Investigation of key interventions for shigellosis outbreak control in China

Molecular Mechanisms of Shigella Pathogenesis; Recent Advances

Shigella species are the main cause of bacillary diarrhoea or shigellosis in humans. These organisms are the inhabitants of the human intestinal tract; however, they are one of the main concerns in public health in both developed and developing countries. In this study, we reviewed and summarised the previous studies and recent advances in molecular mechanisms of pathogenesis of Shigella Dysenteriae and non-Dysenteriae species. Regarding the molecular mechanisms of pathogenesis and the presence of virulence factor encoding genes in Shigella strains, species of this bacteria are categorised into Dysenteriae and non-Dysenteriae clinical groups. Shigella species uses attachment, invasion, intracellular motility, toxin secretion and host cell interruption mechanisms, causing mild diarrhoea, haemorrhagic colitis and haemolytic uremic syndrome diseases in humans through the expression of effector delivery systems, protein effectors, toxins, host cell immune system evasion and iron uptake genes. The investigation of these genes and molecular mechanisms can help us to develop and design new methods to detect and differentiate these organisms in food and clinical samples and determine appropriate strategies to prevent and treat the intestinal and extraintestinal infections caused by these enteric pathogens.

Application of logistic differential equation models for early warning of infectious diseases in Jilin Province

Background

There is still a relatively serious disease burden of infectious diseases and the warning time for different infectious diseases before implementation of interventions is important. The logistic differential equation models can be used for predicting early warning of infectious diseases. The aim of this study is to compare the disease fitting effects of the logistic differential equation (LDE) model and the generalized logistic differential equation (GLDE) model for the first time using data on multiple infectious diseases in Jilin Province and to calculate the early warning signals for different types of infectious diseases using these two models in Jilin Province to solve the disease early warning schedule for Jilin Province throughout the year.

Methods

Collecting the incidence of 22 infectious diseases in Jilin Province, China. The LDE and GLDE models were used to calculate the recommended warning week (RWW), the epidemic acceleration week (EAW) and warning removed week (WRW) for acute infectious diseases with seasonality, respectively.

Results

Five diseases were selected for analysis based on screening principles: hemorrhagic fever with renal syndrome (HFRS), shigellosis, mumps, Hand, foot and mouth disease (HFMD), and scarlet fever. The GLDE model fitted the above diseases better (0.80 ≤ R2 ≤ 0.94, P <  0. 005) than the LDE model. The estimated warning durations (per year) of the LDE model for the above diseases were: weeks 12–23 and 40–50; weeks 20–36; weeks 15–24 and 43–52; weeks 26–34; and weeks 16–25 and 41–50. While the durations of early warning (per year) estimated by the GLDE model were: weeks 7–24 and 36–51; weeks 13–37; weeks 11–26 and 39–54; weeks 23–35; and weeks 12–26 and 40–50.

Conclusions

Compared to the LDE model, the GLDE model provides a better fit to the actual disease incidence data. The RWW appeared to be earlier when estimated with the GLDE model than the LDE model. In addition, the WRW estimated with the GLDE model were more lagged and had a longer warning time.

Study of Risk Factors for Total Attack Rate and Transmission Dynamics of Norovirus Outbreaks, Jiangsu Province, China, From 2012 to 2018

Objective: To describe the epidemiological characteristics of norovirus outbreaks in Jiangsu Province, utilize the total attack rate (TAR) and transmissibility (R_unc) as the measurement indicators of the outbreak, and a statistical difference in risk factors associated with TAR and transmissibility was compared. Ultimately, this study aimed to provide scientific suggestions to develop the most appropriate prevention and control measures.

Method: We collected epidemiological data from investigation reports of all norovirus outbreaks in Jiangsu Province from 2012 to 2018 and performed epidemiological descriptions, sequenced the genes of the positive specimens collected that were eligible for sequencing, created a database and calculated the TAR, constructed SEIAR and SEIARW transmission dynamic models to calculate R_unc, and performed statistical analyses of risk factors associated with the TAR and R_unc.

Results: We collected a total of 206 reported outbreaks, of which 145 could be used to calculate transmissibility. The mean TAR in was 2.6% and the mean R_unc was 12.2. The epidemiological characteristics of norovirus outbreaks showed an overall increasing trend in the number of norovirus outbreaks from 2012 to 2018; more outbreaks in southern Jiangsu than northern Jiangsu; more outbreaks in urban areas than in rural areas; outbreaks occurred mostly in autumn and winter. Most of the sites where outbreaks occurred were schools, especially primary schools. Interpersonal transmission accounted for the majority. Analysis of the genotypes of noroviruses revealed that the major genotypes of the viruses changed every 3 years, with the GII.2 [P16] type of norovirus dominating from 2016 to 2018. Statistical analysis of TAR associated with risk factors found statistical differences in all risk factors, including time (year, month, season), location (geographic location, type of settlement, type of premises), population (total number of susceptible people at the outbreak site), transmission route, and genotype (P < 0.05). Statistical analysis of transmissibility associated with risk factors revealed that only transmissibility was statistically different between sites.

Conclusions: The number of norovirus outbreaks in Jiangsu Province continues to increase during the follow-up period. Our findings highlight the impact of different factors on norovirus outbreaks and identify the key points of prevention and control in Jiangsu Province.

Biological Indicators for Fecal Pollution Detection and Source Tracking: A Review

Fecal pollution, commonly detected in untreated or less treated sewage, is associated with health risks (e.g., waterborne diseases and antibiotic resistance dissemination), ecological issues (e.g., release of harmful gases in fecal sludge composting, proliferative bacterial/algal growth due to high nutrient loads) and economy losses (e.g., reduced aqua farm harvesting). Therefore, the discharge of untreated domestic sewage to the environment and its agricultural reuse are growing concerns. The goals of fecal pollution detection include fecal waste source tracking and identifying the presence of pathogens, therefore assessing potential health risks. This review summarizes available biological fecal indicators focusing on host specificity, degree of association with fecal pollution, environmental persistence, and quantification methods in fecal pollution assessment. The development of practical tools is a crucial requirement for the implementation of mitigation strategies that may help confine the types of host-specific pathogens and determine the source control point, such as sourcing fecal wastes from point sources and nonpoint sources. Emerging multidisciplinary bacterial enumeration platforms are also discussed, including individual working mechanisms, applications, advantages, and limitations.

