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Modeling emergence and dynamics of new COVID-19 variants in the UK

Jacob Scott

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While the coronavirus disease 19 (COVID-19) pandemic is still ongoing, the global prophylactic vaccination drive has successfully achieved a remarkable milestone with approximately half of the world population having already received at least a first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine dose.


Study: Modelling the interplay of SARS-CoV-2 variants in the United Kingdom. Image Credit: Axel_Kock/Shutterstock


As the virus spreads, its genome replicates creating mutations that lead to virus variants. Several new variants have been identified in the SARS-CoV-2 genome, of which some clinically relevant variants (variants of concern), are transmitted more efficiently than the original ones and that can even cause more severe disease.


The most widely prevalent strains include the ones first detected in the United Kingdom (Alpha or B.1.1.7), South Africa (Beta or B.1.351), Brazil (Gamma or P.1), and India (Delta or B.1.617.2). The emergence of these new COVID-19 variants has resulted in the appearance of fast reinfections and co-infections and has raised doubts about the effectiveness of vaccines.


Given such global impact of the COVID-19 pandemic, a reliable model to analyze the dissemination of SARS-CoV-2 variants is crucial to explore effective mitigation strategies.


Effects of vaccination and non-pharmaceutical measures


In their recent work published on the medRxiv* preprint server, researchers from Argentina and Mexico have presented a geo-stochastic SEIRS-V model that provides a means of accurately describing the dynamics of the pandemic. The model, that reliably analyzes the spread of the different virus variants, has a unique property that it conveniently separates the parameters related to the disease from the ones related to social behavior and mobility restrictions, which enables to explain some global features observed in the daily number of worldwide cases. For instance, the model demonstrates that the surge of periodical waves is not only related to the appearance of new variants but is also associated with varying vaccination and social-distancing schemes.


The team highlighted that,


It consists of an extended compartmental model that includes various strains and vaccination strategies, allowing to study the emergence and dynamics of the new COVID-19 variants”.


The team uses this model to simulate the local dynamics of infection spreading, taking place in each cell of an area of a few km2, with average population density. Global dynamics, considers the geographical spread to neighboring cells and along terrestrial roads or aerial routes; governmental non-pharmaceutical interventions, and social behavior are reflected in the mobility parameters used.


Model application


In the current study, the team applied this model to the case of the United Kingdom (UK) to take advantage of the reliably available data. The information on density map and the main routes of country were extracted. The dynamics of different strains of the virus is very well documented in the UK, consequently the available information suffices to fit the parameters of the model for the different variants. Only the most abundant strains over time namely, EU1 strain (B. 1.177 originated in Europe), the Alpha (B.1.1.7) and the Delta (B.1.617.2) were considered in the adjustment. The rest of the less abundant variants were grouped together under the name “other strains”.



Figure 1: Diagram showing the geo-stochastic model scheme. (A) represents the local dynamics. Susceptible, Recovered, Vaccinated, Exposed and Infected with different strains, are taken into account. Vaccinated people can get infected with a certain variant k with a ?k probability. The exposed, infectious and immune periods for the k- th strain are ?k, ?k and ?k, respectively. The variables vr and ? stand for the vaccination rate and the immunity period conferred by the vaccine. (B) The global dynamics on a geographical area, divided into a grid of cells, is followed by placing a SEIRS-V model on each one and allowing contagions between them. Three mobility processes are considered: movement to neighbor and far cells and thermal noise.

Restricting the spread of the virus


The model predicts for new COVID-19 waves in the future, if highly transmissible, vaccine-resistant variants are present. This would imply the need for new vaccines, including strain-specific proteins. However, mass vaccination is clearly essential to reduce the appearance of new variants of concern and, consequently, the need for those specific vaccines.


If vaccinated people get a mild version of the infection, COVID-19 will turn out to be a common, relatively harmless, influenza-like disease and there will be less susceptible people over time. Under that scenario, mobility restrictions should be applied mainly to contain the spread of new variants of concern and boosters should only be given to high-risk groups in the near future.


The results of the present study seem to imply that the world’s population would probably need to be vaccinated periodically in the years to come.


The team identified the epidemiological parameters which determine the dominant variant i.e. the one possessing a larger transmission coefficient or smaller exposed period before becoming infectious will eventually become dominant. Interestingly, as new variants with higher transmission coefficients appear, they quickly become the prevalent strain.


This model is useful to predict future scenarios, testing pharmaceutical and non-pharmaceutical interventions, and in particular to optimize the timing of vaccination boosters in order to minimize the appearance of new waves of the disease”, the team concludes.



