Can ship travel contain COVID-19 outbreak after re-opening: a Bayesian meta-analysis.

Large gatherings of people on cruise ships and warships are often at high risk of COVID-19 infections. To assess the transmissibility of SARS-CoV-2 on warships and cruise ships and to quantify the effectiveness of the containment measures, the transmission coefficient (ß), basic reproductive number (R0), and time to deploy containment measures were estimated by the Bayesian Susceptible-Exposed-Infected-Recovered model. A meta-analysis was conducted to predict vaccine protection with or without non-pharmaceutical interventions (NPIs). The analysis showed that implementing NPIs during voyages could reduce the transmission coefficients of SARS-CoV-2 by 50%. Two weeks into the voyage of a cruise that begins with 1 infected passenger out of a total of 3,711 passengers, we estimate there would be 45 (95% CI:25-71), 33 (95% CI:20-52), 18 (95% CI:11-26), 9 (95% CI:6-12), 4 (95% CI:3-5), and 2 (95% CI:2-2) final cases under 0%, 10%, 30%, 50%, 70%, and 90% vaccine protection, respectively, without NPIs. The timeliness of strict NPIs along with implementing strict quarantine and isolation measures is imperative to contain COVID-19 cases in cruise ships. The spread of COVID-19 on ships was predicted to be limited in scenarios corresponding to at least 70% protection from prior vaccination, across all passengers and crew.

Evaluation of the Canadian government policies on controlling the COVID-19 outbreaks

In this paper, we investigate the COVID-19 pandemic in Canada and evaluate the Canadian government policies on controlling COVID-19 outbreaks. The first case of COVID-19 was reported in Ontario on 25 January 2020. Since then, there have been over million cases by now. During this time period, the federal, provincial and local governments have implemented regulations and policies in order to control the pandemic. To evaluate these government policies, which may be done by analysing the infection rate, infection period and reproductive number of COVID-19, we approach the problem by introducing an extended susceptible-exposed-infectious-removed (SEIR) model and conducting the model inference by using the iterated filter ensemble adjustment Kalman filter (IF-EAKF) algorithm. We first divide the time period into phases according to the policy intensities in each province by segmenting the time period from 4 March 2020 to 31 October 2020 into three time phases: the exploding phase, the strict policy implementation phase, and the provincial reopening phase. We then use IF-EAKF algorithm to obtain the estimates of the model parameters. We show that the infection rate in the second phase is lower than that in both first and third phases. We also discuss the number of new COVID-19 cases under different policy intensities and different policy durations in the third wave of the pandemic. © 2023 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

Estimation of infection fields and pathways for SARS-CoV-2 and its variant based on the relationship among dose-response function parameter, quantum emission rate, and basic reproductive number

The theoretical model of the relationship among dose-response function parameters, quantum emission rate, and basic reproductive number for SARS-CoV-2 was constructed. Then, using this model, infection fields and pathways for SARS-CoV-2 and its variant were estimated. The parameters of the time activity, the number of contacts by the microenvironments and groups, and the COVID-19 risk from multiple pathways in near and far fields were used. Consequently, in lower transmissibility, droplet spray transmission in the near field was dominant, whereas in higher transmissibility, transmission from inhalation of smaller aerosols in the far field was dominant. Moreover, it was suggested that transmission from droplet spray, indirect contacts, and inhalation of smaller aerosols in the near field and inhalation of smaller aerosols in the far field was dominant for the wild-type strain, while transmission from inhalation of smaller aerosols in the far field were dominant for the Delta variant. © 2022 17th International Conference on Indoor Air Quality and Climate, INDOOR AIR 2022. All rights reserved.

Use of community SARS-CoV2 case counts and instantaneous reproductive number to predict short-term COVID-19 hospital admission volumes.

