Identification of Marker Genes in Infectious Diseases from ScRNA-seq Data Using Interpretable Machine Learning.

A common result of infection is an abnormal immune response, which may be detrimental to the host. To control the infection, the immune system might undergo regulation, therefore producing an excess of either pro-inflammatory or anti-inflammatory pathways that can lead to widespread inflammation, tissue damage, and organ failure. A dysregulated immune response can manifest as changes in differentiated immune cell populations and concentrations of circulating biomarkers. To propose an early diagnostic system that enables differentiation and identifies the severity of immune-dysregulated syndromes, we built an artificial intelligence tool that uses input data from single-cell RNA sequencing. In our results, single-cell transcriptomics successfully distinguished between mild and severe sepsis and COVID-19 infections. Moreover, by interpreting the decision patterns of our classification system, we identified that different immune cells upregulating or downregulating the expression of the genes CD3, CD14, CD16, FOSB, S100A12, and TCRɣδ can accurately differentiate between different degrees of infection. Our research has identified genes of significance that effectively distinguish between infections, offering promising prospects as diagnostic markers and providing potential targets for therapeutic intervention.

Understanding knowledge, attitudes and practices on Ebola Virus Disease: a multi-site mixed methods survey on preparedness in Rwanda.

BACKGROUND: The overall goal of this survey was to understand the knowledge, attitudes, and practices related to the Ebola Virus Disease (EVD) in Rwanda. METHODS: This mixed-method cross-sectional survey was conducted in five selected districts of Rwanda. Quantitative data were collected from 1,010 participants using Kobo Collect Software and the analysis was performed using SPSS and Python software. Qualitative data were specifically collected from 98 participants through Key Informant Interviews (KIIs) and Focus Group Discussion (FGDs). Interview transcripts were imported into NVIVO 8 for coding and subsequent analysis. RESULTS: As per our quantitative findings, we report that from the 1,010 respondents, 99.6% reported having previously heard of Ebola, 97.2% believed that vaccination is important in combatting the disease and 93.3% of individuals reported a willingness to receive vaccination should one become available. Around 54% of the respondents were correct in identifying that the disease is of a viral origin which originates from wild animals (42.1%). When asked if they believed that Rwanda is at risk of an EVD outbreak, 90% of the respondents believe that the country is at risk of an EVD outbreak, and the cofactors *gender* and *whether people dwell in Rubavu/Rusizi* were found to significantly impact their perception of threat. As per our qualitative findings, the respondents mentioned that both geographical proximity and relations with the Democratic Republic of Congo place Rwanda at risk of developing an internal outbreak. Although the respondents seemed to be aware of the Ebola prevention behaviours, it was noted that some of them will require significant time before reintegrating into the community an EVD survivor, as they will first need assurance that the patient has fully recovered. Therefore, the qualitative findings reinforce what we originally reported in the quantitative approach to this study. CONCLUSION: Our results show that there was high EVD-related knowledge and awareness among the general population in Rwanda. However, for strong public health awareness, preparedness, and protection, a massive investment should always be made in education about EVD with a special focus on districts neighboring countries where the disease is consistently being reported.

Coronary microvascular ischemia in hypertrophic cardiomyopathy - a pixel-wise quantitative cardiovascular magnetic resonance perfusion study.