Estimating the transmissibility of hepatitis C: A modelling study in Yichang City, China

Yichang is a city in central China in the Hubei Province. This study aimed to estimate the dynamics of the transmissibility of hepatitis C using a mathematical model and predict the transmissibility of hepatitis C in 2030. Data of hepatitis C cases from 13 counties or districts (cities) in Yichang from 2008 to 2016 were collected. A susceptible-infectious-chronic-recovered (SICR) model was developed to fit the data. The transmissibility of hepatitis C at the counties or districts was calculated based on new infections (including infected or chronically infected cases) reported monthly in the city caused by one infectious individual (MNI). The trend of the MNI was fitted and predicted using 11 models, with the coefficient of determination (R² ) was being used to test the goodness of fit of these models. A total of 3065 cases of hepatitis C were reported in Yichang from 2008 to 2016. The median MNI of Yichang was 0.0768. According to the fitting results and analysis, the trend of transmissibility of hepatitis C in Yichang City conforms with the logarithmic (R²  = 0.918, p < 0.001):MNI = 0.265-0.108 log(t) and exponential (R²  = 0.939, p < 0.001): MNI = 0.344e^(-0.278t) models. Hence, the transmission of hepatitis C virus at the county level has a downward trend. In conclusion, the transmissibility of hepatitis C in Yichang has a downward trend. With the current preventive and control measures in place, the spread of hepatitis C can be controlled.

Review of fractional epidemic models

The global impact of corona virus (COVID-19) has been profound, and the public health threat it represents is the most serious seen in a respiratory virus since the 1918 influenza A(H1N1) pandemic. In this paper, we have focused on reviewing the results of epidemiological modelling especially the fractional epidemic model and summarized different types of fractional epidemic models including fractional Susceptible-Infective-Recovered (SIR), Susceptible-Exposed-Infective-Recovered (SEIR), Susceptible-Exposed-Infective-Asymptomatic-Recovered (SEIAR) models and so on. Furthermore, we propose a general fractional SEIAR model in the case of single-term and multi-term fractional differential equations. A feasible and reliable parameter estimation method based on modified hybrid Nelder-Mead simplex search and particle swarm optimisation is also presented to fit the real data using fractional SEIAR model. The effective methods to solve the fractional epidemic models we introduced construct a simple and effective analytical technique that can be easily extended and applied to other fractional models, and can help guide the concerned bodies in preventing or controlling, even predicting the infectious disease outbreaks.

Relative transmissibility of shigellosis among different age groups: A modeling study in Hubei Province, China

Shigellosis is a heavy disease burden in China especially in children aged under 5 years. However, the age-related factors involved in transmission of shigellosis are unclear. An age-specific Susceptible-Exposed-Infectious/Asymptomatic-Recovered (SEIAR) model was applied to shigellosis surveillance data maintained by Hubei Province Centers for Disease Control and Prevention from 2005 to 2017. The individuals were divided into four age groups (≤ 5 years, 6-24 years, 25-59 years, and ≥ 60 years). The effective reproduction number (Reff), including infectivity (RI) and susceptibility (RS) was calculated to assess the transmissibility of different age groups. From 2005 to 2017, 130,768 shigellosis cases were reported in Hubei Province. The SEIAR model fitted well with the reported data (P < 0.001). The highest transmissibility (Reff) was from ≤ 5 years to the 25-59 years (mean: 0.76, 95% confidence interval [CI]: 0.34-1.17), followed by from the 6-24 years to the 25-59 years (mean: 0.69, 95% CI: 0.35-1.02), from the ≥ 60 years to the 25-59 years (mean: 0.58, 95% CI: 0.29-0.86), and from the 25-59 years to 25-59 years (mean: 0.50, 95% CI: 0.21-0.78). The highest infectivity was in ≤ 5 years (RI = 1.71), and was most commonly transmitted to the 25-59 years (45.11%). The highest susceptibility was in the 25-59 years (RS = 2.51), and their most common source was the ≤ 5 years (30.15%). Furthermore, "knock out" simulation predicted the greatest reduction in the number of cases occurred by when cutting off transmission routes among ≤ 5 years and from 25-59 years to ≤ 5 years. Transmission in ≤ 5 years occurred mainly within the group, but infections were most commonly introduced by individuals in the 25-59 years. Infectivity was highest in the ≤ 5 years and susceptibility was highest in the 25-59 years. Interventions to stop transmission should be directed at these age groups.

Transmission pattern of shigellosis in Wuhan City, China: a modelling study

The article aims to estimate and forecast the transmissibility of shigellosis and explore the association of meteorological factors with shigellosis. The mathematical model named Susceptible–Exposed–Symptomatic/Asymptomatic–Recovered–Water/Food (SEIARW) was used to explore the feature of shigellosis transmission based on the data of Wuhan City, China, from 2005 to 2017. The study applied effective reproduction number (R_eff) to estimate the transmissibility. Daily meteorological data from 2008 to 2017 were used to determine Spearman's correlation with reported new cases and R_eff. The SEIARW model fit the data well (χ² = 0.00046, p > 0.999). The simulation results showed that the reservoir-to-person transmission of the shigellosis route has been interrupted. The R_eff would be reduced to a transmission threshold of 1.00 (95% confidence interval (CI) 0.82–1.19) in 2035. Reducing the infectious period to 11.25 days would also decrease the value of R_eff to 0.99. There was a significant correlation between new cases of shigellosis and atmospheric pressure, temperature, wind speed and sun hours per day. The correlation coefficients, although statistically significant, were very low (<0.3). In Wuhan, China, the main transmission pattern of shigellosis is person-to-person. Meteorological factors, especially daily atmospheric pressure and temperature, may influence the epidemic of shigellosis.

