Ph.D

感染症疫学

性感染症

数理生物学

インフルエンザ

理論疫学

病原体の進化

Life Science, Evolutionary biology, 数理生物学

Life Science, Hygiene and public health: excluding laboratory approach, 理論疫学

Life Science, Hygiene and public health: including laboratory approach, 理論疫学

Life Science, Medical management and medical sociology, 理論疫学

Doctoral (PhD) degree program, Graduate School of Infectious Diseases

Mar. 2022, 第59回獣医疫学会学術集会優秀発表賞
養殖における魚病疫学解析の問題とその解決法－実験と 観察を繋ぐ為の数理モデルの活用－
大森亮介;松山亮太;降幡充;笠井久会

Mar. 2021, 獣医疫学会, 第57回獣医疫学会学術集会一般口頭演題優秀学会発表賞
我が国の2018年以降の豚熱流行初期における野生イノシシの死亡率、回復率、および致命率の推定
松山亮太;大森亮介

2013, 日本数理生物学会, 日本数理生物学会研究奨励賞

Estimation of sample size required to detect an outbreak of highly pathogenic avian influenza in a poultry farm during emergency surveillance for secondarily infected farms
Jiro Iwamoto; Kohei Makita; Ryosuke Omori
Preventive Veterinary Medicine, 252, 106847, 106847, Elsevier BV, Jul. 2026, [Peer-reviewed], [Corresponding author]
Scientific journal

Secondary severe acute respiratory syndrome coronavirus 2 transmission from childcare workers versus teachers in school-associated screening events, Okinawa, Japan, January-March 2022
Kaoru Ogawa; Yining S. Xu; Yusuke Shimakawa; Gerardo Chowell; Ryosuke Omori; Ryota Matsuyama; Yoshihiro Takayama; Kenji Mizumoto
International Journal of Infectious Diseases, 167, 108672, 108672, Elsevier BV, Jun. 2026, [Peer-reviewed]
Scientific journal

A novel surveillance-based method for estimating the waning of immunity following natural infection
Ryosuke Omori; Hiam Chemaitelly; Laith J. Abu-Raddad
Public Health, 249, 106017, 106017, Elsevier BV, Dec. 2025, [Peer-reviewed], [Lead author, Corresponding author]
Scientific journal

Determinants of COVID-19 Outbreak Size in Elderly Residential Facilities in Okinawa Prefecture, Japan, April to June 2022
Yining S Xu; Yusuke Shimakawa; Gerardo Chowell; Ryota Matsuyama; Tetsuharu Nagamoto; Ryosuke Omori; Takashi Nakamura; Toru Itokazu; Yoshihiro Takayama; Kenji Mizumoto
IJID Regions, 100813, 100813, Elsevier BV, Nov. 2025, [Peer-reviewed]
Scientific journal

Pre-travel health awareness and perceptions of voluntary airport PCR testing during COVID-19: A cross-sectional study in Okinawa, Japan
Masahiro Kozuka; Yusuke Shimakawa; Gerardo Chowell; Tetsuharu Nagamoto; Ryota Matsuyama; Ryosuke Omori; Yining S Xu; Yoshiro Shimoji; Kaoru Ogawa; Yoshihiro Takayama; Kenji Mizumoto
IJID Regions, 100817, 100817, Elsevier BV, Nov. 2025, [Peer-reviewed]
Scientific journal

Inferring the timing of individual mobility decisions from accommodation reservation data during the COVID-19 outbreak
Koichi Ito; Shunsuke Kanemitsu; Ryusuke Kimura; Ryosuke Omori
Royal Society Open Science, 12, 7, The Royal Society, 30 Jul. 2025, [Peer-reviewed], [Corresponding author]
Scientific journal, Understanding the changes in human mobility in response to outbreaks is important for controlling emerging infectious disease outbreaks. This requires an understanding of the mechanism of human behavioural response as well as the timing of decisions for future mobility. However, most human mobility data only record the executed mobility that results from decision-making, and not the timing of decisions. In this study, we used accommodation reservation data to extract the decision-making process in response to the changing epidemic situation and compared it with data on executed mobility, ‘stay time’ in workplaces and stay time in places other than home or workplaces to clarify when people decide on their mobility. We confirmed that the decision-making process estimated from accommodation reservation data can accurately predict human mobility. The decision-making process estimated from accommodation reservation data was more strongly associated with stay time in places other than home or workplaces than stay time in workplaces. Furthermore, the comparison between the estimated decision-making process and mobility data quantitatively revealed that mobility was the result of integrating two types of decisions made in recent weeks (within two and five weeks for mobility to workplaces and places other than home or workplaces, respectively) and previous weeks.

