Estimating the basic reproductive number in the general epidemic model with an unknown initial number of susceptible individuals

Abstract.  In any epidemic, there may exist an unidentified subpopulation which might be naturally immune or isolated and who will not be involved in the transmission of the disease. Estimation of key parameters, for example, the basic reproductive number, without accounting for this possibility would underestimate the severity of the epidemics. Here, we propose a procedure to estimate the basic reproductive number (R0) in an epidemic model with an unknown initial number of susceptibles. The infection process is usually not completely observed, but is reconstructed by a kernel‐smoothing method under a counting process framework. Simulation is used to evaluate the performance of the estimators for major epidemics. We illustrate the procedure using the Abakaliki smallpox data

Reply to: Is presymptomatic spread a major contributor to COVID-19 transmission?

Reply to: Is presymptomatic spread a major contributor to COVID-19 transmission

Re: "a chain multinomial model for estimating the real-time fatality rate of a disease, with an application to severe acute respiratory syndrome" [3]

Re: "a chain multinomial model for estimating the real-time fatality rate of a disease, with an application to severe acute respiratory syndrome" [3

A note on the estimation of the initial number of susceptible individuals in the general epidemic model

Traditional inference for epidemic models depends on knowledge of the initial number of susceptible individuals. However, this may be difficult to obtain in practice. In this short note we show that it is possible to use data from a major epidemic to estimate the number of individuals initially susceptible to a disease and an approximate asymptotic variance is derived. The results are confirmed in simulations of major epidemics. An application to a data set on smallpox is given. © 2004 Elsevier B.V. All rights reserved

School Closure to Reduce Influenza Transmission : In response

School Closure to Reduce Influenza Transmission : In respons

Dynamic interactions of influenza viruses in Hong Kong during 1998-2018

Influenza epidemics cause substantial morbidity and mortality every year worldwide. Currently, two influenza A subtypes, A(H1N1) and A(H3N2), and type B viruses co-circulate in humans and infection with one type/subtype could provide cross-protection against the others. However, it remains unclear how such ecologic competition via cross-immunity and antigenic mutations that allow immune escape impact influenza epidemic dynamics at the population level. Here we develop a comprehensive model-inference system and apply it to study the evolutionary and epidemiological dynamics of the three influenza types/subtypes in Hong Kong, a city of global public health significance for influenza epidemic and pandemic control. Utilizing long-term influenza surveillance data since 1998, we are able to estimate the strength of cross-immunity between each virus-pairs, the timing and frequency of punctuated changes in population immunity in response to antigenic mutations in influenza viruses, and key epidemiological parameters over the last 20 years including the 2009 pandemic. We find evidence of cross-immunity in all types/subtypes, with strongest crossimmunity from A(H1N1) against A(H3N2). Our results also suggest that A(H3N2) may undergo antigenic mutations in both summers and winters and thus monitoring the virus in both seasons may be important for vaccine development. Overall, our study reveals intricate epidemiological interactions and underscores the importance of simultaneous monitoring of population immunity, incidence rates, and viral genetic and antigenic changes

Waning Immunity after Receipt of Pertussis, Diphtheria, Tetanus, and Polio-Related Vaccines: A Systematic Review and Meta-analysis

Pertussis, diphtheria, and tetanus (DTP)-containing vaccines combined with polio vaccines are recommended by the World Health Organization as part of routine immunization programs. The decline of immunity after vaccination has been considered as a possible reason for the reemergence of vaccine-preventable diseases worldwide. In this study, we evaluated the potential duration of protective immunity of pertussis, diphtheria, tetanus, and polio through a systematic review and meta-analysis. We examined data on immunological and clinical outcomes. We observed evidence of waning postvaccination immunity for pertussis and diphtheria, whereas tetanus and polio vaccines provided sustained protection. Further research on the risk factors of waning immunity after vaccination and the optimal timing of booster doses for pertussis and diphtheria is needed

Estimating the Severity Profile of Enterovirus A71 Infections in Children: A Bayesian Synthesis Framework

Enterovirus A71 (EV-A71) is responsible for the majority of severe cases of hand, foot, and mouth disease, but little evidence is available on the severity profile of EV-A71 infections. We formulated a hierarchical Bayesian model that synthesized data on diseases/events associated with EV-A71 and EV-A71 antibody responses to infection among unvaccinated children from large clinical trials of EV-A71 vaccination, which were conducted in Jiangsu and Beijing during 2012 and 2013, to reconstruct the severity profile in a unified framework. On average, 15.1% of the children aged 6-35 months were infected by EV-A71 during 1-year follow-up in a mild epidemic season. We estimated that 9.7%, 2.2%, and 0.6% of children infected with EV-A71 were diagnosed with EV-A71-associated diseases, were hospitalized, and showed severe complications, respectively. We estimated on average 1 death per 10,000 EV-A71 infections for children aged 6-35 months. Approximately 70% of children had ≥4-fold rises in antibody titers after infection. Most EV-A71 infections in young children are mild, and overall 2.2% of the infected patients were hospitalized in the 2 trials. There remain several uncertainties about the immune response after infection and the duration of immunity against EV-A71 reinfection

Epidemiology of reemerging scarlet fever, Hong Kong, 2005–2015

Annual incidence of scarlet fever in Hong Kong remained elevated after an upsurge in 2011. Incidence increased from 3.3/10,000 children <5 years of age during 2005–2010 to 18.1/10,000 during 2012–2015. Incidence was higher among boys and was 32%–42% lower in the week following school holidays

Estimating the incubation period of hand, foot and mouth disease for children in different age groups

Hand, foot and mouth disease (HFMD) is a childhood disease causing large outbreaks frequently in Asia and occasionally in Europe and the US. The incubation period of HFMD was typically described as about 3-7 days but empirical evidence is lacking. In this study, we estimated the incubation period of HFMD from school outbreaks in Hong Kong, utilizing information on symptom onset and sick absence dates of students diagnosed with HFMD. A total of 99 HFMD cases from 12 schools were selected for analysis. We fitted parametric models accounting for interval censoring. Based on the best-fitted distributions, the estimated median incubation periods were 4.4 (95% CI 3.8-5.1) days, 4.7 (95% CI 4.5-5.1) days and 5.7 (95% CI 4.6-7.0) days for children in kindergartens, primary schools and secondary schools respectively. From the fitted distribution, the estimated incubation periods can be longer than 10 days for 8.8% and 23.2% of the HFMD cases in kindergarten and secondary schools respectively. Our results show that the incubation period of HFMD for secondary schools students can be longer than the ranges commonly described. An extended period of enhanced personal hygiene practice and disinfection of the environment may be needed to control outbreaks