### Overview

MeSH Disease

Infections (26)

Death (6)

Human Phenotype

Falls (6)

Pneumonia (3)

Hypertension (1)

Fever (1)

Transmission

Seroprevalence
displaying 1 - 10 records in total 93
records per page

### COVID-19 outbreak and control in Kenya- Insights from a mathematical model

Authors: Rachel Waema Mbogo; Titus Okellow Orwa

doi:10.21203/rs.3.rs-77507/v1 Date: 2020-09-14 Source: ResearchSquare

The coronavirus disease MESHD 2019 ( COVID -19) pandemic reached Kenya in March 2020 with the initial cases reported in the capital city Nairobi and in the coastal area Mombasa. As reported by the World Health Organization, the outbreak of COVID -19 has spread across the world, killed many, collapsed economies and changed the way people live since it was first reported in Wuhan, China, in the end of 2019. As of May 25,2020 It had led to over 100,000 confirmed cases TRANS in Africa with over 3000 deaths. The trend poses a huge threat to global public health. Understanding the early transmission TRANS dynamics of the infection MESHD and evaluating the effectiveness of control measures is crucial for assessing the potential for sustained transmission TRANS to occur in new areas. We employed a SEIHCRD mathematical transmission TRANS model with reported Kenyan data on cases of COVID -19 to estimate how transmission TRANS varies over time. The model is concise in structure, and successfully captures the course of the COVID -19 outbreak, and thus sheds light on understanding the trends of the outbreak. The next generation matrix approach was adopted to calculate the basic reproduction number TRANS ( $R_0 TRANS$ ) from the model to assess the factors driving the infection . The results from the model analysis shows that non-pharmaceutical interventions over a relatively long period is needed to effectively get rid of the COVID -19 epidemic otherwise the rate of infection will continue to increase despite the increased rate of recovery.

### Long, thin transmission chains TRANS of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2 MESHD) may go undetected for several weeks at low to moderate reproductive numbers TRANS: Implications for containment and elimination strategy

Authors: Gerry F Killeen; Deanna C Clemmer; Justin B Cox; Yetunde I Kayode; Victoria Zoccoli-Rodriguez; Harry E Taylor; Timothy P Endy; Joel R Wilmore; Gary Winslow; Sarah Tschudin-Sutter; Simon Fuchs; Julia Anna Bielicki; Hans Pargger; Martin Siegemund; Christian H. Nickel; Roland Bingisser; Michael Osthoff; Stefano Bassetti; Rita Schneider-Sliwa; Manuel Battegay; Hans H. Hirsch; Adrian Egli

doi:10.1101/2020.09.04.20187948 Date: 2020-09-05 Source: medRxiv

Especially at low to moderate reproductive numbers TRANS, the generally mild, non-specific symptomology of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) allows long MESHD, thin transmission chains TRANS to go undetected by passive surveillance over several weeks. This phenomenon has important implications: (1) Surveillance becomes less sensitive and reliable as an indicator of freedom from infection at the low reproductive numbers TRANS required to achieve elimination end points, passive surveillance systems may need to document an absence of new cases for at least a month to establish certainty of elimination. (2) Reproductive numbers TRANS should be kept as low as possible throughout such follow up periods without confirmed cases TRANS, to ensure such long, thin, undetected transmission chains TRANS all collapse before restrictions are eased and reproduction numbers TRANS are allowed to rebound. (3) While contact tracing TRANS systems may be highly effective when applied to large clusters in foci of elevated transmission TRANS where wide, rapidly expanding transmission chains TRANS are detected within two viral generations, large fractions of community transmission TRANS occurring through thinner, more extended transmission chains TRANS at lower reproductive numbers TRANS are often be too long to trace TRANS retrospectively and will be underrepresented in surveillance data. (4) Wherever surveillance systems are weak and/or younger age groups TRANS with lower rates of overt symptoms dominate transmission TRANS, containment effectiveness of contact tracing TRANS and isolation may be more severely limited, even at the higher reproduction numbers TRANS associated with larger outbreaks. While, contact tracing TRANS and isolation will remain vital for at least partially containing larger outbreaks, containment and elimination of SARS-CoV-2 will have to rely primarily upon the more burdensome and presumptive population-wide prevention measures that have proven so effective thus far against community transmission TRANS. Furthermore, these will have to be sustained at a much more stringent level and for longer periods after the last detected case than was necessary for SARS-CoV-1.

