A unique insert in the genomes of high-risk human papillomaviruses with a predicted dual role in conferring oncogenic risk

Improvement in Pulmonary Hypertension Following Metabolic and Bariatric Surgery: a Brief Review and Meta-analysis

We reviewed the available evidence on the outcome of metabolic and bariatric surgery (MBS) in patients with pulmonary hypertension (PH). Five studies examining 174 patients were included; the mean age was 54.5 ± 9.27 years; the mean BMI before surgery and at the end of follow-up were 47.2 ± 5.95 kg/m2 and 37.4 ± 2.51 kg/m2, respectively. Furthermore, the results showed a significant decrease in the right ventricle systolic pressure (RVSP) after MBS with a mean difference of 10.11% (CI 95%: 3.52, 16.70, I2 = 85.37%, p =  < 0.001), at 16.5  ±  3.8 month follow-up with a morbidity rate of 26% and 0 mortality. Thirty-day postoperative complications included respiratory failure, pulmonary embolism, pulmonary edema, and anastomotic leak. There appears to be a significant improvement in PH with a decrease in medication requirements after MBS.

RNA elements that control human papillomavirus mRNA splicing-targets for therapy?

Human papillomaviruses (HPVs) cause more than 4.5% of all cancer in the world and more than half of these cases are attributed to human papillomavirus type 16 (HPV16). Prophylactic vaccines are available but antiviral drugs are not. Novel targets for therapy are urgently needed. Alternative RNA splicing is extensively used by HPVs to express all their genes and HPV16 is no exception. This process must function to perfection since mis-splicing could perturb the HPV gene expression program by altering mRNA levels or by generating dysfunctional mRNAs. Cis-acting RNA elements on the viral mRNAs and their cognate cellular trans-acting factors control papillomavirus RNA splicing. The precise but delicate nature of the splicing process renders splicing sensitive to interference. As such, papillomavirus RNA splicing is a potential target for therapy. Here we summarize our current understanding of cis-acting HPV16 RNA elements that control HPV16 mRNA splicing via cellular proteins and discuss how they may be exploited as targets for therapy to papillomavirus infections and cancer.

Comparison of the cardiovascular risk profile of rheumatoid arthritis versus hand osteoarthritis patients

It is clear that there is an increased cardiovascular (CV) risk in rheumatoid arthritis (RA) as a result of systemic inflammation. Hand osteoarthritis (HOA) patients, also have an increased CV risk, but the causes are still debated. Our objective was to compare CV risk factors and risk scores between HOA and RA patients. Thirty-five HOA patients were matched by age (< 3 years) and sex to 35 RA patients in a case-control study. We compared their CV risk profiles and their risk of occurrence of CV events at 10 years using the risk equations SCORE1, SCORE2, and QRISK3. There was a significant increase in SCORE1, SCORE2, but not in QRISK3 in the RA group compared to the HOA group, provided that the multiplication coefficient for RA was applied. This increase was found to no longer be significant for SCORE1 when RA patients have low disease activity (DAS28 ≤ 3.2; n = 8). There was no difference between groups in the frequency of metabolic syndrome, blood pressure, abdominal circumference, body mass index, uricemia, triglyceridemia, HDL cholesterolemia, or pain intensity. Conversely, HOA patients had higher LDL cholesterol and fasting blood glucose levels, in the main analysis and in the subgroup of moderate/high RA activity patients (DAS28 > 3.2; n = 26). We found a higher CV risk in RA compared to HOA patients with moderate/high disease activity. The increased CV risk reported in OA remains to be confirmed in HOA, but these patients appear to have a pro-atherogenic lipid and glycemic profile.

