scholarly journals Evolving SARS-CoV-2 variants and mutational cascades

2021 ◽  
Author(s):  
John M Halley ◽  
Despoina Vokou ◽  
Georgios Pappas ◽  
Ioannis Sainis
Keyword(s):  
Exponential Growth ◽  
Systemic Response ◽  
Relevant Research ◽  
Novel Mutations ◽  
Preparedness Planning ◽  
Transmission Parameters ◽  
Novel Variants ◽  
Partial Immunity

The emergence of novel SARS-CoV-2 variants of concern (VOC), in late 2020, with selective transmission advantage and partial immunity escape potential, threatens a pandemic resurgence. The timing of mutational evolution and its limits are thus of paramount importance in preparedness planning. Here, we present a model predicting the pattern of epidemic growth including the emergence of variants through mutation. It is based on the SEIR (Susceptible, Exposed, Infected, Removed) model, but its equations are modifiable according to the transmission parameters of novel variants. Since more transmissible strains will drive a further increase in the number of cases, they will also lead to further novel mutations. As one cannot predict whether there is a viral mutational evolutionary limit, we model a cascade that could lead to hyper-exponential growth involving the emergence of even more transmissible mutants that could overwhelm systemic response. Our results are consistent with the timing, since the beginning of the pandemic, of the concurrent and independent emergence of the VOCs. We examine conditions that favor the expected appearance of similar variants, thus enabling better preparedness and relevant research.

Culture in Virtual Communities

2008 ◽  
pp. 1009-1013
Author(s):  
Li Xiao
Keyword(s):  
Knowledge Sharing ◽  
Sense Of Community ◽  
Exponential Growth ◽  
Virtual Communities ◽  
Cultural Issues ◽  
Relevant Research ◽  
Technological Infrastructure ◽  
Culture Model ◽  
The World ◽  
New Challenges

With exponential growth of virtual communities, more and more studies are carried out to examine how they change people’s life (Bieber et al., 2002; Blanchard & Markus, 2004; Bruckman, 2002; Burnett, 2002; Burnett, Dickey, Kazmer, & Chudoba, 2003). Among those studies, many researchers focus on the architectures and infrastructures to enable knowledge sharing, such as Bieber et al. (2002), Bruckman (2002) and Marshall (2000). The human behavioral side of virtual communities, however, still remains mysterious. While virtual communities are inconceivable without the technological infrastructure and protocols that support them, they are equally inconceivable without human users. It is the users or the sense of community rather than the technologies that give virtual communities their significance (Burnett, 2002). The interactions of users in electronically mediated environments bring up new challenges and questions for researchers. For example, how do we understand culture in virtual communities? What kind of cultural issues are involved in virtual communities? Interacting with people from all over the world, how does one’s national and ethnic culture background influence his or her activities in the virtual communities (Burnett et al., 2003)? The list of questions can go on. This article proposes one possible way to answer the first question of how to understand culture in virtual communities. We argue that the culture model by Schein (1992) can be applied to obtain an understanding of culture in virtual communities. In this article, we first review relevant research on cultural issues in virtual communities. Then we propose that Schein’s model can be applied to understand culture in virtual communities. Next, we analyze the trends for research on the topic and discuss our conclusion.

Culture in Virtual Communities

2011 ◽  
pp. 102-104
Author(s):  
Li Xiao
Keyword(s):  
Knowledge Sharing ◽  
Sense Of Community ◽  
Exponential Growth ◽  
Virtual Communities ◽  
Cultural Issues ◽  
Relevant Research ◽  
Technological Infrastructure ◽  
Culture Model ◽  
The World ◽  
New Challenges

With exponential growth of virtual communities, more and more studies are carried out to examine how they change people’s life (Bieber et al., 2002; Blanchard & Markus, 2004; Bruckman, 2002; Burnett, 2002; Burnett, Dickey, Kazmer, & Chudoba, 2003). Among those studies, many researchers focus on the architectures and infrastructures to enable knowledge sharing, such as Bieber et al. (2002), Bruckman (2002) and Marshall (2000). The human behavioral side of virtual communities, however, still remains mysterious. While virtual communities are inconceivable without the technological infrastructure and protocols that support them, they are equally inconceivable without human users. It is the users or the sense of community rather than the technologies that give virtual communities their significance (Burnett, 2002). The interactions of users in electronically mediated environments bring up new challenges and questions for researchers. For example, how do we understand culture in virtual communities? What kind of cultural issues are involved in virtual communities? Interacting with people from all over the world, how does one’s national and ethnic culture background influence his or her activities in the virtual communities (Burnett et al., 2003)? The list of questions can go on. This article proposes one possible way to answer the first question of how to understand culture in virtual communities. We argue that the culture model by Schein (1992) can be applied to obtain an understanding of culture in virtual communities. In this article, we first review relevant research on cultural issues in virtual communities. Then we propose that Schein’s model can be applied to understand culture in virtual communities. Next, we analyze the trends for research on the topic and discuss our conclusion.