The SARS-CoV2 pandemic and high hospitalization rates placed a tremendous strain on hospital resources necessitating models to predict hospital volumes and the associated resource requirements. Complex epidemiologic models have been developed and published, but many require continued adjustment of input parameters. We developed a simplified model for short-term bed need predictions that self-adjusts to changing patterns of disease in the community and admission rates. The model utilizes public health data on community new case counts for SARS-CoV2 and projects anticipated hospitalization rates. The model was retrospectively evaluated after the second wave of SARS-CoV2 2 in New York (October 2020-April 2021) for its accuracy in predicting number of COVID-19 admissions at three, five, seven and 10 days into the future comparing predicted admissions with actual admissions for each day at a large integrated healthcare delivery network. Mean absolute percent error of the model was found to be low when evaluated across the entire health system, for a single region of the health system or for a single large hospital (6.1%-7.6% for 3-day predictions, 9.2%-10.4% for five-day predictions, 12.4%-13.2% for seven-day predictions, and 17.1-17.8% for 10-day predictions).

Quantifying Mycobacterium tuberculosis transmission dynamics across global settings: a systematic analysis.

The degree to which individual heterogeneity in the production of secondary cases ("superspreading") affects tuberculosis (TB) transmission has not been systematically studied. We searched for population-based or surveillance studies in which whole genome sequencing was used to estimate TB transmission and the size distributions of putative TB transmission clusters were enumerated. We fit cluster size distribution data to a negative binomial branching process model to jointly infer the transmission parameters $R$ (the reproductive number) and dispersion parameter, $k$, which quantifies the propensity of superspreading in a population (generally, lower values of $k$ ($<1.0$) suggest increased heterogeneity). Of 4,796 citations identified in our initial search, nine studies met inclusion criteria ($n=5$ all TB; $n=4$ drug resistant TB) from eight global settings. Estimated $R$ values (range: 0.10, 0.73) were below 1.0, consistent with declining epidemics in the included settings; estimated $k$ values were well below 1.0 (range: 0.02, 0.48), indicating the presence of substantial individual-level heterogeneity in transmission across all settings. We estimated that a minority of cases (range 2-31%) drive the majority (80%) of ongoing transmission at the population level. Identifying sources of heterogeneity and accounting for them in TB control may have a considerable impact on mitigating TB transmission.

Tradeoff between speed and reproductive number in pathogen evolution

The rapid succession of new variants of SARS-CoV-2 emphasizes the need to understand the factors driving pathogen evolution. Here, we investigate a possible tradeoff between the rate of progression of a disease and its reproductive number. Using an SEIR framework, we show that in the exponential growth phase of an epidemic, there is an optimal disease duration that balances the advantage of a fast disease progression with that of causing many secondary infections. This result offers one possible explanation for the ever shorter generation times of novel variants of SARS-CoV-2, as it progressed from the original strain to the Alpha, Delta, and, from late 2021 onwards, to several Omicron variant subtypes. In the endemic state, the optimum disappears and longer disease duration becomes advantageous for the pathogen. However, selection pressures depend on context: mitigation strategies such as quarantine of infected individuals may slow down the evolution towards longer-lasting, more infectious variants. This work then suggests that, in the future, the trend towards shorter generation times may reverse, and SARS-CoV-2 may instead evolve towards longer-lasting variants. © 2023 authors. Published by the American Physical Society. Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI.

Weather variability and transmissibility of COVID-19: a time series analysis based on effective reproductive number.

COVID-19 is causing a significant burden on medical and healthcare resources globally due to high numbers of hospitalisations and deaths recorded as the pandemic continues. This research aims to assess the effects of climate factors (i.e., daily average temperature and average relative humidity) on effective reproductive number of COVID-19 outbreak in Wuhan, China during the early stage of the outbreak. Our research showed that effective reproductive number of COVID-19 will increase by 7.6% (95% Confidence Interval: 5.4% ~ 9.8%) per 1°C drop in mean temperature at prior moving average of 0-8 days lag in Wuhan, China. Our results indicate temperature was negatively associated with COVID-19 transmissibility during early stages of the outbreak in Wuhan, suggesting temperature is likely to effect COVID-19 transmission. These results suggest increased precautions should be taken in the colder seasons to reduce COVID-19 transmission in the future, based on past success in controlling the pandemic in Wuhan, China.

