[Estimating the basic reproduction number of COVID-19 in Wuhan, China]

Improved time-varying reproduction numbers using the generation interval for COVID-19

Estimating key epidemiological parameters, such as incubation period, serial interval (SI), generation interval (GI) and latent period, is essential to quantify the transmissibility and effects of various interventions of COVID-19. These key parameters play a critical role in quantifying the basic reproduction number. With the hard work of epidemiological investigators in South Korea, estimating these key parameters has become possible based on infector-infectee surveillance data of COVID-19 between February 2020 and April 2021. Herein, the mean incubation period was estimated to be 4.9 days (95% CI: 4.2, 5.7) and the mean generation interval was estimated to be 4.3 days (95% CI: 4.2, 4.4). The mean serial interval was estimated to be 4.3, with a standard deviation of 4.2. It is also revealed that the proportion of presymptomatic transmission was ~57%, which indicates the potential risk of transmission before the disease onset. We compared the time-varying reproduction number based on GI and SI and found that the time-varying reproduction number based on GI may result in a larger estimation of Rt, which refers to the COVID-19 transmission potential around the rapid increase of cases. This highlights the importance of considering presymptomatic transmission and generation intervals when estimating the time-varying reproduction number.

Update on COVID-19 and Effectiveness of a Vaccination Campaign in a Global Context

The COVID-19 pandemic caused by SARS-CoV-2 remains a significant issue for global health, the economy, and society. When SARS-CoV-2 began to spread, the most recent serious infectious disease of this century around the world, with its high morbidity and mortality rates, it is understandable why such infections have generally been spread in the past, mainly from international travel movements. This perspective review aimed to provide an update for clinicians on the recent developments related to the microbiological perspectives in pandemics, diagnostics, prevention (such as the spread of a virus), vaccination campaigns, treatment options, and health consequences for COVID-19 based on the current literature. In this way, the authors attempt to raise awareness on the transversal nature of these challenges by identifying the main risk/vulnerability factors that the scientific community must face including our current knowledge on the virus capacity of the mechanism of entry into the cells, the current classifications of viral variants, the knowledge of the mathematical model on the spread of viruses (the possible routes of transmission), and the effectiveness of vaccination campaigns in a global context of pandemic, particularly from COVID-19, with a look at new or future vaccines.

Epidemiological Characteristics of COVID-19 Outbreak in Yangzhou, China, 2021

Objective

Epidemiological characteristics of COVID-19 outbreak in Yangzhou city caused by the highly contagious Delta variant strain of SARS-CoV-2 virus were investigated in this retrospective descriptive study to provide prevention and control guidelines for outbreaks in the future.

Methods

All the epidemiological data used in this study were collected manually from the official website of the Yangzhou Municipal Health Committee from 28 July to 26 August 2021, and then were analyzed systematically and statistically in this study.

Results

A total of 570 COVID-19 cases were reported during the short-term outbreak in Yangzhou City. The ages of infected individuals ranged from 1 to 90 years with the average age at 49.47 ± 22.69 years. As for gender distributions, the ratio of male- to-female patients was 1:1.36 (242:328). Geographic analysis showed that 377 patients (66.1%) were in Hanjiang District while 188 patients (33.0%) were in Guangling District. Clinical diagnosis showed that 175 people (30.7%) had mild symptoms, 385 people were in moderate conditions (67.5%), and 10 people were in severe situations (1.8%). Significant age differences were found among the three groups (P < 0.001). However, no significant difference was identified in terms of gender ratio (P > 0.05). Based on the transmission chain formed by 6 generations of infected persons with a clear transmission relationship, the age showed a gradually decreasing trend, while the median time of diagnosis in 2 adjacent generations was 3 days. In addition, the estimated basic reproduction number R 0 of the Delta variant was 3.3651 by the classical Susceptible, Infectious, and/or Recovered (SIR) model.

Conclusion

The Delta variant of SARS-CoV-2 was highly infectious and has obvious clustering characteristics during the Yangzhou outbreak in China.

Feasibility of using a mobile App to monitor and report COVID-19 related symptoms and people's movements in Uganda

BACKGROUND

Feasibility of mobile Apps to monitor diseases has not been well documented particularly in developing countries. We developed and studied the feasibility of using a mobile App to collect daily data on COVID-19 symptoms and people's movements.