Figure 2: Model results for three different scenarios. Red, green and violet solid lines are the model simulation results under scenarios 1,2 and 3 (see text), respectively. Shaded areas on each color represent the standard deviation from 100 model runs for each scenario. Yellow dash-dot vertical line indicates the day when immunization started. Blue bars and solid orange lines are the actual daily cases and their 7 day rolling average, respectively. In scenario 1, a short vaccination immunity period implies a growth of the daily cases in the near future, if current mobility is sustained. Under scenario 2, people are expected to be immune for a longer time and breakthrough infections will act as antibodies boosters, prolonging the defence against the pandemic. In scenario 3 most people will be immune in the near future, lowering the number of cases, and a new wave would appear when vaccine immunity ends.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:

Barreiro NL, et al. (2021) Modelling the interplay of SARS-CoV-2 variants in the United Kingdom. medRxiv. doi: https://doi.org/10.1101/2021.11.26.21266485 https://www.medrxiv.org/content/10.1101/2021.11.26.21266485v1

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Genetic bottlenecks could impact Wyoming toads’ ability to respond to new pathogens

Jacob Scott

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A new study from North Carolina State University examines immune system diversity in the critically endangered Wyoming toad and finds that genetic bottlenecks could impact a species’ ability to respond to new pathogens. The findings could inform captive breeding strategies for endangered animal populations.

The Wyoming toad, Anaxyrus baxteri, suffered a severe population decline throughout the latter part of the 20th century due to factors including habitat destruction and fungal infection. The toad was brought into a captive breeding program in the 1990s in order to save the species. Scientists estimate a current wild population of only 400 to 1,500 animals, meaning that the toad is considered critically endangered.

Population reduction in this species created a genetic bottleneck to begin with, meaning the level of genetic diversity is already very small. This is the first study to look specifically at genetic diversity in the immune systems of these toads and how it could impact them as a population.”

Jeff Yoder, professor of comparative immunology at NC State and co-corresponding author of paper

Yoder, with co-corresponding author Alex Dornburg of the University of North Carolina at Charlotte, performed RNA sequencing on immune tissues from three healthy, retired Wyoming toad breeders. Study co-author Michael Stoskopf, who was on the Wyoming Toad Recovery Implementation Team established in 2008, obtained the samples.

“We were focused specifically on sequences encoding toll-like receptors – TLRs – and the proteins of the major histocompatibility complex, or MHC, expressed in these tissues,” says Kara Carlson, first author of the study and current Ph.D. candidate at NC State. “These sets of genes are major components of the immune system.”

TLRs are the first responders of the immune system, and are similar, or well-conserved, between species. The MHC, on the other hand, is a large and diverse group of genes that varies between species and individuals. It can determine why one group is more resistant to a particular pathogen than another.

“MHC genes are some of the most rapidly evolving sequences in the genome,” Carlson says. “So in a healthy population there’s a lot of variety that gets passed along to descendants, enabling the species at large to adapt to different pathogens. However, if disease survivors do so because of their MHC, then that group would have a similar MHC.

“The Wyoming toads that were brought into captivity to save the species were all able to resist the fungus that had decimated the population, but that could mean that their immune diversity is reduced.”

The researchers compared the TLR and MHC of the three Wyoming toads to each other, as well as to samples from a common toad and a cane toad. Both the common toad and the cane toad showed more MHC diversity than the Wyoming toad, even though the cane toad underwent a similar genetic bottleneck.

“The small sample size in this study – which was unavoidable due to the endangered status of the toad – nevertheless lays an important framework for conservation,” Carlson says.

“Amphibians in general don’t have as many genomic resources as other organisms,” Yoder says. “And captive breeding from a small population further decreases genetic diversity. But while these toads may be better protected against the fungal infection that nearly wiped them out, they may not be equipped to deal with new pathogens down the road.”

“While we weren’t necessarily surprised by the lack of immunogenic diversity in the Wyoming toad, it does spark an important question,” Dornburg says. “How equipped are other species of conservation concern for a battle with an emergent pathogen?”

“By understanding the genetic diversity of the immune system we can inform captive breeding to increase the chance of a species to resist disease in the wild,” Yoder adds. “Studies like this one are invaluable for captive breeding practices going forward.”

Source:
Journal reference:

Carlson, K.B., et al. (2022) Transcriptome annotation reveals minimal immunogenetic diversity among Wyoming toads, Anaxyrus baxteri. Conservation Genetics. doi.org/10.1007/s10592-022-01444-8.

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Video conferencing hinders creativity

Jacob Scott

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In-person teamwork has now transformed into virtual collaboration due to the COVID-19 pandemic. But does this affect innovation and creativity?