BBLN triggers CAMK2D pathology in mice under cardiac pressure overload and potentially in unrepaired hearts with tetralogy of Fallot

Tetralogy of Fallot (TOF) is one of the most prevalent congenital heart defects, with adverse cardiac remodeling and long-term cardiac complications. Here, searching for pathomechanisms, we find upregulated bublin coiled-coil protein (BBLN) in heart specimens of TOF patients with cyanosis, which positively correlates with cardiac remodeling pathways. Human BBLN, a protein with largely unknown function, promoted heart failure features, with increased mortality when overexpressed in mice, in a protein dosage-dependent manner. BBLN enhanced cardiac inflammation, fibrosis and necroptosis by calcium/calmodulin-dependent protein kinase II delta (CAMK2D) activation, whereas a BBLN mutant with impaired CAMK2D binding was inert. Downregulation of CAMK2D by an interfering RNA retarded BBLN-induced symptoms of heart failure. Endogenous BBLN was induced by hypoxia as a major TOF feature in human patients and by chronic pressure overload in mice, and its downregulation decreased CAMK2D hyperactivity, necroptosis and cardiovascular dysfunction. Thus, BBLN promotes CAMK2D-induced pathways to pathological cardiac remodeling, which are triggered by hypoxia in TOF.

Proteomic meta-study harmonization, mechanotyping and drug repurposing candidate prediction with ProHarMeD

Proteomics technologies, which include a diverse range of approaches such as mass spectrometry-based, array-based, and others, are key technologies for the identification of biomarkers and disease mechanisms, referred to as mechanotyping. Despite over 15,000 published studies in 2022 alone, leveraging publicly available proteomics data for biomarker identification, mechanotyping and drug target identification is not readily possible. Proteomic data addressing similar biological/biomedical questions are made available by multiple research groups in different locations using different model organisms. Furthermore, not only various organisms are employed but different assay systems, such as in vitro and in vivo systems, are used. Finally, even though proteomics data are deposited in public databases, such as ProteomeXchange, they are provided at different levels of detail. Thus, data integration is hampered by non-harmonized usage of identifiers when reviewing the literature or performing meta-analyses to consolidate existing publications into a joint picture. To address this problem, we present ProHarMeD, a tool for harmonizing and comparing proteomics data gathered in multiple studies and for the extraction of disease mechanisms and putative drug repurposing candidates. It is available as a website, Python library and R package. ProHarMeD facilitates ID and name conversions between protein and gene levels, or organisms via ortholog mapping, and provides detailed logs on the loss and gain of IDs after each step. The web tool further determines IDs shared by different studies, proposes potential disease mechanisms as well as drug repurposing candidates automatically, and visualizes these results interactively. We apply ProHarMeD to a set of four studies on bone regeneration. First, we demonstrate the benefit of ID harmonization which increases the number of shared genes between studies by 50%. Second, we identify a potential disease mechanism, with five corresponding drug targets, and the top 20 putative drug repurposing candidates, of which Fondaparinux, the candidate with the highest score, and multiple others are known to have an impact on bone regeneration. Hence, ProHarMeD allows users to harmonize multi-centric proteomics research data in meta-analyses, evaluates the success of the ID conversions and remappings, and finally, it closes the gaps between proteomics, disease mechanism mining and drug repurposing. It is publicly available at https://apps.cosy.bio/proharmed/ .

A Case Report of Extreme Oral Lesions: A Rare Indicator of Bullying-Associated Non-suicidal Self-Injury

Bullying has reached epidemic proportions, affecting one in three students worldwide. A pervasive issue that carries profound physical, mental, and social consequences, significantly increasing the risk of non-suicidal self-injury (NSSI) and suicidal behaviors among those who experience this type of harassment and hazing. While physicians and most caregivers are fully aware and competent in identifying signs of self-harming behavior such as scratching, cutting, or burning the skin, oral self-injury is often overlooked as a potential indicator and is associated with unintentional soft tissue biting or specific conditions. We present a rare case of a 14-year-old male who sought medical attention due to severe bilateral tongue ulcers, leading to his admittance to the emergency department (ED) with excruciating pain and feeding difficulties. In the reported case, although the traumatic biting of the tongue emerged as the most probable etiological factor, a specific underlying motive and contextual comprehension were initially absent. It was only after successfully establishing a foundation of trust with the patient, enabling an honest response, that it became evident that the observed lesions represented a manifestation of bullying-induced non-suicidal self-injury. However, patients rarely openly acknowledge intentional self-inflicted lesions and/or their experiences of bullying, underscoring the necessity to maintain vigilance for alternative indicators such as behavioral changes or a noticeable decline in academic productivity. The significance of this case also goes beyond its presentation, highlighting the largely unexplored issue of how a patient's dentofacial features can serve as substantial catalysts for bullying. Therefore, it is only through equally prioritizing awareness of uncommon signs, symptoms, and context that one can expedite early diagnosis and intervention, emphasizing the essential need for comprehensive and timely management of such cases.

