The ongoing global pandemic of the coronavirus 2019 (COVID-19) disease is caused by the virus SARS-CoV-2, with very few highly effective antiviral treatments currently available. The machinery responsible for the replication and transcription of viral RNA during infection is made up of several important proteins. Two of these are nsp12, the catalytic subunit of the viral polymerase, and nsp9, a cofactor of nsp12 involved in the capping and priming of viral RNA. While several recent studies have determined the structural details of the interaction of nsp9 with nsp12 in the context of RNA capping, very few biochemical or biophysical details are currently available. In this study, we have used a combination of surface plasmon resonance (SPR) experiments, size exclusion chromatography (SEC) experiments, and biochemical assays to identify specific nsp9 residues that are critical for nsp12 binding as well as RNAylation, both of which are essential for the RNA capping process. Our data indicate that nsp9 dimerization is unlikely to play a significant functional role in the virus. We confirm that a set of recently discovered antiviral peptides inhibit nsp9-nsp12 interaction by specifically binding to nsp9; however, we find that these peptides do not impact RNAylation. In summary, our results have important implications for future drug discovery efforts to combat SARS-CoV-2 and any newly emerging coronaviruses.

OBJECTIVE: The objective of this study was to assess the impact of the coronavirus pandemic on gynecology surgical training.
METHODS: A national cross-sectional online survey was distributed to all trainees and trainers in the higher specialist training program for obstetrics and gynecology in Ireland. The survey consisted of questions on topics which included: the volume of surgical procedures performed before and since the pandemic, confidence in performing various gynecologic procedures before and since the pandemic and questions regarding the impact of the pandemic on wellbeing and work practices.
RESULTS: Trainers and trainees experienced a significant reduction in operative volumes for most procedure types. Analysis showed a significant reduction in the number of minor procedures performed by trainees (z = -2.7, P = 0.007) and a significant reduction in the number of all procedure types performed by trainers (minor procedures z = -3.78, P = <0.001; intermediate procedures z = -4.48, P = < 0.001; major procedures z = -3.69, P = < 0.001). Respondents reported they had less time for research and audit, were less able to attend courses or conferences and worried about the impact of their work on their families.
CONCLUSIONS: In conclusion, this study has highlighted the current difficulties facing surgical trainees in gynecology because of the COVID-19 pandemic. These challenges have compounded an already challenging training environment for gynecology trainees. Efforts must be made to continue to provide high-quality tailored training to ensure the development of the next generation of gynecologic surgeons.

The study aimed to investigate molecularly the presence of flea-borne viruses in infested small ruminants with fleas. It was carried out in Egypt\'s Northern West Coast (NWC) and South Sinai Governorate (SSG). Three specific primers were used targeting genes, ORF103 (for Capripoxvirus and Lumpy skin disease virus), NS3 (for Bluetongue virus), and Rdrp (for Coronavirus), followed by gene sequencing and phylogenetic analyses. The results revealed that 78.94% of sheep and 65.63% of goats were infested in the NWC area, whereas 49.76% of sheep and 77.8% of goats were infested in the SSG region. Sheep were preferable hosts for flea infestations (58.9%) to goats (41.1%) in the two studied areas. Sex and age of the animals had no effects on the infestation rate (p > 0.05). The season and site of infestation on animals were significantly different between the two areas (p < 0.05). Ctenocephalides felis predominated in NWC and Ctenocephalides canis in SSG, and males of both flea species were more prevalent than females. Molecular analysis of flea DNA revealed the presence of Capripoxvirus in all tested samples, while other viral infections were absent. Gene sequencing identified three isolates as sheeppox viruses, and one as goatpox virus. The findings suggest that Capripoxvirus is adapted to fleas and may be transmitted to animals through infestation. This underscores the need for ongoing surveillance of other pathogens in different regions of Egypt.

OBJECTIVE: To describe the clinical-laboratory profile and analyze the factors associated with the severity of COVID-19.
METHODS: A prospective cohort study involving patients with COVID-19 admitted to a tertiary hospital in Recife, Brazil. All cases were confirmed by RT-PCR and classified according to severity criteria. A descriptive statistical analysis of the population\'s characteristics was conducted. Risk factors associated with the outcome of the case according to severity were analyzed by calculating the odds ratio (OR) using the general equation estimation (GEE) model.
RESULTS: Among the 75 cases included, 64% were female, and 62.7% were aged 65 years or older. The median length of stay was 9 days (6 - 14). Hypertension (65.3%) and Diabetes Mellitus (36%) were the most frequent comorbidities. Severe forms of COVID-19 constituted 41.3% of the sample. The factors associated with severity were a history of asthma (OR=4.58, 95%CI:1.13 - 18.7), report of anorexia (OR=1, 12, 95%CI:1.01-1.24), and laboratory changes that included elevated platelets (OR=1.00, 95% CI:1.00-1.01), elevated D\'Dimer (OR=1, 26, 95% CI:1.04-1.52), elevated aspartate aminotransferase (OR=1.00, 95% CI:1.00-1.01), and gamma-glutamyl transferase (OR=1.22, IC95 %:0.98-1.51), hypernatremia (OR=1.31, 95%CI:1.12-1.52), and hyperkalemia (OR=1.21, 95% CI:1.04-1.41).
CONCLUSIONS: Multisystemic involvement with a tendency for thrombophilia, electrolyte disturbances, and hepatic aggression, reflected by laboratory changes, were factors associated with the severity of COVID-19.