Asymptomatic transmission shifts epidemic dynamics

Asymptomatic transmission of infectious diseases has been recognized recently in several epidemics or pandemics. There is a great need to incorporate asymptomatic transmissions into traditional modeling of infectious diseases and to study how asymptomatic transmissions shift epidemic dynamics. In this work, we propose a compartmental model with asymptomatic transmissions for waterborne infectious diseases. We conduct a detailed analysis and numerical study with shigellosis data. Two parameters, the proportion $p$ of asymptomatic infected individuals and the proportion $k$ of asymptomatic infectious individuals who can asymptomatically transmit diseases, play major rules in the epidemic dynamics. The basic reproduction number $\mathscr{R}_{0}$ is a decreasing function of parameter $p$ when parameter $k$ is smaller than a critical value while $\mathscr{R}_{0}$ is an increasing function of $p$ when $k$ is greater than the critical value. $\mathscr{R}_{0}$ is an increasing function of $k$ for any value of $p$. When $\mathscr{R}_{0}$ passes through 1 as $p$ or $k$ varies, the dynamics of epidemics is shifted. If asymptomatic transmissions are not counted, $\mathscr{R}_{0}$ will be underestimated while the final size may be overestimated or underestimated. Our study provides a theoretical example for investigating other asymptomatic transmissions and useful information for public health measurements in waterborne infectious diseases.

How Food Affects Colonization Resistance Against Enteropathogenic Bacteria

Food has a major impact on all aspects of health. Recent data suggest that food composition can also affect susceptibility to infections by enteropathogenic bacteria. Here, we discuss how food may alter the microbiota as well as mucosal defenses and how this can affect infection. Salmonella Typhimurium diarrhea serves as a paradigm, and complementary evidence comes from other pathogens. We discuss the effects of food composition on colonization resistance, host defenses, and the infection process as well as the merits and limitations of mouse models and experimental foods, which are available to decipher the underlying mechanisms.

Feasibility of containing shigellosis in Hubei Province, China: a modelling study

Background

The transmission features and the feasibility of containing shigellosis remain unclear among a population-based study in China.

Methods

A population–based Susceptible – Exposed – Infectious / Asymptomatic – Recovered (SEIAR) model was built including decreasing the infectious period (DIP) or isolation of shigellosis cases. We analyzed the distribution of the reported shigellosis cases in Hubei Province, China from January 2005 to December 2017, and divided the time series into several stages according to the heterogeneity of reported incidence during the period. In each stage, an epidemic season was selected for the modelling and assessing the effectiveness of DIP and case isolation.

Results

A total of 130,770 shigellosis cases were reported in Hubei Province. The median of R_eff was 1.13 (range: 0.86–1.21), 1.10 (range: 0.91–1.13), 1.09 (range: 0.92–1.92), and 1.03 (range: 0.94–1.22) in 2005–2006 season, 2010–2011 season, 2013–2014 season, and 2016–2017 season, respectively. The reported incidence decreased significantly (trend χ² = 8260.41, P <  0.001) among four stages. The incidence of shigellosis decreased sharply when DIP implemented in three scenarios (γ = 0.1, 0.1429, 0.3333) and when proportion of case isolation increased.

Conclusions

Year heterogeneity of reported shigellosis incidence exists in Hubei Province. It is feasible to contain the transmission by implementing DIP and case isolation.

Optimal Control of Shigellosis with Cost-Effective Strategies

In this paper, we apply optimal control theory to the model for shigellosis. It is assumed that education campaign, sanitation, and treatment are the main controls for this disease. The aim is to minimize the number of infections resulting from contact with careers, infectious population, and contaminated environments while keeping the cost of associated controls minimum. We achieve this aim through the application of Pontryagin's Maximum Principle. Numerical simulations are carried out by using both forward and backward in time fourth-order Runge-Kutta schemes. We simulate the model under different strategies to investigate which option could yield the best results. The findings show that the strategy combining all three control efforts (treatment, sanitation, and education campaign) proves to be more beneficial in containing shigellosis than the rest. On the other hand, cost-effectiveness analysis is performed via incremental cost-effectiveness ratio (ICER). The findings from the ICER show that a strategy incorporating all three controls (treatment, sanitation, and education campaign) is the most cost-effective of all strategies considered in the study.

Mathematical modelling on phase based transmissibility of Coronavirus

Mathematical and epidemiological simulation plays a pivotal role in predicting, anticipating, and controlling present and future epidemics. To better understand and model the dynamics of a specific infection, researchers need to consider the influence of many variables ranging from micro-host-pathogen interactions to host-to-host encounters, and the prevailing cultural, social, economic, and local customs worldwide. As reported by the WHO, a novel corona virus (COVID-19) is identified as the etiological virus through Wuhan pneumonia for unknown etiology with Chinese administration on Jan 7, 2020. This virus is designated as an unsympathetic SARS-Cov-2 by International Commission for Taxonomy of Viruses on Feb 11, 2020. The main aim is to enlarge a phase based mathematical modelling to specify the transferability of this disease. It is developed Reservoir-individuals spreading set of connections modelling for imitating the prospective broadcast as of the infectivity foundation in the direction of the person infectivity. In view of the fact that, the Reservoir has set of connections to rigid to see the sights obviously as well as communal anxieties are concentrating on top of the spreading starting reservoir to individuals. The subsequent generation matrix methodology is endorsed towards compute the fundamental reproduction number (R 0 ) through the RP modelling to measure the transferability by the COVID-19. The values ofR 0 are estimated from reservoir to human being as well as starting individual to individual, that is to say, the accepted quantity of less important diseases this consequence from presenting a solitary contaminated personality addicted to differently susceptible inhabitants. The present model demonstrated that the spreading of COVID-19 is superior to the Middle-East pulmonary infirmity during the Middle-East nationals, analogous to harsh sensitive pulmonary infirmity, but inferior than Middle-East pulmonary infirmity within the Republic of Korea. It can also extend this study to some other countries, including Saudi Arabia, Italy, and Germany etc. The COVID-19 pandemic has become the leading societal concern. The pandemic has shown that the public health concern is not only a medical problem, but also affects society as a whole; so, it has also become the leading scientific concern.

Relative transmissibility of shigellosis among male and female individuals: a modeling study in Hubei Province, China

BACKGROUND

Developing countries exhibit a high disease burden from shigellosis. Owing to the different incidences in males and females, this study aims to analyze the features involved in the transmission of shigellosis among male (subscript m) and female (subscript f) individuals using a newly developed sex-based model.