METHODS

We used an open source software "KoBo Toolbox" to develop the App and installed it on low cost smart mobile phones. We named this App "Wetaase" ("protect yourself"). The App was tested on 30 selected households from 3 densely populated areas of Kampala, Uganda, and followed them for 3 months. One trained member per household captured the data in the App for each enrolled member and uploaded it to a virtual server on a daily basis. The App is embedded with an algorithm that flags participants who report fever and any other COVID-19 related symptom.

RESULTS

A total of 101 participants were enrolled; 61% female; median age 23 (interquartile range (IQR): 17-36) years. Usage of the App was 78% (95% confidence interval (CI): 77.0%-78.8%). It increased from 40% on day 1 to a peak of 81% on day 45 and then declined to 59% on day 90. Usage of the App did not significantly vary by site, sex or age. Only 57/6617 (0.86%) records included a report of at least one of the 17 listed COVID-19 related symptoms. The most reported symptom was flu/runny nose (21%) followed by sneezing (15%), with the rest ranging between 2% and 7%. Reports on movements away from home were 45% with 74% going to markets or shops. The participants liked the "Wetaase" App and recommended it for use as an alert system for COVID-19.

CONCLUSION

Usage of the "Wetaase" App was high (78%) and it was similar across the three study sites, sex and age groups. Reporting of symptoms related to COVID-19 was low. Movements were mainly to markets and shops. Users reported that the App was easy to use and recommended its scale up. We recommend that this App be assessed at a large scale for feasibility, usability and acceptability as an additional tool for increasing alerts on COVID-19 in Uganda and similar settings.

Current Status and Associated Factors of Depression and Anxiety Among the Chinese Residents During the Period of Low Transmission of COVID-19

Background: The outbreak of coronavirus disease 2019 (COVID-19) has contributed to depression and anxiety among the general population in China. The purpose of this study is to investigate the prevalence and associated factors of these psychological problems among Chinese adults during the period of low transmission, which could reflect the long-term depression and anxiety of the COVID-19 outbreak. Methods: A cross-sectional survey was conducted in China from 4 to 26 February 2021. Convenient sampling strategy was adopted to recruit participators. Participants were asked to filled out the questions that assessed questionnaire on the residents' depression and anxiety. Results: A total of 2,361 residents filled out the questionnaire. The mean age was 29.72 years (SD = 6.94) and majority of respondents were female (60.10%). Among the respondents, 421 (17.83%), 1470 (62.26%), and 470 (19.91%) were from eastern, central, and western China, respectively. 1704 (72.17%) consented COVID-19 information has been disclosed timely. 142 (6.01%) and 130 (5.51%) patients suffered from depression and anxiety symptoms. Furthermore, some influencing factors were found, including marital status, place of residence, employment status. Conclusion: This study revealed that anxiety and depression still are potential depression and anxiety for some residents, which suggested early recognition and initiation of interventions during the period of low transmission is still indispensable.

Basic Reproduction Number of the 2019 Novel Coronavirus Disease in the Major Endemic Areas of China: A Latent Profile Analysis

Objective: The aim of this study is to analyze the latent class of basic reproduction number (R₀) trends of the 2019 novel coronavirus disease (COVID-19) in the major endemic areas of China.

Methods: The provinces that reported more than 500 cases of COVID-19 till February 18, 2020 were selected as the major endemic areas. The Verhulst model was used to fit the growth rate of cumulative confirmed cases. The R₀ of COVID-19 was calculated using the parameters of severe acute respiratory syndrome (SARS) and COVID-19. The latent class of R₀ was analyzed using the latent profile analysis (LPA) model.

Results: The median R₀ calculated from the SARS and COVID-19 parameters were 1.84–3.18 and 1.74–2.91, respectively. The R₀ calculated from the SARS parameters was greater than that calculated from the COVID-19 parameters (Z = −4.782 to −4.623, p < 0.01). Both R₀ can be divided into three latent classes. The initial value of R₀ in class 1 (Shandong Province, Sichuan Province, and Chongqing Municipality) was relatively low and decreased slowly. The initial value of R₀ in class 2 (Anhui Province, Hunan Province, Jiangxi Province, Henan Province, Zhejiang Province, Guangdong Province, and Jiangsu Province) was relatively high and decreased rapidly. Moreover, the initial R₀ value of class 3 (Hubei Province) was in the range between that of classes 1 and 2, but the higher R₀ level lasted longer and decreased slowly.