Advances in the Applications of Bioinformatics and Chemoinformatics

Chemoinformatics involves integrating the principles of physical chemistry with computer-based and information science methodologies, commonly referred to as "in silico techniques", in order to address a wide range of descriptive and prescriptive chemistry issues, including applications to biology, drug discovery, and related molecular areas. On the other hand, the incorporation of machine learning has been considered of high importance in the field of drug design, enabling the extraction of chemical data from enormous compound databases to develop drugs endowed with significant biological features. The present review discusses the field of cheminformatics and proposes the use of virtual chemical libraries in virtual screening methods to increase the probability of discovering novel hit chemicals. The virtual libraries address the need to increase the quality of the compounds as well as discover promising ones. On the other hand, various applications of bioinformatics in disease classification, diagnosis, and identification of multidrug-resistant organisms were discussed. The use of ensemble models and brute-force feature selection methodology has resulted in high accuracy rates for heart disease and COVID-19 diagnosis, along with the role of special formulations for targeting meningitis and Alzheimer's disease. Additionally, the correlation between genomic variations and disease states such as obesity and chronic progressive external ophthalmoplegia, the investigation of the antibacterial activity of pyrazole and benzimidazole-based compounds against resistant microorganisms, and its applications in chemoinformatics for the prediction of drug properties and toxicity-all the previously mentioned-were presented in the current review.

Development and Validation of a Delirium Risk Prediction Model for Elderly Patients Undergoing Elective Orthopedic Surgery

Purpose

This study aimed to develop and validate a post-operative delirium (POD) nomogram in a population of elderly patients undergoing elective orthopedic surgery.

Patients and Methods

A predictive model was developed based on a training dataset of 474 elderly patients undergoing elective orthopedic surgery from March 2021 to May 2022. POD was identified using the Confusion Assessment Methods (CAM). The least absolute shrinkage and selection operator (LASSO) method was used to screen risk factors, and prediction models were created by combining the outcomes with logistic regression analysis. We employ bootstrap validation for internal validation to examine the model's repeatability. The results were validated using a prospective study on 153 patients operated on from January 2022 to May 2022 at another institution.

Results

The predictors in the POD nomogram included age, the Mini-Mental State Examination(MMSE), sleep disorder, neurological disorders, preoperative serum creatinine (Pre-SCR), and ASA classification. The c-index of the model was 0.928 (95% confidence interval 0.898 ~ 0.957) and the bootstrap validation still achieved a high c-index of 0.912. The c-index of the external validation was 0.921. The calibration curve for the diagnostic probability showed good agreement between prediction by nomogram and actual observation.

Conclusion

By combining preoperative and intraoperative clinical risk factors, we created a POD risk nomogram to predict the probability of POD in elderly patients who undergo elective orthopedic surgery. It could be a tool for guiding individualized interventions.

Luteolin Protects Against Obese Sarcopenia in Mice with High-Fat Diet-Induced Obesity by Ameliorating Inflammation and Protein Degradation in Muscles

SCOPE

Although sarcopenia is mainly caused by aging, sarcopenia due to obesity has become an emerging issue given the increase in obesity among people of various ages. There are studies on obesity or sarcopenia, our understanding of obesity-mediated sarcopenia is insufficient. Luteolin (LU) has exhibited antiobesity effects, but no studies have investigated the LU effects on antisarcopenia. This study therefore investigated the effects of LU on obese sarcopenia in mice with high-fat diet (HFD)-induced obesity.

METHODS AND RESULTS

To evaluate its inhibitory efficacy against obese sarcopenia, 5-week-old mice are fed an HFD supplemented with LU for 20 weeks. LU exerts suppressive effects on obesity, inflammation, and protein degradation in the HFD-fed obese mice. It also inhibits lipid infiltration into the muscle and decreases p38 activity and the mRNA expression of inflammatory factors, including TNF-α, Tlr2, Tlr4, MCP1, and MMP2, in the muscle. The suppression of muscle inflammation by LU leads to the inhibition of myostatin, FoxO, atrogin, and MuRF expression. These effects of LU affect inhibition of protein degradation and improvement of muscle function.

