Two bovine hepacivirus genome sequences from U.S. cattle.

Bovine hepacivirus (BoHV) is closely related to the hepatitis C virus (HCV) in humans and can cause both acute and chronic liver infections in cattle. BoHV was first identified in Ghana and Germany in 2015 and since then it has been detected and characterized in other countries around the world, but no strains have been sequenced from U.S. cattle. To date, BoHV has been classified into 2 genotypes (1 and 2), with genotype 1 being further divided into 11 subtypes (A-K). However, the true genetic diversity of BoHV is likely underestimated given limited surveillance and a lack of published genome sequences. Here, we sequenced 2 nearly complete BoHV genomes from serum samples collected in 2019 from beef cattle in Missouri. Sequence comparisons and phylogenetic analysis showed that isolate MARC/2019/60 had high sequence homology with genotype 1, subtype E isolates from China. In contrast, isolate MARC/2019/50 represented a novel BoHV subtype within genotype 2. Thus, we report the first genomic characterization of BoHV isolates from U.S. cattle, and the second complete BoHV2 genome worldwide. This work increases our knowledge of the global genetic diversity of BoHV and demonstrates the co-circulation of divergent BoHV strains in U.S. cattle.

First gene-edited calf with reduced susceptibility to a major viral pathogen.

Bovine viral diarrhea virus (BVDV) is one of the most important viruses affecting the health and well-being of bovine species throughout the world. Here, we used CRISPR-mediated homology-directed repair and somatic cell nuclear transfer to produce a live calf with a six amino acid substitution in the BVDV binding domain of bovine CD46. The result was a gene-edited calf with dramatically reduced susceptibility to infection as measured by reduced clinical signs and the lack of viral infection in white blood cells. The edited calf has no off-target edits and appears normal and healthy at 20 months of age without obvious adverse effects from the on-target edit. This precision bred, proof-of-concept animal provides the first evidence that intentional genome alterations in the CD46 gene may reduce the burden of BVDV-associated diseases in cattle and is consistent with our stepwise, in vitro and ex vivo experiments with cell lines and matched fetal clones.

Blood chemistry and rectal temperature changes in a population of healthy, fall-born, suckling beef calves from birth to 72 h of age.

To determine changes in suckling neonatal beef calf blood chemistry and body temperature during the first 72 h of life, jugular blood samples and rectal temperatures were obtained from 24 healthy, fall-born Angus-cross and Hereford calves (average calving date = September 11) at 0 (after standing, but pre-suckling), 6, 12, 24, 48, and 72 h postnatally. Serum chemistry panels were conducted, and plasma triglycerides and serum non-esterified fatty acids (NEFA) were also determined. Data were analyzed using sampling hour as a repeated effect, and individual data points were compared to adult bovine reference intervals. All serum chemistry measures were affected by hour of age except bicarbonate (P = 0.48). Serum glucose, total protein, and globulin concentrations increased (P < 0.001) from 0 to 24 h. Plasma triglycerides increased (P < 0.001) from 0 to 6 h and 24 to 72 h. Serum urea nitrogen increased (P < 0.001) from 0 to 6 h and decreased (P = 0.01) from 48 to 72 h. Serum NEFA and creatine kinase (CK) increased (P < 0.001) from 0 to 6 h, but decreased (P ≤ 0.02) from 12 to 72 h. Serum magnesium, aspartate aminotransferase (AST), and total and direct bilirubin increased (P < 0.001) during the first 12 h, then decreased (P < 0.001) from 24 to 72 h. Gamma-glutamyl transpeptidase (GGT) increased (P < 0.001) from 0 to 12, and then decreased (P < 0.003) from 12 to 48 h. Serum creatinine decreased (P < 0.001) from 0 to 72 h, and albumin decreased (P < 0.01) from 0 to 12 h but increased (P < 0.001) from 24 to 48 h. Anion gap decreased (P ≤ 0.05) from 6 to 24 h. No serum components measured were within adult bovine reference intervals for all calves at all sampling times. All serum albumin concentrations were outside of reference intervals, and the majority of serum glucose, calcium, phosphorus, potassium, CK, GGT, and total bilirubin were outside of reference intervals. More serum chemistry measures diverged from reference intervals in the first 24 h of neonatal life. Rectal temperature decreased (P = 0.003) from 0 to 6 h of age, then increased (P ≤ 0.02) from 12 to 48 h. In summary, blood chemistry profiles of healthy, suckling neonatal beef calves change over the first 72 h of life, indicating rapid changes in metabolism and physiology. Bovine reference intervals based on adults do not appear to represent neonatal calves; thus, neonatal status and animal age should be taken into consideration when interpreting serum chemistry in a clinical or research setting.

Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies.

Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. Here we generate haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT is sufficient to produce two haplotype-resolved assemblies meeting standards set by the Vertebrate Genomes Project. Structural variant-based pangenomes created from the haplotype-resolved assemblies demonstrate significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identifies 90 thousand structural variants including 931 overlapping with coding sequences; this approach reveals variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46, and GC that have potential to affect phenotype.

Association of ARRDC3 and NFIA variants with bovine congestive heart failure in feedlot cattle.

Background: Bovine congestive heart failure (BCHF) has become increasingly prevalent among feedlot cattle in the Western Great Plains of North America with up to 7% mortality in affected herds. BCHF is an untreatable complex condition involving pulmonary hypertension that culminates in right ventricular failure and death. Genes associated with BCHF in feedlot cattle have not been previously identified. Our aim was to search for genomic regions associated with this disease. Methods: A retrospective, matched case-control design with 102 clinical BCHF cases and their unaffected pen mates was used in a genome-wide association study. Paired nominal data from approximately 560,000 filtered single nucleotide polymorphisms (SNPs) were analyzed with McNemar's test. Results: Two independent genomic regions were identified as having the most significant association with BCHF: the arrestin domain-containing protein 3 gene ( ARRDC3), and the nuclear factor IA gene ( NFIA, mid- p-values, 1x10 -8 and 2x10 -7, respectively). Animals with two copies of risk alleles at either gene were approximately eight-fold more likely to have BCHF than their matched pen mates with either one or zero risk alleles at both genes (CI 95 = 3-17). Further, animals with two copies of risk alleles at both genes were 28-fold more likely to have BCHF than all others ( p-value = 1×10 -7, CI 95 = 4-206). A missense variant in ARRDC3 (C182Y) represents a potential functional variant since the C182 codon is conserved among all other jawed vertebrate species observed. A two-SNP test with markers in both genes showed 29% of 273 BCHF cases had homozygous risk genotypes in both genes, compared to 2.5% in 198 similar unaffected feedlot cattle. This and other DNA tests may be useful for identifying feedlot animals with the highest risk for BCHF in the environments described here. Conclusions: Although pathogenic roles for variants in the ARRDC3 and NFIA genes are unknown, their discovery facilitates classifying animals by genetic risk and allows cattle producers to make informed decisions for selective breeding and animal health management.

A Reference Genome Assembly of American Bison, Bison bison bison.

Bison are an icon of the American West and an ecologically, commercially, and culturally important species. Despite numbering in the hundreds of thousands today, conservation concerns remain for the species, including the impact on genetic diversity of a severe bottleneck around the turn of the 20th century and genetic introgression from domestic cattle. Genetic diversity and admixture are best evaluated at genome-wide scale, for which a high-quality reference is necessary. Here, we use trio binning of long reads from a bison-Simmental cattle (Bos taurus taurus) male F1 hybrid to sequence and assemble the genome of the American plains bison (Bison bison bison). The male haplotype genome is chromosome-scale, with a total length of 2.65 Gb across 775 scaffolds (839 contigs) and a scaffold N50 of 87.8 Mb. Our bison genome is ~13× more contiguous overall and ~3400× more contiguous at the contig level than the current bison reference genome. The bison genome sequence presented here (ARS-UCSC_bison1.0) will enable new research into the evolutionary history of this iconic megafauna species and provide a new tool for the management of bison populations in federal and commercial herds.

A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus.

Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison-cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS_Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date.

Efficacy of sodium iodide for prevention of respiratory disease in preweaned dairy calves.