Conclusion: The results indicated that the overall R₀ trend is decreased with the strengthening of comprehensive prevention and control measures of China for COVID-19, however, there are regional differences.

Impact of the gate-keeping policies of China's primary healthcare model on the future burden of tuberculosis in China: a protocol for a mathematical modelling study

INTRODUCTION

In the past three decades, China has made great strides in the prevention and treatment of tuberculosis (TB). However, the TB burden remains high. In 2019, China accounted for 8.4% of global incident cases of TB, the third highest in the world, with a higher prevalence in rural areas. The Healthy China 2030 highlights the gate-keeping role of primary healthcare (PHC). However, the impact of PHC reforms on the future TB burden is unclear. We propose to use mathematical models to project and evaluate the impacts of different gate-keeping policies.

METHODS AND ANALYSIS

We will develop a deterministic, population-level, compartmental model to capture the dynamics of TB transmission within adult rural population. The model will incorporate seven main TB statuses, and each compartment will be subdivided by service providers. The parameters involving preference for healthcare seeking will be collected using discrete choice experiment (DCE) method. We will solve the deterministic model numerically over a 20-year (2021-2040) timeframe and predict the TB prevalence, incidence and cumulative new infections under the status quo or various policy scenarios. We will also conduct an analysis following standard protocols to calculate the average cost-effectiveness for each policy scenario relative to the status quo. A numerical calibration analysis against the available published TB prevalence data will be performed using a Bayesian approach.

ETHICS AND DISSEMINATION

Most of the data or parameters in the model will be obtained based on secondary data (eg, published literature and an open-access data set). The DCE survey has been reviewed and approved by the Ethics Committee of the School of Public Health, Sun Yat-sen University. The approval number is SYSU [2019]140. Results of the study will be disseminated through peer-reviewed journals, media and conference presentations.

Assessment of basic reproductive number for COVID-19 at global level: A meta-analysis

BACKGROUND

There are large knowledge gaps regarding how transmission of 2019 novel coronavirus disease (COVID-19) occurred in different settings across the world. This study aims to summarize basic reproduction number (R0) data and provide clues for designing prevention and control measures.

METHODS

Several databases and preprint platforms were retrieved for literature reporting R0 values of COVID-19. The analysis was stratified by the prespecified modeling method to make the R0 values comparable, and by country/region to explore whether R0 estimates differed across the world. The average R0 values were pooled using a random-effects model.

RESULTS

We identified 185 unique articles, yielding 43 articles for analysis. The selected studies covered 5 countries from Asia, 5 countries from Europe, 12 countries from Africa, and 1 from North America, South America, and Australia each. Exponential growth rate model was most favored by researchers. The pooled global R0 was 4.08 (95% CI, 3.09-5.39). The R0 estimates for new and shifting epicenters were comparable or even higher than that for the original epicenter Wuhan, China.

CONCLUSIONS

The high R0 values suggest that an extraordinary combination of control measures is needed for halting COVID-19.

A study on the effects of containment policies and vaccination on the spread of SARS-CoV-2

This paper presents a method to predict the spread of the SARS-CoV-2 in a population with a known age-structure, and then, to quantify the effects of various containment policies, including those policies that affect each age-group differently. The model itself is a compartmental model in which each compartment is divided into a number of age-groups. The parameters of the model are estimated using an optimisation scheme and some known results from the theory of monotone systems such that the model output agrees with some collected data on the spread of SARS-CoV-2. To highlight the strengths of this framework, a few case studies are presented in which different populations are subjected to different containment strategies. They include cases in which the containment policies switch between scenarios with different levels of severity. Then a case study on herd immunity due to vaccination is presented. And then it is shown how we can use this framework to optimally distribute a limited number of vaccine units in a given population to maximise their impact and reduce the total number of infectious individuals.