An interesting study on virtual communication led by Dr. Melanie S. Brucks from Columbia University and Prof. Jonathan Levav from Stanford University is published in the journal Nature. The study examines whether videoconferencing affects creative idea generation.

Study: Virtual communication curbs creative idea generation. Image Credit: Andrey_Popov / Shutterstock

Communication and collaboration

Collaboration is essential for several workplace tasks. It leads to innovation and idea generation. Historically, these collaborations have been in-person and required sharing of the same physical space. The use of traditional communication technologies like letters, emails, and phone calls hinder the smooth exchange of information and limits collaboration.

Now, due to advances in audio-visual technology, face-to-face interaction is possible via videoconferencing, allowing virtual collaboration. Videoconferencing has replaced in-person interactions due to pandemic-driven social distancing. Video interaction and in-person interaction allow communication of the same information.

While videoconferencing replacing in-person interaction has been beneficial in the social scenario, does it come with a cost in the workplace scenario? For example, does it affect collaborative idea generation?

Experiments

The investigators performed a Laboratory experiment and a field experiment to test the difference between in-person interaction and videoconferencing in collaborative idea generation. First, they recruited participants and divided them into pairs: half of the pairs were assigned to an in-person setting, and the rest were assigned to a virtual setting.

Laboratory experiment

A total of 602 participants were recruited for the laboratory experiment and divided into pairs. The participants were in separate rooms in the virtual setting and communicated through videoconferencing. The pairs were allotted five minutes to generate creative uses for a frisbee (150 pairs) or bubble wrap (151 pairs) and then one minute to select their most innovative idea.

The pairs were evaluated by counting the number of creative ideas and ideas they generated. The virtual pairs generated significantly fewer total and creative ideas compared to in-person pairs.

So, virtual collaboration hampered creative ideas. This could be because the virtual space narrows the visual scope, which in turn narrows the cognitive scope. To assess the visual focus, two methods were used. Firstly, the participants had to recollect the individual props in the room and point them on a worksheet. Secondly, the participants’ eye gaze was recorded during the experiment.

The virtual pairs narrowed their focus to the screen. Compared to in-person pairs, they spent significantly more time looking directly at their partner and less time looking at the surrounding room, and remembered significantly fewer props in the surrounding room.

As a consequence, the virtual medium narrowed the visual focus and inhibited the generation of ideas.

However, these results are in the context of a controlled laboratory setting.

Field experiment

The experiment was repeated in ‘the field’ under actual work conditions within a large multinational telecommunications company to see if these results could be extrapolated to the real world. The field experiment was conducted in five country sites – in Europe, the Middle East, and South Asia. In this setting, the participants knew their partners and used video conferencing regularly for work. Moreover, it included domain experts highly invested in the outcome of the collaboration.

A total of 1,490 engineers were recruited to participate in an ideation workshop and randomly divided into pairs. The pairs were allotted an hour to generate product ideas and submit one idea as future product innovation for the company.

The engineer pairs who worked on the task virtually generated fewer total ideas and creative ideas than in-person pairs at all five sites.

However, the decision quality was not affected by virtual collaboration. The in-person pairs generated a significantly higher top-scoring idea, but the selected idea did not significantly differ in quality between the virtual pairs and in-person pairs.

Other reasons for reduced creativity

The could be other reasons why virtual collaboration negatively affected idea generation. Therefore, the investigators explored the alternative explanations.

More ideas

Since the in-person collaborators generated more total and creative ideas than the virtual collaborators, they could generate additional ideas similar to each other. However, upon semantic analysis, it was observed that they generated diverse and disconnected ideas.

Feelings of connection and trust

Studies have shown that feelings of connection and trust can foster team creativity. The virtual pairs may have reduced feelings of connection and trust toward their partner.

However, when assessed for subjective feelings of closeness, verbal and non-verbal behaviors, and mimicry, the virtual pairs were similar to in-person pairs in the laboratory experiment.

Thus, virtual and in-person interactions are very similar in terms of social connection or social behavior.

Communication coordination

Usually, there is a lack of coordination in a conversation in virtual interactions due to the absence of eye contact. However, it could not wholly explain the effect of virtual interaction on idea generation.

Interpersonal processes

This study also assessed the effect of interpersonal processes on idea generation. Interpersonal processes fear of evaluation, dominance, social facilitation, social loafing, social sensitivity, perceptions of performance, and production blocking were affected in virtual collaborations and these, in turn, affected idea generation.

