosylation sites in 12/24 strains. A statistically robust recombination event was detected in strain 42_Montana2019 (lineage 1A), with a putative major parent MH719138_1 (lineage 1A, Peru-2016/5 variant; 95.3% sequence similarity) and an unknown minor parent, although strain 36_Montana2019 showed the closest phylogenetic affinity. Genetic diversity analysis revealed 530 polymorphic sites, and Tajimas D test yielded a value of -0.78746, indicating high genetic variability within the Lima cohort. Overall, this study provides the first comprehensive molecular characterization of ORF5 (GP5) genetic variability in sublineage 1A (NADC34) Betaarterivirus americense strains circulating in swine farms in Lima. Broader and temporally structured sampling is warranted to assess nationwide evolutionary patterns.