Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

Background The SARS-CoV-2 variant B.1.1.7 was first identified in December, 2020, in England. We aimed to investigate whether increases in the proportion of infections with this variant are associated with differences in symptoms or disease course, reinfection rates, or transmissibility. Methods We did an ecological study to examine the association between the regional proportion of infections with the SARS-CoV-2 B.1.1.7 variant and reported symptoms, disease course, rates of reinfection, and transmissibility. Data on types and duration of symptoms were obtained from longitudinal reports from users of the COVID Symptom Study app who reported a positive test for COVID-19 between Sept 28 and Dec 27, 2020 (during which the prevalence of B.1.1.7 increased most notably in parts of the UK). From this dataset, we also estimated the frequency of possible reinfection, defined as the presence of two reported positive tests separated by more than 90 days with a period of reporting no symptoms for more than 7 days before the second positive test. The proportion of SARS-CoV-2 infections with the B.1.1.7 variant across the UK was estimated with use of genomic data from the COVID-19 Genomics UK Consortium and data from Public Health England on spike-gene target failure (a non-specific indicator of the B.1.1.7 variant) in community cases in England. We used linear regression to examine the association between reported symptoms and proportion of B.1.1.7. We assessed the Spearman correlation between the proportion of B.1.1.7 cases and number of reinfections over time, and between the number of positive tests and reinfections. We estimated incidence for B.1.1.7 and previous variants, and compared the effective reproduction number, Rt, for the two incidence estimates. Findings From Sept 28 to Dec 27, 2020, positive COVID-19 tests were reported by 36 920 COVID Symptom Study app users whose region was known and who reported as healthy on app sign-up. We found no changes in reported symptoms or disease duration associated with B.1.1.7. For the same period, possible reinfections were identified in 249 (0·7% [95% CI 0·6–0·8]) of 36 509 app users who reported a positive swab test before Oct 1, 2020, but there was no evidence that the frequency of reinfections was higher for the B.1.1.7 variant than for pre-existing variants. Reinfection occurrences were more positively correlated with the overall regional rise in cases (Spearman correlation 0·56–0·69 for South East, London, and East of England) than with the regional increase in the proportion of infections with the B.1.1.7 variant (Spearman correlation 0·38–0·56 in the same regions), suggesting B.1.1.7 does not substantially alter the risk of reinfection. We found a multiplicative increase in the Rt of B.1.1.7 by a factor of 1·35 (95% CI 1·02–1·69) relative to pre-existing variants. However, Rt fell below 1 during regional and national lockdowns, even in regions with high proportions of infections with the B.1.1.7 variant. Interpretation The lack of change in symptoms identified in this study indicates that existing testing and surveillance infrastructure do not need to change specifically for the B.1.1.7 variant. In addition, given that there was no apparent increase in the reinfection rate, vaccines are likely to remain effective against the B.1.1.7 variant. Funding Zoe Global, Department of Health (UK), Wellcome Trust, Engineering and Physical Sciences Research Council (UK), National Institute for Health Research (UK), Medical Research Council (UK), Alzheimer's Society

Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission

Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was associated with a lower rate of contacts, and the impact of quarantine was greatest in the 16–20 age-group. 186 SARS-CoV-2 genomes were sufficiently unique to identify travel-related clusters. Fewer genomically-linked cases were observed for index cases who returned from countries with quarantine requirement compared to countries with no quarantine requirement. This difference was explained by fewer importation events per identified genome for these cases, as opposed to fewer onward contacts per case. Overall, our study demonstrates that a 14-day quarantine period reduces, but does not completely eliminate, the onward transmission of imported cases, mainly by dissuading travel to countries with a quarantine requirement

Efficacy of Manufacturer Recommendations for the Control of Salmonella Typhimurium and Listeria monocytogenes in Food Ink Capsules Utilized in 3D Food Printing Systems

The adoption of 3D food printing systems has allowed for the personalization of food properties such as color, shape, and texture. This study aimed to determine if manufacturer cleaning recommendations for stainless steel food ink capsules utilized in 3D food printers adequately control foodborne pathogens of concern, as the recommendations have not been tested. A cocktail of ∼9 log10 CFU/mL each of Salmonella Typhimurium and Listeria monocytogenes was inoculated onto the interior surface of the capsules. Capsules were either unsoiled or soiled with one of the following: butter, protein powder solution, powdered sugar solution, or a mixture containing all three food components. The prepared capsules underwent one of three hygienic protocols: manual washing (MW), a dishwasher speed cycle (DSC), or a dishwasher heavy cycle (DHC). The interaction effect between DSC and the soil mixture was significant (P = 0.01), with the combination achieving an estimated mean log reduction of 5.28 (95% CI: 4.61, 6.05) for L. monocytogenes and 6.69 (95% CI: 6.03, 7.41) for S. Typhimurium. The DSC was the least effective method of cleaning when compared with MW and the DHC. No significant differences were found by placing capsules on the right or left side of the dishwasher (P > 0.1). The interaction effect between wash type and capsule position was significant (P = 0.0007), with the soil mixture and DSC combination achieving an estimated mean log reduction of 3.48 (95% CI: 2.72, 4.45) for the front-most position versus 7.92 (95% CI: 6.72, 9.31) for the back-most position. Soil matrix, cleaning protocol, and capsule position all significantly impact capsule cleanability and therefore food safety risk. The DHC is recommended, and the corners should be avoided during dishwasher loading. The current study provides practical information for consumers, restaurants, industry, and regulatory industries regarding the best practices for cleaning 3D food printers

