African Swine Fever-Vitamin Supply Chain Workshop Notes

An African swine fever-vitamin meal supply chain workshop involving key industry stakeholders was conducted on April 26, 2019 on the University of Minnesota St. Paul campus. Several vitamins are produced exclusively in China, while others are also primarily produced in China by a few manufacturers. Likewise, most vitamin manufacturers produce human and animal grade vitamins using the same quality assurance and controls that meet human grade standards. Most meeting participants consider the risk of ASF introduction from vitamins to be low but recognize that, if contaminated, vitamins can be a vehicle for virus introduction in the U.S. Several research and development priorities were identified including 1) develop a surrogate for ASF virus for monitoring processes that can inactivate the virus if it was present, 2) develop third party biosecurity modules and audits that can be implemented for feed ingredient manufacturers, 3) conduct a risk assessment of virus transmission throughout the vitamin supply chain, and 4) explore the use of blockchain technology for greater transparency and trust in the vitamin supply chain. Several education and communication priorities were also identified. A clear, transparent, and unified message is needed to educate the feed and pork industry to decrease confusion and suspicion of the perceived risks of virus transmission in the vitamin supply chain. Key components of this story include: 1) what is known about ASF virus characteristics, survival, and inactivation, 2) general description of raw materials, chemical and fermentation processes used to produce various vitamins, 3) current quality assurance programs, 4) packaging and transport, 5) potential for cross contamination from other porcine derived feed ingredients in multi-species feed mills, 6) approved sources vs. brokers and traders, and 7) holding times, origin of carriers, and premix manufacturing processes used before delivery to feed mills and commercial swine farms. Vitamin suppliers have industry wide standards for ingredient safety that minimize the opportunity for virus introduction. However, pork producers are responsible for knowing their suppliers and asking the right questions to screen potential suppliers that do not follow standards of safety. A comprehensive description of the entire vitamin supply chain is needed and a unified, accurate, and consistent message to the pork industry.Swine Health Information Center, Ames, I

Guidelines for developing a risk-based plan to mitigate virus transmission from imported feed ingredients

There is increasing concern regarding the risk of swine disease transmission via feed ingredients, whether imported or domestically produced. This risk may be reduced in the feed ingredient supply chain by identifying and implementing preventive controls (supply chain, sanitation, transportation, and process) at different steps of the chain. The objective of this study was to develop a practical guide to help feed ingredient suppliers and buyers to safely manufacture, package, transport, and use feed ingredients in swine feeding programs. The Food Safety Modernization Act (FSMA) provides the basis of this study because these regulations require proactive risk-based preventive control processes that are applied in the food supply chain to prevent or reduce the risk of hazards from being present in the final product. Using this conceptual framework, implementation of preventive controls in the feed production chain can control or decrease the potential introduction of foreign animal viruses through feed ingredients into the U.S. A decision tree was developed as a first step in identifying preventive controls and potential high-risk feed ingredient sourcing scenarios. A case-study using Porcine Epidemic Diarrhea virus (PEDV) and the corresponding decision tree was developed as an illustration on how to use this new approach. Although this approach is based on swine viral diseases, it can serve as a template for other pathogenic viruses and species.Swine Health Information Center, Ames, I

Survival of a surrogate African swine fever virus-like algal virus in feed matrices using a 23-day commercial United States truck transport model

African swine fever virus (ASFV) is a member of the nucleocytoplasmic large DNA viruses (NCLDVs) and is stable in a variety of environments, including animal feed ingredients as shown in previous laboratory experiments and simulations. virus (EhV) is another member of the NCLDVs, which has a restricted host range limited to a species of marine algae called . This algal NCLDV has many similar morphological and physical characteristics to ASFV thereby making it a safe surrogate, with results that are applicable to ASFV and suitable for use in real-world experiments. Here we inoculated conventional soybean meal (SBMC), organic soybean meal (SBMO), and swine complete feed ( ) matrices with EhV strain 86 (EhV-86) at a concentration of 6.6 × 10 virus g , and then transported these samples in the trailer of a commercial transport vehicle for 23 days across 10,183 km covering 29 states in various regions of the United States. Upon return, samples were evaluated for virus presence and viability using a previously validated viability qPCR (V-qPCR) method. Results showed that EhV-86 was detected in all matrices and no degradation in EhV-86 viability was observed after the 23-day transportation event. Additionally, sampling sensitivity (we recorded unexpected increases, as high as 49% in one matrix, when virus was recovered at the end of the sampling period) rather than virus degradation best explains the variation of virus quantity observed after the 23-day transport simulation. These results demonstrate for the first time that ASFV-like NCLDVs can retain viability in swine feed matrices during long-term transport across the continental United States

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Blockchain Technology and the Potential Applicability in the Feed Industry