METHODS

The data of reported shigellosis cases were collected from the China Information System for Disease Control and Prevention in Hubei Province from 2005 to 2017. A sex-based Susceptible-Exposed-Infectious/Asymptomatic-Recovered (SEIAR) model was applied to explore the dataset, and a sex-age-based SEIAR model was applied in 2010 to explore the sex- and age-specific transmissions.

RESULTS

From 2005 to 2017, 130 770 shigellosis cases (including 73 981 male and 56 789 female cases) were reported in Hubei Province. The SEIAR model exhibited a significant fitting effect with the shigellosis data (P <  0.001). The median values of the shigellosis transmission were 2.3225 × 10⁸ for SAR_mm (secondary attack rate from male to male), 2.5729 × 10⁸ for SAR_mf, 2.7630 × 10^-8 for SAR_fm, and 2.1061 × 10^-8 for SAR_ff. The top five mean values of the transmission relative rate in 2010 (where the subscript 1 was defined as male and age ≤ 5 years, 2 was male and age 6 to 59 years, 3 was male and age ≥ 60 years, 4 was female and age ≤ 5 years, 5 was female and age 6 to 59 years, and 6 was male and age ≥ 60 years) were 5.76 × 10^-8 for β₆₁, 5.32 × 10^-8 for β₃₁, 4.01 × 10^-8 for β₃₄, 7.52 × 10^-9 for β₆₂, and 6.04 × 10^-9 for β₆₄.

CONCLUSIONS

The transmissibility of shigellosis differed among male and female individuals. The transmissibility between the genders was higher than that within the genders, particularly female-to-male transmission. The most important route in children (age ≤ 5 years) was transmission from the elderly (age ≥ 60 years). Therefore, the greatest interventions should be applied in females and the elderly.

Epidemiological characteristics and transmissibility of shigellosis in Hubei Province, China, 2005 - 2017

BACKGROUND

Shigellosis is one of the main diarrhea diseases in developing countries. However, the transmissibility of shigellosis remains unclear.

METHODS

We used the dataset of shigellosis cases reported between January 2005 and December 2017, from Hubei Province, China. A mathematical model was developed based on the natural history and the transmission mechanism of the disease. By fitting the data using the model, transmission relative rate from person to person (b) and from reservoir to person (bw), and the effective reproduction number (Reff) were estimated. To simulate the contribution of b and bw during the transmission, we performed a "knock-out" simulation in four scenarios: A) b = 0 and bw = 0; B) b = 0; C) bw = 0; D) control (no intervention).

RESULTS

A total of 130,770 shigellosis cases were reported in Hubei province, among which 13 cases were dead. The median annual incidence was 19.96 per 100,000 persons (range: 5.99 per 100,000 persons - 29.47 per 100,000 persons) with a decreased trend (trend χ2 = 25,470.27, P < 0.001). The mean values of b and bw were 0.0898 (95% confidence interval [CI]: 0.0851-0.0946) and 1.1264 × 10- 9 (95% CI: 4.1123 × 10- 10-1.8416 × 10- 9), respectively. The "knock-out" simulation showed that the number of cases simulated by scenario A was almost the same as scenario B, and scenario C was almost the same as scenario D. The mean value of Reff of shigellosis was 1.19 (95% CI: 1.13-1.25) and decreased slightly with a Linear model until it decreased to an epidemic threshold of 0.99 (95% CI: 0.65-1.34) in 2029.

CONCLUSIONS

The incidence of shigellosis is still in high level. The transmissibility of the disease is low in Hubei Province. The transmission would be interrupted in the year of 2029.

The study on the early warning period of varicella outbreaks based on logistic differential equation model

Chickenpox is a common acute and highly contagious disease in childhood; moreover, there is currently no targeted treatment. Carrying out an early warning on chickenpox plays an important role in taking targeted measures in advance as well as preventing the outbreak of the disease. In recent years, the infectious disease dynamic model has been widely used in the research of various infectious diseases. The logistic differential equation model can well demonstrate the epidemic characteristics of epidemic outbreaks, gives the point at which the early epidemic rate changes from slow to fast. Therefore, our study aims to use the logistic differential equation model to explore the epidemic characteristics and early-warning time of varicella. Meanwhile, the data of varicella cases were collected from first week of 2008 to 52nd week of 2017 in Changsha. Finally, our study found that the logistic model can be well fitted with varicella data, besides the model illustrated that there are two peaks of varicella at each year in Changsha City. One is the peak in summer–autumn corresponding to the 8th–38th week; the other is in winter–spring corresponding to the time from the 38th to the seventh week next year. The ‘epidemic acceleration week’ average value of summer–autumn and winter–spring are about the 16th week (ranging from the 15th to 17th week) and 45th week (ranging from the 44th to 47th week), respectively. What is more, taking warning measures during the acceleration week, the preventive effect will be delayed; thus, we recommend intervene during recommended warning weeks which are the 15th and 44th weeks instead.

A mathematical model for simulating the phase-based transmissibility of a novel coronavirus

Background

As reported by the World Health Organization, a novel coronavirus (2019-nCoV) was identified as the causative virus of Wuhan pneumonia of unknown etiology by Chinese authorities on 7 January, 2020. The virus was named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by International Committee on Taxonomy of Viruses on 11 February, 2020. This study aimed to develop a mathematical model for calculating the transmissibility of the virus.

Methods

In this study, we developed a Bats-Hosts-Reservoir-People transmission network model for simulating the potential transmission from the infection source (probably be bats) to the human infection. Since the Bats-Hosts-Reservoir network was hard to explore clearly and public concerns were focusing on the transmission from Huanan Seafood Wholesale Market (reservoir) to people, we simplified the model as Reservoir-People (RP) transmission network model. The next generation matrix approach was adopted to calculate the basic reproduction number (R₀) from the RP model to assess the transmissibility of the SARS-CoV-2.

Results

The value of R₀ was estimated of 2.30 from reservoir to person and 3.58 from person to person which means that the expected number of secondary infections that result from introducing a single infected individual into an otherwise susceptible population was 3.58.