The Epidemiology of COVID-19 in Malaysia.

BACKGROUND: COVID-19 has rapidly spread across the globe. Critical to the control of COVID-19 is the characterisation of its epidemiology. Despite this, there has been a paucity of evidence from many parts of the world, including Malaysia. We aim to describe the epidemiology of COVID-19 in Malaysia to inform prevention and control policies better. METHODS: Malaysian COVID-19 data was extracted from 16 March 2020 up to 31 May 2021. We estimated the following epidemiological indicators: 7-day incidence rates, 7-day mortality rates, case fatality rates, test positive ratios, testing rates and the time-varying reproduction number (Rt). FINDINGS: Between 16 March 2020 and 31 May 2021, Malaysia has reported 571,901 cases and 2,796 deaths. Malaysia's average 7-day incidence rate was 26•6 reported infections per 100,000 population (95% CI: 17•8, 38•1). The average test positive ratio and testing rate were 4•3% (95% CI: 1•6, 10•2) and 0•8 tests per 1,000 population (95% CI: <0•1, 3•7), respectively. The case fatality rates (CFR) was 0•6% (95% CI: <0•1, 3•7). Among the 2,796 cases who died, 87•3% were ≥ 50 years. INTERPRETATION: The public health response was successful in the suppression of COVID-19 transmission or the first half of 2020. However, a state election and outbreaks in institutionalised populations have been the catalyst for more significant community propagation. This rising community transmission has continued in 2021, leading to increased incidence and strained healthcare systems. Calibrating NPI based on epidemiological indicators remain critical for us to live with the virus. (243 words). FUNDING: This study is part of the COVID-19 Epidemiological Analysis and Strategies (CEASe) Project with funding from the Ministry of Science, Technology and Innovation (UM.0000245/HGA.GV).

ACE2 enhance viral infection or viral infection aggravate the underlying diseases.

ACE2 plays a critical role in SARS-CoV-2 infection to cause COVID-19 and SARS-CoV-2 spike protein binds to ACE2 and probably functionally inhibits ACE2 to aggravate the underlying diseases of COVID-19. The important factors that affect the severity and fatality of COVID-19 include patients' underlying diseases and ages. Therefore, particular care to the patients with underlying diseases is needed during the treatment of COVID-19 patients.

Analyzing the effects of social distancing on the COVID-19 pandemic in Korea using mathematical modeling.

OBJECTIVES: During the 6 months since the first coronavirus disease 2019 (COVID-19) patient was diagnosed in Korea on January 20, 2020, various prevention and control measures have been implemented according to the COVID-19 epidemic pattern. Therefore, this study aimed to estimate the reproductive numbers (R) for each epidemic stage to analyze the effects of the preventive measures and to predict the COVID-19 transmission trends. METHODS: We estimated the transmission rates for each epidemic stage by fitting a COVID-19 transmission model, based on a deterministic mathematical model, to the data on confirmed cases. The effects of preventive measures such as social distancing by time period were analyzed, and the size and trends of future COVID-19 outbreaks were estimated. RESULTS: The value of R was 3.53 from February18, 2020 to February 28, 2020, and the mean R reduced to 0.45 from March 14, 2020 to April 29, 2020, but it significantly increased to 2.69 from April 30, 2020 to May13, 2020 and it was maintained at 1.03 from May 14, 2020 to July 23, 2020. CONCLUSIONS: According to the estimated R, it had fallen to below 1 and was maintained at that level owing to the isolation of infected persons by the public health authorities and social distancing measures followed by the general public. Then, the estimated R increased rapidly as the contact among individuals increased during the long holiday period from April 30, 2020 to May 5, 2020. Thereafter, the value of R dropped, with the continued use of preventive measures but remained higher than 1.00, indicating that the COVID-19 outbreak can be prolonged and develop into a severe outbreak at any time.

