scholarly journals COVID-19 pandemic dynamics in India and impact of the SARS-CoV-2 Delta (B.1.617.2) variant

Author(s):  
Wan Yang ◽  
Jeffrey Shaman

The Delta SARS-CoV-2 variant has spread quickly since first being identified. To better understand its epidemiological characteristics and impact, we utilize multiple datasets and comprehensive model-inference methods to reconstruct COVID-19 pandemic dynamics in India, where Delta first emerged. Using model-inference estimates from March 2020 to May 2021, we estimate the Delta variant can escape adaptive immunity induced by prior wildtype infection roughly half of the time and is around 60% more infectious than wildtype SARS-CoV-2. In addition, our analysis suggests that the recent case decline in India was likely due to implemented non-pharmaceutical interventions and weather conditions less conducive for SARS-CoV-2 transmission during March - May, rather than high population immunity. Model projections show infections could resurge as India enters its monsoon season, beginning June, if intervention measures are lifted prematurely.

2021 ◽  
Author(s):  
Wan Yang ◽  
Jeffrey Shaman

Within days of first detection, Omicron SARS-CoV-2 variant case numbers grew exponentially and spread globally. To better understand variant epidemiological characteristics, we utilize a model-inference system to reconstruct SARS-CoV-2 transmission dynamics in South Africa and decompose novel variant transmissibility and immune erosion. Accounting for under-detection of infection, infection seasonality, nonpharmaceutical interventions, and vaccination, we estimate that the majority of South Africans had been infected by SARS-CoV-2 before the Omicron wave. Based on findings for Gauteng province, Omicron is estimated 100.3% (95% CI: 74.8 - 140.4%) more transmissible than the ancestral SARS-CoV-2 and 36.5% (95% CI: 20.9 - 60.1%) more transmissible than Delta; in addition, Omicron erodes 63.7% (95% CI: 52.9 - 73.9%) of the population immunity, accumulated from prior infections and vaccination, in Gauteng.


2021 ◽  
Author(s):  
Sebastian Mader ◽  
Tobias Rüttenauer

Background: Most governments have introduced various non-pharmaceutical interventions (NPIs) in response to the pandemic outbreak of Coronavirus disease (COVID-19) since early 2020. While NPIs aim at avoiding fatalities related to COVID-19, the previous literature on their efficacy has focused on infections and on data of the first half of 2020. Still, findings of early NPI studies may be subject to underreporting and missing timeliness of reporting of cases. Moreover, the low variation in treatment timing during the first wave makes identification of robust treatment effects difficult.Methods: To circumvent problems of reporting and treatment variation, we analyse data on daily confirmed COVID-19-related deaths per capita from Our World in Data, and on 10 different NPIs from the Oxford COVID-19 Government Response Tracker for 169 countries from 1st July 2020 to 31st May 2021. To identify the causal effects of introducing NPIs on COVID-19-related confirmed fatalities per capita, we apply the generalized synthetic control (GSC) method to each NPI, while controlling for the remaining NPIs, weather conditions, vaccinations, and NPI-residualized COVID-19 cases.Findings: We do not find substantial and consistent mitigating effects of any NPI under investigation on COVID-19-related deaths per capita. We see a tentative change in the trend of COVID-19-related deaths around 30 days after workplace closing, public transport closing, and stay at home rules have been implemented, but none of them exerts a statistically significant effect.Interpretation: The study enhances the literature on the effectivity of NPIs with respect to the time frame, the number of countries, and the analytical approach. The results provide further guidance to judge the proportionality of NPIs.


2020 ◽  
Vol 13 (2) ◽  
pp. 564
Author(s):  
Renata Cristina Mafra ◽  
Mayara Maezano Faita Pinheiro ◽  
Rejane Ennes Cicerelli ◽  
Lucas Prado Osco ◽  
Marcelo Rodrigo Alves ◽  
...  

