No abstract

Non-pharmaceutical interventions (NPIs) to mitigate the spread of SARS-CoV-2 were often implemented under considerable uncertainty and a lack of scientific evidence. Assessing the effectiveness of the individual interventions is critical to inform future preparedness response plans. Here we quantify the impact of 4,579 NPIs implemented in 76 territories on the effective reproduction number, Rt, of COVID-19. We use a hierarchically coded data set of NPIs and propose a novel modelling approach that combines four computational techniques, which together allow for a worldwide consensus rank of the NPIs based on their effectiveness in mitigating the spread of COVID-19. We show how the effectiveness of individual NPIs strongly varies across countries and world regions, and in relation to human and economic development as well as different dimensions of governance. We quantify the effectiveness of each NPI with respect to the epidemic age of its adoption, i.e., how early into the epidemics. The emerging picture is one in which no one-fits-all solution exists, and no single NPI alone can decrease Rt below one and that a combination of NPIs is necessary to curb the spread of the virus. We show that there are NPIs considerably less intrusive and costly than lockdowns that are also highly effective, such as certain risk communication strategies and voluntary measures that strengthen the healthcare system. By allowing to simulate ``what-if'' scenarios at the country level, our approach opens the way for planning the most likely effectiveness of future NPIs.

A random effect meta-analysis was performed to estimate the worldwide pooled bovine viral diarrhoea virus (BVDV) prevalences of persistently infected (PI), viraemic (VI) and antibody-positive (AB) animals and herds. The meta-analysis covered 325 studies in 73 countries that determined the presence or absence of BVDV infections in cattle from 1961 to 2016. In total, 6.5 million animals and 310,548 herds were tested for BVDV infections in the global cattle population. The worldwide pooled PI prevalences at animal level ranged from low (≤0.8% Europe, North America, Australia), medium (>0.8% to 1.6% East Asia) to high (>1.6% West Asia). The PI and AB prevalences in Europe decreased over time, while BVDV prevalence increased in North America. The highest mean pooled PI prevalences at animal level were identified in countries that had failed to implement any BVDV control and/or eradication programmes (including vaccination). Our analysis emphasizes the need for more standardised epidemiological studies to support decision-makers implementing animal health policies for non-globally-regulated animal diseases.

Subacute ruminal acidosis (SARA) is a prevalent metabolic disorder in cattle, characterized by intermittent drops in ruminal pH. This study investigated the effect of a gradual adaptation and continuously induced long-term SARA challenge diet on the epimural bacterial community structure in the rumen of cows. Eight rumen-cannulated nonlactating Holstein cows were transitioned over 1 wk from a forage-based baseline feeding diet (grass silage-hay mix) to a SARA challenge diet, which they were fed for 4 wk. The SARA challenge diet consisted of 60% concentrates (dry matter basis) and 40% grass silage-hay mix. Rumen papillae biopsies were taken at the baseline, on the last day of the 1-wk adaptation, and on the last day of the 4-wk SARA challenge period; ruminal pH was measured using wireless sensors. We isolated DNA from papillae samples for 16S rRNA gene amplicon sequencing using Illumina MiSeq. Sequencing results of most abundant key phylotypes were confirmed by quantitative PCR. Although they were fed similar amounts of concentrate, cows responded differently in terms of ruminal pH during the SARA feeding challenge. Cows were therefore classified as responders (n = 4) and nonresponders (n = 4): only responders met the SARA criterion of a ruminal pH drop below 5.8 for longer than 330 min/d. Data showed that Proteobacteria, Firmicutes, and Bacteroidetes were the most abundant phyla, and at genus level, Campylobacter and Kingella showed highest relative abundance, at 15.5 and 7.8%, respectively. Diversity analyses revealed a significant increase of diversity after the 1-wk adaptation but a decrease of diversity and species richness after the 4-wk SARA feeding challenge, although without distinction between responders and nonresponders. At the level of the operational taxonomic unit, we detected diet-specific shifts in epimural community structure, but in the overall epimural bacterial community structure, we found no differences between responders and nonresponders. Correlation analysis revealed significant associations between grain intake and operational taxonomic unit abundance. The study revealed major shifts in the 3 dominating phyla and, most importantly, a loss of diversity in the epimural bacterial communities during a long-term SARA diet challenge, in which 60% concentrate supply for 4 wk was instrumental rather than the magnitude of the drop of ruminal pH below 5.8.

Bovine viral diarrhoea virus (BVDV) is an important infectious agent of cattle worldwide that affects herd productivity and reproduction. In this systematic review of the impact of BVDV, studies were analysed with a particular focus on the monetary implications and types of direct losses, the initial infection status of herds, production systems, time periods of assessment, calculation level, study types and whether or not country-specific assessments were published. A linear mixed model was applied to analyse factors that influence the level of monetary direct losses due to BVDV infection. The 44 studies included in this review covered 15 countries and assessed direct monetary losses due to BVDV incurred over the past 30 years. Direct losses between and within countries were largely heterogeneous with respect to the monetary level and types of direct losses, ranging from 0.50 to 687.80 US dollars (USD) per animal. Average direct losses per naïve dairy cow were USD24.85 higher than per beef cow. Country-specific assessments of direct losses due to BVDV were provided in 38/44 (86.4%) studies. Mortality, morbidity, premature culling, stillbirths, abortion, reinfection, country and study type had a significant influence on the monetary level of direct losses (r = 0.69). Countries recording direct losses were more likely to carry out voluntary or compulsory control and eradication programmes (odds ratio = 10.2; 95% confidence interval 1.7-81.9; P = 0.004).

