Seasonal effects decouple SARS-CoV-2 haplotypes worldwide

Background: Variants of concern (VOCs) have been replacing each other during the still rampant COVID-19 pandemic. As a result, SARS-CoV-2 populations have evolved increasingly intricate constellations of mutations that often enhance transmissibility, disease severity, and other epidemiological characteristics. The origin and evolution of these constellations remain puzzling. Methods: Here we study the evolution of VOCs at the proteome level by analyzing about 12 million genomic sequences retrieved from GISAID on July 23, 2022. A total 183,276 mutations were identified and filtered with a relevancy heuristic. The prevalence of haplotypes and free-standing mutations was then tracked monthly in various latitude corridors of the world. Results: A chronology of 22 haplotypes defined three phases driven by protein flexibility-rigidity, environmental sensing, and immune escape. A network of haplotypes illustrated the recruitment and coalescence of mutations into major VOC constellations and seasonal effects of decoupling and loss. Protein interaction networks mediated by haplotypes predicted communications impacting the structure and function of proteins, showing the increasingly central role of molecular interactions involving the spike (S), nucleocapsid (N), and membrane (M) proteins. Haplotype markers either affected fusogenic regions while spreading along the sequence of the S-protein or clustered around binding domains. Modeling of protein structure with AlphaFold2 showed that VOC Omicron and one of its haplotypes were major contributors to the distortion of the M-protein endodomain, which behaves as a receptor of other structural proteins during virion assembly. Remarkably, VOC constellations acted cooperatively to balance the more extreme effects of individual haplotypes. Conclusions: Our study uncovers seasonal patterns of emergence and diversification occurring amid a highly dynamic evolutionary landscape of bursts and waves. The mapping of genetically-linked mutations to structures that sense environmental change with powerful ab initio modeling tools demonstrates the potential of deep-learning for COVID-19 predictive intelligence and therapeutic intervention.

The emergence of SARS-CoV-2 variants of concern in Australia by haplotype coalescence reveals a continental link to COVID-19 seasonality

SARS-CoV-2 continues to evolve, even after implementation of public-wide vaccination, as can be observed by an increasing number of mutations over time. Compared to responses by the United States and European countries, the disease mitigation strategies employed by the Australian government have been swift and effective. This provides a unique opportunity to study the emergence of variants of concern (VOCs) at many latitude levels in a country that has been able to control infection for the majority of the pandemic. In the present study, we explored the occurrence and accumulation of major mutations typical of VOCs in different regions of Australia and the effects that latitude has on the establishment of VOC-induced disease. We also studied the constellation of mutations characteristic of VOCs to determine if the mutation sets acted as haplotypes. Our goal was to explore processes behind the emergence of VOCs as the viral disease progresses towards becoming endemic. Most reported COVID-19 cases were in largest cities located within a -30°S to - 50°S latitude corridor previously identified to be associated with seasonal behavior. Accumulation plots of individual amino acid variants of major VOCs showed that the first major haplotypes reported worldwide were also present in Australia. A classification of accumulation plots revealed the existence of 18 additional haplotypes associated with VOCs alpha, delta and omicron. Core mutant constellations for these VOCs and curve overlaps for variants in each set of haplotypes demonstrated significant decoupling patterns, suggesting processes of emergence. Finally, construction of a "haplotype network" that describes the viral population landscape of Australia throughout the COVID-19 pandemic revealed significant and unanticipated seasonal patterns of emergence and diversification. These results provide a unique window into our evolutionary understanding of a human pathogen of great significance. They may guide future research into mitigation and prediction strategies for future VOCs.

