Complete Genome Sequence of Highly Virulent Porcine Reproductive and Respiratory Syndrome Virus Variants That Recently Emerged in the United States

A recent outbreak of particularly virulent disease caused by porcine reproductive and respiratory syndrome virus has occurred in swine herds across the United States. We report here the complete genome sequence of eight viral isolates from four Nebraska herds experiencing an outbreak of severe disease in 2016

Complete Genome Sequences of Two Genotype A2 Small Ruminant Lentiviruses Isolated from Infected U.S. Sheep

Two distinct subgroups of genotype A2 small ruminant lentiviruses (SRLVs) have been identified in the United States that infect sheep with specific host trans- membrane protein 154 (TMEM154) diplotypes. Here, we report the first two com- plete genome sequences of SRLV strains infecting U.S. sheep belonging to genotype A2, subgroups 1 and 2

Classification of small ruminant lentivirus subtype A2, subgroups 1 and 2 based on whole genome comparisons and complex recombination patterns

Background: Small ruminant lentiviruses (SRLVs) cause a multisystemic chronic wasting disease in sheep across much of the world. SRLV subtype A2 is prevalent in North America and further classified into multiple subgroups based on variation in the group antigens gene (gag) and envelope (env) genes. In sheep, the ovine transmembrane protein 154 (TMEM154) gene is associated with SRLV susceptibility. Ewes with at least one copy of TMEM154 encoding a fulllength protein with glutamate at position 35 (E35; haplotypes 2 and 3), are highly susceptible to SRLV infection while ewes with any combination of TMEM154 haplotypes which encodes lysine (K35; haplotype 1), or truncated proteins (haplotypes 4 and 6) are several times less so. A2 subgroups 1 and 2 are associated with host TMEM154 genotypes; subgroup 1 with the K35/K35 genotype and subgroup 2 with the E35/E35 genotype. Methods: The goals of this study were to analyze sequence variation within and among SRLV subtype A2 subgroups 1 and 2 and to identify genome-scale recombination patterns. This was done using full-length assemblies of virus samples. Results: Consensus viral genomes were assembled for 23 infected sheep, including animals of assorted TMEM154 genotypes comprised of haplotypes 1, 2, or 3. Viral genome analysis identified viral subgroups 1 and 2 among the samples, and revealed additional substructure within subgroup 2 based on models predicting complex patterns of recombination between the two subgroups in several genomes. Animals with evidence of dual subgroup infection also possessed the most diverse quasi-species and the most highly recombined genomes. Conclusions: The viral subgroup framework developed to classify SRLV consensus genomes along a continuum of recombination suggests that animals with the TMEM154 E35/K35 genotype may represent a reservoir for producing viral genomes representing recombination between A2 subgroups 1 and 2

Resolving \u3ci\u3eBovine viral diarrhea virus\u3c/i\u3e subtypes from persistently infected U.S. beef calves with complete genome sequence

Bovine viral diarrhea virus (BVDV) is classified into 2 genotypes, BVDV-1 and BVDV-2, each of which contains distinct subtypes with genetic and antigenic variation. To effectively control BVDV by vaccination, it is important to know which subtypes of the virus are circulating and how their prevalence is changing over time. Accordingly, the purpose of our study was to estimate the current prevalence and diversity of BVDV subtypes from persistently infected (PI) beef calves in the central United States. Phylogenetic analysis of the 5′-UTR (5′ untranslated region) for 119 virus strains revealed that a majority (82%) belonged to genotype 1b, and the remaining strains were distributed between genotypes 1a (9%) and 2 (8%); however, BVDV-2 subtypes could not be confidently resolved. Therefore, to better define the variability of U.S. BVDV isolates and further investigate the division of BVDV-2 isolates into subtypes, complete genome sequences were obtained for these isolates as well as representatives of BVDV-1a and -1b. Phylogenetic analyses of the complete coding sequence provided more conclusive genetic classification and revealed that U.S. BVDV-2 isolates belong to at least 3 distinct genetic groups that are statistically supported by both complete and individual coding gene analyses. These results show that a more complex set of BVDV-2 subtypes has been circulating in this region than was previously thought

Resolving \u3ci\u3eBovine viral diarrhea virus\u3c/i\u3e subtypes from persistently infected U.S. beef calves with complete genome sequence

Bovine viral diarrhea virus (BVDV) is classified into 2 genotypes, BVDV-1 and BVDV-2, each of which contains distinct subtypes with genetic and antigenic variation. To effectively control BVDV by vaccination, it is important to know which subtypes of the virus are circulating and how their prevalence is changing over time. Accordingly, the purpose of our study was to estimate the current prevalence and diversity of BVDV subtypes from persistently infected (PI) beef calves in the central United States. Phylogenetic analysis of the 5′-UTR (5′ untranslated region) for 119 virus strains revealed that a majority (82%) belonged to genotype 1b, and the remaining strains were distributed between genotypes 1a (9%) and 2 (8%); however, BVDV-2 subtypes could not be confidently resolved. Therefore, to better define the variability of U.S. BVDV isolates and further investigate the division of BVDV-2 isolates into subtypes, complete genome sequences were obtained for these isolates as well as representatives of BVDV-1a and -1b. Phylogenetic analyses of the complete coding sequence provided more conclusive genetic classification and revealed that U.S. BVDV-2 isolates belong to at least 3 distinct genetic groups that are statistically supported by both complete and individual coding gene analyses. These results show that a more complex set of BVDV-2 subtypes has been circulating in this region than was previously thought