Assessing the regional impact of Japan's COVID-19 state of emergency declaration: a population-level observational study using social networking services

OBJECTIVE

On 7 April 2020, the Japanese government declared a state of emergency in response to the novel coronavirus outbreak. To estimate the impact of the declaration on regional cities with low numbers of COVID-19 cases, large-scale surveillance to capture the current epidemiological situation of COVID-19 was urgently conducted in this study.

DESIGN

Cohort study.

SETTING

Social networking service (SNS)-based online survey conducted in five prefectures of Japan: Tottori, Kagawa, Shimane, Tokushima and Okayama.

PARTICIPANTS

127 121 participants from the five prefectures surveyed between 24 March and 5 May 2020.

INTERVENTIONS

An SNS-based healthcare system named COOPERA (COvid-19: Operation for Personalized Empowerment to Render smart prevention And care seeking) was launched. It asks questions regarding postcode, personal information, preventive actions, and current and past symptoms related to COVID-19.

PRIMARY AND SECONDARY OUTCOME MEASURES

Empirical Bayes estimates of age-sex-standardised incidence rate (EBSIR) of symptoms and the spatial correlation between the number of those who reported having symptoms and the number of COVID-19 cases were examined to identify the geographical distribution of symptoms in the five prefectures.

RESULTS

97.8% of participants had no subjective symptoms. We identified several geographical clusters of fever with significant spatial correlation (r=0.67) with the number of confirmed COVID-19 cases, especially in the urban centres of prefectural capital cities.

CONCLUSIONS

Given that there are still several high-risk areas measured by EBSIR, careful discussion on which areas should be reopened at the end of the state of emergency is urgently required using real-time SNS system to monitor the nationwide epidemic.

Ten Epidemiological Parameters of COVID-19: Use of Rapid Literature Review to Inform Predictive Models During the Pandemic

Objective: To describe the methods used in a rapid review of the literature and to present the main epidemiological parameters that describe the transmission of SARS-Cov-2 and the illness caused by this virus, coronavirus disease 2019 (COVID-19).

Methods: This is a methodological protocol that enabled a rapid review of COVID-19 epidemiological parameters.

Findings: The protocol consisted of the following steps: definition of scope; eligibility criteria; information sources; search strategies; selection of studies; and data extraction. Four reviewers and three supervisors conducted this review in 40 days. Of the 1,266 studies found, 65 were included, mostly observational and descriptive in content, indicating relative homogeneity as to the quality of the evidence. The variation in the basic reproduction number, between 0.48 and 14.8; and the median of the hospitalization period, between 7.5 and 20.5 days stand out as key findings.

Conclusion: We identified and synthesized 10 epidemiological parameters that may support predictive models and other rapid reviews to inform modeling of this and other future public health emergencies.

Estimation of the Outbreak Severity and Evaluation of Epidemic Prevention Ability of COVID-19 by Province in China

Objectives. To compare the epidemic prevention ability of COVID-19 of each province in China and to evaluate the existing prevention and control capacity of each province.Methods. We established a quasi-Poisson linear mixed-effects model using the case data in cities outside Wuhan in Hubei Province, China. We adapted this model to estimate the number of potential cases in Wuhan and obtained epidemiological parameters. We estimated the initial number of cases in each province by using passenger flowrate data and constructed the extended susceptible-exposed-infectious-recovered model to predict the future disease transmission trends.Results. The estimated potential cases in Wuhan were about 3 times the reported cases. The basic reproductive number was 3.30 during the initial outbreak. Provinces with more estimated imported cases than reported cases were those in the surrounding provinces of Hubei, including Henan and Shaanxi. The regions where the number of reported cases was closer to the predicted value were most the developed areas, including Beijing and Shanghai.Conclusions. The number of confirmed cases in Wuhan was underestimated in the initial period of the outbreak. Provincial surveillance and emergency response capabilities vary across the country.