BACKGROUND: Microvascular dysfunction in HCM has been associated with adverse clinical outcomes. Advances in quantitative cardiovascular magnetic resonance (CMR) perfusion imaging now allow myocardial blood flow to be quantified at the pixel level. We applied these techniques to investigate the spectrum of microvascular dysfunction in hypertrophic cardiomyopathy (HCM) and to explore its relationship with fibrosis and wall thickness. METHODS: CMR perfusion imaging was undertaken during adenosine-induced hyperemia and again at rest in 35 patients together with late gadolinium enhancement (LGE) imaging. Myocardial blood flow (MBF) was quantified on a pixel-by-pixel basis from CMR perfusion images using a Fermi-constrained deconvolution algorithm. Regions-of-interest (ROI) in hypoperfused and hyperemic myocardium were identified from the MBF pixel maps. The myocardium was also divided into 16 AHA segments. RESULTS: Resting MBF was significantly higher in the endocardium than in the epicardium (mean ± SD: 1.25 ± 0.35 ml/g/min versus 1.20 ± 0.35 ml/g/min, P<0.001), a pattern that reversed with stress (2.00 ± 0.76 ml/g/min versus 2.36 ± 0.83 ml/g/min, P<0.001). ROI analysis revealed 11 (31%) patients with stress MBF lower than resting values (1.05 ± 0.39 ml/g/min versus 1.22 ± 0.36 ml/g/min, P=0.021). There was a significant negative association between hyperemic MBF and wall thickness (ß=-0.047 ml/g/min per mm, 95% CI: -0.057 to -0.038, P<0.001) and a significantly lower probability of fibrosis in a segment with increasing hyperemic MBF (odds ratio per ml/g/min: 0.086, 95% CI: 0.078 to 0.095, P=0.003). CONCLUSIONS: Pixel-wise quantitative CMR perfusion imaging identifies a subgroup of patients with HCM that have localised severe microvascular dysfunction which may give rise to myocardial ischemia.

The impact of public transportation on the transmission of COVID-19 in Rwanda.

Introduction: The onset of the COVID-19 pandemic has placed a significant burden on healthcare systems worldwide, particularly in sub-Saharan regions where healthcare resources are limited. The transmission of SARS-CoV-2 is facilitated by the movement of people from place to place. Therefore, implementing measures that restrict movement of people and contacts is crucial in controlling the spread of the disease. Following the identification of the first COVID-19 case in Rwanda, the government implemented stringent measures, including a complete nationwide lockdown, border closures, curfews, reduced capacity in public transportation and businesses, and mandatory testing. This study aims to assess epidemiological trends in COVID-19 cases in relation to changes in population mobility within the public transportation system. Methods: A descriptive analysis using publicly available data on COVID-19 epidemiological indicators (cases, deaths, vaccinations, and stringency index) and mobility data was conducted. Results: The results reveal a strong correlation between mobility in public transportation and other activities, underscoring Rwanda's reliance on its public transportation system. The study also identifies a pattern where increases in transit station mobility preceded spikes in COVID-19 cases, suggesting that the subsequent rise in public transportation usage may contribute to higher infection rates. Discussion: Therefore, this study emphasizes the importance of ongoing vigilance and regulatory measures regarding public transportation during infectious disease outbreaks.

Complete Genome Sequencing, Annotation, and Mutational Profiling of the Novel Clade I Human Mpox Virus, Kamituga Strain.

INTRODUCTION: Human Mpox (formerly monkeypox) infection is an emerging zoonotic disease caused by the Mpox virus (MPXV). We describe the complete genome annotation, phylogeny, and mutational profile of a novel, sustained Clade I Mpox outbreak in the city of Kamituga in Eastern Democratic Republic of the Congo (DRC). METHODOLOGY: A cross-sectional, observational, cohort study was performed among patients of all ages admitted to the Kamituga Hospital with Mpox infection symptoms between late September 2023 and late January 2024. DNA was isolated from Mpox swabbed lesions and sequenced followed by phylogenetic analysis, genome annotation, and mutational profiling. RESULTS: We describe an ongoing Clade I Mpox outbreak in the city of Kamituga, South Kivu Province, Democratic Republic of Congo. Whole-genome sequencing of the viral RNA samples revealed, on average, 201.5 snps, 28 insertions, 81 deletions, 2 indels, 312.5 total variants, 158.3 amino acid changes, 81.66 intergenic variants, 72.16 synonymous mutations, 106 missense variants, 41.16 frameshift variants, and 3.33 inframe deletions across six samples. By assigning mutations at the proteome level for Kamituga MPXV sequences, we observed that seven proteins, namely, C9L (OPG047), I4L (OPG080), L6R (OPG105), A17L (OPG143), A25R (OPG151), A28L (OPG153), and B21R (OPG210) have emerged as hot spot mutations based on the consensuses inframe deletions, frameshift variants, synonymous variants, and amino acids substitutions. Based on the outcome of the annotation, we found a deletion of the D14L (OPG032) gene in all six samples. Following phylogenetic analysis and whole genome assembly, we determined that this cluster of Mpox infections is genetically distinct from previously reported Clade I outbreaks, and thus propose that the Kamituga Mpox outbreak represents a novel subgroup (subgroup VI) of Clade I MPXV. CONCLUSIONS: Here we report the complete viral genome for the ongoing Clade I Mpox Kamituga outbreak for the first time. This outbreak presents a distinct mutational profile from previously sequenced Clade I MPXV oubtreaks, suggesting that this cluster of infections is a novel subgroup (we term this subgroup VI). These findings underscore the need for ongoing vigilance and continued sequencing of novel Mpox threats in endemic regions.