CONCLUSION

Here, it demonstrates that LU's antiobesity and antiinflammatory functionality affect inhibition of muscle protein degradation, and consequently, these interactions by LU exerts a protective effect against obese sarcopenia.

Human papillomavirus genomics: Understanding carcinogenicity

Human papillomavirus (HPV) causes virtually all cervical cancers and many cancers at other anatomical sites in both men and women. However, only 12 of 448 known HPV types are currently classified as carcinogens, and even the most carcinogenic type - HPV16 - only rarely leads to cancer. HPV is therefore necessary but insufficient for cervical cancer, with other contributing factors including host and viral genetics. Over the last decade, HPV whole genome sequencing has established that even fine-scale within-type HPV variation influences precancer/cancer risks, and that these risks vary by histology and host race/ethnicity. In this review, we place these findings in the context of the HPV life cycle and evolution at various levels of viral diversity: between-type, within-type, and within-host. We also discuss key concepts necessary for interpreting HPV genomic data, including features of the viral genome; events leading to carcinogenesis; the role of APOBEC3 in HPV infection and evolution; and methodologies that use deep (high-coverage) sequencing to characterize within-host variation, as opposed to relying on a single representative (consensus) sequence. Given the continued high burden of HPV-associated cancers, understanding HPV carcinogenicity remains important for better understanding, preventing, and treating cancers attributable to infection.

Biventricular shape modes discriminate pulmonary valve replacement in tetralogy of Fallot better than imaging indices

Current indications for pulmonary valve replacement (PVR) in repaired tetralogy of Fallot (rTOF) rely on cardiovascular magnetic resonance (CMR) image-based indices but are inconsistently applied, lead to mixed outcomes, and remain debated. This study aimed to test the hypothesis that specific markers of biventricular shape may discriminate differences between rTOF patients who did and did not require subsequent PVR better than standard imaging indices. In this cross-sectional retrospective study, biventricular shape models were customized to CMR images from 84 rTOF patients. A statistical atlas of end-diastolic shape was constructed using principal component analysis. Multivariate regression was used to quantify shape mode and imaging index associations with subsequent intervention status (PVR, n = 48 vs. No-PVR, n = 36), while accounting for confounders. Clustering analysis was used to test the ability of the most significant shape modes and imaging indices to discriminate PVR status as evaluated by a Matthews correlation coefficient (MCC). Geometric strain analysis was also conducted to assess shape mode associations with systolic function. PVR status correlated significantly with shape modes associated with right ventricular (RV) apical dilation and left ventricular (LV) dilation (p < 0.01), RV basal bulging and LV conicity (p < 0.05), and pulmonary valve dilation (p < 0.01). PVR status also correlated significantly with RV ejection fraction (p < 0.05) and correlated marginally with LV end-systolic volume index (p < 0.07). Shape modes discriminated subsequent PVR better than standard imaging indices (MCC = 0.49 and MCC = 0.28, respectively) and were significantly associated with RV and LV radial systolic strain. Biventricular shape modes discriminated differences between patients who did and did not require subsequent PVR better than standard imaging indices in current use. These regional features of cardiac morphology may provide insight into adaptive vs. maladaptive types of structural remodeling and point toward an improved quantitative, patient-specific assessment tool for clinical use.

Effect of sedative premedication with oral midazolam on postanesthesia care unit delirium in older adults: a secondary analysis following an uncontrolled before-after design

BACKGROUND

Sedative premedication with benzodiazepines has been linked with prolonged recovery and inadequate emergence during the immediate postoperative period. We aimed to analyze the association between postanesthesia care unit (PACU) delirium and sedative premedication with oral midazolam.

METHODS

We performed a secondary analysis of prospectively collected data before (midazolam cohort) and after (non-midazolam cohort) implementation of a restrictive strategy for oral premedication with midazolam. From March 2015 until July 2018, we included patients 60 years and older, who underwent elective radical prostatectomy for prostate cancer. Exclusion criteria were contraindications to premedication with midazolam, preoperative anxiety, and a history of neurological disorders. Patients, who were scheduled for postoperative admission to the intensive care unit, were excluded. Between 2015 and 2016, patients received 7.5 mg oral midazolam preoperatively (midazolam cohort). Patients included between 2017 and 2018 did not receive any sedative medication preoperatively (non-midazolam cohort). The primary endpoint was the incidence of PACU delirium.

