Genetic variability, N-glycosylation, and recombination in sublineage 1A of Betaarterivirus americense from commercial pig farms in Lima, 2019

Porcine reproductive and respiratory syndrome virus (PRRSV) is highly variable, and emerging variants have been responsible for severe outbreaks with unprecedented economic losses. Lima represents a major center of pig production; however, the absence of a structured epidemiological surveillance program has facilitated the spread of divergent variants in commercial farms. The present study provides an initial assessment of GP5 variability in a high-risk production setting. The aim of this study was to characterize the genetic variability, N-glycosylation sites, and recombination events within this region. Bioinformatic tools and servers were used for phylogenetic analyses, revealing that all 24 analyzed strains clustered within sublineage 1A, with evidence of divergent variants. Several amino acid substitutions were identified in domains associated with neutralizing and non-neutralizing antibody responses, including A27V/S (12/24), A31T (1/24), N32S/G/R/E (16/24), S34N/T (3/24), S35N/I (6/24), H38L (1/24), L39F (7/24), Q40L/R (6/24), L41Y/V (3/24), I42V (1/24), Y43H (4/24), N44I (4/24), L45R (4/24), T46A (4/24), K58E/V/R (15/24), and S59H/R/N (8/24) in GP5. Nine N-glycosylation patterns (A–I) were identified, with nine putative sites at N30, N32, N33, N34, N35, N44, N50, N51, and N57. Patterns A, B, E, and G exhibited five to six potential glycosylation sites in 12/24 strains. A recombination event was detected in strain RC05088942.1_montana/PERU/2019-R, with RC05088941.1_montana/PERU/2019 as the putative major parent (96.1% similarity) and an unidentified minor parent; however, strain RC05088939.1_montana/PERU/2019 showed the closest phylogenetic relationship. Genetic diversity analysis revealed 172 polymorphic sites. Tajima’s D test yielded a value of −0.84020, which was not statistically significant ( P > 0.10), indicating that the null hypothesis of neutral evolution could not be rejected. Overall, this study provides the first detailed characterization of ORF5 gene diversity in PRRSV strains detected in pigs suspected of infection from commercial farms in Lima in 2019. Broader sampling with temporal resolution is required to better understand nationwide evolutionary patterns.