Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.02.24.707833

Molecular Diversity and Recombination Patterns of the ORF7 (Nucleocapsid) Gene in Betaarterivirus americense Variants Circulating from Lima, Peru

Cotaquispe, R. Y.
View original source ↗Export metadata ↓

Abstract

Porcine reproductive and respiratory syndrome (PRRS) is a globally distributed disease caused by Betaarterivirus europensis (PRRSV-1) and Betaarterivirus americense (PRRSV-2). Its clinical presentation ranges from subclinical infection to severe disease, depending on viral evolution and the emergence of novel variants. The aim of this study was to characterize the genetic diversity and identify recombination events in the ORF7 (nucleocapsid, N) gene of ten PRRSV-2 strains circulating in pig farms in Lima, Peru. Bioinformatic analyses were performed using DNAMAN v10.0, MEGA 6, BepiPred-2.0, DnaSP v6, and RDP v4.101. Phylogenetic analysis revealed two well-defined lineages: eight strains clustered within lineage 1A (NADC34-like), and two within lineage 5A (VR2332-like), demonstrating the co-circulation of genetically distinct variants in the region. Comparative sequence analysis identified significant amino acid substitutions in eight strains (15, 16, 17, 20, 21, 22, 23, and 24), with strain 24 being the most divergent, accumulating multiple substitutions, including T81I, R109S, I115F, R116S, and A119K within the C-terminal region encompassing antigenic domains I-V. B-cell epitope prediction using BepiPred-2.0 identified six epitope patterns (A-F) comprising nine potential B-cell epitope regions (positions 5-19, 33-72, 33-73, 84-85, 87-98, 84-98, 87-97, 84, and 119). Patterns B, E, and F exhibited four to five predicted epitope sites and corresponded to strains 21, 22, 23, and 24. Recombination analysis using RDP v4.101 detected a statistically robust recombination event in strain 18_montana2020-R (lineage 5A), with strain 24_montana2020-WT (lineage 1A) identified as the putative major parent (100% similarity) and the vaccine-like VR2332 strain (lineage 5A) as the minor parent (99.3% similarity). Secondary evidence of the same recombination event was observed in strain 19_montana2020-R. Genetic diversity analysis of the ORF7 gene identified 50 polymorphic nucleotide sites and 52 mutations. Overall, these findings demonstrate substantial genetic variability in the ORF7 gene of PRRSV-2 circulating in Lima, Peru, characterized by lineage co-circulation and inter-lineage recombination. Continuous molecular surveillance is warranted to monitor viral evolution, assess potential antigenic implications, and support effective PRRS control strategies in the Peruvian swine industry.

Explore related subjects

molecular biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Cotaquispe, R. Y.. 2026-02-26. Molecular Diversity and Recombination Patterns of the ORF7 (Nucleocapsid) Gene in Betaarterivirus americense Variants Circulating from Lima, Peru. https://doi.org/10.64898/2026.02.24.707833

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Plasmid architecture determines the stability of inverted terminal repeats in adeno-associated virus vectors

