Genomic characterization of a NADC30-like PRRSV strain harboring a unique "111+2+1+19" amino acid deletion in NSP2 in northern Xinjiang, China, 2026.

ORF5-Based Molecular Characterization of PRRSV Reveals Multiple Co-circulating Lineages in Vietnam, 2021-2026.

Porcine reproductive and respiratory syndrome virus (PRRSV) continues to pose a major challenge to swine production in Vietnam because of its rapid evolution and genetic diversity. Here, we analyzed 69 PRRSV-positive samples collected from 20 provinces in Vietnam between 2021 and 2026 using ORF5 gene sequencing to characterize the genetic diversity of circulating strains. Phylogenetic analysis demonstrated the co-circulation of multiple PRRSV-2 lineages (L1, L3, L5, L8, and L10), together with a limited presence of PRRSV-1, indicating a genetically diverse PRRSV population within the analyzed diagnostic samples. Among the PRRSV-2 strains, lineage 8 (L8), particularly sub-lineage L8E, was the most frequently detected, whereas lineage 10 (L10) accounted for 24.6% of the sequenced isolates and was detected only in samples collected from 2023 onwards. Independent maximum-likelihood phylogenetic and pairwise ORF5 distance analyses showed that the Vietnamese L10 strains formed a distinct monophyletic cluster within lineage 10. Analysis of the GP5 protein identified amino acid variation in previously described antigenic regions, providing descriptive information on the genetic diversity of circulating Vietnamese PRRSV strains. Collectively, these findings provide updated insights into the molecular epidemiology of PRRSV in Vietnam and highlight the value of continuous molecular surveillance for monitoring the emergence and distribution of PRRSV lineages.

First Draft genome sequence of strain MF0224, representing an unclassified Fusobacterium-related lineage isolated from coastal sediments of Puducherry, India

The genome provides a valuable resource for investigating anaerobic carbon metabolism, acetate biosynthesis, sulfur-associated pathways, and the ecological adaptation of Fusobacterium-related bacteria in coastal sediment ecosystems.

Single amino acid substitution in RdRp reduces viral recombination frequency of NADC30-like porcine reproductive and respiratory syndrome virus type 2

Porcine reproductive and respiratory syndrome (PRRS) is one of the most significant diseases, causing tremendous economic losses to the global swine industry. Accumulating evidence indicates that recombination between PRRSV-2 strains, particularly those involving NADC30-like PRRSV-2 variants, has been responsible for outbreaks across several countries. However, the key proteins or amino acids associated with PRRSV-2 recombination remain unclear. In this study, two representative PRRSV-2 strains (the NADC30-like HeB108 strain from lineage 1 and the HP-PRRSV HuN4 strain from lineage 8) were serially passaged in the presence of ribavirin. Amino acid substitutions associated with ribavirin resistance were identified in the RNA-dependent RNA polymerase (RdRp) and helicase of the passaged viruses. Using the infectious clones PRRSV-2 HeB108 and HuN4, ribavirin-resistant mutants with single or multiple amino acid substitutions were generated. Notably, the mutants HeB108-VGSS and HuN4-TNII, with multiple amino acid substitutions, showed higher fidelity and lower pathogenicity in infected piglets than their parental viruses. Furthermore, the potential decreased recombination risk correlated with increased polymerase fidelity. In an inter-lineage co-infection assay on primary alveolar macrophages, the I360V substitution in RdRp reduced the recombination frequency of NADC30-like PRRSV-2 HeB108 as determined by both Sanger sequencing and nanopore long-read RNA sequencing. The results identified a key amino acid associated with viral recombination in NADC30-like PRRSV-2 and provide an editing target for developing safer vaccines that are less prone to recombination.

Metatranscriptomic analysis reveals two new viruses and highly expressed endogenous elements in pepper in Iraq

Pepper plants exhibiting severe leaf curling and deformation in open fields in Iraq were investigated to characterize their associated virome using metatranscriptomic sequencing. High-throughput sequencing (HTS) revealed the presence of bell pepper alphaendornavirus (BPEV) and pepper cryptic virus 2 (PCV-2), together with fragmented sequences related to tobacco vein clearing virus (TVCV). A nearly complete genome of the Iraqi BPEV isolate (14,700 bp) and both genomic segments of PCV-2 (1,623 bp and 1,513 bp) were assembled and deposited in GenBank. Phylogenetic analysis showed that the BPEV isolate clustered closely with isolates from South Korea, Jamaica, and the Dominican Republic, whereas both PCV-2 genomic segments were most closely related to Turkish isolates, indicating high genetic conservation among geographically distant populations. In addition, transcriptome mapping revealed abundant expression of ten endogenous pararetroviral elements integrated within the pepper genome, with most transcripts corresponding to reverse transcriptase (RT-LTR) and RNase H domains. This study represents the first comprehensive metatranscriptomic characterization of the pepper virome in Iraq, documenting the first detection of BPEV and PCV-2 in the country while revealing extensive expression of endogenous viral elements. These findings expand current knowledge of pepper-associated viruses in the Middle East and demonstrate the value of metatranscriptomic sequencing for detecting both exogenous viruses and endogenous viral components.

Reassessment of PRRSV-2 ORF5 sequence diversity in Japan identifies a previously unrecognized candidate lineage-level clade

Characterization and pathogenicity of single-farm-isolated PRRSV 1 and PRRSV 2 strain in China

ABSTRACT Porcine reproductive and respiratory syndrome virus (PRRSV) remains a major threat to the swine industry globally. In China, the dominance of PRRSV 2 is complicated by the emergence and co-circulation of genetically distinct strains, including a rising number of PRRSV 1 cases. In this study, the concurrent circulation of PRRSV 1 and PRRSV 2 was identified, and two novel strains AHB1 and Chah2022 were isolated from a single sow farm experiencing reproductive failure. Genetic analysis revealed that AHB1 shared 81.6%-83.6% nucleotide identity with subtype 1 strains of PRRSV 1 and clustered within a new evolutionary branch, characterized by a continuous 54-amino acid deletion in nsp2 and 1-amino acid deletion in the GP3-GP4 overlap region. In contrast, Chah2022 was identified as a recombinant virus with NADC30-like (lineage 1) and highly pathogenic PRRSV-like (lineage 8) strains. Pathogenicity assessment in nursery piglet model demonstrated that both AHB1 and Chah2022 had established systemic and persistent infections, although with low or moderate clinical signs. Our findings provide the evidence of PRRSV 1 and PRRSV 2 concurrent circulation in the single sow farm in China, which highlights the ongoing evolution of both Chinese PRRSV species and underscores the urgent need for enhanced surveillance and updated control strategies.