Food retail businesses experienced a pronounced increase in sales when food hospitality outlets closed in the early stages of the COVID-19 pandemic in Canada. This study investigates how pandemic-related modifications to food retail businesses in Ontario, Canada affected the well-being of workers. Semi-structured interviews were conducted with 17 food retail employees between June 2020 and May 2021 as part of the Food Retail Environment Study for Health and Economic Resiliency (FRESHER). Transcripts were analyzed inductively, and themes were refined using the Effort Reward Imbalance Model. Themes were connected to the main components of this model: extrinsic effort, intrinsic effort, money, esteem, status control, and burnout. Results indicate that, for food retail employees, the presence of an imbalance between efforts and rewards threatens well-being via symptoms of burnout. Further study is needed to examine how this inequality and burnout among this population might be measured and addressed.

Viruses are obligate parasites that depend on the cellular machinery for their propagation. Several viruses also incorporate cellular proteins that facilitate viral spread. Defining these cellular proteins is critical to decipher viral life cycles and delineate novel therapeutic strategies. While numerous studies have explored the importance of host proteins in coronavirus spread, information about their presence in mature virions is limited. In this study, we developed a protocol to highly enrich mature HCoV-OC43 virions and characterize them by proteomics. Recognizing that cells release extracellular vesicles whose content is modulated by viruses, and given our ability to separate virions from these vesicles, we also analyzed their protein content in both uninfected and infected cells. We uncovered 69 unique cellular proteins associated with virions including 31 high-confidence hits. These proteins primarily regulate RNA metabolism, enzymatic activities, vesicular transport, cell adhesion, metabolite interconversion, and translation. We further discovered that the virus had a profound impact on exosome composition, incorporating 47 novel cellular proteins (11 high confidence) and excluding 92 others (61 high confidence) in virus-associated extracellular vesicles compared to uninfected cells. Moreover, a dsiRNA screen revealed that 11 of 18 select targets significantly impacted viral yields, including proteins found in virions or extracellular vesicles. Overall, this study provides new and important insights into the incorporation of numerous host proteins into HCoV-OC43 virions, their biological significance, and the ability of the virus to modulate extracellular vesicles.
OBJECTIVE: In recent years, coronaviruses have dominated global attention, making it crucial to develop methods to control them and prevent future pandemics. Besides viral proteins, host proteins play a significant role in viral propagation and offer potential therapeutic targets. Targeting host proteins is advantageous because they are less likely to mutate and develop resistance compared to viral proteins, a common issue with many antiviral treatments. In this study, we examined the protein content of the less virulent biosafety level 2 HCoV-OC43 virus as a stand-in for the more virulent SARS-CoV-2. Our findings reveal that several cellular proteins incorporated into the virion regulate viral spread. In addition, we report that the virus extensively modulates the content of extracellular vesicles, enhancing viral dissemination. This underscores the critical interplay between the virus, host proteins, and extracellular vesicles.

Nanopore direct RNA sequencing (DRS) enables the capture and full-length sequencing of native RNAs, without recoding or amplification bias. Resulting data sets may be interrogated to define the identity and location of chemically modified ribonucleotides, as well as the length of poly(A) tails, on individual RNA molecules. The success of these analyses is highly dependent on the provision of high-resolution transcriptome annotations in combination with workflows that minimize misalignments and other analysis artifacts. Existing software solutions for generating high-resolution transcriptome annotations are poorly suited to small gene-dense genomes of viruses due to the challenge of identifying distinct transcript isoforms where alternative splicing and overlapping RNAs are prevalent. To resolve this, we identified key characteristics of DRS data sets that inform resulting read alignments and developed the nanopore guided annotation of transcriptome architectures (NAGATA) software package (https://github.com/DepledgeLab/NAGATA). We demonstrate, using a combination of synthetic and original DRS data sets derived from adenoviruses, herpesviruses, coronaviruses, and human cells, that NAGATA outperforms existing transcriptome annotation software and yields a consistently high level of precision and recall when reconstructing both gene sparse and gene-dense transcriptomes. Finally, we apply NAGATA to generate the first high-resolution transcriptome annotation of the neglected pathogen human adenovirus type F41 (HAdV-41) for which we identify 77 distinct transcripts encoding at least 23 different proteins.
OBJECTIVE: The transcriptome of an organism denotes the full repertoire of encoded RNAs that may be expressed. This is critical to understanding the biology of an organism and for accurate transcriptomic and epitranscriptomic-based analyses. Annotating transcriptomes remains a complex task, particularly in small gene-dense organisms such as viruses which maximize their coding capacity through overlapping RNAs. To resolve this, we have developed a new software nanopore guided annotation of transcriptome architectures (NAGATA) which utilizes nanopore direct RNA sequencing (DRS) datasets to rapidly produce high-resolution transcriptome annotations for diverse viruses and other organisms.

