Ryosuke Omori

Since the novel coronavirus disease (COVID-19) emerged in December 2019 in China, it has rapidly spread around the world, leading to one of the most significant pandemic events of recent history. Deriving reliable estimates of the COVID-19 epidemic growth rate is quite important to guide the timing and intensity of intervention strategies. Indeed, many studies have quantified the epidemic growth rate using time-series of reported cases during the early phase of the outbreak to estimate the basic

Among Italy, Spain, and Japan, the age distributions of COVID-19 mortality show only small variation even though the number of deaths per country shows large variation. To understand the determinant for this situation, we constructed a mathematical model describing the transmission dynamics and natural history of COVID-19 and analyzed the dataset of mortality in Italy, Spain, and Japan. We estimated the parameter which describes the age-dependency of susceptibility by fitting the model to report

Severe cases are twice as likely to be diagnosed and reported when compared to other cases. Considering that reported cases are usually dominated by non-severe cases, the adjusted total number of cases is also approximately double the observed count. This finding is critical in interpreting the reported data, and it is advised that the mild case data for COVID-19 should always be interpreted as under-ascertained [Au?1].

Network statistics produced similar and differential effects on HIV/HSV-2 transmission, and explained most of the variation in HIV and HSV-2 prevalences. HIV prevalence reflected primarily mean and variance of number of partners, but HSV-2 prevalence was affected by a range of network statistics. HSV-2 prevalence (as a proxy) can forecast a population's HIV epidemic potential, thereby informing interventions.

It is difficult to control for sexual-behaviour confounding in observational studies. The observed HIV/HSV-2 association appears more consistent with two infections sharing the same mode of transmission, rather than with HSV-2 enhancing HIV acquisition.

Until the early 1990 s, incidences of Mycoplasma pneumoniae (MP) infection showed three to five year epidemic cycles in multiple countries, however, the mechanism for the MP epidemic cycle has not been understood. Here, we investigate the determinant of periodicity in MP incidence by employing a mathematical model describing MP transmission dynamics. Three candidates for the determinant of periodicity were evaluated: school-term forcing, minor variance in the duration of immunity, and epidemiolo

The actual number of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is difficult to estimate using a case-reporting system (i.e., passive surveillance) alone because of asymptomatic infection. While wastewater-based epidemiology has been implemented as an alternative/additional monitoring tool to reduce reporting bias, the relationship between passive and wastewater surveillance data has not yet been explicitly examined. As there is strong age dependency i

Non-cohabiting sex appears to be a random 'opportunistic' phenomenon linked to situations that may facilitate it. The mean values and variances of number of partners in SSA show wide variation by country, marital status and sex. Unmarried individuals have larger mean values than their married counterparts, and men have larger mean values than women. Unmarried individuals appear to play a disproportionate role in driving heterogeneity in sexual networks and possibly epidemiology of sexually trans

A strong long-lasting partial immunity against <i>C. trachomatis</i> reinfection should be present to explain observed prevalence patterns. The mechanism of immunity could be either a reduction in susceptibility to reinfection or a reduction in duration of infection on reinfection. <i>C. trachomatis</i> infection appears to naturally elicit a strong long-lasting immune response, supporting the concept of vaccine development.

It is essential to understand the transmission dynamics of non-vaccine strains so that epidemiological methods can appropriately measure both the direct and indirect population impact of vaccination. For pathogens with interacting antigenic types, the most valid estimates of VE, that are unlikely to be biased by the transmission dynamics, may be obtained from longitudinal prospective studies that permit estimation of the VE based on the relative risk of infection among vaccinated compared to unv

The prediction of the lineage dynamics of influenza B viruses for the next season is one of the largest obstacles for constructing an appropriate influenza trivalent vaccine. Seasonal fluctuation of transmissibility and epidemiological interference between the two major influenza B lineages make the lineage dynamics complicated. Here we construct a parsimonious model describing the lineage dynamics while taking into account seasonal fluctuation of transmissibility and epidemiological interferenc

STI epidemiologies demonstrate substantial overlap and associations, alongside nuanced differences that shape a unique pattern for each STI. Gonorrhea exhibits an "intermediate STI epidemiology," reflected by the highest average correlation coefficient with other STIs.

To estimate and predict the transmission dynamics of respiratory viruses, the estimation of the basic reproduction number, <i>R</i>₀, is essential. Recently, approximate Bayesian computation methods have been used as likelihood free methods to estimate epidemiological model parameters, particularly <i>R</i>₀. In this paper, we explore various machine learning approaches, the multi-layer perceptron, convolutional neural network, and long-short term memory, to learn and estim