RESULTS

PACU delirium rates were 49% in the midazolam cohort (n = 214) and 33% in the non-midazolam cohort (n = 218). This difference was not statistically significant on multivariable logistic regression analysis (OR 0.847 [95% CI 0.164; 4.367]; P = 0.842). Age (OR 1.102 [95% CI 1.050; 1.156]; P < 0.001), the cumulative dose of sufentanil (OR 1.014 [95% CI 1.005; 1.024]; P = 0.005), and propofol-sufentanil for anesthesia maintenance (OR 2.805 [95% CI 1.497; 5.256]; P = 0.001) were significantly associated with PACU delirium.

CONCLUSION

Midazolam for sedative premedication was not significantly associated with PACU delirium. The reduction in the incidence of PACU delirium throughout the study period may be attributable to improvements in perioperative management other than a more restrictive preoperative benzodiazepine administration.

Immune-based combinations for metastatic triple negative breast cancer in clinical trials: current knowledge and therapeutic prospects

INTRODUCTION

Immune checkpoint inhibitor (ICI) monotherapy appears to be effective in a small cohort of patients with metastatic triple negative breast cancer (mTNBC). This supports the exploration of strategies for increasing the efficacy of immunotherapy. To enhance overall response and clinical outcomes, several immune-based combinations are being investigated.

AREAS COVERED

The authors present a synopsis of current, state-of-art immune-based combinations in this setting and reflect on future possibilities. They shed light on recently presented and published clinical trials and ongoing studies. A literature search was conducted in October 2021; in addition, abstracts of international cancer meetings were reviewed.

EXPERT OPINION

Clinical trials suggest that ICI monotherapy could be beneficial in a minority of mTNBC patients; conversely, several immune-based combinations have reported notable results in recently presented or published studies. Some of these combination strategies have been approved for mTNBC - as in the case of chemoimmunotherapy in PD-L1 positive patients. Numerous trials are investigating novel ICI-based combinations and their results are eagerly awaited.

The biology of papillomavirus PDZ associations: what do they offer papillomaviruses?

The high-risk α-type papillomaviruses have a C-terminal PDZ-binding motif (PBM) on one of the two major oncoproteins E6 or E7; the vast majority on E6. The PBM is essential for the high-risk HPV life cycle, for episomal maintenance of the virus genome, and for maintaining the mitotic stability of the infected cell. The question is why only these viruses have PBMs - are there specific constraints imposed by the mucosal epithelium in which these viruses replicate? However the low-risk α-HPVs, such as HPV-6 and HPV-11 replicate extremely efficiently without a PBM, while viruses of the alpha8 group, such as HPV-40, replicate well with a very primitive PBM. So what does PDZ-binding capacity contribute to the fitness of the virus?

Human papillomaviruses: diversity, infection and host interactions

Human papillomaviruses (HPVs) are an ancient and highly successful group of viruses that have co-evolved with their host to replicate in specific anatomical niches of the stratified epithelia. They replicate persistently in dividing cells, hijack key host cellular processes to manipulate the cellular environment and escape immune detection, and produce virions in terminally differentiated cells that are shed from the host. Some HPVs cause benign, proliferative lesions on the skin and mucosa, and others are associated with the development of cancer. However, most HPVs cause infections that are asymptomatic and inapparent unless the immune system becomes compromised. To date, the genomes of almost 450 distinct HPV types have been isolated and sequenced. In this Review, I explore the diversity, evolution, infectious cycle, host interactions and disease association of HPVs.