The pandemic due to severe respiratory syndrome coronavirus 2 (SARS-Cov-2) was one of the most damaging healthcare emergencies the world has ever seen. Co-infection with dengue virus in COVID-19-positive patients is an additional challenge especially in dengue-endemic areas. Both dengue and COVID-19 infection cause increased morbidity and adverse outcomes in pregnant women, and simultaneous infection of these two illnesses can be further detrimental and sometimes fatal in pregnant women. Here, we present a case of a pregnant woman in her early second trimester with co-infection of dengue and moderate COVID-19 disease who was managed successfully and had a favorable outcome.

UNASSIGNED: Syndromic surveillance represents a potentially inexpensive supplement to test-based COVID-19 surveillance. By strengthening surveillance of COVID-19-like illness (CLI), targeted and rapid interventions can be facilitated that prevent COVID-19 outbreaks without primary reliance on testing.
UNASSIGNED: This study aims to assess the temporal relationship between confirmed SARS-CoV-2 infections and self-reported and health care provider-reported CLI in university and county settings, respectively.
UNASSIGNED: We collected aggregated COVID-19 testing and symptom reporting surveillance data from Cornell University (2020-2021) and Tompkins County Health Department (2020-2022). We used negative binomial and linear regression models to correlate confirmed COVID-19 case counts and positive test rates with CLI rate time series, lagged COVID-19 cases or rates, and day of the week as independent variables. Optimal lag periods were identified using Granger causality and likelihood ratio tests.
UNASSIGNED: In modeling undergraduate student cases, the CLI rate (P=.003) and rate of exposure to CLI (P<.001) were significantly correlated with the COVID-19 test positivity rate with no lag in the linear models. At the county level, the health care provider-reported CLI rate was significantly correlated with SARS-CoV-2 test positivity with a 3-day lag in both the linear (P<.001) and negative binomial model (P=.005).
UNASSIGNED: The real-time correlation between syndromic surveillance and COVID-19 cases on a university campus suggests symptom reporting is a viable alternative or supplement to COVID-19 surveillance testing. At the county level, syndromic surveillance is also a leading indicator of COVID-19 cases, enabling quick action to reduce transmission. Further research should investigate COVID-19 risk using syndromic surveillance in other settings, such as low-resource settings like low- and middle-income countries.

We investigated nurses\' experiences of hospital-acquired pressure injury (PI) prevention in acute care services to better understand how PI prevention may be optimised. We used the Theoretical Domains Framework to systematically identify barriers and enablers to evidence-based preventive practices as required by the International Guideline. This study was one element of a complex capacity building project on PI surveillance and prevention within the acute health service partners of Monash Partners Academic Health Science Centre, an accredited academic health partnership located in Melbourne, Australia. We adopted a qualitative descriptive design. We interviewed 32 nurses that provided care in intensive care units, general wards and COVID wards of four acute care services. Nurses were recruited from four large acute care services (three public, one private) located in Melbourne. Most of them worked with patients who were at high risk of hospital-acquired PI on a daily basis. Interview transcripts were coded and analysed using thematic analysis guided by the Theoretical Domains Framework. The domains referred to most frequently by all participants included: Knowledge, Skills, Social/Professional Role and Identity, Beliefs about Capabilities, and Environmental Context and Resources. The key barriers discussed by nurses included gaps in nurses\' knowledge and skills related to identification and staging of PI, heavy nursing workload and inadequate staffing levels, stigma and self-blame related to PI identification, and exacerbating impacts of the COVID-19 pandemic. Main facilitators discussed were training programmes, nursing audits and feedback, and teamwork. Participants suggested improvements including accessible and tailored training, visual reminders, and addressing heavy workloads and emotional barriers nurses face. Investing in tailored training initiatives to improve nurses\' knowledge and organisational changes to address low level staffing and heavy workloads are urgently needed to support nurses in delivering optimal care and preventing hospital-acquired PI.