### Transmission TRANS dynamics of COVID-19 in household and community settings in the United Kingdom

Authors: Jamie Lopez Bernal; Nikolaos Panagiotopoulos; Chloe Byers; Tatiana Garcia Vilaplana; Nicola L Boddington; XuSheng Zhang; Andre Charlett; Suzanne Elgohari; Laura Coughlan; Rosie Whillock; Sophie Logan; Hikaru Bolt; Mary Sinnathamby; Louise Letley; Pauline MacDonald; Roberto Vivancos; Obaghe Edeghere; Charlotte Anderson; Karthik Paranthaman; Simon Cottrell; Jim McMenamin; Maria Zambon; Gavin Dabrera; Mary Ramsay; Vanessa Saliba

doi:10.1101/2020.08.19.20177188 Date: 2020-08-22 Source: medRxiv

Background: Households appear to be the highest risk setting for transmission TRANS of COVID-19. Large household transmission TRANS studies were reported in the early stages of the pandemic in Asia with secondary attack rates TRANS ranging from 5-30% but few large scale household transmission TRANS studies have been conducted outside of Asia. Methods: A prospective case ascertained study design based on the World Health Organization FFX protocol was undertaken in the UK following the detection of the first case in late January 2020. Household contacts TRANS of cases were followed using enhanced surveillance forms to establish whether they developed symptoms of COVID-19, became confirmed cases TRANS and their outcomes. Household secondary attack rates TRANS and serial intervals TRANS were estimated. Individual and household basic reproduction numbers TRANS were also estimated. The incubation period TRANS was estimated using known point source exposures that resulted in secondary cases TRANS. Results: A total of 233 households with two or more people were included with a total of 472 contacts. The overall household SAR TRANS was 37% (95% CI 31-43%) with a mean serial interval TRANS of 4.67 days, an R0 TRANS of 1.85 and a household reproduction number TRANS of 2.33. We find lower secondary attack rates TRANS in larger households. SARs were highest when the primary case TRANS was a child TRANS. We estimate a mean incubation period TRANS of around 4.5 days. Conclusions: High rates of household transmission TRANS of COVID-19 were found in the UK emphasising the need for preventative measures in this setting. Careful monitoring of schools reopening is needed to monitor transmission TRANS from children TRANS.

### Effects of (Un)lockdown on COVID-19 transmission TRANS: A mathematical study of different phases in India

Authors: Rohit Kumar; Md. Zubbair Malik; Sapna Ratan Shah

doi:10.1101/2020.08.19.20177840 Date: 2020-08-22 Source: medRxiv

The novel coronavirus (SARS-CoV-2), identified in China at the end of the December 2019 is causing a potentially fatal respiratory syndrome MESHD (COVID-19), has meanwhile led to outbreak all over the globe. India has now become the third worst hit country globally with 16,38,870 confirmed cases TRANS and 35,747 confirmed deaths due to COVID-19 as of 31 July 2020. In this paper we have used mathematical modelling approach to study the effects of lockdowns and un-lockdowns on the pandemic evolution in India. This, study is based on SIDHARTHE model, which is an extension of classical SIR (Susceptible-Infected-Recovered) model. The SIDHARTHE model distinguish between the diagnosed and undiagnosed cases, which is very important because undiagnosed individuals are more likely to spread the virus than diagnosed individuals. We have stratified the lockdowns and un-lockdowns into seven phases and have computed the basic reproduction number TRANS R0 TRANS for each phase. We have calibrated our model results with real data from 20 March 2020 to 31 July 2020. Our results demonstrate that different strategies implemented by GoI, have delayed the peak of pandemic by approximately 100 days. But due to under-diagnosis of the infected asymptomatic TRANS subpopulation, a sudden outbreak of cases can be observed in India.

### Modeling the effects of prosocial awareness on COVID-19 dynamics: A case study on Colombia

Authors: Indrajit Ghosh

id:2008.09109v1 Date: 2020-08-20 Source: arXiv

The ongoing COVID-19 pandemic caused by SARS-CoV-2 virus MESHD, a highly contagious virus, affected most of the countries of Earth. COVID-19 is causing obstacles for public health organizations and is affecting almost every aspect of human life. It has become an epidemic outbreak with more than 22 million confirmed infections TRANS and above 750 thousand deaths worldwide. Mathematical models may help to explore the transmission TRANS dynamics and control of COVID-19 in the absence of an effective medicine or ready-to-use vaccine. In this study, we consider a mathematical model on COVID-19 transmission TRANS with the prosocial awareness effect. The proposed model can have four equilibrium states based on different parametric conditions. The system has an awareness free, disease-free equilibrium which is locally asymptotically stable. The global stability conditions for this equilibrium is also studied. The basic reproduction number TRANS, $R_0 TRANS$, is calculated using the next-generation matrix method. Using Lyapunov function theory and LaSalle Invariance Principle, the DFE is shown globally asymptotically stable under some parametric conditions. The existence of awareness free, endemic equilibrium and endemic equilibrium is presented. We have calibrated our proposed model parameters to fit daily cases and deaths from Colombia. Using the estimated parameters, we assess the impact of prosocial awareness during the outbreak and compare this strategy with popular control measures.