scholarly journals Growth, reproduction numbers and factors affecting the spread of SARS-CoV-2 novel variants of concern in the UK from October 2020 to July 2021: a modelling analysis

BMJ Open ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. e056636
Author(s):  
Thomas Ward ◽  
Alex Glaser ◽  
Alexander Johnsen ◽  
Feng Xu ◽  
Ian Hall ◽  
...  
Keyword(s):  
Growth Rate ◽  
Exponential Growth ◽  
Doubling Time ◽  
Reproduction Number ◽  
Age Groups ◽  
Instantaneous Growth Rate ◽  
Rt Pcr ◽  
Gene Target ◽  
Novel Variants ◽  
The Uk

ObjectivesImportations of novel variants of concern (VOC), particularly B.1.617.2, have become the impetus behind recent outbreaks of SARS-CoV-2. Concerns around the impact on vaccine effectiveness, transmissibility and severity are now driving the public health response to these variants. This paper analyses the patterns of growth in hospitalisations and confirmed cases for novel VOCs by age groups, geography and ethnicity in the context of changing behaviour, non-pharmaceutical interventions (NPIs) and the UK vaccination programme. We seek to highlight where strategies have been effective and periods that have facilitated the establishment of new variants.DesignWe have algorithmically linked the most complete testing and hospitalisation data in England to create a data set of confirmed infections and hospitalisations by SARS-CoV-2 genomic variant. We have used these linked data sets to analyse temporal, geographic and demographic distinctions.Setting and participantsThe setting is England from October 2020 to July 2021. Participants included all COVID-19 tests that included RT-PCR CT gene target data or underwent sequencing and hospitalisations that could be linked to these tests.MethodsTo calculate the instantaneous growth rate for VOCs we have developed a generalised additive model fit to multiple splines and varying day of the week effects. We have further modelled the instantaneous reproduction number Rt for the B.1.1.7 and B.1.617.2 variants and included a doubly interval censored model to temporally adjust the confirmed variant cases.ResultsWe observed a clear replacement of the predominant B.1.1.7 by the B.1.617.2 variant without observing sustained exponential growth in other novel variants. Modelled exponential growth of RT PCR gene target triple-positive cases was initially detected in the youngest age groups, although we now observe across all ages a very small doubling time of 10.7 (95% CI 9.1 to 13.2) days and 8 (95% CI 6.9 to 9.1) days for cases and hospitalisations, respectively. We observe that growth in RT PCR gene target triple-positive cases was first detected in the Indian ethnicity group in late February, with a peak of 0.06 (95% CI 0.07 to 0.05) in the instantaneous growth rate, but is now maintained by the white ethnicity groups, observing a doubling time of 6.8 (95% CI 4.9 to 11) days. Rt analysis indicates a reproduction number advantage of 0.45 for B.1.617.2 relative to B.1.1.7, with the Rt value peaking at 1.85 for B.1.617.2.ConclusionsOur results illustrate a clear transmission advantage for the B.1.617.2 variant and the growth in hospitalisations illustrates that this variant is able to maintain exponential growth within age groups that are largely doubly vaccinated. There are concerning signs of intermittent growth in the B.1.351 variant, reaching a 28-day doubling time peak in March 2021, although this variant is presently not showing any evidence of a transmission advantage over B.1.617.2. Step 1b of the UK national lockdown easing was sufficient to precipitate exponential growth in B.1.617.2 cases for most regions and younger adult age groups. The final stages of NPI easing appeared to have a negligible impact on the growth of B.1.617.2 with every region experiencing sustained exponential growth from step 2. Nonetheless, early targeted local NPIs appeared to markedly reduced growth of B.1.617.2. Later localised interventions, at a time of higher prevalence and greater geographic dispersion of this variant, appeared to have a negligible impact on growth.

