Porcine reproductive and respiratory syndrome virus (PRRSV) is an important swine pathogen affecting the global swine industry. The first open reading frame 5 (ORF5)-based genetic lineage classification system describing global PRRSV-2 genetic diversity was introduced over a decade ago. Although refinements have been proposed for the predominant lineage in the USA (lineage 1), PRRSV-2 phylogenetic classification system at international levels has not been thoroughly evaluated and updated since 2010. In this study, based on analysis of 82,237 global ORF5 sequences reported during 1989–2021, we classified PRRSV-2 into 11 genetic lineages (L1‒L11) and 21 sublineages (L1A‒L1F, L1H‒L1J, L5A‒L5B, L8A‒L8E, and L9A‒L9E). The proposed classification system is flexible for growth if additional lineages, sublineages, or more granular classifications are needed. For example, for more fine-scale epidemiological investigation, L1C was further divided into five groups (L1C.1‒L1C.5), with L1C.5 corresponding to the recently emerged L1C variant. Comparison between restriction fragment length polymorphism (RFLP) typing and phylogenetic classification revealed the inaccuracy of using RFLP to determine PRRSV-2 genetic relatedness in most scenarios. Genetic homology of six commercial PRRSV-2 vaccines to each lineage/sublineage and detection frequency of vaccine-like viruses were determined. Global geographic distribution of each lineage/sublineage was presented. Temporal dynamic changes of PRRSV-2 in the USA during 1989–2021 were investigated by analyzing 73,092 ORF5 sequences. In summary, this study refined PRRSV-2 ORF5-based phylogenetic classification and investigated the geographic distribution and temporal changes of PRRSV-2 at the lineage/sublineage levels. The refined classification system and molecular epidemiology data in this study will be invaluable for future characterization of PRRSV-2.IMPORTANCE: In this study, comprehensive analysis of 82,237 global porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) open reading frame 5 sequences spanning from 1989 to 2021 refined PRRSV-2 genetic classification system, which defines 11 lineages and 21 sublineages and provides flexibility for growth if additional lineages, sublineages, or more granular classifications are needed in the future. Geographic distribution and temporal changes of PRRSV-2 were investigated in detail. This is a thorough study describing the molecular epidemiology of global PRRSV-2. In addition, the reference sequences based on the refined genetic classification system are made available to the public for future epidemiological and diagnostic applications worldwide. The data from this study will facilitate global standardization and application of PRRSV-2 genetic classification.

Porcine reproductive and respiratory syndrome (PRRS) is one of the most significant swine diseases. However, the phylogenetic and genomic recombination properties of the PRRS virus (PRRSV) have not been completely elucidated. In this study, we systematically compared differences in the lineage distribution, recombination, NSP2 polymorphisms, and evolutionary dynamics between North American (NA)-type PRRSVs in China and in the United States. Strikingly, we found high frequency of interlineage recombination hot spots in nonstructural protein 9 (NSP9) and in the GP2 to GP3 region. Also, intralineage recombination hot spots were scattered across the genome between Chinese and US strains. Furthermore, we proposed novel methods based on NSP2 indel patterns for the classification of PRRSVs. Evolutionary dynamics analysis revealed that NADC30-like PRRSVs are undergoing a decrease in population genetic diversity, suggesting that a dominant population may occur and cause an outbreak. Our findings offer important insights into the recombination of PRRSVs and suggest the need for coordinated international epidemiological investigations.

Precision swine production can benefit from autonomous, noninvasive, and affordable devices that conduct frequent checks on the well-being status of pigs. Here, we present a remote monitoring tool for the objective measurement of some behavioral indicators that may help in assessing the health and welfare status—namely, posture, gait, vocalization, and external temperature. The multiparameter electronic sensor board is characterized by laboratory measurements and by animal tests. Relevant behavioral health indicators are discussed for implementing machine learning algorithms and decision support tools to detect animal lameness, lethargy, pain, injury, and distress. The roadmap for technology adoption is also discussed, along with challenges and the path forward. The presented technology can potentially lead to efficient management of farm animals, targeted focus on sick animals, medical cost savings, and less use of antibiotics.

In March 2024, the emergence of highly pathogenic avian influenza (HPAI) A (H5N1) infections in dairy cattle was detected in the United Sates for the first time. We genetically characterize HPAI viruses from dairy cattle showing an abrupt drop in milk production, as well as from two cats, six wild birds, and one skunk. They share nearly identical genome sequences, forming a new genotype B3.13 within the 2.3.4.4b clade. B3.13 viruses underwent two reassortment events since 2023 and exhibit critical mutations in HA, M1, and NS genes but lack critical mutations in PB2 and PB1 genes, which enhance virulence or adaptation to mammals. The PB2 E627 K mutation in a human case associated with cattle underscores the potential for rapid evolution post infection, highlighting the need for continued surveillance to monitor public health threats.

Influenza A Virus (IAV) causes respiratory disease in swine and is a zoonotic pathogen. Uncontrolled IAV in swine herds not only affects animal health, it also impacts production through increased costs associated with treatment and prevention efforts. The Iowa State University Veterinary Diagnostic Laboratory (ISU VDL) diagnoses influenza respiratory disease in swine and provides epidemiological analyses on samples submitted by veterinarians. To assess the incidence of IAV in swine and inform stakeholders, the ISU FLUture website was developed as an interactive visualization tool that allows the exploration of the ISU VDL swine IAV aggregate data in the clinical diagnostic database. The information associated with diagnostic cases has varying levels of completeness and is anonymous, but minimally contains: sample collection date, specimen type, and IAV subtype. Many IAV positive samples are sequenced, and in these cases, the hemagglutinin (HA) sequence and genetic classification are completed. These data are collected and presented on ISU FLUture in near real-time, and more than 6,000 IAV positive diagnostic cases and their epidemiological and evolutionary information since 2003 are presented to date. The database and web interface provides rapid and unique insight into the trends of IAV derived from both large- and small-scale swine farms across the United States of America. ISU FLUture provides a suite of web-based tools to allow stakeholders to search for trends and correlations in IAV case metadata in swine from the ISU VDL. Since the database infrastructure is updated in near real-time and is integrated within a high-volume veterinary diagnostic laboratory, earlier detection is now possible for emerging IAV in swine that subsequently cause vaccination and control challenges. The access to real-time swine IAV data provides a link with the national USDA swine IAV surveillance system and allows veterinarians to make objective decisions regarding the management and control of IAV in swine. The website is publicly accessible at http://influenza.cvm.iastate.edu .