OBJECTIVE: To determine the pharmacokinetics of sodium iodide (NaI) following oral administration to preweaned dairy calves, and to assess the efficacy of NaI for prevention of bovine respiratory disease (BRD) in preweaned calves at a commercial calf-raising facility. ANIMALS: 434 healthy preweaned dairy calves. PROCEDURES: In the first of 2 experimental trials, each of 7 calves received NaI (20 mg/kg, PO) once. Blood and nasal fluid samples were collected at predetermined times before (baseline) and for 72 hours after NaI administration for determination of iodine concentrations. Pharmacokinetic parameters were determined by noncompartmental analysis. In the second trial, 427 calves at a calf-raising facility were randomly assigned to receive NaI (20 mg/kg, PO, 2 doses 72 hours apart; n = 211) or serve as untreated controls (216). Health outcomes were compared between the 2 groups. RESULTS: For all 7 calves in the pharmacokinetic trial, the iodine concentration in both serum and nasal fluid samples was significantly increased from the baseline concentration and exceeded the presumed therapeutic iodine concentration (6.35 µg/mL) throughout the sampling period. In the on-farm trial, the odds of being treated for BRD before weaning for NaI-treated calves were twice those for control calves (OR, 2.04; 95% CI, 1.38 to 3.00). CONCLUSIONS AND CLINICAL RELEVANCE: Results suggested that, although oral administration of NaI (20 mg/kg) to preweaned dairy calves achieved iodine concentrations presumed to be effective in both serum and nasal fluid, it was not effective for prevention of BRD in preweaned calves at a commercial calf-raising facility.

Detection of bovine viral diarrhea virus in stable flies following consumption of blood from persistently infected cattle.

Control of bovine viral diarrhea virus (BVDV) relies on resource-intensive sampling to detect and remove persistently infected (PI) cattle. Herd-level surveillance tools would be useful for herds with unknown BVDV status and for monitoring herds with BVDV-free status. Our objective was to determine the feasibility of using stable flies as a sampling tool to detect BVDV at the herd level. Stable flies (Stomoxys calcitrans) were fed citrated blood from either BVDV-PI or BVDV-free cattle to establish pools of 100 flies with various proportions of BVDV-fed flies (0%, 1%, 10%, 20%, 40%, or 100% in each pool). BVDV-fed flies in these pools were harvested either 1, 2, or 3 d after consuming BVDV-PI blood to determine the impact of time after feeding. Two replicates of a 3-d by 6-dilution level matrix were produced. BVDV RNA was consistently detected on day 1 when ≥10% of the flies in the pool consumed PI blood. On days 2 and 3, positive BVDV RNA detection was variable and became less consistent. Our results demonstrate that BVDV RNA can be detected in stable flies after feeding on blood from PI cattle. Successful use of stable flies as a surveillance tool will require validation under field conditions.

Evaluation of EPAS1 variants for association with bovine congestive heart failure.

Background:  Bovine congestive heart failure (BCHF) has become increasingly prevalent in feedlot cattle in the Western Great Plains of North America. BCHF is an untreatable complex condition involving pulmonary hypertension that culminates in right ventricular failure and death. A protein variant of hypoxia-inducible factor 2 alpha (HIF2α, encoded by the endothelial PAS domain-containing protein 1 gene, EPAS1) was previously reported to be associated with pulmonary hypertension at altitudes exceeding 2,000 m. Our aim was to evaluate EPAS1 haplotypes for association with BCHF in feedlot cattle raised at moderate altitudes (1,200 m). Methods: Paired samples of clinical cases and unaffected controls were collected at four feedlots in Nebraska and Wyoming. Each pair (n =102) was matched for source, pen, breed type, sex, arrival date, and management conditions. Cases were identified by animal caretakers, euthanized, and diagnosis was confirmed at necropsy. Cases were derived from 30 different ranch operations, with the largest source contributing 32. Animals were tested for eight EPAS1 haplotypes encoding 36 possible different diploid combinations. Results: The common, ancestral EPAS1 haplotype encoding HIF2α with alanine (A) at position 606 and glycine (G) at position 610 was equally frequent in cases and controls (0.67). The EPAS1 variant haplotype reported to be associated with disease (encoding threonine (T) at position 606 and serine (S) at position 610) was not enriched in cases compared with controls (0.21 and 0.25, respectively). Frequencies of other EPAS1 haplotypes (e.g., encoding Q270, L362, or G671) were each less than 0.05 overall. McNemar's test with 45 discordant pairs showed the linked T606/S610 variant was not associated with BCHF (OR = 0.73, CI 95 0.38 -1.4, p-value = 0.37). Conclusions: HIF2α polypeptide variants were not significantly associated with BCHF in feedlot cattle at moderate altitudes. Thus, a wider search is needed to identify genetic risk factors underlying this disease.