O processo erosivo é um fenômeno que acontece devido às condições climáticas ou uso inadequado da terra. O mapeamento dos níveis de vulnerabilidade à erosão de uma área pode ocorrer usando diferentes modelos de inferência geográfica. No entanto, definir o método apropriado é ainda uma questão a ser respondida. Este trabalho apresenta uma abordagem de validação de mapa de vulnerabilidade à erosão elaborado por diferentes métodos de inferência. Como estudo de caso, adotou-se uma bacia hidrográfica e considerou-se os seguintes critérios: geomorfologia, pedologia, declividade, densidade de drenagem e cobertura da terra. Dentre os métodos testados tem-se: Combinação Linear Ponderada (CLP) e três operadores Fuzzy: soma algébrica, produto algébrico e gamma, variando o expoente “γ” entre os valores 0,4; 0,6 e 0,8. Os pesos dos critérios foram definidos com base no Processo Analítico Hierárquico. A validação dos mapas ocorreu usando 1902 pontos, sendo 951 pontos de erosão na área, definidos com base em imagens do Google Earth Pro, e 951 pontos sem erosão, gerados aleatoriamente no QGIS 3.8. O modelo de regressão logística foi usado parar comparar o desempenho de cada mapa ao apontar as áreas com maior e menor grau de vulnerabilidade. A melhor modelagem foi alcançada com o operador Fuzzy gamma quando parametrizado com γ = 0,6. Embora o CLP seja a abordagem recorrente em estudos ambientais envolvendo inferência geográfica, nossos resultados demostram que outros operadores podem produzir resultados mais próximos aos encontrados com a realidade observada em campo.  Machine learning erosion and vulnerability map validation A B S T R A C TErosion is a natural phenomenon that happens in all ecosystems, whether due to weather conditions or inappropriate land use. Mapping the erosion vulnerability levels of an area can occur using different methods of geographic inference. However, defining the appropriate method is still a question to be answered. This paper presents an erosion vulnerability map validation approach elaborated by different inference methods. As a case study, a watershed was adopted and the following criteria were considered: geomorphology, pedology, slope, drainage density and land cover. Among the tested methods are: Weighted Linear Combination (WLC) and three Fuzzy operators: algebraic sum, algebraic product and gamma, varying the exponent “γ” between the values 0.4; 0.6 and 0.8. The weights of the criteria were defined based on the Hierarchical Analytical Process. The validation of the maps took place using 1902 points, with 951 erosion points in the area defined based on Google Earth Pro images and 951 points without erosion randomly generated in QGIS 3.8. The logistic regression model was used to compare the performance of each map by pointing out the areas with the highest and lowest degree of vulnerability. The best modeling was achieved with the Fuzzy gamma operator when parameterized with γ = 0.6. Although WLC is the recurring approach in environmental studies involving geographic inference, our results show that other operators can produce results closer to those encountered with the reality observed in the field.Keywords: Geographical inference; multicriteria analysis; data validation; environmental impact.


BMJ Open ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. e047227
Author(s):  
Xiaoming Cui ◽  
Lin Zhao ◽  
Yuhao Zhou ◽  
Xin Lin ◽  
Runze Ye ◽  
...  

ObjectiveTo evaluate epidemiological characteristics and transmission dynamics of COVID-19 outbreak resurged in Beijing and to assess the effects of three non-pharmaceutical interventions.DesignDescriptive and modelling study based on surveillance data of COVID-19 in Beijing.SettingOutbreak in Beijing.ParticipantsThe database included 335 confirmed cases of COVID-19.MethodsTo conduct spatiotemporal analyses of the outbreak, we collected individual records on laboratory-confirmed cases of COVID-19 from 11 June 2020 to 5 July 2020 in Beijing, and visitor flow and products transportation data of Xinfadi Wholesale Market. We also built a modified susceptible-exposed-infected-removed model to investigate the effect of interventions deployed in Beijing.ResultsWe found that the staff working in the market (52.2%) and the people around 10 km to this epicentre (72.5%) were most affected, and the population mobility entering-exiting Xinfadi Wholesale Market significantly contributed to the spread of COVID-19 (p=0.021), but goods flow of the market had little impact on the virus spread (p=0.184). The prompt identification of Xinfadi Wholesale Market as the infection source could have avoided a total of 25 708 (95% CI 13 657 to 40 625) cases if unnoticed transmission lasted for a month. Based on the model, we found that active screening on targeted population by nucleic acid testing alone had the most significant effect.ConclusionsThe non-pharmaceutical interventions deployed in Beijing, including localised lockdown, close-contact tracing and community-based testing, were proved to be effective enough to contain the outbreak. Beijing has achieved an optimal balance between epidemic containment and economic protection.


Author(s):  
Li-Chien Chien ◽  
Christian K. Beÿ ◽  
Kristi L. Koenig

ABSTRACT The authors describe Taiwan’s successful strategy in achieving control of coronavirus disease (COVID-19) without economic shutdown, despite the prediction that millions of infections would be imported from travelers returning from Chinese New Year celebrations in Mainland China in early 2020. As of September 2, 2020, Taiwan reports 489 cases, 7 deaths, and no locally acquired COVID-19 cases for the last 135 days (greater than 4 months) in its population of over 23.8 million people. Taiwan created quasi population immunity through the application of established public health principles. These non-pharmaceutical interventions, including public masking and social distancing, coupled with early and aggressive identification, isolation, and contact tracing to inhibit local transmission, represent a model for optimal public health management of COVID-19 and future emerging infectious diseases.


Author(s):  
Dmitry Avdyukhin ◽  
Daniil Chivilikhin ◽  
Georgiy Korneev ◽  
Vladimir Ulyantsev ◽  
Anatoly Shalyto

2020 ◽  
Vol 21 (1) ◽  
pp. 1-7
Author(s):  
Grace Russell ◽  
Marcus Bridge ◽  
Maja Nimak-Wood