Information on the current applications of blockchain in food systems and the potential applicability, uses, and limitations of blockchain for feed ingredients common to the swine industry was gathered from a multitude of sources. The information on applications representative of supply chain logistics for imported feed ingredients was evaluated and limitations of blockchain in tracing lots of packaged ingredients vs. ingredients in bulk transportation was assessed. Overall, blockchain application is a viable technology to ensure traceability of feed ingredients. Blockchain provides key benefits including transaction security, auditability, and transparency. However, these benefits are accompanied by costs including, most importantly, the need for all-in participation and a value-driven incentive to participate that is shared across the supply chain. In addition, due to the bulk commodity nature of many feed ingredients common to the swine industry, traceability to individual manufacturer or producer through any technology becomes limited to the largest storage and/or transportation unit in the supply chain. Ingredients that move through the supply chain as discreetly packaged products, whether in kilogram packages or metric ton super sacks, have an easier entry into and more optimal traceability within blockchain technology. These concepts were modeled into a scenario for potential soybean shipments including where suppliers may verify the implementation of key preventive controls to decrease the risk of disease transmission via feed distribution.Swine Health Information Cente

Blockchain Technology and the Potential Applicability in the Feed Industry - Condensed

Blockchain applications offer the feed supply chain incredible benefits and efficiencies in the goal to improve feed safety and animal health. The power of utilizing blockchain technology in feed supply chain transactions is in allowing parties to trade in the absence of a mediator or trusting relationship. This is the cornerstone of all blockchain applications - secure trading of ‘things’, both physical and virtual, without middlemen and historical relationships. However, implementation of the technology will experience hurdles and will require consensus among the industry for standards and methods of data collection and sharing. In addition, the cost of entry to access the data and who will pay for it will be a driving factor in the success of blockchain technology adoption. And finally, it should be recognized that blockchain applications depend absolutely on the reputability and accuracy of the data included in the blocks that are recorded in the chain.Swine Health Information Cente

Research Protocol

This protocol was developed in accordance with the Joanna Briggs Institute (JBI) Reviewers' Manual 2015 - Methodology for JBI Scoping Reviews. This protocol outlines the predefined methodology to be implemented during this research

African Swine Fever-Soybean Meal Supply China Workshop – Workshop Summary and Supplemental Information

An African swine fever-Soybean meal supply chain workshop involving key industry stakeholders was conducted on July 10, 2019 on the University of Minnesota St. Paul campus. The objectives were to 1) identify and discuss the various segments and potential risk factors of the soy supply chain in North America, 2) identify and discuss potential prevention, mitigation, and product differentiation (country of origin) strategies for soy products used in the U.S. pork industry, and 3) identify research and education needs related to foreign animal viruses and soy products. The group identified potential risk factors for African swine fever virus introduction into the United States through imported soy products including 1) contamination during transport, 2) inadequate virus inactivation in soybean hulls during processing if contaminated, 3) imported organic soybean products used in fertilizers, and 4) risk of virus spreading through manure and other routes if introduced. Prevention, mitigation, and differentiation strategies were discussed and included 1) develop a diagnostic test to assess African swine fever virus in feed, 2) explore alternatives to inter-port shipment of soybean products among U.S. ports of entry, and 3) identify and educate importers about consequences of African swine fever virus introduction and suggest prevention and mitigation methods. Several research and education outcomes were identified including 1) improve data collection on country of origin for imported soy products, 2) write a report describing the soy supply chain including reasons for imports and benefits of exports, 3) conduct more research on survivability of the virus in different feed ingredient matrices that is reproducible, 4) determine whether the virus is present in feed ingredient supply chains, 5) determine the most accurate methods to assess virus survival, and 6) determine specific factors that cause the African swine fever virus to survive in soybean meal for extended periods of time.Swine Health Information Center, Ames, I

A genome sequencing program for novel undiagnosed diseases

PURPOSE: The Scripps Idiopathic Diseases of huMan (IDIOM) study aims to discover novel gene-disease relationships and provide molecular genetic diagnosis and treatment guidance for individuals with novel diseases using genome sequencing integrated with clinical assessment and multidisciplinary case review. METHODS: Here we describe the IDIOM study operational protocol and initial results. RESULTS: 121 cases underwent first tier review by the principal investigators to determine if the primary inclusion criteria were satisfied, 59 (48.8%) underwent second tier review by our clinician-scientist review panel, and 17 (14.0%) patients and their family members were enrolled. 60% of cases resulted in a plausible molecular diagnosis. 18% of cases resulted in a confirmed molecular diagnosis. 2 of 3 confirmed cases led to the identification of novel gene-disease relationships. In the third confirmed case, a previously described but unrecognized disease was revealed. In all three confirmed cases, a new clinical management strategy was initiated based on the genetic findings. CONCLUSIONS: Genome sequencing provides tangible clinical benefit for individuals with idiopathic genetic disease, not only in the context of molecular genetic diagnosis of known rare conditions, but also in cases where prior clinical information regarding a new genetic disorder is lacking