scholarly journals Preliminary modeling estimates of the relative transmissibility and immune escape of the Omicron SARS-CoV-2 variant of concern in South Africa

2022 ◽  
Author(s):  
Nicolò Gozzi ◽  
Matteo Chinazzi ◽  
Jessica T. Davis ◽  
Kunpeng Mu ◽  
Ana Pastore y Piontti ◽  
...  
Keyword(s):  
South Africa ◽  
Parameter Space ◽  
Generation Time ◽  
Immune Escape ◽  
Current Knowledge ◽  
Unknown Origin ◽  
Epidemiological Data ◽  
Initial Seeding ◽  
Epidemic Wave ◽  
Pharmaceutical Interventions

We develop a stochastic, multi-strain, compartmental epidemic model to estimate the relative transmissibility and immune escape of the Omicron variant of concern (VOC) in South Africa. The model integrates population, non-pharmaceutical interventions, vaccines, and epidemiological data and it is calibrated in the period May 1st, 2021 - November 23rd, 2021. We explore a parameter space of relative transmissibility with respect to the Delta variant and immune escape for Omicron by assuming an initial seeding, from unknown origin, in the first week of October 2021. We identify a region of the parameter space where combinations of relative transmissibility and immune escape are compatible with the growth of the epidemic wave. We also find that changes in the generation time associated with Omicron infections strongly affect the results concerning its relative transmissibility. The presented results are informed by current knowledge of Omicron and subject to changes.

scholarly journals Estimation of the test to test distribution as a proxy for generation interval distribution for the Omicron variant in England

2022 ◽  
Author(s):  
Sam Abbott ◽  
Katharine Sherratt ◽  
Moritz Gerstung ◽  
Sebastian Funk
Keyword(s):  
South Africa ◽  
Standard Deviation ◽  
Generation Time ◽  
Time Distribution ◽  
Immune Escape ◽  
Credible Interval ◽  
Contact Tracing ◽  
Time Varying ◽  
Daily Growth ◽  
Gene Target

Background Early estimates from South Africa indicated that the Omicron COVID-19 variant may be both more transmissible and have greater immune escape than the previously dominant Delta variant. The rapid turnover of the latest epidemic wave in South Africa as well as initial evidence from contact tracing and household infection studies has prompted speculation that the generation time of the Omicron variant may be shorter in comparable settings than the generation time of the Delta variant. Methods We estimated daily growth rates for the Omicron and Delta variants in each UKHSA region from the 23rd of November to the 23rd of December 2021 using surveillance case counts by date of specimen and S-gene target failure status with an autoregressive model that allowed for time-varying differences in the transmission advantage of the Delta variant where the evidence supported this. By assuming a gamma distributed generation distribution we then estimated the generation time distribution and transmission advantage of the Omicron variant that would be required to explain this time varying advantage. We repeated this estimation process using two different prior estimates for the generation time of the Delta variant first based on household transmission and then based on its intrinsic generation time. Results Visualising our growth rate estimates provided initial evidence for a difference in generation time distributions. Assuming a generation time distribution for Delta with a mean of 2.5-4 days (90% credible interval) and a standard deviation of 1.9-3 days we estimated a shorter generation time distribution for Omicron with a mean of 1.5-3.2 days and a standard deviation of 1.3-4.6 days. This implied a transmission advantage for Omicron in this setting of 160%-210% compared to Delta. We found similar relative results using an estimate of the intrinsic generation time for Delta though all estimates increased in magnitude due to the longer assumed generation time. Conclusions We found that a reduction in the generation time of Omicron compared to Delta was able to explain the observed variation over time in the transmission advantage of the Omicron variant. However, this analysis cannot rule out the role of other factors such as differences in the populations the variants were mixing in, differences in immune escape between variants or bias due to using the test to test distribution as a proxy for the generation time distribution.

scholarly journals Projected epidemiological consequences of the Omicron SARS-CoV-2 variant in England, December 2021 to April 2022