TRIMs: selective recruitment at different steps of the NF-κB pathway-determinant of activation or resolution of inflammation

TNF-α-induced NF-κB pathway is an essential component of innate and adaptive immune pathway, and it is tightly regulated by various post-translational modifications including ubiquitination. Oscillations in NF-κB activation and temporal gene expression are emerging as critical determinants of inflammatory response, however, the regulators of unique outcomes in different patho-physiological conditions are not well understood. Tripartite Motif-containing proteins (TRIMs) are RING domain-containing E3 ligases involved in the regulation of cellular homeostasis, metabolism, cell death, inflammation, and host defence. Emerging reports suggest that TRIMs are recruited at different steps of TNF-α-induced NF-κB pathway and modulate via their E3 ligase activity. TRIMs show synergy and antagonism in the regulation of the NF-κB pathway and also regulate it in a feedback manner. TRIMs also regulate pattern recognition receptors (PRRs) mediated inflammatory pathways and may have evolved to directly regulate a specific arm of immune signalling. The review emphasizes TRIM-mediated ubiquitination and modulation of TNF-α-regulated temporal and NF-κB signaling and its possible impact on unique transcriptional and functional outcomes.

Does Covera-19 know 'when to hold 'em or 'when to fold 'em? A translational thought experiment

The function of proteins depends on their structure. The structural integrity of proteins is dynamic and depends on interacting nearby neighboring moieties that influence their properties and induce folding and structural changes. The conformational changes induced by these nearby neighbors in the micro-environmental milieu at that moment are guided by chemical or electrical bonding attractions. There are few literature references that describe the potential for environmental milieu changes to disfavor SARS-CoV-2 attachment to a receptor for survival outside of a host. There are many studies on the effects of pH (acid and base balance) supporting its importance for protein structure and function, but few focus on pH role in extracellular or intracellular protein or actionable requirements of Covera-19. 'Fold 'em or Hold 'em' is seen by the various functions and effects of furin as it seeks an acidic milieu for action or compatible amino acid sequences which is currently aided by its histidine component and the structural changes of proteins as they enter or exit the host. Questions throughout the text are posed to focus on current thoughts as reviewing applicable COVID-19 translational research science in order to understand the complexities of Covid-19. The pH needs of COVID-19 players and its journey through the human host and environment as well as some efficacious readily available repurposed drugs and out-of-the box and easily available treatments are reviewed.

Impact of pulmonary valve replacement on left ventricular rotational mechanics in repaired tetralogy of Fallot

BACKGROUND

In repaired tetralogy of Fallot (rTOF), abnormal left ventricular (LV) rotational mechanics are associated with adverse clinical outcomes. We performed a comprehensive analysis of LV rotational mechanics in rTOF patients using cardiac magnetic resonance (CMR) prior to and following surgical pulmonary valve replacement (PVR).

METHODS

In this single center retrospective study, we identified rTOF patients who (1) had both a CMR ≤ 1 year before PVR and ≤ 5 years after PVR, (2) had no other intervening procedure between CMRs, (3) had a body surface area > 1.0 m2 at CMR, and (4) had images suitable for feature tracking analysis. These subjects were matched to healthy age- and sex-matched control subjects. CMR feature tracking analysis was performed on a ventricular short-axis stack of balanced steady-state free precession images. Measurements included LV basal and apical rotation, twist, torsion, peak systolic rates of rotation and torsion, and timing of events. Associations with LV torsion were assessed.

RESULTS

A total of 60 rTOF patients (23.6 ± 7.9 years, 52% male) and 30 healthy control subjects (20.8 ± 3.1 years, 50% male) were included. Compared with healthy controls, rTOF patients had lower apical and basal rotation, twist, torsion, and systolic rotation rates, and these parameters peaked earlier in systole. The only parameters that were correlated with LV torsion were right ventricular (RV) end-systolic volume (r = - 0.28, p = 0.029) and RV ejection fraction (r = 0.26, p = 0.044). At a median of 1.0 year (IQR 0.5-1.7) following PVR, there was no significant change in LV rotational parameters versus pre-PVR despite reductions in RV volumes, RV mass, pulmonary regurgitation, and RV outflow tract obstruction.

CONCLUSION

In this comprehensive study of CMR-derived LV rotational mechanics in rTOF patients, rotation, twist, and torsion were diminished compared to controls and did not improve at a median of 1 year after PVR despite favorable RV remodeling.