Estimating waning immunity against classical swine fever virus among adult wild boar: A case study in Japan
Ryota Matsuyama; Takehisa Yamamoto; Yoko Hayama; Ryosuke Omori
Preventive Veterinary Medicine, 237, 106440, 106440, Elsevier BV, Apr. 2025, [Peer-reviewed], [Last author, Corresponding author]
Scientific journal

Descriptive Epidemiological Analysis for the First Outbreak of Lumpy Skin Disease in Japan in 2024
Yoko Hayama; Ryosuke Omori; Ryota Matsuyama; Sonoko Kondo; Emi Yamaguchi; Yuzu Kamata; Takehisa Yamamoto
Transboundary and Emerging Diseases, 2025, 1, Wiley, 2025
Scientific journal, Lumpy skin disease (LSD) is a transboundary emerging disease of cattle and water buffaloes that threatens the livestock industry globally. Japan experienced its first outbreak in November 2024. This study aimed to describe the spatial and temporal characteristics of this outbreak and estimate the transmissibility using a mathematical model for within‐farm transmission. The first and second cases were confirmed on dairy farms in Itoshima City, Fukuoka Prefecture, southern Japan, on November 6, 2024. Twenty‐two farms were confirmed during this outbreak, with 17 cases in Itoshima City and the other two municipalities in Fukuoka Prefecture. The third case occurred in Kumamoto Prefecture on November 8, 2024, and was linked to the long‐distance movement of potentially infected cattle via the livestock market from the first case on October 18, 2024. Two additional cases were detected near the third case. Control measures included isolation and voluntary culling of infected cattle; voluntary movement restrictions on infected, suspected, and apparently healthy cattle on the same premises; and voluntary suspension of the raw milk and semen shipments from infected and suspected animals. These measures were voluntary; however, no violations were reported. Vector control was achieved with insecticides and insect‐proof netting. Voluntary vaccination was conducted within a 20 km radius of affected farms in Fukuoka Prefecture. Mathematical modeling of within‐farm transmission dynamics revealed a transmission rate of 0.0031 (95% CI: 0.002–0.0044) per day. The basic reproduction number was 3.51 (95% CI: 2.26–4.98) based on a herd size of 49 and an infectious period of 23.1 days. Although the outbreak was geographically limited, this study highlights key epidemiological features of LSD, including its high transmission rate and long‐distance transmission via cattle movement. Japan has a persisting LSD virus (LSDV)incursion risk due to recent outbreaks in Asia. Strengthening preparedness, including awareness among farmers and veterinarians, emergency vaccination plans, vector control, traceability, and quarantine protocols for cattle movement, is essential to mitigate future outbreaks.

Can the Prevalence of One STI Serve as a Predictor for Another? A Mathematical Modeling Analysis
Ryosuke Omori; Hiam Chemaitelly; Laith J. Abu-Raddad
Infectious Disease Modelling, Elsevier BV, Dec. 2024, [Peer-reviewed], [Lead author, Corresponding author]
Scientific journal

Environmental and host factors underlying tick-borne virus infection in wild animals: Investigation of the emerging Yezo virus in Hokkaido, Japan
Mebuki Ito; Miku Minamikawa; Anastasiia Kovba; Hideka Numata; Tetsuji Itoh; Takuma Ariizumi; Asako Shigeno; Yuki Katada; Shiho Niwa; Yurie Taya; Yuto Shiraki; Gita Sadaula Pandey; Nariaki Nonaka; Ryo Nakao; Ryosuke Omori; Yuma Ohari; Norikazu Isoda; Michito Shimozuru; Toshio Tsubota; Keita Matsuno; Mariko Sashika
Ticks and Tick-borne Diseases, 15, 6, 102419, 102419, Elsevier BV, Nov. 2024
Scientific journal

SARS-CoV-2 Infection in School Settings, Okinawa Prefecture, Japan, 2021–2022
Yoshihiro Takayama; Yusuke Shimakawa; Ryota Matsuyama; Gerardo Chowell; Ryosuke Omori; Tetsuharu Nagamoto; Taro Yamamoto; Kenji Mizumoto
Emerging Infectious Diseases, 30, 11, Centers for Disease Control and Prevention (CDC), Nov. 2024, [Peer-reviewed]
Scientific journal