2021 ◽  
Author(s):  
Rosanna C Barnard ◽  
Nicholas G Davies ◽  
Carl A B Pearson ◽  
Mark Jit ◽  
W John Edmunds
Keyword(s):  
Health Outcomes ◽  
Compartmental Model ◽  
Hospital Admissions ◽  
Immune Escape ◽  
Epidemiological Data ◽  
Control Measures ◽  
Gene Target ◽  
S Gene ◽  
Failure Data ◽  
Pharmaceutical Interventions

The Omicron B.1.1.529 SARS-CoV-2 variant was first detected in late November 2021 and has since spread to multiple countries worldwide. We model the potential consequences of the Omicron variant on SARS-CoV-2 transmission and health outcomes in England between December 2021 and April 2022, using a deterministic compartmental model fitted to epidemiological data from March 2020 onwards. Because of uncertainty around the characteristics of Omicron, we explore scenarios varying the extent of Omicron's immune escape and the effectiveness of COVID-19 booster vaccinations against Omicron, assuming the level of Omicron's transmissibility relative to Delta to match the growth in observed S gene target failure data in England. We consider strategies for the re-introduction of control measures in response to projected surges in transmission, as well as scenarios varying the uptake and speed of COVID-19 booster vaccinations and the rate of Omicron's introduction into the population. These results suggest that Omicron has the potential to cause substantial surges in cases, hospital admissions and deaths in populations with high levels of immunity, including England. The reintroduction of additional non-pharmaceutical interventions may be required to prevent hospital admissions exceeding the levels seen in England during the previous peak in winter 2020-2021.

scholarly journals The Impact of Non-Pharmaceutical Interventions on the First COVID-19 Epidemic Wave in South Africa

2021 ◽  
Author(s):  
Thabo Mabuka ◽  
Nesisa Ncube ◽  
Michael Ross ◽  
Andrea Silaji ◽  
Willie Macharia ◽  
...  
Keyword(s):  
South Africa ◽  
South African ◽  
African Population ◽  
South African Population ◽  
Seir Model ◽  
The Government ◽  
The Impact ◽  
Epidemic Wave ◽  
Pharmaceutical Interventions ◽  
Excess Deaths

On the 5th of March 2020, South Africa reported its first cases of COVID-19. This signalled the onset of the first COVID-19 epidemic wave in South Africa. The response by the Government of South Africa to the COVID-19 epidemic in South Africa was the use of non-pharmaceutical interventions (NPIs). In this study, a semi-reactive COVID-19 model, the ARI COVID-19 SEIR model, was used to investigate the impact of NPIs in South Africa to understand their effectiveness in the reduction of COVID-19 transmission in the South African population. This study also investigated the COVID-19 testing, reporting, hospitalised cases and excess deaths in the first COVID-19 epidemic wave in South Africa.

scholarly journals Current and future neutrino oscillation constraints on leptonic unitarity

2020 ◽  
Vol 2020 (12) ◽  
Author(s):  
Sebastian A. R. Ellis ◽  
Kevin J. Kelly ◽  
Shirley Weishi Li
Keyword(s):  
Precise Measurement ◽  
Sterile Neutrino ◽  
Current Knowledge ◽  
Unknown Origin ◽  
Neutrino Masses ◽  
Matrix Elements ◽  
Neutrino Mixing ◽  
Next Generation ◽  
Active Neutrino ◽  
Mixing Matrix

Abstract The unitarity of the lepton mixing matrix is a critical assumption underlying the standard neutrino-mixing paradigm. However, many models seeking to explain the as-yet-unknown origin of neutrino masses predict deviations from unitarity in the mixing of the active neutrino states. Motivated by the prospect that future experiments may provide a precise measurement of the lepton mixing matrix, we revisit current constraints on unitarity violation from oscillation measurements and project how next-generation experiments will improve our current knowledge. With the next-generation data, the normalizations of all rows and columns of the lepton mixing matrix will be constrained to ≲10% precision, with the e-row best measured at ≲1% and the τ-row worst measured at ∼10% precision. The measurements of the mixing matrix elements themselves will be improved on average by a factor of 3. We highlight the complementarity of DUNE, T2HK, JUNO, and IceCube Upgrade for these improvements, as well as the importance of ντ appearance measurements and sterile neutrino searches for tests of leptonic unitarity.