PASC (Post Acute Sequelae of COVID-19) is associated with decreased neutralizing antibody titers in both biological sexes and increased ANG-2 and GM-CSF in females.

Post-acute sequelae of COVID-19 (PASC) or the continuation of COVID-19 (Coronavirus disease 2019) symptoms past 12 weeks may affect as many as 30% of people recovering from a SARS-CoV-2 (severe acute respiratory coronavirus 2) infection. The mechanisms regulating the development of PASC are currently not known; however, hypotheses include virus reservoirs, pre-existing conditions, microblood clots, immune dysregulation, as well as poor antibody responses. Importantly, virus neutralizing antibodies are essential for COVID-19 recovery and protection from reinfection but there is currently limited information on these immune regulators and associated cytokines in PASC patients. Understanding the key drivers of general and specific symptoms associated with Long COVID and the presence of virus neutralizing antibodies in PASC will aid in the development of therapeutics, diagnostics, and vaccines which currently do not exist. We designed a cross-sectional study to investigate systemic antibody and cytokine responses during COVID-19 recovery and PASC. In total, 195 participants were recruited in one of four groups: (1) Those who never had COVID-19 (No COVID); (2) Those in acute COVID-19 recovery (Acute Recovery) (4-12 weeks post infection); (3) Those who recovered from COVID-19 (Recovered) (+ 12 weeks from infection); and (4) those who had PASC (PASC) (+ 12 weeks from infection). Participants completed a questionnaire on health history, sex, gender, demographics, experiences with COVID-19 acute and COVID-19 recovery/continuing symptoms. Serum samples collected were evaluated for antibody binding to viral proteins, virus neutralizing antibody titers, and serum cytokine levels using Ella SimplePlex Immunoassay™ panels. We found participants with PASC reported more pre-existing conditions (e.g. such as hypertension, asthma, and obesity), and PASC symptoms (e.g. fatigue, brain fog, headaches, and shortness of breath) following COVID-19 than COVID-19 Recovered individuals. Importantly, we found PASC individuals to have significantly decreased levels of neutralizing antibodies toward both SARS-CoV-2 and the Omicron BA.1 variant. Sex analysis indicated that female PASC study participants had sustained antibody levels as well as levels of the inflammatory cytokines GM-CSF and ANG-2 over time following COVID-19. Our study reports people experiencing PASC had lower levels of virus neutralizing antibodies; however, the results are limited by the collection time post-COVID-19 and post-vaccination. Moreover, we found females experiencing PASC had sustained levels of GM-CSF and ANG-2. With lower levels of virus neutralizing antibodies, this data suggests that PASC individuals not only have had a suboptimal antibody response during acute SARS-CoV-2 infection but may also have increased susceptibility to subsequent infections which may exacerbate or prolong current PASC illnesses. We also provide evidence suggesting GM-CSF and ANG-2 to play a role in the sex-bias of PASC. Taken together, our findings maybe important for understanding immune molecular drivers of PASC and PASC subgroups.