Prevention and control of COVID-19 in public transportation: Experience from China

Due to continuous spread of coronavirus disease 2019 (COVID-19) worldwide, long-term effective prevention and control measures should be adopted for public transport facilities, as they are increasing in popularity and serve as the principal modes for travel of many people. The human infection risk could be extremely high due to length of exposure time window, transmission routes and structural characteristics during travel or work. This can result in the rapid spread of the infection. Based on the transmission characteristics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and the nature of public transport sites, we identified comprehensive countermeasures toward the prevention and control of COVID-19, including the strengthening of personnel management, personal protection, environmental cleaning and disinfection, and health education. Multi-pronged strategies can enhance safety of public transportation. The prevention and control of the disease during the use of public transportation will be particularly important when all countries in the world resume production. The aim of this study is to introduce experience of the prevention and control measures for public transportation in China to promote the global response to COVID-19.

Statistically-based methodology for revealing real contagion trends and correcting delay-induced errors in the assessment of COVID-19 pandemic

COVID-19 pandemic has reshaped our world in a timescale much shorter than what we can understand. Particularities of SARS-CoV-2, such as its persistence in surfaces and the lack of a curative treatment or vaccine against COVID-19, have pushed authorities to apply restrictive policies to control its spreading. As data drove most of the decisions made in this global contingency, their quality is a critical variable for decision-making actors, and therefore should be carefully curated. In this work, we analyze the sources of error in typically reported epidemiological variables and usual tests used for diagnosis, and their impact on our understanding of COVID-19 spreading dynamics. We address the existence of different delays in the report of new cases, induced by the incubation time of the virus and testing-diagnosis time gaps, and other error sources related to the sensitivity/specificity of the tests used to diagnose COVID-19. Using a statistically-based algorithm, we perform a temporal reclassification of cases to avoid delay-induced errors, building up new epidemiologic curves centered in the day where the contagion effectively occurred. We also statistically enhance the robustness behind the discharge/recovery clinical criteria in the absence of a direct test, which is typically the case of non-first world countries, where the limited testing capabilities are fully dedicated to the evaluation of new cases. Finally, we applied our methodology to assess the evolution of the pandemic in Chile through the Effective Reproduction Number R_t , identifying different moments in which data was misleading governmental actions. In doing so, we aim to raise public awareness of the need for proper data reporting and processing protocols for epidemiological modelling and predictions.

Predicting the Impact of COVID-19 and the Potential Impact of the Public Health Response on Disease Burden in Uganda

The COVID-19 pandemic and public health "lockdown" responses in sub-Saharan Africa, including Uganda, are now widely reported. Although the impact of COVID-19 on African populations has been relatively light, it is feared that redirecting focus and prioritization of health systems to fight COVID-19 may have an impact on access to non-COVID-19 diseases. We applied age-based COVID-19 mortality data from China to the population structures of Uganda and non-African countries with previously established outbreaks, comparing theoretical mortality and disability-adjusted life years (DALYs) lost. We then predicted the impact of possible scenarios of the COVID-19 public health response on morbidity and mortality for HIV/AIDS, malaria, and maternal health in Uganda. Based on population age structure alone, Uganda is predicted to have a relatively low COVID-19 burden compared with an equivalent transmission in comparison countries, with 12% of the mortality and 19% of the lost DALYs predicted for an equivalent transmission in Italy. By contrast, scenarios of the impact of the public health response on malaria and HIV/AIDS predict additional disease burdens outweighing that predicted from extensive SARS-CoV-2 transmission. Emerging disease data from Uganda suggest that such deterioration may already be occurring. The results predict a relatively low COVID-19 impact on Uganda associated with its young population, with a high risk of negative impact on non-COVID-19 disease burden from a prolonged lockdown response. This may reverse hard-won gains in addressing fundamental vulnerabilities in women and children's health, and underlines the importance of tailoring COVID-19 responses according to population structure and local disease vulnerabilities.

The basic reproduction number of SARS-CoV-2 in Wuhan is about to die out, how about the rest of the World?

The virologically confirmed cases of a new coronavirus disease (COVID-19) in the world are rapidly increasing, leading epidemiologists and mathematicians to construct transmission models that aim to predict the future course of the current pandemic. The transmissibility of a virus is measured by the basic reproduction number ( R0 ), which measures the average number of new cases generated per typical infectious case. This review highlights the articles reporting rigorous estimates and determinants of COVID-19 R0 for the most affected areas. Moreover, the mean of all estimated R0 with median and interquartile range is calculated. According to these articles, the basic reproduction number of the virus epicentre Wuhan has now declined below the important threshold value of 1.0 since the disease emerged. Ongoing modelling will inform the transmission rates seen in the new epicentres outside of China, including Italy, Iran and South Korea.