The Impact of a Delay on the Evolution of Epidemics

: Based on a discrete model of the spread of infection in a closed population, the corresponding form of differential equations with delay is found. It is shown that the development of the epidemic is determined by four key parameters: the number of infectious persons, the average number of dangerous contacts of one infectious person per day, the probability of infection as a result of such contact, and the average time interval during which the sick person is able to infect others. The decision also depends on the size of the population and on the initial number of infected persons. The four named parameters have a clear meaning and are related to the well-known concept of reproductive number in the continuous Susceptible–Infectious–Recovered (SIR) and Susceptible–Infected–Infectious–Recovered (SEIR) models. The epidemic saturation conditions are established by solving the obtained differential equations. It is shown that, due to the long virus carrying characteristic of COVID-19, the solutions proposed here differ significantly from the SIR model. © 2022, Pleiades Publishing, Ltd.

The reproduction rate of severe acute respiratory syndrome coronavirus 2 different variants recently circulated in human: a narrative review.

SARS-COV-2 is responsible for the current worldwide pandemic, which started on December 2019 in Wuhan, China. On March 2020 World Health Organization announced COVID-19 as the new pandemic. Some SARS-COV-2 variants have increased transmissibility, cause more severe disease (e.g., increased hospitalizations or deaths), are resistant to antibodies produced by the previous infection or vaccination, and there is more difficulty in treatment and diagnosis of them. World Health Organization considered them as SARS-CoV-2 variants of concern. The introductory reproduction rate (R0) is an epidemiologic index of the transmissibility of the virus, defined as the average number of persons infected by the virus after known contact with an infectious person in a susceptible population. An R0 > 1 means that the virus is spreading exponentially, and R0 < 1, means that the outbreak is subsiding. In various studies, the estimated R and VOC growth rates were reported to be greater than the ancestral strains. However, it was also a low level of concordance between the estimated Rt of the same variant in different studies. It is because the R of a variant not only dependent on the biological and intrinsic factors of the virus but also several parameters can affect the R0, including the duration of contagiousness and the likelihood of infection per contact. Evaluation of changes in SARS-CoV-2 has shown that the rate of human-to-human transmission of this virus has increased. Like other viruses with non-human sources which succeeded in surviving in the human population, SARS-CoV-2 has gradually adapted to the human population, and its ability to transmit from human to human has increased. Of course, due to the continuous changes in this virus, it is crucial to survey the rate of transmission of the virus over time.

How the effective reproductive number impacts global stock markets

The pandemic caused by the novel coronavirus COVID-19 has impact the economies of countries across the world. In a short period of time, researchers have begun to analyse the effect of the pandemic on global stock markets. Although the most known measurements of COVID-19 are the number of new cases and deaths, there are more robust indicators. In particular, the effective reproductive number is one of the most important indicators to analyse the pandemic which indicates the degree to which the spread is under control. In this paper, we assess the impact that the Effective Reproductive Number (Rt) has on 26 countries around the world (32 stock market indexes) comparing the performance of various forms of Generalized AutoRegressive Conditional Heteroskedasticity models. The results demonstrate that of the 32 stock markets analysed, 37.5% had a negative effect with respect to Rt and only in 12.5% of the cases was the effect of the variation of Rt positive. This implies that in more than a third of the stock markets analysed as the pandemic progressed uncontrolled the result was a decrease in the value of the market index. The 11 of the 26 countries analysed had a negative and significant effect (Brazil, Germany, Indonesia, Israel, Italy, Japan, Russia, South Korea, Sweden, Taiwan, and United States). Findings suggest that the Effective Reproductive Number volatility had a significant impact on 10 of the 26 countries analysed (38.5%) (Australia, Brazil, Canada, China, India, Italy, Mexico, Russia, Singapore and United Kingdom). © 2023 John Wiley & Sons Ltd.