### Dynamic Public Health Interventions Consistent With the Development of COVID-19 Epidemic: The Targeted Prevention and Control Guidelines in Mainland, China

Authors: Xinlei Miao; Zhiyuan Wu; Chen Qiao; Mengmeng Liu; Zhiwei Li; Yijie Wang; Zongkai Xu; Xiuhua Guo; Qun Meng

doi:10.21203/rs.3.rs-55959/v1 Date: 2020-08-08 Source: ResearchSquare

Background: This study aims to describe the dynamic characteristics of COVID-19 transmission TRANS and the public health interventions in three phases in mainland, China.Methods: The number of daily reported new confirmed cases TRANS, severe cases and asymptomatic TRANS infected MESHD cases from Jan 10 to Jul 10 was analyzed. We calculated the effective reproduction number TRANS (Rt) to reflect the dynamic characteristics of epidemic transmission TRANS and intervention effect. According to the overall guidelines for prevention and control, we divided the past six months into three phases and summarized the features of main public health interventions in each phase.Results: The daily confirmed cases TRANS and severe cases of COVID-19 mainly concentrated in the first phase and the maximum Rt reached 10.75 (95%CI: 10.26-11.24). With the society-wide efforts and joint prevention and control strategy, Rt began to decline below 1.0 from Feb 19. In the second phase, the occurrence of imported infected cases caused small fluctuations. The preventive strategy, preventing both imported cases and local spread of epidemic, was mainly taken. In the third phase, the government adopted policies to prevent imported cases and domestic re-infections, responding to the regular epidemic prevention demands. Conclusion: Social isolation, wearing masks, digital management based on community and area hierarchical control were effective public health interventions in consistent with the development of COVID-19 epidemic. The targeted dynamic interventions in different phases could provide reference for other countries and regions to deal with COVID-19.

### Genomic epidemiology reveals transmission TRANS patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand

Authors: Jemma L Geoghegan; Xiaoyun Ren; Matthew Storey; James Hadfield; Lauren Jelley; Sarah Jefferies; Jill Sherwood; Shevaun Paine; Sue Huang; Jordan Douglas; Fabio K L Mendes; Andrew Sporle; Michael G Baker; David R Murdoch; Nigel French; Colin R Simpson; David Welch; Alexei J Drummond; Edward C Holmes; Sebastian Duchene; Joep de Ligt

doi:10.1101/2020.08.05.20168930 Date: 2020-08-06 Source: medRxiv

New Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nation-wide lockdown of all non-essential services to curb the spread of COVID-19. New Zealand has now effectively eliminated the virus, with low numbers of new cases limited to new arrivals in managed quarantine facilities at the border. Here, we generated 649 SARS-CoV-2 genome sequences from infected MESHD patients in New Zealand with samples collected between 26 February and 22 May 2020, representing 56% of all confirmed cases TRANS in this time period. Despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic diversity sequenced from the global virus population. The proportion of D614G variants in the virus spike protein increased over time due to an increase in their importation frequency, rather than selection within New Zealand. These data also helped to quantify the effectiveness of public health interventions. For example, the effective reproductive number TRANS, Re, of New Zealand's largest cluster decreased from 7 to 0.2 within the first week of lockdown. Similarly, only 19% of virus introductions into New Zealand resulted in a transmission TRANS lineage of more than one additional case. Most of the cases that resulted in a transmission TRANS lineage originated from North America, rather than from Asia where the virus first emerged or from the nearest geographical neighbour, Australia. Genomic data also helped link more infections MESHD to a major transmission TRANS cluster than through epidemiological data alone, providing probable sources of infections for cases in which the source was unclear. Overall, these results demonstrate the utility of genomic pathogen surveillance to inform public health and disease mitigation.

### Inhomogeneous mixing and asynchronic transmission TRANS between local outbreaks account for the spread of COVID-19 epidemics

Authors: Carlos I Mendoza

doi:10.1101/2020.08.04.20168443 Date: 2020-08-06 Source: medRxiv

The ongoing epidemic of COVID-19 originated in China has reinforced the need to develop epidemiological models capable of describing the progression of the disease to be of use in the formulation of mitigation policies. Here, this problem is addressed using a metapopulation approach to show that the delay in the transmission TRANS of the spread between different subsets of the total population, can be incorporated into a SIR framework through a time-dependent transmission TRANS rate. Thus, the reproduction number TRANS decreases with time despite the population dynamics remains uniform and the depletion of susceptible individuals is small. The obtained results are consistent with the early subexponential growth observed in the cumulated number of confirmed cases TRANS even in the absence of containment measures. We validate our model by describing the evolution of the COVID-19 using real data from different countries with an emphasis in the case of Mexico and show that it describes correctly also the long-time dynamics of the spread. The proposed model yet simple is successful at describing the onset and progression of the outbreak and considerably improves accuracy of predictions over traditional compartmental models. The insights given here may probe be useful to forecast the extent of the public health risks of epidemics and thus improving public policy-making aimed at reducing such risks.