Conclusions

Our model showed that the transmissibility of SARS-CoV-2 was higher than the Middle East respiratory syndrome in the Middle East countries, similar to severe acute respiratory syndrome, but lower than MERS in the Republic of Korea.

A mathematical model for simulating the phase-based transmissibility of a novel coronavirus

BACKGROUND

As reported by the World Health Organization, a novel coronavirus (2019-nCoV) was identified as the causative virus of Wuhan pneumonia of unknown etiology by Chinese authorities on 7 January, 2020. The virus was named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by International Committee on Taxonomy of Viruses on 11 February, 2020. This study aimed to develop a mathematical model for calculating the transmissibility of the virus.

METHODS

In this study, we developed a Bats-Hosts-Reservoir-People transmission network model for simulating the potential transmission from the infection source (probably be bats) to the human infection. Since the Bats-Hosts-Reservoir network was hard to explore clearly and public concerns were focusing on the transmission from Huanan Seafood Wholesale Market (reservoir) to people, we simplified the model as Reservoir-People (RP) transmission network model. The next generation matrix approach was adopted to calculate the basic reproduction number (R₀) from the RP model to assess the transmissibility of the SARS-CoV-2.

RESULTS

The value of R₀ was estimated of 2.30 from reservoir to person and 3.58 from person to person which means that the expected number of secondary infections that result from introducing a single infected individual into an otherwise susceptible population was 3.58.

CONCLUSIONS

Our model showed that the transmissibility of SARS-CoV-2 was higher than the Middle East respiratory syndrome in the Middle East countries, similar to severe acute respiratory syndrome, but lower than MERS in the Republic of Korea.

Incidence dynamics and investigation of key interventions in a dengue outbreak in Ningbo City, China

Background

The reported incidence of dengue fever increased dramatically in recent years in China. This study aimed to investigate and to assess the effectiveness of intervention implemented in a dengue outbreak in Ningbo City, Zhejiang Province, China.

Methods

Data of a dengue outbreak were collected in Ningbo City in China by a field epidemiological survey according to a strict protocol and case definition. Serum specimens of all cases were collected for diagnosis and the virological characteristics were detected by using polymerase chain reaction (PCR) and gene sequencing. Vector surveillance was implemented during the outbreak to collect the larva and adult mosquito densities to calculate the Breteau Index (BI) and human biting rate (HBR), respectively. Data of monthly BI and light-trap density in 2018 were built to calculate the seasonality of the vector. A transmission mathematical model was developed to dynamic the incidence of the disease. The parameters of the model were estimated by the data of the outbreak and vector surveillance data in 2018. The effectiveness of the interventions implemented during the outbreak was assessed by the data and the modelling.

Results

From 11 August to 8 September, 2018, a dengue outbreak was reported with 27 confirmed cases in a population of 5536-people community (community A) of Ningbo City. Whole E gene sequences were obtained from 24 cases and were confirmed as dengue virus type 1 (DENV-1). The transmission source of the outbreak was origin from community B where a dengue case having the same E gene sequence was onset on 30 July. Aedes albopictus was the only vector species in the area. The value of BI and HBR was 57.5 and 12 per person per hour respectively on 18 August, 2018 and decreased dramatically after interventions. The transmission model fitted well (χ² = 6.324, P = 0.388) with the reported cases data. With no intervention, the total simulated number of the cases would be 1728 with a total attack rate (TAR) of 31.21% (95%CI: 29.99%– 32.43%). Case isolation and larva control (LC) have almost the same TAR and duration of outbreak (DO) as no intervention. Different levels of reducing HBR (rHBR) had different effectiveness with TARs ranging from 1.05% to 31.21% and DOs ranging from 27 days to 102 days. Adult vector control (AVC) had a very low TAR and DO. “LC+AVC” had a similar TAR and DO as that of AVC. “rHBR_100%+LC”, “rHBR_100%+AVC”, “rHBR_100%+LC+AVC” and “rHBR_100%+LC+AVC+Iso” had the same effectiveness.

Conclusions

Without intervention, DENV-1 could be transmitted rapidly within a short period of time and leads to high attack rate in community in China. AVC or rHBR should be recommended as primary interventions to control rapid transmission of the dengue virus at the early stage of an outbreak.

Dengue has led to heavy disease burden in China. The reported incidence of the disease increased dramatically in recent years and cases have expanded from southern to central and northern part of China. In this study, the findings include that DENV-1 can transmit rapidly with a short period of time and leads to high attack rate in community, and that rHBR or AVC should be recommended as primary interventions to control rapid transmission of dengue virus at the early stage of an outbreak. Therefore, dengue outbreak is at high risk in many areas in China because of the potential high receptivity (widely distribution of Ae. albopictus) and vulnerability (high frequency of the importation) of the transmission. The high transmissibility of the virus makes it hard and urgent to control the outbreak. Delayed intervention (larvae control or case isolation) is hard to show its effectiveness and the interventions without delay are strongly recommended. Bed net or mosquito repellents were encouraged to use in the community to reduce HBR, and space spraying of insecticides were recommended to control adult vector during the outbreak.

Evaluating the effects of control interventions and estimating the inapparent infections for dengue outbreak in Hangzhou, China

Background

The number of dengue fever (DF) cases and the number of dengue outbreaks have increased in recent years in Zhejiang Province, China. An unexpected dengue outbreak was reported in Hangzhou in 2017 and caused more than one thousand dengue cases. This study was undertaken to evaluate the effectiveness of the actual control measures, estimate the proportion of inapparent infections during this outbreak and simulate epidemic development based on different levels of control measures taking inapparent infections into consideration.

Methods

The epidemic data of dengue cases in Hangzhou, Zhejiang Province, in 2017 and the number of the people exposed to the outbreaks were obtained from the China Information Network System of Disease Prevention and Control. The epidemic without intervention measures was used to estimate the unknown parameters. A susceptible-exposed-infectious/inapparent-recovered (SEIAR) model was used to estimate the effectiveness of the control interventions. The inapparent infections were also evaluated at the same time.