scholarly journals SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Marta Giovanetti ◽  
Eleonora Cella ◽  
Francesca Benedetti ◽  
Brittany Rife Magalis ◽  
Vagner Fonseca ◽  
...  
Keyword(s):  
Public Health ◽  
Epidemiological Data ◽  
Health Interventions ◽  
Transmission Dynamics ◽  
Public Health Interventions ◽  
Viral Spread ◽  
Three Phase ◽  
Phylodynamic Analysis ◽  
Epidemic Wave ◽  
Over Time

AbstractWe investigated SARS-CoV-2 transmission dynamics in Italy, one of the countries hit hardest by the pandemic, using phylodynamic analysis of viral genetic and epidemiological data. We observed the co-circulation of multiple SARS-CoV-2 lineages over time, which were linked to multiple importations and characterized by large transmission clusters concomitant with a high number of infections. Subsequent implementation of a three-phase nationwide lockdown strategy greatly reduced infection numbers and hospitalizations. Yet we present evidence of sustained viral spread among sporadic clusters acting as “hidden reservoirs” during summer 2020. Mathematical modelling shows that increased mobility among residents eventually catalyzed the coalescence of such clusters, thus driving up the number of infections and initiating a new epidemic wave. Our results suggest that the efficacy of public health interventions is, ultimately, limited by the size and structure of epidemic reservoirs, which may warrant prioritization during vaccine deployment.

scholarly journals Mycotoxins and health risks

1986 ◽  
Vol 5 (3) ◽  
pp. 154-156
Author(s):  
P. G. Thiel
Keyword(s):  
South Africa ◽  
Immune System ◽  
Health Risks ◽  
Chronic Exposure ◽  
Epidemiological Data ◽  
Domestic Animals ◽  
Agricultural Products ◽  
Farm Animals ◽  
Fungal Contamination ◽  
Experimental Animals

Fungal contamination of agricultural products can prove to be harmful to humans and domestic animals as these fungi produce a variety of mycotoxins which can eventually occur in food. Acute intoxications with mycotoxins occur regularly in farm animals but, fortunately, are infrequently observed in humans. However, the chronic exposure of humans to mycotoxins occurs regularly. Such exposures are potentially teratogenic and carcmogenic and can suppress the immune system. It is presently impossible to establish safe levels of exposure for most mycotoxins due to scanty epidemiological data and insufficient observations on experimental animals. With respect to aflatoxin all available data point to a real health risk. Risk analysis based on epidemiological observations shows that the liver-cancer risk for individuals in South Africa is potentially increased by continued exposure to the present legally permitted level of aflatoxin in food.

scholarly journals Service life design and modelling of concrete structures – background, developments, and implementation

2018 ◽  
Vol 8 (3) ◽  
pp. 224-245 ◽  
Author(s):  
Mark Gavin Alexander
Keyword(s):  
South Africa ◽  
Service Life ◽  
Current Knowledge ◽  
Concrete Structures ◽  
International Experience ◽  
Durability Design ◽  
Service Life Design ◽  
International View ◽  
Life Design ◽  
Service Life Modelling

The paper presents an overview of current knowledge and progress in service life design and modelling of concrete structures, taking an international view but also giving local examples from South Africa. It raises the question of why service life modelling is needed, and indicates that modern demands for longevity, durability, and sustainability of concrete structures cannot be fulfilled without service life modelling. It addresses the current approaches to durability design and specification and concludes that a move to performance-based approaches is imperative if progress is to be made. Examples from international experience are cited to illustrate progress that has been made. Lastly, the paper discusses ways of moving forward, recognizing that the philosophical bases are already firmly in place in the form of general code formulations, but these need to be converted into useful approaches.

scholarly journals Tumor-Intrinsic Mechanisms Regulating Immune Exclusion in Liver Cancers

2021 ◽  
Vol 12 ◽  
Author(s):  
Katherine E. Lindblad ◽  
Marina Ruiz de Galarreta ◽  
Amaia Lujambio
Keyword(s):  
Liver Cancer ◽  
Rational Design ◽  
Immune Escape ◽  
Current Knowledge ◽  
Treatment Options ◽  
Health Concern ◽  
Patient Stratification ◽  
Tumor Immune Evasion ◽  
Advanced Hcc ◽  
Liver Cancers