Recombinant vectors derived from adeno-associated viruses (rAAVs) are a mainstay of human gene therapy. rAAVs are produced from plasmids containing transgene cassettes flanked by inverted terminal repeats (ITRs), which form structured DNA elements that stabilize the ends of the single-stranded viral genome and are the only viral sequences required in cis for genome packaging. For decades, it has been recognized that propagation of ITR-containing plasmids can result in deletions and other mutations, prompting the use of specialized bacterial strains, modified growth conditions, and truncated or altered ITRs. Despite these practices, ITR instability remains a persistent source of plasmid heterogeneity. To identify determinants of ITR stability, we evaluated ITR integrity in one of the original cloned AAV2 genome isolates, a reconstructed AAV2 plasmid, and a synthetic rAAV vector containing full-length native AAV2 ITRs. We established a quantitative bioinformatic workflow for analyzing ITR-containing plasmids and virus preparations from raw Oxford Nanopore sequencing data. These experiments showed that ITRs were highly stable during short-term culture, whereas prolonged culture revealed strong positional effects, with preferential loss or mutation of the ITR nearest the plasmid origin of replication. Consistent with this model, a survey of 7,041 sequence-verifiable AAV plasmids from the Addgene repository identified a widely disseminated 11-bp ITR deletion in 4,773 plasmids; among analyzable two-ITR plasmids, this deletion was located in the origin-proximal ITR in 95.3% of cases. Guided by these findings, we constructed a novel rAAV entry vector with stable full-length native AAV2 ITRs that enabled efficient packaging of a 4,750-bp all-in-one CRISPR-Cas9 cassette. Finally, we developed a cell-based strategy to compare the effects of ITR mutations on rAAV genome integration, providing preliminary evidence that ITR sequence variation can influence integration outcomes. Together, these findings show that ITR instability is a preventable, position-dependent property of plasmid architecture and identify ITR integrity as an important variable in rAAV vector design and quality control.

molecular biology↗
bioRxiv2026

Single-point mutation alters odorant receptor sensitivity associated with host plant specialization in Spodoptera moths

Host specialization in herbivorous insects is often associated with divergence in chemosensory abilities. Here, we investigated the possible contribution of odorant receptors (ORs) in host plant restriction in the lily moth Spodoptera picta, a species specialized on Amaryllidaceae. Manual annotation of S. picta ORs in its genome revealed a repertoire similar in size and composition to those of its polyphagous sister species, S. littoralis and S. litura, suggesting that specialization did not involve major gene loss or expansion in the lily moth. To assess functional divergence beyond gene number, we applied a large scaled structure-based virtual screening approach to the entire OR repertoires of these three Spodoptera species, generating ligand-binding profiles for 120,591 volatile compounds. Among 69 1:1:1 OR orthologs, 24 exhibited divergent predicted binding spectra. We pinpointed OR29 that we also found to be highly expressed in both male and female antennae of S. picta through a RNAseq approach. Functional assays demonstrated that S. picta OR29 acquired heightened sensitivity to limonene enantiomers, volatiles emitted by host Amaryllidaceae inflorescences. Site-directed mutagenesis revealed that a single amino acid substitution within the predicted binding region underlies this shift in sensitivity. These results show that host specialization in S. picta has not been accompanied by significant OR repertoire remodeling, but rather by subtle molecular changes that fine-tune receptor sensitivity to host-derived volatiles.

molecular biology↗
bioRxiv2026

Arc represses gene expression in IS605-family transposons

Bacterial insertion sequences (IS) are compact transposable elements that encode proteins required for their mobility and maintenance, yet many also encode accessory proteins with poorly understood functions. For example, IS605-family elements often encode a transposase called TnpA and an RNA-guided nuclease called TnpB that supports transposon maintenance, alongside an additional ribbon-helix-helix protein named Arc. Though the roles of TnpA and TnpB have been extensively studied in recent years, the enigmatic function of Arc has not been investigated. Here, we show that Arc acts as a transcriptional repressor to directly bind the transposon's native promoter sequence regulating TnpA and TnpB gene expression. By systematically testing Arc-containing IS605 elements, we identified a conserved binding pattern at intergenic transposon sequences neighboring protein-coding genes through chromatin immunoprecipitation and sequencing analyses. We then used fluorescence reporter assays and demonstrated that these intergenic sequences function as strong promoters, and that the presence of Arc dramatically reduces their gene expression. Together, these findings identify Arc as a transposon-encoded transcriptional repressor, revealing a regulatory layer that may promote long-term persistence of IS605-family elements by keeping their activity in check. The widespread association of Arc homologs with diverse mobile elements and cellular genes suggests that these compact regulators may more broadly restrain the expression of neighboring genetic machinery across varied genomic contexts. neighboring genetic machinery across varied genomic contexts.

molecular biology↗