Results

In total, 1137 indigenous dengue cases were reported in Hangzhou in 2017. The number of indigenous dengue cases was estimated by the SEIAR model. This number was predicted to reach 6090 by the end of November 2, 2017, if no control measures were implemented. The total number of reported cases was reduced by 81.33% in contrast to the estimated incidence without intervention. The number of average daily inapparent cases was 10.18 times higher than the number of symptomatic cases. The earlier and more rigorously the vector control interventions were implemented, the more effective they were. The results showed that implementing vector control continuously for more than twenty days was more effective than every few days of implementation. Case isolation is not sufficient enough for epidemic control and only reduced the incidence by 38.10% in contrast to the estimated incidence without intervention, even if case isolation began seven days after the onset of the first case.

Conclusions

The practical control interventions in the outbreaks that occurred in Hangzhou City were highly effective. The proportion of inapparent infections was large, and it played an important role in transmitting the disease during this epidemic. Early, continuous and high efficacy vector control interventions are necessary to limit the development of a dengue epidemic. Timely diagnosis and case reporting are important in the intervention at an early stage of the epidemic.

Mobile population dynamics and malaria vulnerability: a modelling study in the China-Myanmar border region of Yunnan Province, China

BACKGROUND

The China-Myanmar border region presents a great challenge in malaria elimination in China, and it is essential to understand the relationship between malaria vulnerability and population mobility in this region.

METHODS

A community-based, cross-sectional survey was performed in five villages of Yingjiang county during September 2016. Finger-prick blood samples were obtained to identify asymptomatic infections, and imported cases were identified in each village (between January 2013 and September 2016). A stochastic simulation model (SSM) was used to test the relationship between population mobility and malaria vulnerability, according to the mechanisms of malaria importation.

RESULTS

Thirty-two imported cases were identified in the five villages, with a 4-year average of 1 case/year (range: 0-5 cases/year). No parasites were detected in the 353 blood samples from 2016. The median density of malaria vulnerability was 0.012 (range: 0.000-0.033). The average proportion of mobile members of the study population was 32.56% (range: 28.38-71.95%). Most mobile individuals lived indoors at night with mosquito protection. The SSM model fit the investigated data (χ² = 0.487, P = 0.485). The average probability of infection in the members of the population that moved to Myanmar was 0.011 (range: 0.0048-0.1585). The values for simulated vulnerability increased with greater population mobility in each village.

CONCLUSIONS

A high proportion of population mobility was associated with greater malaria vulnerability in the China-Myanmar border region. Mobile population-specific measures should be used to decrease the risk of malaria re-establishment in China.

Simulation of key interventions for seasonal influenza outbreak control at school in Changsha, China

Objective

To use a mathematical model to simulate an influenza outbreak in a school in order to assess the effectiveness of isolation (Iso), antiviral therapeutics, antiviral prophylactics (P), vaccination prior to the outbreak, and school closure (for 1 [S1w], 2 or 3 weeks).

Methods

This study developed a susceptible–exposed–infectious/asymptomatic–recovered model to estimate the effectiveness of commonly used interventions for seasonal influenza outbreaks in school.

Results

The most effective single-intervention strategy was isolation with a total attack rate of 1.99% and an outbreak duration of 30 days. The additional effectiveness of antiviral therapeutics and prophylactics and vaccination (prior to the outbreak) strategies were not obvious. Although Iso+P, P+Iso+S1w, four-, and five-combined intervention strategies had commendable effectiveness, total attack rate decreased only slightly, and outbreak duration was shortened by 9 days maximum, compared with the single-intervention isolation strategy. School closure for 1, 2 or 3 weeks was futile or even counterproductive.

Conclusion

Isolation, as a single intervention, was the most effective in terms of reducing the total attack rate and the duration of the outbreak.

Virulence and Stress Responses of Shigella flexneri Regulated by PhoP/PhoQ

The two-component signal transduction system PhoP/PhoQ is an important regulator for stress responses and virulence in most Gram-negative bacteria, but characterization of PhoP/PhoQ in Shigella has not been thoroughly investigated. In the present study, we found that deletion of phoPQ (ΔphoPQ) from Shigella flexneri 2a 301 (Sf301) resulted in a significant decline (reduced by more than 15-fold) in invasion of HeLa cells and Caco-2 cells, and less inflammation (− or +) compared to Sf301 (+++) in the guinea pig Sereny test. In low Mg²⁺ (10 μM) medium or pH 5 medium, the ΔphoPQ strain exhibited a growth deficiency compared to Sf301. The ΔphoPQ strain was more sensitive than Sf301 to polymyxin B, an important antimicrobial agent for treating multi-resistant Gram-negative infections. By comparing the transcriptional profiles of ΔphoPQ and Sf301 using DNA microarrays, 117 differentially expressed genes (DEGs) were identified, which were involved in Mg²⁺ transport, lipopolysaccharide modification, acid resistance, bacterial virulence, respiratory, and energy metabolism. Based on the reported PhoP box motif [(T/G) GTTTA-5nt-(T/G) GTTTA], we screened 38 suspected PhoP target operons in S. flexneri, and 11 of them (phoPQ, mgtA, slyB, yoaE, yrbL, icsA, yhiWX, rstA, hdeAB, pagP, and shf–rfbU-virK-msbB2) were demonstrated to be PhoP-regulated genes based on electrophoretic mobility shift assays and β-galactosidase assays. One of these PhoP-regulated genes, icsA, is a well-known virulence factor in S. flexneri. In conclusion, our data suggest that the PhoP/PhoQ system modulates S. flexneri virulence (in an icsA-dependent manner) and stress responses of Mg²⁺, pH and antibacterial peptides.

Outbreak detection and evaluation of a school-based influenza-like-illness syndromic surveillance in Tianjin, China

School-based influenza-like-illness (ILI) syndromic surveillance can be an important part of influenza community surveillance by providing early warnings for outbreaks and leading to a fast response. From September 2012 to December 2014, syndromic surveillance of ILI was carried out in 4 county-level schools. The cumulative sum methods(CUSUM) was used to detect abnormal signals. A susceptible-exposed-infectious/asymptomatic-recovered (SEIAR) model was fit to the influenza outbreak without control measures and compared with the actual influenza outbreak to evaluate the effectiveness of early control efforts. The ILI incidence rates in 2014 (14.51%) was higher than the incidence in 2013 (5.27%) and 2012 (3.59%). Ten school influenza outbreaks were detected by CUSUM. Each outbreak had high transmissibility with a median R_unc of 4.62. The interventions in each outbreak had high effectiveness and all R_con were 0. The early intervention had high effectiveness within the school-based ILI syndromic surveillance. Syndromic surveillance within schools can play an important role in controlling influenza outbreaks.