Environmental and host factors underlying tick infestation in invasive raccoons (Procyon lotor) in Hokkaido, Japan
Mebuki Ito; Miku Minamikawa; Anastasiia Kovba; Hideka Numata; Tetsuji Itoh; Yuki Katada; Shiho Niwa; Yurie Taya; Yuto Shiraki; Gita Sadaula Pandey; Samuel Kelava; Nariaki Nonaka; Ryo Nakao; Ryosuke Omori; Yuma Ohari; Norikazu Isoda; Michito Shimozuru; Toshio Tsubota; Keita Matsuno; Mariko Sashika
Ticks and Tick-borne Diseases, 15, 6, 102389, 102389, Elsevier BV, Nov. 2024, [Peer-reviewed]
Scientific journal

Estimating the impact of sarcoptic mange epidemic on the population size of wild raccoon dogs (Nyctereutes procyonoides) from wildlife rescue data
Ryota Matsuyama; Nobuhide Kido; Ryosuke Omori
International Journal for Parasitology: Parasites and Wildlife, 101010, 101010, Elsevier BV, Oct. 2024, [Peer-reviewed], [Corresponding author]
Scientific journal, Abstract

Background: The impact of infectious diseases on host populations is often not quantified because it is difficult to observe the host population and infectious disease dynamics. To address this problem, we developed a state-space model to simultaneously estimate host population and disease dynamics using wildlife rescue data. Using this model, we aimed to quantify the impact of sarcoptic mange on a Japanese racoon dog population by estimating the change in their relative population size.Methods: We classified the status of rescued raccoon dogs into four categories: i) rescued due to infection with mange, ii) rescued due to traffic accidents without mange, iii) rescued due to traffic accidents with mange, and iv) rescued due to causes other than traffic accidents or mange. We modelled the observation process for each categoryand fitted the model to the reported number of raccoon dogs rescued between 1990 and 2010 at three wildlife rescue facilities in Kanagawa Prefecture, Japan.Results: The mortality rate induced by mange was estimated to be 1.09 (95% credible interval (CI): 0.47–1.72) per year. The estimated prevalence of sarcoptic mange ranged between 4–80% in the study period. When a substantial prevalence of mange was observed (1995 to 2002), the host population size decreased by 91.2% (95% credible intervals: 86.3–94.7).Conclusion: We show that the impact of infectious disease outbreak on the wildlife population can be estimated from the time-series data of wildlife rescue events due to multiple causes. Our estimates suggest that sarcoptic mange triggered a substantial decrease in the Japanese wild raccoon dog populations.

SARS-CoV-2 IgG seroprevalence in the Okinawa Main Island and remote islands in Okinawa, Japan, 2020-2021.
Yoshihiro Takayama; Yusuke Shimakawa; Yoshiaki Aizawa; Christian Butcher; Naomi Chibana; Mary Collins; Kohei Kamegai; Tae Gyun Kim; Satoshi Koyama; Ryota Matsuyama; Melissa M. Matthews; Tomoari Mori; Tetsuharu Nagamoto; Masashi Narita; Ryosuke Omori; Noriko Shibata; Satoshi Shibata; Souichi Shiiki; Shunichi Takakura; Naoki Toyozato; Hiroyuki Tsuchiya; Matthias Wolf; Taro Yamamoto; Shuhei Yokoyama; Sho Yonaha; Kenji Mizumoto
Japanese Journal of Infectious Diseases, Editorial Committee of Japanese Journal of Infectious Diseases, National Institute of Infectious Dis, 30 Sep. 2024, [Peer-reviewed]
Scientific journal

Dynamics of Neisseria gonorrhoeae transmission among female sex workers and clients: A mathematical modeling study
Houssein H. Ayoub; Milan Tomy; Hiam Chemaitelly; Ryosuke Omori; Kent Buse; Nicola Low; Sarah Hawkes; Laith J. Abu-Raddad
Epidemics, 48, 100785, 100785, Elsevier BV, Sep. 2024, [Peer-reviewed]
Scientific journal

Advancing Public Health Surveillance: Integrating Modeling and GIS in the Wastewater-Based Epidemiology of Viruses, a Narrative Review
Diego F. Cuadros; Xi Chen; Jingjing Li; Ryosuke Omori; Godfrey Musuka
Pathogens, 13, 8, 685, 685, MDPI AG, 14 Aug. 2024, [Peer-reviewed]
Scientific journal, This review article will present a comprehensive examination of the use of modeling, spatial analysis, and geographic information systems (GIS) in the surveillance of viruses in wastewater. With the advent of global health challenges like the COVID-19 pandemic, wastewater surveillance has emerged as a crucial tool for the early detection and management of viral outbreaks. This review will explore the application of various modeling techniques that enable the prediction and understanding of virus concentrations and spread patterns in wastewater systems. It highlights the role of spatial analysis in mapping the geographic distribution of viral loads, providing insights into the dynamics of virus transmission within communities. The integration of GIS in wastewater surveillance will be explored, emphasizing the utility of such systems in visualizing data, enhancing sampling site selection, and ensuring equitable monitoring across diverse populations. The review will also discuss the innovative combination of GIS with remote sensing data and predictive modeling, offering a multi-faceted approach to understand virus spread. Challenges such as data quality, privacy concerns, and the necessity for interdisciplinary collaboration will be addressed. This review concludes by underscoring the transformative potential of these analytical tools in public health, advocating for continued research and innovation to strengthen preparedness and response strategies for future viral threats. This article aims to provide a foundational understanding for researchers and public health officials, fostering advancements in the field of wastewater-based epidemiology.