Computational Modeling of Reaction-Diffusion COVID-19 Model Having Isolated Compartment

Cases of COVID-19 and its variant omicron are raised all across the world. The most lethal form and effect of COVID-19 are the omicron version, which has been reported in tens of thousands of cases daily in numerous nations. Following WHO (World health organization) records on 30 December 2021, the cases of COVID-19 were found to be maximum for which boarding individuals were found 1,524,266, active, recovered, and discharge were found to be 82,402 and 34,258,778, respectively. While there were 160,989 active cases, 33,614,434 cured cases, 456,386 total deaths, and 605,885,769 total samples tested. So far, 1,438,322,742 individuals have been vaccinated. The coronavirus or COVID-19 is inciting panic for several reasons. It is a new virus that has affected the whole world. Scientists have introduced certain ways to prevent the virus. One can lower the danger of infection by reducing the contact rate with other persons. Avoiding crowded places and social events with many people reduces the chance of one being exposed to the virus. The deadly COVID-19 spreads speedily. It is thought that the upcoming waves of this pandemic will be even more dreadful. Mathematicians have presented several mathematical models to study the pandemic and predict future dangers. The need of the hour is to restrict the mobility to control the infection from spreading. Moreover, separating affected individuals from healthy people is essential to control the infection. We consider the COVID-19 model in which the population is divided into five compartments. The present model presents the population's diffusion effects on all susceptible, exposed, infected, isolated, and recovered compartments. The reproductive number, which has a key role in the infectious models, is discussed. The equilibrium points and their stability is presented. For numerical simulations, finite difference (FD) schemes like nonstandard finite difference (NSFD), forward in time central in space (FTCS), and Crank Nicolson (CN) schemes are implemented. Some core characteristics of schemes like stability and consistency are calculated. © 2023 Tech Science Press. All rights reserved.

A Predictive Model for R0(SARS-COV2)

Due to the rapid spread of the COVID-19, scientists are constantly monitoring the evolution of the number of infections in a region. In particular, the basic reproductive number (R0) is studied, because it indicates if the number of cases will increase and the infection will last, or if it will decrease and stability will be reached. The present contribution is focused on forecasting this ratio, based on the extreme gradient boosting tree approach. Gradient reinforcement trees are used. Using public data of the COVID-19 outbreak in the Caribbean and some countries, this value is computed. © 2022 IEEE.

Epidemiology of SARS-CoV-2 Omicron BA.5 Infections, Macau, June-July 2022.

A SARS-CoV-2 Omicron BA.5 outbreak occurred in Macau from mid-June through July 2022. Out of >1,800 laboratory-confirmed cases, most were mild or asymptomatic; only 6 deaths were recorded. The outbreak was controlled through stringent public health and social measures, such as repeated universal testing and a stay-at-home order lasting 2 weeks.

Modeling shield immunity to reduce COVID-19 transmission in long-term care facilities.

PURPOSE: Nursing homes and long-term care facilities have experienced severe outbreaks and elevated mortality rates of COVID-19. When available, vaccination at-scale has helped drive a rapid reduction in severe cases. However, vaccination coverage remains incomplete among residents and staff, such that additional mitigation and prevention strategies are needed to reduce the ongoing risk of transmission. One such strategy is that of "shield immunity", in which immune individuals modulate their contact rates and shield uninfected individuals from potentially risky interactions. METHODS: Here, we adapt shield immunity principles to a network context, by using computational models to evaluate how restructured interactions between staff and residents affect SARS-CoV-2 epidemic dynamics. RESULTS: First, we identify a mitigation rewiring strategy that reassigns immune healthcare workers to infected residents, significantly reducing outbreak sizes given weekly testing and rewiring (48% reduction in the outbreak size). Second, we identify a preventative prewiring strategy in which susceptible healthcare workers are assigned to immunized residents. This preventative strategy reduces the risk and size of an outbreak via the inadvertent introduction of an infectious healthcare worker in a partially immunized population (44% reduction in the epidemic size). These mitigation levels derived from network-based interventions are similar to those derived from isolating infectious healthcare workers. CONCLUSIONS: This modeling-based assessment of shield immunity provides further support for leveraging infection and immune status in network-based interventions to control and prevent the spread of COVID-19.