Representing the fourth leading cause of cancer-related mortality worldwide, liver cancers constitute a major global health concern. Hepatocellular carcinoma (HCC), the most frequent type of liver cancer, is associated with dismal survival outcomes and has traditionally had few treatment options available. In fact, up until 2017, treatment options for advanced HCC were restricted to broad acting tyrosine kinase inhibitors, including Sorafenib, which has been the standard of care for over a decade. Since 2017, a multitude of mono- and combination immunotherapies that include pembrolizumab, nivolumab, ipilumumab, atezolizumab, and bevacizumab have been FDA-approved for the treatment of advanced HCC with unprecedented response rates ranging from 20 to 30% of patients. However, this also means that ~70% of patients do not respond to this treatment and currently very little is known regarding mechanisms of action of these immunotherapies as well as predictors of response to facilitate patient stratification. With the recent success of immunotherapies in HCC, there is a pressing need to understand mechanisms of tumor immune evasion and resistance to these immunotherapies in order to identify biomarkers of resistance or response. This will enable better patient stratification as well as the rational design of combination immunotherapies to restore sensitivity in resistant patients. The aim of this review is to summarize the current knowledge to date of tumor-intrinsic mechanisms of immune escape in liver cancer, specifically in the context of HCC.

Migraine and ovarian steroid hormones

Cephalalgia ◽  
1997 ◽  
Vol 17 (20_suppl) ◽  
pp. 12-16 ◽  
Author(s):  
Kma Welch
Keyword(s):  
Steroid Hormones ◽  
Clinical Presentation ◽  
Current Knowledge ◽  
Epidemiological Data ◽  
Special Treatment ◽  
Ovarian Hormone ◽  
Ovarian Steroid ◽  
Ovarian Steroids ◽  
Treatment Considerations ◽  
Hormone Sensitive

This chapter reviews clinical and epidemiological data that support a role for ovarian steroid hormones in the migraine syndrome. Changes in the clinical presentation of migraine are discussed on the basis of current knowledge of biochemistry and pharmacology of ovarian steroids. Finally, special treatment considerations of ovarian hormone-sensitive migraine are discussed.

scholarly journals Role of indoleamine 2,3-dioxygenase in pathology of the gastrointestinal tract

2018 ◽  
Vol 11 ◽  
pp. 175628481881533 ◽  
Author(s):  
Aleksandar Acovic ◽  
Marina Gazdic ◽  
Nemanja Jovicic ◽  
C. Randall Harrell ◽  
Crissy Fellabaum ◽  
...  
Keyword(s):  
Immune Response ◽  
Gastrointestinal Tract ◽  
Immune Escape ◽  
Current Knowledge ◽  
Gastrointestinal System ◽  
Gastrointestinal Tumors ◽  
Malignant Diseases ◽  
Cellular Mechanisms ◽  
Indoleamine 2,3 Dioxygenase ◽  
New Therapeutic Approaches

Indoleamine 2,3-dioxygenase (IDO) has the most important role in modulation of tryptophan-dependent effects in the gastrointestinal tract, including modulation of intestinal immune response. An increased IDO activity maintains immune tolerance and attenuates ongoing inflammation but allows immune escape and uncontrolled growth of gastrointestinal tumors. Accordingly, IDO represents a novel therapeutic target for the treatment of inflammatory and malignant diseases of the gastrointestinal tract. In this review article, we summarize current knowledge about molecular and cellular mechanisms that are involved in IDO-dependent effects. We provide a brief outline of experimental and clinical studies that increased our understanding of how enhanced IDO activity: controls host–microbiota interactions in the gut; regulates detrimental immune response in inflammatory disorders of the gastrointestinal system; and allows immune escape and uncontrolled growth of gastrointestinal tumors. Additionally, we present future perspectives regarding modulation of IDO activity in the gut as possible new therapeutic approaches for the treatment of inflammatory and malignant diseases of the gastrointestinal system.

Sign in / Sign up

Export Citation Format

Share Document