Observations of 37 individual blue whales (Balaenoptera musculus) were recorded off the southern coast of Sri Lanka during the Southwest Monsoon Season (SWM). Sightings were made during a scientific geophysical survey campaign conducted in July and August 2017. Whilst blue whales are regularly recorded on the continental slope of southern Sri Lanka during the Northeast Monsoon Season (NEM) (December - March) and during the two inter-monsoonal periods (March - April and September - October), limited data is available for the SWM (May - September) mostly due to unfavourable weather conditions and very little survey effort. In the northern hemisphere blue whales undertake seasonal migrations from higher latitude feeding grounds to lower latitude breeding and wintering areas. However it has been suggested that a population of blue whales in the Northern India Ocean (NIO) remains in lower latitudes year round taking advantage of the rich upwelling areas off Somalia, southwest Arabia and western Sri Lanka. Data from this study nevertheless support a theory that a certain number of individuals remain off the southern coast off Sri Lanka during the SWM, suggesting that the productivity in this region is sufficient to support their year-round presence. This study therefore fills a knowledge gap regarding the presence and movement of blue whales in the NIO highlighting the importance of data obtained from platforms of opportunity.


microLife ◽  
2021 ◽  
Author(s):  
M Campos ◽  
J M Sempere ◽  
J C Galán ◽  
A Moya ◽  
C Llorens ◽  
...  

ABSTRACT Epidemics caused by microbial organisms are part of the natural phenomena of increasing biological complexity. The heterogeneity and constant variability of hosts, in terms of age, immunological status, family structure, lifestyle, work activities, social and leisure habits, daily division of time, and other demographic characteristics make it extremely difficult to predict the evolution of epidemics. Such prediction is, however, critical for implementing intervention measures in due time and with appropriate intensity. General conclusions should be precluded, given that local parameters dominate the flow of local epidemics. Membrane computing models allows us to reproduce the objects (viruses, hosts) and their interactions (stochastic but also with defined probabilities) with an unprecedented level of detail. Our LOIMOS model helps reproduce the demographics and social aspects of a hypothetical town of 10,320 inhabitants in an average European country where COVID-19 is imported from the outside. The above-mentioned characteristics of hosts and their lifestyle are minutely considered. For the data in the Hospital and the ICU we took advantage of the observations at the Nursery Intensive Care Unit of the Consortium University General Hospital, Valencia, Spain (included as author). The dynamics of the epidemics are reproduced and include the effects on viral transmission of innate and acquired immunity at various ages. The model predicts the consequences of delaying the adoption of non-pharmaceutical interventions (between 15 and 45 days after the first reported cases) and the effect of those interventions on infection and mortality rates (reducing transmission by 20%, 50%, and 80%) in immunological response groups. The lockdown for the elderly population as a single intervention appears to be effective. This modelling exercise exemplifies the application of membrane computing for designing appropriate multilateral interventions in epidemic situations.


Author(s):  
Chaolong Wang ◽  
Li Liu ◽  
Xingjie Hao ◽  
Huan Guo ◽  
Qi Wang ◽  
...  

ABSTRACTBACKGROUNDWe described the epidemiological features of the coronavirus disease 2019 (Covid-19) outbreak, and evaluated the impact of non-pharmaceutical interventions on the epidemic in Wuhan, China.METHODSIndividual-level data on 25,961 laboratory-confirmed Covid-19 cases reported through February 18, 2020 were extracted from the municipal Notifiable Disease Report System. Based on key events and interventions, we divided the epidemic into four periods: before January 11, January 11-22, January 23 - February 1, and February 2-18. We compared epidemiological characteristics across periods and different demographic groups. We developed a susceptible-exposed-infectious-recovered model to study the epidemic and evaluate the impact of interventions.RESULTSThe median age of the cases was 57 years and 50.3% were women. The attack rate peaked in the third period and substantially declined afterwards across geographic regions, sex and age groups, except for children (age <20) whose attack rate continued to increase. Healthcare workers and elderly people had higher attack rates and severity risk increased with age. The effective reproductive number dropped from 3.86 (95% credible interval 3.74 to 3.97) before interventions to 0.32 (0.28 to 0.37) post interventions. The interventions were estimated to prevent 94.5% (93.7 to 95.2%) infections till February 18. We found that at least 59% of infected cases were unascertained in Wuhan, potentially including asymptomatic and mild-symptomatic cases.CONCLUSIONSConsiderable countermeasures have effectively controlled the Covid-19 outbreak in Wuhan. Special efforts are needed to protect vulnerable populations, including healthcare workers, elderly and children. Estimation of unascertained cases has important implications on continuing surveillance and interventions.


2021 ◽  
Author(s):  
Marta Galanti ◽  
Sen Pei ◽  
Teresa K. Yamana ◽  
Frederick J. Angulo ◽  
Apostolos Charos ◽  
...  

AbstractNearly one year into the COVID-19 pandemic, the first SARS-COV-2 vaccines received emergency use authorization and vaccination campaigns began. A number of factors can reduce the averted burden of cases and deaths due to vaccination. Here, we use a dynamic model, parametrized with Bayesian inference methods, to assess the effects of non-pharmaceutical interventions, and vaccine administration and uptake rates on infections and deaths averted in the United States. We estimate that high compliance with non-pharmaceutical interventions could avert more than 60% of infections and 70% of deaths during the period of vaccine administration, and that increasing the vaccination rate from 5 to 11 million people per week could increase the averted burden by more than one third. These findings underscore the importance of maintaining non-pharmaceutical interventions and increasing vaccine administration rates.


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