Evaluating the effectiveness of lockdowns and restrictions during SARS-CoV-2 variant waves in the Canadian province of Nova Scotia.

Introduction: After the initial onset of the SARS-CoV-2 pandemic, the government of Canada and provincial health authorities imposed restrictive policies to limit virus transmission and mitigate disease burden. In this study, the pandemic implications in the Canadian province of Nova Scotia (NS) were evaluated as a function of the movement of people and governmental restrictions during successive SARS-CoV-2 variant waves (i.e., Alpha through Omicron). Methods: Publicly available data obtained from community mobility reports (Google), the Bank of Canada Stringency Index, the "COVID-19 Tracker" service, including cases, hospitalizations, deaths, and vaccines, population mobility trends, and governmental response data were used to relate the effectiveness of policies in controlling movement and containing multiple waves of SARS-CoV-2. Results: Our results indicate that the SARS-CoV-2 pandemic inflicted low burden in NS in the initial 2 years of the pandemic. In this period, we identified reduced mobility patterns in the population. We also observed a negative correlation between public transport (-0.78), workplace (-0.69), retail and recreation (-0.68) and governmental restrictions, indicating a tight governmental control of these movement patterns. During the initial 2 years, governmental restrictions were high and the movement of people low, characterizing a 'seek-and-destroy' approach. Following this phase, the highly transmissible Omicron (B.1.1.529) variant began circulating in NS at the end of the second year, leading to increased cases, hospitalizations, and deaths. During this Omicron period, unsustainable governmental restrictions and waning public adherence led to increased population mobility, despite increased transmissibility (26.41-fold increase) and lethality (9.62-fold increase) of the novel variant. Discussion: These findings suggest that the low initial burden caused by the SARS-CoV-2 pandemic was likely a result of enhanced restrictions to contain the movement of people and consequently, the spread of the disease. Easing public health restrictions (as measured by a decline in the BOC index) during periods of high transmissibility of circulating COVID-19 variants contributed to community spread, despite high levels of immunization in NS.

Molecular mechanisms responsible for SARS-CoV-2 antibody waning and vaccine escape in Omicron sublineages BA.4 and BA.5.

Mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome continue to threaten the global landscape of the coronavirus disease 2019 (COVID-19) pandemic. The Omicron variant (B.1.1.529) rapidly displaced previous 'variants of concern' (VoC) in 2021 due to its high rate of transmissibility and multitude of mutations. This global influx of infections saturated healthcare systems, overwhelmed testing capacity and case reporting, and increased the COVID-19 death toll. Global health leaders are now being faced with the most transmissible COVID-19 variants yet, the Omicron sublineages BA.4 and BA.5, which contain additional spike protein (S) mutations from previous Omicron and VoC serotypes. With universally observed antibody waning, increasing vaccine-variant mismatch, and resuming international travel, the stage is set for unprecedented levels of breakthrough infections and superspreading events. In this paper, we raise awareness to these novel variants and provide context for the high likelihood of an upcoming wave of infection capable of inflicting significant disease burden on a global scale.

Treatment of Failed Latarjet With Arthroscopic Anatomic Glenoid Reconstruction.

PURPOSE: Various methods have been described for the treatment of anterior shoulder instability with glenoid bone loss. The incidence of recurrent dislocations following surgical intervention is high and, therefore, necessitates a reliable and replicable revision procedure. The purpose of this Technical Note is to describe a method of arthroscopic anatomic glenoid reconstruction using a distal tibial allograft and screw fixation in the setting of a failed Latarjet procedure with significant glenoid bone loss. METHODS: We describe in detail patient positioning, portal placement, steps of the diagnostic arthroscopy, and graft preparation using imaging and a detailed intraoperative arthroscopic technique. LEVEL OF EVIDENCE: Level 1, Shoulder; Level 2, Instability.