The seasonal behaviour of COVID-19 and its galectin-like culprit of the viral spike

Seasonal behaviour is an attribute of many viral diseases. Like other 'winter' RNA viruses, infections caused by the causative agent of COVID-19, SARS-CoV-2, appear to exhibit significant seasonal changes. Here we discuss the seasonal behaviour of COVID-19, emerging viral phenotypes, viral evolution, and how the mutational landscape of the virus affects the seasonal attributes of the disease. We propose that the multiple seasonal drivers behind infectious disease spread (and the spread of COVID-19 specifically) are in 'trade-off' relationships and can be better described within a framework of a 'triangle of viral persistence' modulated by the environment, physiology, and behaviour. This 'trade-off' exists as one trait cannot increase without a decrease in another. We also propose that molecular components of the virus can act as sensors of environment and physiology, and could represent molecular culprits of seasonality. We searched for flexible protein structures capable of being modulated by the environment and identified a galectin-like fold within the N-terminal domain of the spike protein of SARS-CoV-2 as a potential candidate. Tracking the prevalence of mutations in this structure resulted in the identification of a hemisphere-dependent seasonal pattern driven by mutational bursts. We propose that the galectin-like structure is a frequent target of mutations because it helps the virus evade or modulate the physiological responses of the host to further its spread and survival. The flexible regions of the N-terminal domain should now become a focus for mitigation through vaccines and therapeutics and for prediction and informed public health decision making.

Cardiology cathlab-based management of thrombotic carotid stenoses in acute ischaemic stroke: tools, techniques, local stroke unit collaboration, challenges and patient outcomes

Background

Shortage of endovascular operators able to deliver thrombectomy in acute ischemic stroke (AIS) on a 24/7/365 basis is a main challenge in health care settings around the world. Another fundamental barrier is getting multispecialy teams to work collaboratively with each other in AIS as is already done (albeit on an elective rather than acute basis) in managing stroke mechanistic pathologies such as AFib (pharmacology/ablation) or PFO (diagnosis/closure).

Purpose

To present accumulating experience en route to a full interventional stroke service on the basis of a cardiac cathlab and local multi-specialty collaboration.

Methods

Withn the PARADIGM-EXTEND (symptomatic and increased-stroke-risk asymptomatic carotid stenosis) all-comer study we have treated, on an emergent basis, 21 patients (15 men, age 58–83 years, median 68 years) with AIS caused by severe carotid artery stenoses. All cases were performed as part of our pathway towards a full 24/7 thrombectomy stroke service.

Results

All lesions (100%) were thrombotic (mobile thrombus - 29%; one was a thrombotic total occusion). Proximal neuroprotection (flow reversal using a CCA±ECA balloon) with thrombus aspiration was used in 19/21 patients (90.5%; in ICA total thrombotic occlusion TigerTrieverXL was used). In 2 patients proximal system use was unfeasible. All cases were done under ACT control and using, consistent with the PARADIGM-EXTEND protocol, the MicroNET-covered embolic prevention stent system (CGuard) that was routinely optimized with large balloons/high pressures.

There were no procedure- or device-related complications. TIMI/TICI-3 was achieved in all cases. Embolism-to-infarct territory was 0% and embolism-to-new territory was 0%. Vascular access closure device use was 76%. A 30-day good clinical outcome (mRS of 0–2) rate was 95.2%. One patient with thrombotic near-occlusion, in whom crescendo stroke episodes superimposing the baseline late presentation event necessitated treatment, had a haemorrhagic stroke transformation on day 2 that finally led to death. By 30 days no new stroke, stent thrombosis, myocardial infarction or other SAE occurred.

Conclusion

Cardiologists skilled in carotid interventions are naturally positioned to deliver AIS treatment. 24/7 interventional services and networks for AMI have long been established and, as demonstrated in our centre, the services and skills can be translated -in collaboration with a local stroke unit/neurology- to AIS. Breaking away from traditionally-perceived “territories” towards working as a multispecialy AIS team is a logical concept that provides an effective healthcare solution for large numbers of stroke patients currently needing -and not receving- thrombectomy. Working hand in hand with neurology and radiology in managing acute carotid syndromes is thus part of a natural evolution towards full interventional stroke services, including thrombectomy, in the cardiology cathlab.