Incorporating Machine Learning into Established Bioinformatics Frameworks

The exponential growth of biomedical data in recent years has urged the application of numerous machine learning techniques to address emerging problems in biology and clinical research. By enabling the automatic feature extraction, selection, and generation of predictive models, these methods can be used to efficiently study complex biological systems. Machine learning techniques are frequently integrated with bioinformatic methods, as well as curated databases and biological networks, to enhance training and validation, identify the best interpretable features, and enable feature and model investigation. Here, we review recently developed methods that incorporate machine learning within the same framework with techniques from molecular evolution, protein structure analysis, systems biology, and disease genomics. We outline the challenges posed for machine learning, and, in particular, deep learning in biomedicine, and suggest unique opportunities for machine learning techniques integrated with established bioinformatics approaches to overcome some of these challenges.

Challenges in the prevention or treatment of RSV with emerging new agents in children from low- and middle-income countries

INTRODUCTION

Respiratory syncytial virus (RSV) causes approximately 120,000 deaths annually in children <5 years, with 99% of fatalities occurring in low- and middle-income countries (LMICs).

AREAS COVERED

There are numerous RSV interventions in development, including long-acting monoclonal antibodies, vaccines (maternal and child) and treatments which are expected to become available soon. We reviewed the key challenges and issues that need to be addressed to maximize the impact of these interventions in LMICs. The epidemiology of RSV in LMICs was reviewed (PubMed search to 30 June 2020 inclusive) and the need for more and better-quality data, encompassing hospital admissions, community contacts, and longer-term respiratory morbidity, emphasized. The requirement for an agreed clinical definition of RSV lower respiratory tract infection was proposed. The pros and cons of the new RSV interventions are reviewed from the perspective of LMICs.

EXPERT OPINION

We believe that a vaccine (or combination of vaccines, if practicable) is the only viable solution to the burden of RSV in LMICs. A coordinated program, analogous to that with polio, involving governments, non-governmental organizations, the World Health Organization, the manufacturers and the healthcare community is required to realize the full potential of vaccine(s) and end the devastation of RSV in LMICs.

Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses

The ongoing COVID-19 pandemic is an urgent, global threat. Here we analyze the genome of the virus that causes COVID-19, SARS-CoV-2, along with other members of the coronavirus family. Our analysis identifies crucial genomic features that are unique to SARS-CoV-2 and two other deadly coronaviruses, SARS-CoV and MERS-CoV. These features correlate with the high fatality rate of these coronaviruses as well as their ability to switch hosts from animals to humans. The identified features could represent crucial elements of coronavirus virulence, and allow for detecting animal coronaviruses that have the potential to make the jump to humans in the future.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses an immediate, major threat to public health across the globe. Here we report an in-depth molecular analysis to reconstruct the evolutionary origins of the enhanced pathogenicity of SARS-CoV-2 and other coronaviruses that are severe human pathogens. Using integrated comparative genomics and machine learning techniques, we identify key genomic features that differentiate SARS-CoV-2 and the viruses behind the two previous deadly coronavirus outbreaks, SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), from less pathogenic coronaviruses. These features include enhancement of the nuclear localization signals in the nucleocapsid protein and distinct inserts in the spike glycoprotein that appear to be associated with high case fatality rate of these coronaviruses as well as the host switch from animals to humans. The identified features could be crucial contributors to coronavirus pathogenicity and possible targets for diagnostics, prognostication, and interventions.

A unique insert in the genomes of high-risk human papillomaviruses with a predicted dual role in conferring oncogenic risk

The differences between high risk and low risk human papillomaviruses (HR-HPV and LR-HPV, respectively) that contribute to the tumorigenic potential of HR-HPV are not well understood but can be expected to involve the HPV oncoproteins, E6 and E7. We combine genome comparison and machine learning techniques to identify a previously unnoticed insert near the 3’-end of the E6 oncoprotein gene that is unique to HR-HPV. Analysis of the insert sequence suggests that it exerts a dual effect, by creating a PDZ domain-binding motif at the C-terminus of E6, as well as eliminating the overlap between the E6 and E7 coding regions in HR-HPV. We show that, as a result, the insert might enable coupled termination-reinitiation of the E6 and E7 genes, supported by motifs complementary to the human 18S rRNA. We hypothesize that the added functionality of E6 and positive regulation of E7 expression jointly account for the tumorigenic potential of HR-HPV.