Assessment of fever screening at airports in detecting domestic passengers infected with SARS-CoV-2, 2020–2022, Okinawa prefecture, Japan
Yoshihiro Takayama; Yining S. Xu; Yusuke Shimakawa; Gerardo Chowell; Masahiro Kozuka; Ryosuke Omori; Ryota Matsuyama; Taro Yamamoto; Kenji Mizumoto
BMC Infectious Diseases, 24, 1, Springer Science and Business Media LLC, 30 May 2024, [Peer-reviewed]
Scientific journal, Abstract

Background

While airport screening measures for COVID-19 infected passengers at international airports worldwide have been greatly relaxed, observational studies evaluating fever screening alone at airports remain scarce. The purpose of this study is to retrospectively assess the effectiveness of fever screening at airports in preventing the influx of COVID-19 infected persons.

Methods

We conducted a retrospective epidemiological analysis of fever screening implemented at 9 airports in Okinawa Prefecture from May 2020 to March 2022. The number of passengers covered during the same period was 9,003,616 arriving at 9 airports in Okinawa Prefecture and 5,712,983 departing passengers at Naha Airport. The capture rate was defined as the proportion of reported COVID-19 cases who would have passed through airport screening to the number of suspected cases through fever screening at the airport, and this calculation used passengers arriving at Naha Airport and surveillance data collected by Okinawa Prefecture between May 2020 and March 2021.

Results

From May 2020 to March 2021, 4.09 million people were reported to pass through airports in Okinawa. During the same period, at least 122 people with COVID-19 infection arrived at the airports in Okinawa, but only a 10 suspected cases were detected; therefore, the capture rate is estimated to be up to 8.2% (95% CI: 4.00-14.56%). Our result of a fever screening rate is 0.0002% (95%CI: 0.0003–0.0006%) (10 suspected cases /2,971,198 arriving passengers). The refusal rate of passengers detected by thermography who did not respond to temperature measurements was 0.70% (95% CI: 0.19–1.78%) (4 passengers/572 passengers).

Conclusions

This study revealed that airport screening based on thermography alone missed over 90% of COVID-19 infected cases, indicating that thermography screening may be ineffective as a border control measure. The fact that only 10 febrile cases were detected after screening approximately 3 million passengers suggests the need to introduce measures targeting asymptomatic infections, especially with long incubation periods. Therefore, other countermeasures, e.g. preboarding RT-PCR testing, are highly recommended during an epidemic satisfying World Health Organization (WHO) Public Health Emergency of International Concern (PHEIC) criteria with pathogen characteristics similar or exceeding SARS-CoV-2, especially when traveling to rural cities with limited medical resources.

Understanding dynamics and overlapping epidemiologies of HIV, HSV-2, chlamydia, gonorrhea, and syphilis in sexual networks of men who have sex with men
Ryosuke Omori; Hiam Chemaitelly; Laith J. Abu-Raddad
Frontiers in Public Health, 12, Frontiers Media SA, 02 Apr. 2024, [Peer-reviewed], [Lead author, Corresponding author]
Scientific journal, Introduction

We aimed to investigate the overlapping epidemiologies of human immunodeficiency virus (HIV), herpes simplex virus type 2 (HSV-2), chlamydia, gonorrhea, and syphilis in sexual networks of men who have sex with men (MSM), and to explore to what extent the epidemiology of one sexually transmitted infection (STI) relates to or differs from that of another STI.

Methods

An individual-based Monte Carlo simulation model was employed to simulate the concurrent transmission of STIs within diverse sexual networks of MSM. The model simulated sexual partnering, birth, death, and STI transmission within each specific sexual network. The model parameters were chosen based on the current knowledge and understanding of the natural history, transmission, and epidemiology of each considered STI. Associations were measured using the Spearman’s rank correlation coefficient (SRCC) and maximal information coefficient (MIC).