Funding Acknowledgement

Type of funding sources: Public hospital(s). Main funding source(s): John Paul II Hospital in Krakow and Jagiellonian University

Identifying False Human Papillomavirus (HPV) Vaccine Information and Corresponding Risk Perceptions From Twitter: Advanced Predictive Models

Background

The vaccination uptake rates of the human papillomavirus (HPV) vaccine remain low despite the fact that the effectiveness of HPV vaccines has been established for more than a decade. Vaccine hesitancy is in part due to false information about HPV vaccines on social media. Combating false HPV vaccine information is a reasonable step to addressing vaccine hesitancy.

Objective

Given the substantial harm of false HPV vaccine information, there is an urgent need to identify false social media messages before it goes viral. The goal of the study is to develop a systematic and generalizable approach to identifying false HPV vaccine information on social media.

Methods

This study used machine learning and natural language processing to develop a series of classification models and causality mining methods to identify and examine true and false HPV vaccine–related information on Twitter.

Results

We found that the convolutional neural network model outperformed all other models in identifying tweets containing false HPV vaccine–related information (F score=91.95). We also developed completely unsupervised causality mining models to identify HPV vaccine candidate effects for capturing risk perceptions of HPV vaccines. Furthermore, we found that false information contained mostly loss-framed messages focusing on the potential risk of vaccines covering a variety of topics using more diverse vocabulary, while true information contained both gain- and loss-framed messages focusing on the effectiveness of vaccines covering fewer topics using relatively limited vocabulary.

Conclusions

Our research demonstrated the feasibility and effectiveness of using predictive models to identify false HPV vaccine information and its risk perceptions on social media.

Cardiology cathlab-based management of thrombotic carotid stenoses in acute ischaemic stroke en route to full interventional stroke service: tools, techniques, challenges and patient outcomes

Background

Shortage of endovascular operators able to deliver manual thrombectomy in acute ischemic stroke (AIS) on a 24/7/365 basis is a main challenge in many health care settings around the world. Another fundamental barrier is getting multispecialy teams to work collaboratively with each other in AIS as is already done (albeit on an elective rather than acute basis and in absence of “territorial” issues) in managing stroke mechanistic pathologies such as atrial fibrillation (pharmacology/ablation) or PFO (diagnosis/closure).

Purpose

To establish a practical path towards a clinically and orranizationally effective cardiology cathlab-based acute ischaemic stroke service, including intracranial manual thrombectomy, in a large multi-specialty hospital with a high-volume stroke unit but absence of neuroradiology service.

Methods

Withn a symptomatic and increased-stroke-risk asymptomatic carotid stenosis all-comer endovascular revascularization study (NeuroVascular Team decision-making) we have treated, on an emergent basis, 17 patients (13 men, age 58–75 years, median 67 years) with AIS caused by severe thrombotic carotid artery stenoses. All cases were performed as part of our pathway towards a full 24/7 thrombectomy stroke service.

Results

All lesions (100%) were thrombotic (mobile thrombus - 29%). Proximal neuroprotection (flow reversal using a common carotid artery±external carotid artery occlusive balloon/s) was used in 15/17 patients (88%). In 2 patients (12%) filter protection was applied as proximal system use was unfeasible for anatomic or clinical reasons. All cases were done under activated clotting time control and using a micronet-covered embolic prevention stent system that was routinely optimized -under an effective neuroprotection- with large balloons/high pressures. There were no procedure- or device-related complications. TIMI/TICI-3 was achieved in all cases.

Vascular access closure device use was 76%.

A 30-day good clinical outcome (mRS of 0–2) rate was 94%. One patient had a haemorrhagic stroke transformation that finally led to death. By 30 days no new stroke, stent thrombosis, myocardial infarction or other SAE occurred

Conclusions

Cardiologists skilled in carotid interventions are naturally positioned to deliver AIS treatment. 24/7 interventional services and networks for acute myocardial infarction have long been established and, as demonstrated in our centre, the services and skills can be translated -in collaboration with a local stroke unit/neurology- to AIS.