Effects of dry or wet conditions during the preweaning phase on subsequent feedlot performance and carcass composition of beef cattle.

Our objective was to determine the effects of dry and wet conditions during the preweaning on subsequent feedlot performance and carcass characteristics of beef cattle. Steers (n = 7,432) and heifers (n = 2,361) finished in 16 feedlots in southwestern Iowa through the Tri-County Steer Carcass Futurity Cooperative were used for a retrospective analysis. Cattle originated in the Midwest (Iowa, Missouri, Indiana, Illinois, and Minnesota) and were born in February, March, or April of 2002 through 2013. Feedlot performance and carcass composition data were obtained for each animal. Palmer Drought Severity Index (PDSI) values were obtained for each animal's preweaning environment on a monthly basis. Mean PDSI values were used to classify conditions as dry (≤-2.0), normal (>-2.0 and <2.0), or wet (≥2.0) for the cool (April and May), warm (June through August), and combined (April through August) forage growing seasons preweaning. Mixed models were used to evaluate the effects of PDSI class on subsequent performance. Calf sex, date of birth (as day of year), year, and feedlot were also included as fixed effects. When considering PDSI class during the cool season, cattle from normal and wet classes had a greater feedlot delivery BW (P < 0.0001) than dry. Dry and normal classes had greater (P ≤ 0.02) delivery BW than wet during the warm and combined seasons, however. For the cool season, average daily gain was greater (P < 0.0001) for the dry class than normal and wet. Cattle from the normal class for the cool season had greater (P = 0.001) final BW than wet, but the wet class had the greatest (P < 0.04) and dry class had the lowest (P < 0.01) final BW during the warm season. During the cool season, HCW was greater (P < 0.007) for the normal than wet class, although HCW was greater (P ≤ 0.02) for wet compared with dry and normal during the warm season. Calculated yield grade was lower (P ≤ 0.006) for the normal class during the cool season compared with dry and wet. For both the warm and combined seasons, the dry class had lower (P ≤ 0.004) calculated yield grade compared with normal and wet. Carcasses from cattle that experienced normal or wet warm seasons had greater (P ≤ 0.0005) marbling scores than dry, and normal had greater (P = 0.0009) marbling score than dry for the combined seasons. In conclusion, these data indicate that both dry and wet conditions during the preweaning phase may impact ultimate feedlot performance and carcass composition.

Bovine viral diarrhea virus antigen detection across whole cattle hides using two antigen-capture enzyme-linked immunosorbent assays.

Bovine viral diarrhea virus is a costly disease of cattle that can be controlled by vaccination, biosecurity, and removal of persistently infected cattle. Development and proficiency testing of assays to identify persistently infected cattle requires substantial quantities of known positive- and negative-sample material. The objective of this study was to determine what sections of bovine skin contained Bovine viral diarrhea virus antigen. Two commercially available antigen-capture enzyme-linked immunoassays were used to test subsamples representing the entire skin of 3 persistently infected calves. Both assays detected Bovine viral diarrhea virus antigen in the samples indicated for use by assay protocol. However, one assay identified all subsamples as positive, while the second assay identified 64.4% of subsamples as positive. These results show that use of samples other than those specified by the assay protocol must be validated for each individual assay. In this study, alternative sample sites and use of the entire hide for proficiency testing would be acceptable for only one of the assays tested.