Implications of the study

This study supports previous research suggesting that pairs perform better than large groups, both in-person and online. Therefore, this study recommends ideation in pairs and in person. Also, this study suggests that larger videoconferencing screens would not impact idea generation.

In-person collaborations offer a cognitive advantage. Now several workplaces are moving towards a hybrid setup. This study indicates that the creative idea generation should be reserved for in-person meetings.

Journal reference:
Brucks, M.S., Levav, J. (2022) Virtual communication curbs creative idea generation. Nature. https://doi.org/10.1038/s41586-022-04643-y, https://www.nature.com/articles/s41586-022-04643-y

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Gum Health Day 2022 calls for prevention, early detection, and effective treatment of gum diseases

Jacob Scott

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“Treat your gums” is the slogan for Gum Health Day 2022, a worldwide awareness campaign organized by the European Federation of Periodontology (EFP). The event aims to inform the public of the detrimental effects of gum diseases – gingivitis, periodontitis, peri-implant mucositis, and peri-implantitis – on both oral and overall health. The campaign calls for the prevention, early detection, and – where necessary – effective treatment of gum diseases.

Although still poorly acknowledged by the public, gum diseases are chronic inflammatory conditions affecting a high proportion of adults worldwide, causing tooth loss and other problems in the mouth. Crucially, gum diseases are also linked to major systemic health issues including diabetes mellitus, cardiovascular diseases, chronic kidney disease, adverse pregnancy outcomes, rheumatoid arthritis, Alzheimer’s disease, erectile dysfunction, certain forms of cancer, and more severe Covid-19 outcomes. This means that gum diseases and their prevention and treatment are of major importance not only for oral health, but also for the whole body.

This year’s campaign focuses heavily on the treatment part – we know that millions of people suffer from gum diseases that can be treated effectively. ‘Treat your gums’ calls for this treatment – with all the documented positive effects for the mouth and whole body – to actually happen.”

Moritz Kebschull, coordinator of Gum Health Day 2022

That is why the hashtag for the campaign is #TreatYourGums, and why the recent EFP-produced clinical practice guidelines on the treatment of periodontitis are a major part of the Gum Health Day 2022 initiative.

“The new EFP-produced clinical practice guidelines on the treatment of all four stages of periodontitis are a crucial development, as they are the first high-quality international guidelines to outline a structured and easily implemented pathway for the efficient and effective treatment of gum disease,” Prof. Kebschull says. “In a nutshell, gum disease treatment that works!”

He adds: “It is important to underline that gum disease is one of the most widespread chronic diseases in the worldwide adult population, and that it is usually painless, so its early detection and successful treatment depends heavily on how fast the patient takes action.”

A major innovation of Gum Health Day 2022 is an EFP-designed “customized content generator”, a feature that allows the federation’s 37 affiliated national societies of periodontology, their individual members – as well as practices, hospitals, and members of the public – to customise their own Gum Health Day 2022 materials, based on a series of graphic templates and catchphrases.

In the framework of Gum Health Day 2022, the EFP encourages periodontists, dentists, researchers, and other health-related professionals to sign and disseminate the EFP Manifesto: Perio and General Health, an international call to action for the prevention, early detection, and treatment of gum disease. Individuals and organisations are invited to endorse it and join the 1,200+ professionals, dental practices, companies, and universities that have so far supported it.


The European Federation of Periodontology (EFP, ww.efp.org) is a non-profit organization dedicated to promoting awareness of periodontal science and the importance of gum health. Its guiding vision is “periodontal health for a better life.”

Founded in 1991, the EFP is a federation of 37 national periodontal societies that represents more than 16,000 periodontists, dentists, researchers, and oral-health professionals from Europe and around the world. It supports evidence-based science in periodontal and oral health, and it promotes events and campaigns aimed at both professionals and the public.

The EFP organizes EuroPerio, the world’s leading congress in periodontology and implant dentistry, as well as other important professional and expert events such as Perio Master Clinic and Perio Workshop. The annual Gum Health Day on May 12, organized by the EFP and its member societies, brings key messages on gum health to millions of people across the world.

The EFP also organizes workshops and outreach campaigns with its partners: projects to date have covered the relationship between periodontal disease and diabetes, cardiovascular disease, and caries, as well as women’s oral health during pregnancy.

The EFP’s Journal of Clinical Periodontology is the most authoritative scientific publication in this field. The federation also publishes JCP Digest, a monthly digest of research, and the Perio Insight magazine, which features experts’ views and debates.

The EFP’s work in education is also highly significant, notably its accreditation programme for postgraduate education in periodontology and implant dentistry.

The EFP has no professional or commercial agenda.

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