Breaking away from traditionally-perceived “territories” towards working as a multispecialy AIS team is a logical concept that provides an effective healthcare solution for large numbers of stroke patients currently needing -and not receving- thrombectomy.

Working hand in hand with neurology and radiology in managing acute carotid syndromes is thus part of a natural evolution towards full interventional stroke services including thrombectomy.

Funding Acknowledgement

Type of funding source: Public Institution(s). Main funding source(s): Jagiellonian University Medical College

Long-term outcomes of the micronet-covered stent system routine use for carotid revsacularization in stroke prevention: PARADIGM-Extend 5 year evidence

Background

Diffusion-weighted magnetic resonance imaging indicates that micronet-covered embolic prevention stent system effectively minimizes peri-procedural and prevents lesion-related post-procedural cerebral embolism in carotid artery stenting but long-term clinical evidence is missing.

Purpose

To provide long-term clinical and duplex ultrasound evaluation of safety and efficacy of the system use in consecutive carotid revascularization patients.

Methods

PARADIGM-EXTEND is in all-comer, all-referrals-tracked study with no exclusion criteria other than lack of NeuroVascular Team-determined indication. Clinically asymptomatic patients receive revascularization only in case of increased-stroke-risk characteristics. Adverse events are independently adjudicated.

Results

Currently 451 patients (48–87 years, 59% symptomatic, 127 women) with 490 arteries crossed the first follow-up window of 30 days. There has been 100% micronet-covered embolic prevention stent system use (ie, no other stent type/s used throughout study). Proximal/distal intra-procedural neuroprotection use was 38.3%/61.7%. Large balloon/high-pressure stent optimization was routine, leading to a single-digit (mean 6.9%) residual diameter stenosis. Independent neurologist and duplex evaluation are before and after revascularization (48h and 30 days, then yearly).

Peri-procedural death or major ischemic stroke rate was 0%. One event (prior infarct scar asymptomatic extension in prolonged hypotension course) was adjudicated as minor stroke (0.22%), and there was 1 periprocedural MI (type 2, in 2-vessel non-revascularizable CTO; 0.22%).

By 30 days there were no further ischaemic strokes (0%) but there was 1 haemorrhagic transformation that led to death (0.22%) and 1 bleeding-related death (0.22%). Thus total 30-day death/stroke was 0.66%, and total death/stroke/MI was 0.88%.

By 60 months there were 3 contralateral, 1 ipsilateral (device-unrelated), and 2 posterior circulation strokes. Baseline internal carotid artery velocities were 3.72±1.25 and 0.63±0.69 m/s (peak-systolic and end-diastolic). Post-procedural in-stent velocities were normal and remained normal throughout the 60-month follow-up period: 0.78±040 and 0.21±0.10 (1y); 0.75±0.36 0.19±0.09 (2y); 0.75±0,35 and 0.21±0.09 (3y); 0.72±0.27 and 0.20±0.07 (4y); 0.79±0.58 and 0.21±0.11m/s (5y).

There were 2 in-stent restenoses by 1y (including 1 that occurred with de novo neck radiotherapy) and 1 other by 2y (total 2y in-stent restenosis of 1.1%) but no further ones (0% in-stent restenosis at 2–5y).

Conclusions

PARADIGM-Extend long-term clinical and duplex ultrasound evidence is consistent with normal healing and sustained safety and stroke prevention efficacy of the micronet-covered embolic prevention stent system used routinely, on top of optimized medical therapy, for stroke prevention in symptomatic and increased-stroke-risk asymptomatic subjects with carotid stenosis recommended for revasularization by the NeuroVascular Team.