Evaluating the effects of common control measures for influenza A (H1N1) outbreak at school in China: A modeling study

BACKGROUND

Influenza A (H1N1) outbreaks have become common at schools in China since 2009. However, the effects of common countermeasures for school influenza outbreak have not been quantified so far, including isolation, vaccination, antivirus and school closure. We conducted a mathematically modeling study to address this unsolved issue.

METHODS

We collected data of all small-scale school outbreaks caused by influenza A that occurred in Changsha city between January 2009 and December 2013. Two outbreaks (one was in 2009 and the other one was in 2013) were used for simulating the effects of single and combined use of common measures, including isolation (Iso), therapeutics (T), prophylactics (P), vaccinating 70% of susceptible individuals prior to the outbreak (VP70), vaccinating 70% of susceptible individuals every day during the outbreak (VD70) and school closure of one week (S1w). A susceptible-exposed-infectious/asymptomatic-recovered (SEIR) model was developed to implement the simulations based on the natural history of influenza A.

RESULTS

When no control measures are taken, the influenza is expected to spread quickly at school for the selected outbreak in 2013; the outbreak would last 56 days, and the total attack rate (TAR) would reach up to 46.32% (95% CI: 46.12-46.52). Of all single control measures, VP70 is most effective to control the epidemic (TAR = 8.68%), followed by VP50, VD70, VD50 and Iso. The use of VP70 with any other measure can reduce TAR to 3.37-14.04% and showed better effects than any other combination of two kinds of measures. The best two-measure combination is 'S1w+VP70' (TAR = 3.37%, DO = 41 days). All combinations of three kinds of measures were not satisfactory when Vp70 and VD70 were excluded. The most effective three-intervention combination was 'Iso+S1w+VP70' (with TAR = 3.23%). When VP70 or VD70 is included, the combinations of four or five kinds of interventions are very effective, reducing TAR to lower than 5%. But the TAR of combination of 'T+P+Iso+S1w' is 23.20%. Similar simulation results were observed for the selected outbreak in 2009.

CONCLUSION

Vaccinating no less than 70% of individuals prior to the outbreak and isolation are recommended as single measures to control H1N1outbreak at school. The combination of VP70+S1w can achieve very good control for school outbreak.

Infectious diarrheal disease caused by contaminated well water in Chinese schools: A systematic review and meta-analysis

Background

In China, waterborne outbreaks of infectious diarrheal disease mainly occur in schools, and contaminated well water is a common source of pathogens. The objective of this review was to present the attack rates, durations of outbreak, pathogens of infectious diarrheal disease, and sanitary conditions of wells in primary and secondary schools in China, and to analyze risk factors and susceptibility of school children.

Methods

Relevant articles and reports were identified by searching PubMed, Web of Science, China National Knowledge Infrastructure, China Information System for Disease Control and Prevention, and the Chinese Field Epidemiology Training Program. Essential information, including urban/rural areas, school types, attack rates, pathogens, durations of outbreak, report intervals, and interventions were extracted from the eligible articles. Wilcoxon signed-rank test, Kruskal–Wallis H test, and Spearman correlation test were conducted in statistical analyses. Sex- and age-specific attack rate ratios were calculated as pooled effect sizes.

Results

We screened 2188 articles and retrieved data of 85 outbreaks from 1987 to 2014. Attack rates of outbreaks in rural areas (median, 12.63 cases/100 persons) and in primary schools (median, 14.54 cases/100 persons) were higher than those in urban areas (median, 5.62 cases/100 persons) and in secondary schools (median, 8.74 cases/100 persons) (P = 0.004 and P = 0.013, respectively). Shigella, pathogenic Escherichia coli, and norovirus were the most common pathogens. Boys tended toward higher attack rates than girls (sex-specific attack rate ratio, 1.13; 95% CI, 1.00–1.29, P = 0.05). Unsanitary conditions of water wells were reported frequently, and unhealthy behavior habits were common in students.

Conclusion

School children were susceptible to waterborne disease in China. Chinese government should make efforts to improve access to safe water in schools. Health education promotion and conscientiousness of school leaders and teachers should be enhanced.

•

School children were susceptible to waterborne disease in China.

•

Attack rates of rural or primary schools were high.

•

Boys trended toward higher risk than girls.

•

Unsanitary conditions of water wells were reported frequently.

Analysis of enteric disease outbreak metrics, British Columbia Centre for Disease Control, 2005-2014

Background

For enteric disease outbreaks, effective control depends on timely intervention. Routine collection of metrics related to outbreak identification, investigation and control can help evaluate and improve interventions and inform further analyses and modelling of intervention effectiveness.

Objective

To analyze data from enteric disease outbreaks in British Columbia, generate outbreak metrics and assess their use in evaluating the impact of outbreak interventions.

Methods

This descriptive study analyzed data from 57 provincial and national enteric disease outbreak investigations involving the British Columbia Centre for Disease Control from 2005 to 2014. Data were extracted from internal files and the Canadian Network for Public Health Intelligence. Outbreak metrics analyzed included days to initiate investigation, days to intervention, number and type of interventions, duration of investigation, duration of outbreak and the total number of cases.

Results

The median time to initiate an outbreak investigation was 36 days and the median duration of investigations was 39 days. The median duration of outbreaks was 40 days and the median time to intervene was 10 days. Identification of the source was associated with use of one or more interventions (P<0.0001). The duration of outbreaks was correlated with the number of days to initiate an investigation (r_s =0.72, P<0.0001) and number of days to intervene (r_s =0.51, P=0.025).

Conclusion

Identification and analysis of outbreak metrics establishes benchmarks that can be compared to other jurisdictions. This may support continuous quality improvement and enhance understanding of the impact of public health activities. Date information for public health actions is essential for evaluating the timing and effectiveness of outbreak interventions.