Growing Safer Greens: Exploring Food Safety Practices and Challenges in Indoor, Soilless Production Through Thematic Analysis of Leafy Greens Grower Interviews

Indoor, soilless production—often referred to more broadly as controlled environment agriculture (CEA)—is increasingly used for the cultivation of leafy greens. Minimal information is currently available regarding food safety practices during production and distribution of leafy greens grown within indoor, soilless environments in the United States (U.S.). This study aimed to describe production challenges and implementation of good agricultural practices among CEA growers. Data collection methods included semi-structured interviews (N = 25) and a supplemental online survey completed by growers (N = 12) in the U.S. Out of 18 total responses (i.e., multiple responses allowed per completed survey), survey data indicated that lettuce (n = 5; 27.8%) was the most commonly grown leafy green, followed by culinary herbs (n = 3; 16.7%) and arugula (n = 3; 16.7%). Most growers (n = 7; 58.3%) grew other agricultural products, specifically other crops in addition to leafy greens. Revenue from sales ranged from US$500 000 per year. Meanwhile, nearly half (n = 5; 45.5%) of respondents (N = 11) were uncertain whether their produce was subject to the FSMA Produce Safety Rule. Most survey respondents used vertical farming techniques (5 out of 11; 45.5%) or some variety of greenhouse (4 out of 11; 36.4%). Based on 35 total responses, leafy greens were most commonly sold to “Commercial Restaurants” (n = 7; 20.0%), “Grocery Stores” (n = 7; 20.0%), “Institutional Foodservice Establishments (hospitals, schools, childcare, long-term care)” (n = 6; 17.1%), and “Wholesaler/Distributers” (n = 6; 17.1%). The 11 interview questions elucidated three major themes: contextual, barriers to risk management and regulatory compliance, and research needs. Thirteen subthemes were identified, and an example of a subtheme within each major theme, respectively, includes worker hygiene and training, regulatory and certification environment, and risk assessments of individual issues

Aqueous Ozone Efficacy for Inactivation of Foodborne Pathogens on Vegetables Used in Raw Meat-Based Diets for Companion Animals

The present study evaluates the efficacy of a batch wash ozone sanitation system (BWOSS) and spray wash ozone sanitation system (SWOSS) against Listeria monocytogenes (two strains) and Salmonella enterica subsp. enterica (three serovars) inoculated on the surface of carrots, sweet potatoes, and butternut squash, commonly used in raw meat-based diets (RMBDs) marketed for companion animals such as dogs and cats. Produce either remained at room temperature for 2 h or were frozen at −20°C and then tempered overnight at 4°C to mimic the preprocessing steps of a raw pet food processing operation (‘freeze-temper’) prior to ozone treatment. Two ozone concentrations (0 and 5 ppm) were applied for either 20 s or 60 s for BWOSS and 20 s for SWOSS. Based on an ANOVA, BWOSS data showed no significant difference (P > 0.05) in microbial reduction between 0 and 5 ppm ozone concentration across all treatment durations for each produce type. BWOSS resulted in mean microbial reductions of up to 1.56 log CFU/mL depending on the treatment time and produce type. SWOSS data were analyzed using a generalized linear model with Quasipoisson errors. Freeze-tempered produce treated with SWOSS had a higher bacterial log reduction at 5 ppm ozone compared to 0 ppm ozone (P = 0.0013) whereas room temperature produce treated with SWOSS did not show any significant difference in microbial reduction between ozone concentrations. The potential to mitigate microbial cross-contamination was also investigated during SWOSS treatment. The results indicate that 5 ppm ozone decreased pathogens in the rinsate and proximal surfaces by 0.63–1.66 log CFU/mL greater than no ozone depending on the pathogen and sample. Overall, data from this study indicate that SWOSS would be more effective compared to BWOSS in reducing the microbial load present on the surface of root tubers and squash subjected to freezing and thawing and has the potential to mitigate cross-contamination within RMDB manufacturing environments

Cultivating Food Safety Together: Insights About the Future of Produce Safety in the U.S. Controlled Environment Agriculture Sector

Controlled environment agriculture (CEA) is a rapidly growing sector that presents unique challenges and opportunities in ensuring food safety. This manuscript highlights critical gaps and needs to promote food safety in CEA systems as identified by stakeholders (n=47) at the Strategizing to Advance Future Extension and Research (S.A.F.E.R.) CEA conference held in April 2023 at The Ohio State University’s Ohio CEA Research Center. Feedback collected at the conference was analyzed using an emergent thematic analysis approach to determine key areas of focus. Research-based guidance is specific to the type of commodity, production system type, and size. Themes include the need for improved supply chain control, cleaning, and sanitization practices, pathogen preventive controls and mitigation methods and training and education. Discussions surrounding supply chain control underscored the significance of the need for approaches to mitigate foodborne pathogen contamination. Effective cleaning and sanitization practices are vital to maintaining a safe production environment, with considerations such as establishing standard operating procedures, accounting for hygienic equipment design, and managing the microbial communities within the system. Data analysis further highlights the need for risk assessments, validated pathogen detection methods, and evidence-based guidance in microbial reduction. In addition, training and education were identified as crucial in promoting a culture of food safety within CEA. The development of partnerships between industry, regulatory, and research institutions are needed to advance data-driven guidance and practices across the diverse range of CEA operations and deemed essential for addressing challenges and advancing food safety practices in CEA. Considering these factors, the CEA industry can enhance food safety practices, foster consumer trust, and support its long-term sustainability