Monitoring SARS-CoV-2 genetic variability: A post-market surveillance workflow for combined bioinformatic and laboratory evaluation of commercial RT-PCR assay performance.

Objective: The speed at which Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is mutating has made it necessary to frequently assess how these genomic changes impact the performance of diagnostic real-time polymerase chain reaction (RT-PCR) assays. Herein, we describe a generic three-step workflow to assess the effect of genomic mutations on inclusivity and sensitivity of RT-PCR assays.

Methods: Sequences collected from the Global Initiative on Sharing All Influenza Data (GISAID) were mapped to a SARS-CoV-2 reference genome to evaluate the position and prevalence of mismatches in the oligonucleotide-binding sites of the QIAstat-Dx, an RT-PCR panel designed to detect SARS-CoV-2.

Application of mixed linear models for the estimation of functional effects on bovine stature based on SNP summary statistics from a whole-genome association study.

Genome-wide association studies (GWAS) help identify polymorphic sites or genes linked to phenotypic variance, but a few identified genes and/or single nucleotide polymorphisms (SNPs) are unlikely to explain a large part of the phenotypic variability of complex traits. In this study, the focus was moved from single loci to functional units, expressed by the metabolic pathways as defined in the Kyoto Encyclopaedia of Genes and Genomes (KEGG) database. Consequently, the aim of this study was to estimate KEGG effects on stature in three Nordic dairy cattle breeds using SNP effects from GWAS as the dependent variable.

Application of a Bio-Economic Model to Demonstrate the Importance of Health Traits in Herd Management of Lithuanian Dairy Breeds.

Assessing the economic importance of traits is crucial for delivering appropriate breeding goals in dairy cattle breeding. The aim of the present study was to calculate economic values (EV) and assign the importance of health traits for three dairy cattle breeds: Lithuanian Black-and-White open population (LBW), Lithuanian Red open population (LR) and Lithuanian Red old genotype (LROG). The EV estimation was carried out using a stochastic bio-economic model SimHerd, which allows the simulation of the expected monetary gain of dairy herds.

Genome-Wide Genomic and Functional Association Study for Workability and Calving Traits in Holstein Cattle.

The goal of our study was to identify the SNPs, metabolic pathways (KEGG), and gene ontology (GO) terms significantly associated with calving and workability traits in dairy cattle. We analysed direct (DCE) and maternal (MCE) calving ease, direct (DSB) and maternal (MSB) stillbirth, milking speed (MSP), and temperament (TEM) based on a Holstein-Friesian dairy cattle population consisting of 35,203 individuals. The number of animals, depending on the trait, ranged from 22,301 bulls for TEM to 30,603 for DCE.

Exploring the Potential Genetic Heterogeneity in the Incidence of Hoof Disorders in Austrian Fleckvieh and Braunvieh Cattle.

Genetic heterogeneity denotes the situation when different genetic architectures underlying diverse populations result in the same phenotype. In this study, we explore the genetic background underlying differences in the incidence of hoof disorders between Braunvieh and Fleckvieh cattle in the context of genetic heterogeneity between the breeds. Despite potentially higher power of testing due to twice as large sample size, none of the SNPs was significantly associated with the total number of hoof disorders in Fleckvieh, while 15 SNPs were significant in Braunvieh.