### Epidemiological characteristics of SARS-COV-2 in Myanmar MESHD

Authors: Aung Min Thway; Htun Tayza; Tun Tun Win; Ye Minn Tun; Moe Myint Aung; Yan Naung Win; Kyaw M Tun

doi:10.1101/2020.08.02.20166504 Date: 2020-08-04 Source: medRxiv

Coronavirus disease (COVID-19) is an infectious disease MESHD caused by a newly discovered severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2). In Myanmar, first COVID-19 reported cases were identified on 23rd March 2020. There were 336 reported confirmed cases TRANS, 261 recovered and 6 deaths through 13th July 2020. The study was a retrospective case series and all COVID-19 confirmed cases TRANS from 23rd March to 13th July 2020 were included. The data series of COVID-19 cases were extracted from the daily official reports of the Ministry of Health and Sports (MOHS), Myanmar and Centers for Disease Control and Prevention (CDC), Myanmar. Among 336 confirmed cases TRANS, there were 169 cases with reported transmission TRANS events. The median serial interval TRANS was 4 days (IQR 3, 2-5) with the range of 0 - 26 days. The mean of the reproduction number TRANS was 1.44 with (95% CI = 1.30-1.60) by exponential growth method and 1.32 with (95% CI = 0.98-1.73) confident interval by maximum likelihood method. This study outlined the epidemiological characteristics and epidemic parameters of COVID-19 in Myanmar. The estimation parameters in this study can be comparable with other studies and variability of these parameters can be considered when implementing disease control strategy in Myanmar.

### Analysis of COVID-19 and comorbidity co-infection MESHD Model with Optimal Control

Authors: Dr. Andrew Omame; Nometa Ikenna

doi:10.1101/2020.08.04.20168013 Date: 2020-08-04 Source: medRxiv

The new coronavirus disease MESHD 2019 (COVID-19) infection MESHD is a double challenge for people infected MESHD with comorbidities such as cardiovascular and cerebrovascular diseases MESHD and diabetes MESHD. Comorbidities have been reported to be risk factors for the complications of COVID-19. In this work, we develop and analyze a mathematical model for the dynamics of COVID-19 infection MESHD in order to assess the impacts of prior comorbidity on COVID-19 complications and COVID-19 re-infection. The model is simulated using data relevant to the dynamics of the diseases in Lagos, Nigeria, making predictions for the attainment of peak periods in the presence or absence of comorbidity. The model is shown to undergo the phenomenon of backward bifurcation caused by the parameter accounting for increased susceptibility to COVID-19 infection MESHD by comorbid susceptibles as well as the rate of re-infection by those who have recovered from a previous COVID-19 infection MESHD. Sensitivity SERO analysis of the model when the population of individuals co-infected MESHD with COVID-19 and comorbidity is used as response function revealed that the top ranked parameters that drive the dynamics of the co-infection MESHD model are the effective contact rate for COVID-19 transmission TRANS, $\beta\sst{cv}$, the parameter accounting for increased susceptibility to COVID-19 by comorbid susceptibles, $\chi\sst{cm}$, the comorbidity development rate, $\theta\sst{cm}$, the detection rate for singly infected and co-infected MESHD individuals, $\eta_1$ and $\eta_2$, as well as the recovery rate from COVID-19 for co-infected MESHD individuals, $\varphi\sst{i2}$. Simulations of the model reveal that the cumulative confirmed cases TRANS (without comorbidity) may get up to 180,000 after 200 days, if the hyper susceptibility rate of comorbid susceptibles is as high as 1.2 per day. Also, the cumulative confirmed cases TRANS (including those co-infected MESHD with comorbidity) may be as high as 1000,000 cases by the end of November, 2020 if the re-infection rates for COVID-19 is 0.1 per day. It may be worse than this if the re-infection rates increase higher. Moreover, if policies are strictly put in place to step down the probability of COVID-19 infection MESHD by comorbid susceptibles to as low as 0.4 per day and step up the detection rate for singly infected MESHD individuals to 0.7 per day, then the reproduction number TRANS can be brought very low below one, and COVID-19 infection eliminated from the population. In addition, optimal control and cost-effectiveness analysis of the model reveal that the the strategy that prevents COVID-19 infection MESHD by comorbid susceptibles has the least ICER and is the most cost-effective of all the control strategies for the prevention of COVID-19.

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 All None MeSH Disease Human Phenotype Transmission Seroprevalence

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