Infection with bovine viral diarrhea virus (BVDV) results in major economic losses either directly through decreased productive performance in cattle herds or indirectly, such as through expenses for control programs. The aim of this systematic review was to review financial and/or economic assessment studies of prevention and/or mitigation activities of BVDV at national, regional and farm level worldwide. Once all predefined criteria had been met, 35 articles were included for this systematic review. Studies were analyzed with particular focus on the type of financially and/or economically-assessed prevention and/or mitigation activities. Due to the wide range of possible prevention and/or mitigation activities, these activities were grouped into five categories: i) control and/or eradication programs, ii) monitoring or surveillance, iii) prevention, iv) vaccination and v) individual culling, control and testing strategies. Additionally, the studies were analyzed according to economically-related variables such as efficiency, costs or benefits of prevention and/or mitigation activities, the applied financial and/or economic and statistical methods, the payers of prevention and/or mitigation activities, the assessed production systems, and the countries for which such evaluations are available. Financial and/or economic assessments performed in Europe were dominated by those from the United Kingdom, which assessed mostly vaccination strategies, and Norway which primarily carried out assessments in the area of control and eradication programs; whereas among non-European countries the United States carried out the majority of financial and/or economic assessments in the area of individual culling, control and testing. More than half of all studies provided an efficiency calculation of prevention and/or mitigation activities and demonstrated whether the inherent costs of implemented activities were or were not justified. The dairy sector was three times more likely to be assessed by the countries than beef production systems. In addition, the dairy sector was approximately eight times more likely to be assessed economically with respect to prevention and/or mitigation activities than calf and youngstock production systems. Furthermore, the private sector was identified as the primary payer of prevention and/or mitigation activities. This systematic review demonstrated a lack of studies relating to efficiency calculations, in particular at national and regional level, and the specific production systems. Thus, we confirmed the need for more well-designed studies in animal health economics in order to demonstrate that the implementation and inherent costs of BVDV prevention and/or mitigation activities are justified.

Microbial food spoilage is responsible for a considerable amount of waste and can cause food-borne diseases in humans, particularly in immunocompromised individuals and children. Therefore, preventing microbial food spoilage is a major concern for health authorities, regulators, consumers, and the food industry. However, the contamination of food products is difficult to control because there are several potential sources during production, processing, storage, distribution, and consumption, where microorganisms come in contact with the product. Here, we use high-throughput full-length 16S rRNA gene sequencing to provide insights into bacterial community structure throughout a pork-processing plant. Specifically, we investigated what proportion of bacteria on meat are presumptively not animal-associated and are therefore transferred during cutting via personnel, equipment, machines, or the slaughter environment. We then created a facility-specific transmission map of bacterial flow, which predicted previously unknown sources of bacterial contamination. This allowed us to pinpoint specific taxa to particular environmental sources and provide the facility with essential information for targeted disinfection. For example, Moraxella spp., a prominent meat spoilage organism, which was one of the most abundant amplicon sequence variants (ASVs) detected on the meat, was most likely transferred from the gloves of employees, a railing at the classification step, and the polishing tunnel whips. Our results suggest that high-throughput full-length 16S rRNA gene sequencing has great potential in food monitoring applications.

The significant economic impacts of bovine viral diarrhoea (BVD) virus have prompted many countries worldwide to embark on regional or national BVD eradication programmes. Unlike other infectious diseases, BVD control is highly feasible in cattle production systems because the pathogenesis is well understood and there are effective tools to break the disease transmission cycle at the farm and industry levels. Coordinated control approaches typically involve directly testing populations for virus or serological screening of cattle herds to identify those with recent exposure to BVD, testing individual animals within affected herds to identify and eliminate persistently infected (PI) cattle, and implementing biosecurity measures such as double‐fencing shared farm boundaries, vaccinating susceptible breeding cattle, improving visitor and equipment hygiene practices, and maintaining closed herds to prevent further disease transmission. As highlighted by the recent DISCONTOOLS review conducted by a panel of internationally recognized experts, knowledge gaps in the control measures are primarily centred around the practical application of existing tools rather than the need for creation of new tools. Further research is required to: (a) determine the most cost effective and socially acceptable means of applying BVD control measures in different cattle production systems; (b) identify the most effective ways to build widespread support for implementing BVD control measures from the bottom‐up through farmer engagement and from the top‐down through national policy; and (c) to develop strategies to prevent the reintroduction of BVD into disease‐free regions by managing the risks associated with the movements of animals, personnel and equipment. Stronger collaboration between epidemiologists, economists and social scientists will be essential for progressing efforts to eradicate BVD from more countries worldwide.