Risk Assessment of Large-Scale Sports Events in the Context of COVID-19

This paper assesses the potential risks of epidemic situation and public opinion during the Beijing Winter Olympic Games by analyzing the epidemic situation and public opinion of the Tokyo Olympic Games. The results show that there is a strong time-lag correlation between the COVID-19 epidemic and the public opinion of the Tokyo Olympics. For the epidemic situation, the multi-agent modeling method is used at the city level to simulate the possible spread of diseases in the city where the event was held. At the Olympic village level, the modified the SEIR transmission model is modified to simulate the virus transmission in the Olympic Village during the Beijing Winter Olympic Games. At the end, the risk analysis of the Beijing Winter Olympic Games is carried out based on the time series prediction model. © 2022, Editorial Board of Journal of the University of Electronic Science and Technology of China. All right reserved.

How the effective reproductive number impacts global stock markets

The pandemic caused by the novel coronavirus COVID-19 has impact the economies of countries across the world. In a short period of time, researchers have begun to analyse the effect of the pandemic on global stock markets. Although the most known measurements of COVID-19 are the number of new cases and deaths, there are more robust indicators. In particular, the effective reproductive number is one of the most important indicators to analyse the pandemic which indicates the degree to which the spread is under control. In this paper, we assess the impact that the Effective Reproductive Number (Rt) has on 26 countries around the world (32 stock market indexes) comparing the performance of various forms of Generalized AutoRegressive Conditional Heteroskedasticity models. The results demonstrate that of the 32 stock markets analysed, 37.5% had a negative effect with respect to Rt and only in 12.5% of the cases was the effect of the variation of Rt positive. This implies that in more than a third of the stock markets analysed as the pandemic progressed uncontrolled the result was a decrease in the value of the market index. The 11 of the 26 countries analysed had a negative and significant effect (Brazil, Germany, Indonesia, Israel, Italy, Japan, Russia, South Korea, Sweden, Taiwan, and United States). Findings suggest that the Effective Reproductive Number volatility had a significant impact on 10 of the 26 countries analysed (38.5%) (Australia, Brazil, Canada, China, India, Italy, Mexico, Russia, Singapore and United Kingdom). © 2023 John Wiley & Sons Ltd.

Decoding the double trouble: A mathematical modelling of co-infection dynamics of SARS-CoV-2 and influenza-like illness.

After the detection of coronavirus disease 2019 (Covid-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, Hubei Province, China in late December, the cases of Covid-19 have spiralled out around the globe. Due to the clinical similarity of Covid-19 with other flulike syndromes, patients are assayed for other pathogens of influenza like illness. There have been reported cases of co-infection amongst patients with Covid-19. Bacteria for example Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, Mycoplasma pneumoniae, Chlamydia pneumonia, Legionella pneumophila etc and viruses such as influenza, coronavirus, rhinovirus/enterovirus, parainfluenza, metapneumovirus, influenza B virus etc are identified as co-pathogens. In our current effort, we develop and analysed a compartmental based Ordinary Differential Equation (ODE) type mathematical model to understand the co-infection dynamics of Covid-19 and other influenza type illness. In this work we have incorporated the saturated treatment rate to take account of the impact of limited treatment resources to control the possible Covid-19 cases. As results, we formulate the basic reproduction number of the model system. Finally, we have performed numerical simulations of the co-infection model to examine the solutions in different zones of parameter space.