Logic in the time of coronavirus

Much has happened here since the local news media trumpeted the first Australian COVID-19 fatality, and stirred up a medieval fear of contagion. We now need to take a step back to examine the logic underlying the use of our limited COVID-19 countermeasures. Emerging infectious diseases by their nature, pose new challenges to the diagnostic-treatment-control nexus, and push our concepts of causality beyond the limits of the conventional Koch-Henle approach to aetiology. We need to use contemporary methods of assessing causality to ensure that clinical, laboratory and public health measures draw on a rational, evidence-based approach to argumentation. The purpose of any aetiological hypothesis is to derive actionable insights into this latest emerging infectious disease. This review is an introduction to a conversation with medical microbiologists, which will be supported by a moderated blog.

Breastfeeding of infants born to mothers with COVID-19: a rapid review

BACKGROUND

Existing recommendations on whether mothers with COVID-19 should continue breastfeeding are still conflicting. We aimed to conduct a rapid review of mother-to-child transmission of COVID-19 during breastfeeding.

METHODS

We systematically searched Medline, Embase, Web of Science, Cochrane Library, China Biology Medicine disc, China National Knowledge Infrastructure, Wanfang, and preprint articles up to March 2020. We included studies relevant to transmission through milk and respiratory droplets during breastfeeding of mothers with COVID-19, SARS, MERS and influenza. Two reviewers independently screened studies for eligibility, extracted data, assessed risk of bias and used GRADE to assess certainty of evidence.

RESULTS

A total of 4,481 records were identified in our literature search. Six studies (five case reports and one case series) involving 58 mothers (16 mothers with COVID-19, 42 mothers with influenza) and their infants proved eligible. Five case reports showed that the viral nucleic acid tests for all thirteen collected samples of breast milk from mothers with COVID-19 were negative. A case series of 42 influenza infected postpartum mothers taking precautions (hand hygiene and wearing masks) before breastfeeding showed that no neonates were infected with influenza during one-month of follow-up.

CONCLUSIONS

The current evidence indicates that SARS-CoV-2 viral nucleic acid has not been detected in breast milk. The benefits of breastfeeding may outweigh the risk of SARS-CoV-2 infection in infants. Mothers with COVID-19 should take appropriate precautions to reduce the risk of transmission via droplets and close contact during breastfeeding.

Breastfeeding of infants born to mothers with COVID-19: a rapid review

Background

Existing recommendations on whether mothers with COVID-19 should continue breastfeeding are still conflicting. We aimed to conduct a rapid review of mother-to-child transmission of COVID-19 during breastfeeding.

Methods

We systematically searched Medline, Embase, Web of Science, Cochrane Library, China Biology Medicine disc, China National Knowledge Infrastructure, Wanfang, and preprint articles up to March 2020. We included studies relevant to transmission through milk and respiratory droplets during breastfeeding of mothers with COVID-19, SARS, MERS and influenza. Two reviewers independently screened studies for eligibility, extracted data, assessed risk of bias and used GRADE to assess certainty of evidence.

Results

A total of 4,481 records were identified in our literature search. Six studies (five case reports and one case series) involving 58 mothers (16 mothers with COVID-19, 42 mothers with influenza) and their infants proved eligible. Five case reports showed that the viral nucleic acid tests for all thirteen collected samples of breast milk from mothers with COVID-19 were negative. A case series of 42 influenza infected postpartum mothers taking precautions (hand hygiene and wearing masks) before breastfeeding showed that no neonates were infected with influenza during one-month of follow-up.

Conclusions

The current evidence indicates that SARS-CoV-2 viral nucleic acid has not been detected in breast milk. The benefits of breastfeeding may outweigh the risk of SARS-CoV-2 infection in infants. Mothers with COVID-19 should take appropriate precautions to reduce the risk of transmission via droplets and close contact during breastfeeding.