First measurement of the polarization observable E in the p→(γ→,π⁺)n reaction up to 2.25 GeV

First results from the longitudinally polarized frozen-spin target (FROST) program are reported. The double-polarization observable E, for the reaction $\vec \gamma \vec p \to \pi^+n$, has been measured using a circularly polarized tagged-photon beam, with energies from 0.35 to 2.37 GeV. The final-state pions were detected with the CEBAF Large Acceptance Spectrometer in Hall B at the Thomas Jefferson National Accelerator Facility. These polarization data agree fairly well with previous partial-wave analyses at low photon energies. Over much of the covered energy range, however, significant deviations are observed, particularly in the high-energy region where high-L multipoles contribute. The data have been included in new multipole analyses resulting in updated nucleon resonance parameters. We report updated fits from the Bonn-Gatchina, J\"ulich, and SAID groups.Comment: 6 pages, 3 figure

First measurement of the helicity asymmetry E in eta photoproduction on the proton

Results are presented for the first measurement of the double-polarization helicity asymmetry E for the $\eta$ photoproduction reaction $\gamma p \rightarrow \eta p$. Data were obtained using the FROzen Spin Target (FROST) with the CLAS spectrometer in Hall B at Jefferson Lab, covering a range of center-of-mass energy W from threshold to 2.15 GeV and a large range in center-of-mass polar angle. As an initial application of these data, the results have been incorporated into the J\"ulich model to examine the case for the existence of a narrow $N^*$ resonance between 1.66 and 1.70 GeV. The addition of these data to the world database results in marked changes in the predictions for the E observable using that model. Further comparison with several theoretical approaches indicates these data will significantly enhance our understanding of nucleon resonances

Photon beam asymmetry Sigma for eta and eta ' photoproduction from the proton

Measurements of the linearly-polarized photon beam asymmetry $\Sigma$ for photoproduction from the proton of $\eta$ and $\eta^\prime$ mesons are reported. A linearly-polarized tagged photon beam produced by coherent bremsstrahlung was incident on a cryogenic hydrogen target within the CEBAF Large Acceptance Spectrometer. Results are presented for the $\gamma p \to \eta p$ reaction for incident photon energies from 1.070 to 1.876 GeV, and from 1.516 to 1.836 GeV for the $\gamma p \to \eta^\prime p$ reaction. For $\gamma p \to \eta p$, the data reported here considerably extend the range of measurements to higher energies, and are consistent with the few previously published measurements for this observable near threshold. For $\gamma p \to \eta^\prime p$, the results obtained are consistent with the few previously published measurements for this observable near threshold, but also greatly expand the incident photon energy coverage for that reaction. Initial analysis of the data reported here with the Bonn-Gatchina model strengthens the evidence for four nucleon resonances -- the $N(1895)1/2^-$, $N(1900)3/2^+$, $N(2100)1/2^+$ and $N(2120)3/2^-$ resonances -- which presently lack the "four-star" status in the current Particle Data Group compilation, providing examples of how these new measurements help refine models of the photoproduction process.Comment: 10 pages, 3 figure

SARS-CoV-2-specific nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination

BACKGROUND: Most studies of immunity to SARS-CoV-2 focus on circulating antibody, giving limited insights into mucosal defences that prevent viral replication and onward transmission. We studied nasal and plasma antibody responses one year after hospitalisation for COVID-19, including a period when SARS-CoV-2 vaccination was introduced. METHODS: In this follow up study, plasma and nasosorption samples were prospectively collected from 446 adults hospitalised for COVID-19 between February 2020 and March 2021 via the ISARIC4C and PHOSP-COVID consortia. IgA and IgG responses to NP and S of ancestral SARS-CoV-2, Delta and Omicron (BA.1) variants were measured by electrochemiluminescence and compared with plasma neutralisation data. FINDINGS: Strong and consistent nasal anti-NP and anti-S IgA responses were demonstrated, which remained elevated for nine months (p < 0.0001). Nasal and plasma anti-S IgG remained elevated for at least 12 months (p < 0.0001) with plasma neutralising titres that were raised against all variants compared to controls (p < 0.0001). Of 323 with complete data, 307 were vaccinated between 6 and 12 months; coinciding with rises in nasal and plasma IgA and IgG anti-S titres for all SARS-CoV-2 variants, although the change in nasal IgA was minimal (1.46-fold change after 10 months, p = 0.011) and the median remained below the positive threshold determined by pre-pandemic controls. Samples 12 months after admission showed no association between nasal IgA and plasma IgG anti-S responses (R = 0.05, p = 0.18), indicating that nasal IgA responses are distinct from those in plasma and minimally boosted by vaccination. INTERPRETATION: The decline in nasal IgA responses 9 months after infection and minimal impact of subsequent vaccination may explain the lack of long-lasting nasal defence against reinfection and the limited effects of vaccination on transmission. These findings highlight the need to develop vaccines that enhance nasal immunity. FUNDING: This study has been supported by ISARIC4C and PHOSP-COVID consortia. ISARIC4C is supported by grants from the National Institute for Health and Care Research and the Medical Research Council. Liverpool Experimental Cancer Medicine Centre provided infrastructure support for this research. The PHOSP-COVD study is jointly funded by UK Research and Innovation and National Institute of Health and Care Research. The funders were not involved in the study design, interpretation of data or the writing of this manuscript