Funding Acknowledgement

Type of funding source: Public Institution(s). Main funding source(s): Jagiellonian University Medical College

New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release

The massive worldwide spread of the SARS-CoV-2 virus is fueling the COVID-19 pandemic. Since the first whole-genome sequence was published in January 2020, a growing database of tens of thousands of viral genomes has been constructed. This offers opportunities to study pathways of molecular change in the expanding viral population that can help identify molecular culprits of virulence and virus spread. Here we investigate the genomic accumulation of mutations at various time points of the early pandemic to identify changes in mutationally highly active genomic regions that are occurring worldwide. We used the Wuhan NC_045512.2 sequence as a reference and sampled 15 342 indexed sequences from GISAID, translating them into proteins and grouping them by month of deposition. The per-position amino acid frequencies and Shannon entropies of the coding sequences were calculated for each month, and a map of intrinsic disorder regions and binding sites was generated. The analysis revealed dominant variants, most of which were located in loop regions and on the surface of the proteins. Mutation entropy decreased between March and April of 2020 after steady increases at several sites, including the D614G mutation site of the spike (S) protein that was previously found associated with higher case fatality rates and at sites of the NSP12 polymerase and the NSP13 helicase proteins. Notable expanding mutations include R203K and G204R of the nucleocapsid (N) protein inter-domain linker region and G251V of the viroporin encoded by ORF3a between March and April. The regions spanning these mutations exhibited significant intrinsic disorder, which was enhanced and decreased by the N-protein and viroporin 3a protein mutations, respectively. These results predict an ongoing mutational shift from the spike and replication complex to other regions, especially to encoded molecules known to represent major β-interferon antagonists. The study provides valuable information for therapeutics and vaccine design, as well as insight into mutation tendencies that could facilitate preventive control.

3048PARADIGM-Extend prospective academic trial: Accumulating long-term evidence for MicroNet-covered stent safety and stroke prevention efficacy

Aims

To provide long-term clinical (incl neurologic) and duplex ultrasound (DUS) evaluation of the CGuard MicroNet-covered embolic prevention stent system (EPS) routine use to perform CAS in all-comer (no exclusion criteria) patients with symptomatic or increased-stroke-risk asymptomatic carotid stenosis recommended for revascularization by the NeuroVascular Team.

Methods and results

PARADIGM-Extend is a non-industry-funded, prospective academic study in all-referrals-tracked symptomatic and asymptomatic carotid stenosis. In asymptomatic lesions, intervention is mandated only in case of increased-stroke-risk features. There is first-line consideration to use the study device, with EPD choice according to tailored-CAS algorithm. Independent neurologist evaluation and DUS are performed before CAS, at 48h, 30 days, and then every 12 months. There is external source data verification, external angiographic corelab, and external statistical analysis. Currently 325 patients (48–87 years, 54.2% symptomatic) crossed the 1st follow-up window. There has been 100% CGuardEPS use. Angiographic DS was reduced from 84±8% to only 6.9±5% (p<0.001, “CEA-like” effect of CAS).

Peri-procedural death or major stroke rate was 0%. One event was CEC-adjudicated as minor stroke (0.3%), and there was one (type2) MI (0.3%). By 30 days there was one haemorrhagic transformation leading to death (0.3%) and one bleeding-related death (0.3%). Thus total death/major stroke/minor stroke rate at 30 days was 0.9%, and total death/major stroke/minor stroke/MI rate at 30 days was 1.2%. At 1- 12 months were no strokes or stroke-related deaths (0%). At 12–24 months there was one cerebellar stroke in an AFib patient that was confirmed on MRI imaging but no carotid-territory stroke or stroke deaths (0%). By 24 and 36 months there was one posterior circulation (cerebellal) infarct but no cerebral infarctions. Post-procedural in-stent velocities were normal and remained normal throughout the 36-month follow-up period (peak-systolic/end-diastolic velocity 0.69±0.29/0.18±0.09 m/s at 30 days, 0.82±0.47/0.22±0.13m/s at 12 months, 0.73±0.31/0.19±0.09m/s at 24months and 0.80±0.31/0.21±0.11 at 24months), indicating normal device healing.