Association between flood and the morbidity of bacillary dysentery in Zibo City, China: a symmetric bidirectional case-crossover study

This study examined the relationship between daily morbidity of bacillary dysentery and flood in 2007 in Zibo City, China, using a symmetric bidirectional case-crossover study. Odds ratios (ORs) and 95 % confidence intervals (CIs) on the basis of multivariate model and stratified analysis at different lagged days were calculated to estimate the risk of flood on bacillary dysentery. A total of 902 notified bacillary dysentery cases were identified during the study period. The median of case distribution was 7-year-old and biased to children. Multivariable analysis showed that flood was associated with an increased risk of bacillary dysentery, with the largest OR of 1.849 (95 % CI 1.229-2.780) at 2-day lag. Gender-specific analysis showed that there was a significant association between flood and bacillary dysentery among males only (ORs >1 from lag 1 to lag 5), with the strongest lagged effect at 2-day lag (OR = 2.820, 95 % CI 1.629-4.881), and the result of age-specific indicated that youngsters had a slightly larger risk to develop flood-related bacillary dysentery than older people at one shorter lagged day (OR = 2.000, 95 % CI 1.128-3.546 in youngsters at lag 2; OR = 1.879, 95 % CI 1.069-3.305 in older people at lag 3). Our study has confirmed that there is a positive association between flood and the risk of bacillary dysentery in selected study area. Males and youngsters may be the vulnerable and high-risk populations to develop the flood-related bacillary dysentery. Results from this study will provide recommendations to make available strategies for government to deal with negative health outcomes due to floods.

The transmissibility estimation of influenza with early stage data of small-scale outbreaks in Changsha, China, 2005-2013

Hundreds of small-scale influenza outbreaks in schools are reported in mainland China every year, leading to a heavy disease burden which seriously impacts the operation of affected schools. Knowing the transmissibility of each outbreak in the early stage has become a major concern for public health policy-makers and primary healthcare providers. In this study, we collected all the small-scale outbreaks in Changsha (a large city in south central China with ~7·04 million population) from January 2005 to December 2013. Four simple and popularly used models were employed to calculate the reproduction number (R) of these outbreaks. Given that the duration of a generation interval Tc = 2·7 and the standard deviation (s.d.)σ = 1·1, the mean R estimated by an epidemic model, normal distribution and delta distribution were 2·51 (s.d. = 0·73), 4·11 (s.d. = 2·20) and 5·88 (s.d. = 5·00), respectively. When Tc = 2·9 and σ = 1·4, the mean R estimated by the three models were 2·62 (s.d. = 0·78), 4·72 (s.d. = 2·82) and 6·86 (s.d. = 6·34), respectively. The mean R estimated by gamma distribution was 4·32 (s.d. = 2·47). We found that the values of R in small-scale outbreaks in schools were higher than in large-scale outbreaks in a neighbourhood, city or province. Normal distribution, delta distribution, and gamma distribution models seem to more easily overestimate the R of influenza outbreaks compared to the epidemic model.

Evidence-Based interventions of Norovirus outbreaks in China

Background

In resource-limited settings where laboratory capacity is limited and response strategy is non-specific, delayed or inappropriate intervention against outbreaks of Norovirus (NoV) are common. Here we report interventions of two norovirus outbreaks, which highlight the importance of evidence-based modeling and assessment to identify infection sources and formulate effective response strategies.

Methods

Spatiotemporal scanning, mathematical and random walk modeling predicted the modes of transmission in the two incidents, which were supported by laboratory results and intervention outcomes.

Results

Simulation results indicated that contaminated water was 14 to 500 fold more infectious than infected individuals. Asymptomatic individuals were not effective transmitters. School closure for up to a week still could not contain the outbreak unless the duration was extended to 10 or more days. The total attack rates (TARs) for waterborne NoV outbreaks reported in China (n = 3, median = 4.37) were significantly (p < 0.05) lower than worldwide (n = 14, median = 41.34). The low TARs are likely due to the high number of the affected population.

Conclusions

We found that school closure alone could not contain Norovirus outbreaks. Overlooked personal hygiene may serve as a hotbed for infectious disease transmission. Our results reveal that evidence-based investigations can facilitate timely interventions of Norovirus transmission.

Electronic supplementary material

The online version of this article (doi:10.1186/s12889-016-3716-3) contains supplementary material, which is available to authorized users.

The Effectiveness of Age-Specific Isolation Policies on Epidemics of Influenza A (H1N1) in a Large City in Central South China

During the early stage of a pandemic, isolation is the most effective means of controlling transmission. However, the effectiveness of age-specific isolation policies is not clear; especially little information is available concerning their effectiveness in China. Epidemiological and serological survey data in the city of Changsha were employed to estimate key model parameters. The average infectious period (date of recovery-date of symptom onset) of influenza A (H1N1) was 5.2 days. Of all infected persons, 45.93% were asymptomatic. The basic reproduction number of the influenza A (H1N1) pandemic was 1.82. Based on the natural history of influenza A (H1N1), we built an extended susceptible-exposed-infectious/asymptomatic-removed model, taking age groups: 0-5, 6-14, 15-24, 25-59, and ≥60 years into consideration for isolation. Without interventions, the total attack rates (TARs) in each age group were 42.73%, 41.95%, 20.51%, 45.03%, and 37.49%, respectively. Although the isolation of 25-59 years-old persons was the most effective, the TAR of individuals of aged 0-5 and 6-14 could not be reduced. Paradoxically, isolating individuals ≥60 year olds was not predicted to be an effective way of reducing the TAR in this group but isolating the age-group 25-59 did, which implies inter-age-group transmission from the latter to the former is significant. Isolating multiple age groups increased effectiveness. The most effective combined isolation target groups were of 6-14 + 25-59 year olds, 6-14 + 15-24 + 25-59 year olds, and 0-5 + 6-14 + 25-59 + ≥60 year olds. The last of these isolation schemas reduced the TAR of the total population from 39.64% to 0.006%, which was exceptionally close to the effectiveness of isolating all five age groups (TAR = 0.004%).