scholarly journals Whole Exome Sequencing Identifies Three Novel Mutations in the ASPM Gene From Saudi Families Leading to Primary Microcephaly

2021 ◽  
Vol 8 ◽  
Author(s):  
Muhammad Imran Naseer ◽  
Angham Abdulrahman Abdulkareem ◽  
Osama Yousef Muthaffar ◽  
Sameera Sogaty ◽  
Hiba Alkhatabi ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Frameshift Mutation ◽  
Genetic Defect ◽  
Deletion Mutation ◽  
Primary Microcephaly ◽  
Novel Mutations ◽  
Whole Exome ◽  
Novel Variants ◽  
Healthy Control

Autosomal recessive primary microcephaly (MCPH) is a neurodevelopmental defect that is characterized by reduced head circumference at birth along with non-progressive intellectual disability. Till date, 25 genes related to MCPH have been reported so far in humans. The ASPM (abnormal spindle-like, microcephaly-associated) gene is among the most frequently mutated MCPH gene. We studied three different families having primary microcephaly from different regions of Saudi Arabia. Whole exome sequencing (WES) and Sanger sequencing were done to identify the genetic defect. Collectively, three novel variants were identified in the ASPM gene from three different primary microcephaly families. Family 1, showed a deletion mutation leading to a frameshift mutation c.1003del. (p.Val335*) in exon 3 of the ASPM gene and family 2, also showed deletion mutation leading to frameshift mutation c.1047del (p.Gln349Hisfs*18), while in family 3, we identified a missense mutation c.5623A>G leading to a change in protein (p.Lys1875Glu) in exon 18 of the ASPM gene underlying the disorder. The identified respective mutations were ruled out in 100 healthy control samples. In conclusion, we found three novel mutations in the ASPM gene in Saudi families that will help to establish a disease database for specified mutations in Saudi population and will further help to identify strategies to tackle primary microcephaly in the kingdom.

scholarly journals Barriers to Impact Factor Growth in Two Major Psychiatry Journals in India

2020 ◽  
pp. 025371762092801
Author(s):  
Migita D’cruz ◽  
Chittaranjan Andrade
Keyword(s):  
Impact Factor ◽  
Exponential Growth ◽  
Impact Factors ◽  
Relevant Research ◽  
The Past ◽  
Indian Journal ◽  
Psychological Medicine ◽  
Citation Metrics

Background: Despite exponential growth in Indian research, Indian journals have low impact factors. A previous study by one of the authors (CA) of this paper showed that articles published in the Indian Journal of Psychiatry (IJP) under-referenced previously published relevant papers in the same journal. Based on this, we decided to investigate the citation characteristics of contemporary scientific articles published in the Indian Journal of Psychological Medicine (IJPM). Methods: The citation characteristics of scientific articles published in 2018 (Vol 40, issues 1–6) in the IJPM were examined to determine how well the authors cited relevant articles published during the past ten years in the IJPM and the IJP. Results: There were 145 and 142 citation-worthy articles in the IJPM and the IJP, respectively; of these, 85.5% and 65.5%, respectively, had not been cited. Conclusions: Authors publishing in the IJPM under-reference previous relevant research published in the IJPM and IJP. This suggests unawareness of, deliberate disregard of, or even disdain for prior Indian research in the field. Additionally, if Indian researchers do not cite previous Indian research in the field published in Indian journals, the citation metrics of Indian journals will not grow.

scholarly journals Estimation of exponential growth rate and basic reproduction number of the coronavirus disease 2019 (COVID-19) in Africa

2020 ◽  
Author(s):  
Salihu S Musa ◽  
Shi Zhao ◽  
Maggie H Wang ◽  
Abdurrazaq G Habib ◽  
Umar T Mustapha ◽  
...  
Keyword(s):  
Growth Rate ◽  
Basic Reproduction Number ◽  
Exponential Growth ◽  
Initial Phase ◽  
Reproduction Number ◽  
Exponential Growth Rate ◽  
Preparedness Planning ◽  
First Case ◽  
Exponential Growth Model ◽  
The Basic Reproduction Number

Abstract Since the first case of coronavirus disease 2019 (COVID-19) was detected on February 14, 2020, the cumulative confirmations reached 834 including 17 deaths by March 19, 2020. We analyzed the initial phase of the epidemic of COVID-19 in Africa between 1 March and 19 March 2020, by using the simple exponential growth model. We estimated the exponential growth rate as 0.22 per day (95%CI: 0.20 – 0.24), and the basic reproduction number to be 2.37 (95%CI: 2.22-2.51) based on the assumption that the exponential growth starting from 1 March, 2020. Our estimates should be useful in preparedness planning.