Conclusions

PARADIGM-Extend accumulating 36-month clinical and DUS evidence is consistent with unprecedented, sustained safety and cerebral embolism prevention efficacy of the CGuard™ MicroNET-covered embolic prevention stent system used routinely for stroke prevention in symptomatic and increased-stroke-risk asymptomatic subjects with carotid stenosis.

Acknowledgement/Funding

K/ZDS/007819 Jagiellonian University Medical College

Evaluation of mandibular bone structure with radio-visiographic method--its usefulness for diagnostic purposes

The noninvasive assessment of the mandible bone structure can be, beside the indices of mineral density and content of mineral elements, the source of valuable information of diagnostic and prognostic importance. The presented examinations aimed at working out a computer program of radiovisiographic picture analysis of the mandible bone, which, on the basis of radiological trabecula algorithm, would enable finding out parameters determining mean number of trabeculas per 1 mm2 of the analysed area, density expressed in percentage of the area covered with trabeculas, mean width and height of radiological trabeculas, and several calculable derivative indices. On the basis of the above mentioned program there was made an analysis of radiovisiograms of 130 patients with diagnosed osteoporosis and of 110 patients without osteoporosis, treated in the Department and Clinic of Dental and Maxillofacial Surgery, Medical University of Lublin. Slight differences conditioned by sex and age of the patients as well as significant changes in structural indices in patients with generalized osteoporosis were found. The performed tests show that standardized radiovisiographic examinations of mandibular bones completed with computer structure analysis by Radiograph Workshop program can be helpful in diagnostic of osseous changes in mandibular bones.

The case of low symptoms carotid cavernous fistula

The authors describe the case of a patient with posttraumatic carotid cavernous sinus fistula with a complex of low clinical syndromes. Attention was drawn to oligosymptomatic fistula causing diagnostic difficulties in maxillofacial surgery practice. The study presents diagnostic and treatment methods and their results.

Iron content in rats' teeth in glucocorticoid-induced osteoporosis

On the basis of atomic absorption spectrophotometry rat teeth iron levels in glucocorticoid-induced osteoporosis were measured. Hydrocortisone caused decreasing of the iron level in rat teeth after both 4 and 8 weeks of the duration of the experiment. The other drugs used in osteoporosis treatment (calcium and calcitonin) administered together with hydrocortisone or separately also influenced the content of this ion in rats' teeth.

The case of the submandibular gland sialolith

The authors describe a case of a sialolith formation in a submandibular gland over 2 years. A large salivary stone is demonstrated radiologically and surgical treatment is described.

Cervicofacial actinomycosis--an issue still present

On the basis of the literature the authors present the etiopathogenesis, entry of the infection and the course of cervicofacial actinomycosis and they describe treatment possibility of patients with actinomycosis. They also concentrate on the present, atypical clinical picture of the disease, especially in the initial period. They find the sanation of the oral cavity is necessary for a complete recovery.

[The evaluation of action of anesthetic drugs: Xylodont and Mepidont]

The aim of the study was to establish the quality of the therapeutical action- of two local anaesthetics Xylodont and Mepidont, produced by MOLTENI pharmaceutical firm. The investigation was performed in 199 patients of our clinic undergoing teeth extractions or other small surgical procedures. The following data were specified in a questionnaire: name of a drug, applied doses, range of anaesthetic effect, kind and duration of a surgical procedure. We also paid the very attention to the systemic side effects of the used drugs. The significant number of surgical procedures (96, 5%) were painless. The application of additional drug was necessary only in few cases. The obtained results show that the tested anaesthetics Xylodont and Mepidont are safe and effectively acting drugs suitable for local anaesthesia.

[Odontogenic mandibular cysts]

In the paper the method is presented of one-step total removal of extensive dentogenous mandibular cysts. The postoperative cavity was covered partly with a flap of regional soft tissue which was fixed with singular sutures and then with an acrylate obturator.