scholarly journals Novel Variants in Phosphodiesterase 6A and Phosphodiesterase 6B Genes and Its Phenotypes in Patients With Retinitis Pigmentosa in Chinese Families

2021 ◽  
Author(s):  
Yuyu Li ◽  
Ruyi Li ◽  
Hehua Dai ◽  
Genlin Li
Keyword(s):  
Retinitis Pigmentosa ◽  
Sanger Sequencing ◽  
Autosomal Recessive ◽  
Eye Disease ◽  
Specific Enzyme ◽  
Novel Mutations ◽  
Chinese Families ◽  
Novel Variants

Abstract Background: Retinitis pigmentosa (RP) is a genetically heterogeneous disease with 65 causative genes identified to date. However, only approximately 60% of RP cases genetically solved to date, predicating that many novel disease-causing variants are yet to be identified. The purpose of this study is to identify novel variants in phosphodiesterase 6A and phosphodiesterase 6B genes and present its phenotypes in patients with retinitis pigmentosa in Chinese families.Methods: Five retinitis pigmentosa patients with PDE6A variants and three with PDE6B variants were identified through a hereditary eye disease enrichment panel (HEDEP), all patients’ medical and ophthalmic histories were collected, and ophthalmological examinations were performed, then we analysed the possible causative variants. Sanger sequencing was used to verify the variants.Results: We identified 20 mutations sites in eight patients, two heterozygous variants were identified per patient of either PDE6A or PDE6B variants, others are from CA4, OPTN, RHO, ADGRA3 variants. We identified two novel variants in PDE6A: c.1246G > A;p.(Asp416Asn) and c.1747T > A;p.(Tyr583Asn). Three novel mutations in PDE6B: c.401T > C;p.(Leu134Pro), c.2293G > C;p.(Ala765Pro) and c.1610-1612del;p.(537-538del).CA4: c.243G > A;p.(Trp81*) and RHO: c.688G>A;p.(Val230Ile) are novel variants and maybe affecting the phenotype. Among them, c.401T > C;p.(Leu134Pro) variant in PDE6B is non- pathogenic; RHO: c.688G>A;p.(Val230Ile) is conflicting interpretations of pathogenicity;Other novel variants are all pathogenic.Conclusions: This study reveals novel and known variants in Chinese families with PDE6A and PDE6B mutations in autosomal recessive RP, expanding the clinical and genetic findings of photoreceptor-specific enzyme deficiencies.

scholarly journals A Short-Term Forecast Scenario for COVID-19 Epidemic and Allocated Hospital Readiness in Egypt

2020 ◽  
Author(s):  
Engy El-Ghitany
Keyword(s):  
Exponential Growth ◽  
Case Fatality Rate ◽  
Case Fatality ◽  
Fatality Rate ◽  
Short Term ◽  
Epidemic Curve ◽  
Preparedness Planning ◽  
The Status ◽  
Hospital Preparedness ◽  
Hospital Readiness

BackgroundThe novel virus COVID-19, also known as SARS-CoV‑2, is currently rapidly spreading around the globe and pushing healthcare systems to the limits of their capacity. One of the functions of predictive models is to timely act for epidemic preparedness including hospital preparedness. In Egypt, like many other countries in the world, the epidemic situation and forecasting have not yet sufficiently studied. ObjectiveThe study was carried out to develop a short-term forecast scenario for the COVID-19 epidemic situation in Egypt and predict the hospital needs to accommodate the growing number of cases.MethodsSecondary data from the COVID-2019 daily reports and the report issued 8th of April by the Egyptian Ministry of Health and Population were used. Due to the daily changing level of knowledge and data, the article reflects the status up to 18 April 2020. The prediction was based on the exponential growth rate model. For the depiction of the situation, the full length of the epidemic timeline was analyzed (from February 14th till April 18th). The growth rates and their rates of decline during the period from the 22nd of March till the 18th of April were calculated and extrapolated in the coming 7 weeks. The predicted hospital needs were assessed against the announced allocated resources.ResultsThe epidemic curve in Egypt is on the ascending arm as of April, 18. The active cases showed exponential growth from the start of the epidemic till April, 18. At the end of this period time, the recovery rate was 23.12% and the case fatality rate (CFR) was7.39. The case fatality rate median level during the last four weeks was 6.64. The active cases are expected to reach more than 20,000 by late May then starts to decline. The allocated regular hospital beds are predicted to show shortage by the time of the release of the paper. The intensive care units (ICU) beds and ventilators are predicted to show insufficiency on May 6.Conclusions: The COVID-19 epidemic in Egypt is expected to continue on the rise for the next few weeks and expected to start to decline late in May, 2020. Our estimates should be useful in preparedness planning. Serious actions should be taken to provide ICU beds and ventilators enough for the predicted number of cases that would need them, not later than the end of April. Mitigation actions have to continue for the coming 6 weeks or until the epidemic situation is more clearly seen.

scholarly journals Novel variants of MEFV and NOD2 genes in familial hidradenitis suppurativa: A case report

2020 ◽  
Vol 8 ◽  
pp. 2050313X2095311
Author(s):  
Abdulhadi Jfri ◽  
Ivan V Litvinov ◽  
Elena Netchiporouk ◽  
Elizabeth O’Brien
Keyword(s):  
Case Report ◽  
Genetic Testing ◽  
Family History ◽  
Hidradenitis Suppurativa ◽  
Periodic Fever ◽  
Autoinflammatory Disorder ◽  
Strong Family History ◽  
Novel Mutations ◽  
Novel Variants ◽  
History Of

We report a two-generation Canadian family of Armenian ancestry with hidradenitis suppurativa where novel mutations in MEVF and NOD2 genes were identified. The father and both children shared a mild-to-moderate hidradenitis suppurativa phenotype together with the features of follicular occlusion (e.g. acne and scalp folliculitis). Based on our findings and previous literature, we recommend considering genetic testing with a periodic fever/autoinflammatory disorder panel in patients with a strong family history of hidradenitis suppurativa and lack of common triggers such as smoking and being overweight.

A Short-Term Forecast Scenario for COVID-19 Epidemic and Allocated Hospital Readiness in Egypt (Preprint)

2020 ◽  
Author(s):  
Engy ElGhitany
Keyword(s):  
Exponential Growth ◽  
Case Fatality Rate ◽  
Case Fatality ◽  
Secondary Data ◽  
Fatality Rate ◽  
Short Term ◽  
Short Term Forecast ◽  
Epidemic Curve ◽  
Preparedness Planning ◽  
Term Forecast

BACKGROUND The novel virus COVID-19, also known as SARS-CoV 2, is currently rapidly spreading around the globe and pushing healthcare systems to the limits of their capacity. One of the functions of predictive models is to timely act for epidemic preparedness including hospital preparedness. In Egypt, like many other countries in the world, the epidemic situation and forecasting have not yet sufficiently studied. OBJECTIVE The study was carried out to develop a short-term forecast scenario for the COVID-19 epidemic situation in Egypt and predict the hospital needs to accommodate the growing number of cases. METHODS Secondary data from the COVID-2019 daily reports and the report issued 8th of April by the Egyptian Ministry of Health and Population were used. Due to the daily changing level of knowledge and data, the article reflects the status up to 18 April 2020. The prediction was based on the exponential growth rate model. For the depiction of the situation, the full length of the epidemic timeline was analyzed (from February 14th till April 18th). The growth rates and their rates of decline during the period from the 22nd of March till the 18th of April were calculated and extrapolated in the coming 7 weeks. The predicted hospital needs were assessed against the announced allocated resources. RESULTS The epidemic curve in Egypt is on the ascending arm as of April, 18. The active cases showed exponential growth from the start of the epidemic till April, 18. At the end of this period time, the recovery rate was 23.12% and the case fatality rate (CFR) was7.39. The case fatality rate median level during the last four weeks was 6.64. The active cases are expected to reach more than 20,000 by late May then starts to decline. The allocated regular hospital beds are predicted to show shortage by the time of the release of the paper. The intensive care units (ICU) beds and ventilators are predicted to show insufficiency on May 6. CONCLUSIONS The COVID-19 epidemic in Egypt is expected to continue on the rise for the next few weeks and expected to start to decline late in May, 2020. Our estimates should be useful in preparedness planning. Serious actions should be taken to provide ICU beds and ventilators enough for the predicted number of cases that would need them, not later than the end of April. Mitigation actions have to continue for the coming 6 weeks or until the epidemic situation is more clearly seen.

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