Results

A total of 500 sexual networks were simulated by varying the mean and variance of the number of partners for both short-term and all partnerships, degree correlation, and clustering coefficient. HSV-2 had the highest current infection prevalence across the simulations, followed by HIV, chlamydia, syphilis, and gonorrhea. Threshold and saturation effects emerged in the relationship between STIs across the simulated networks, and all STIs demonstrated moderate to strong associations. The strongest current infection prevalence association was between HIV and gonorrhea, with an SRCC of 0.84 (95% CI: 0.80–0.87) and an MIC of 0.81 (95% CI: 0.74–0.88). The weakest association was between HSV-2 and syphilis, with an SRCC of 0.54 (95% CI: 0.48–0.59) and an MIC of 0.57 (95% CI, 0.49–0.65). Gonorrhea exhibited the strongest associations with the other STIs while syphilis had the weakest associations. Across the simulated networks, proportions of the population with zero, one, two, three, four, and five concurrent STI infections were 48.6, 37.7, 11.1, 2.4, 0.3, and < 0.1%, respectively. For lifetime exposure to these infections, these proportions were 13.6, 21.0, 22.9, 24.3, 13.4, and 4.8%, respectively.

Conclusion

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.

Estimating the basic reproduction number and final epidemic size of white spot syndrome virus outbreak in Penaeus japonicus in aquaculture ponds
Ryosuke Omori; Teruyoshi Hagino; Puttirungroj Pattama; Kenichi Ozaki; Ikuo Hirono
Aquaculture, 582, 740548, 740548, Elsevier BV, Mar. 2024, [Peer-reviewed], [Lead author, Corresponding author]
Scientific journal

Human movement avoidance decisions during Coronavirus disease 2019 in Japan
Ryosuke Omori; Koichi Ito; Shunsuke Kanemitsu; Ryusuke Kimura; Yoh Iwasa
Journal of Theoretical Biology, 111795, 111795, Elsevier BV, Mar. 2024, [Peer-reviewed], [Lead author, Corresponding author]
Scientific journal

Extraction of the CDRH3 sequence of the mouse antibody repertoire selected upon influenza virus infection by subtraction of the background antibody repertoire
Masashi Shingai; Sayaka Iida; Naoko Kawai; Mamiko Kawahara; Toshiki Sekiya; Marumi Ohno; Naoki Nomura; Chimuka Handabile; Tomomi Kawakita; Ryosuke Omori; Junya Yamagishi; Kaori Sano; Akira Ainai; Tadaki Suzuki; Kazuo Ohnishi; Kimihito Ito; Hiroshi Kida
Journal of Virology, American Society for Microbiology, 07 Feb. 2024, [Peer-reviewed]
Scientific journal, As specific interactions between antigens and cell-surface antibodies trigger the proliferation of B-cell clones, the frequency of each antibody sequence in the samples reflects the size of each clonal population. Nevertheless, it is extremely difficult to extract antigen-specific antibody sequences from the comprehensive bulk antibody sequences obtained from blood samples due to repertoire bias influenced by exposure to dietary antigens and other infectious agents. This issue can be addressed by subtracting the background noise from the post-immunization or post-infection repertoire data. In the present study, we propose a method to quantify repertoire data from comprehensive repertoire data. This method allowed subtraction of the background repertoire, resulting in more accurate extraction of expanded antibody repertoires upon influenza virus infection. This accurate extraction of antigen- or infection-specific repertoire information is a useful tool for vaccine evaluation.

Identifying Effective Biosecurity Measures for Preventing the Introduction of Classical Swine Fever in Pig Farms in Japan: Under the Condition of Absence/Presence of Observable Infected Wild Boar
Makoto Ukita; Ryota Matsuyama; Norikazu Isoda; Ryosuke Omori; Takehisa Yamamoto; Kohei Makita
Transboundary and Emerging Diseases, 2024, 1, Wiley, Jan. 2024, [Peer-reviewed]
Scientific journal, The outbreak of infectious diseases in swine, such as classical swine fever (CSF), has become a significant concern in the pig‐farming industry. In Japan, after the re‐emergence of CSF in 2018, farms are now exposed to the risk of transmission from infected wild boar and CSF‐contaminated farms. This study aimed to identify biosecurity measures that were effective for the prevention of CSF introduction into farms during the period from the beginning of the CSF epidemic to the implementation of a vaccination campaign for domestic pigs at risk. The probability of virus introduction was assumed to be increased by the elevated risk from CSF‐infected wild boar and infected farms around the farm. The risk from infected wild boar was represented by the prevalence of CSF in wild boar or the occupancy of 1‐km grid cells with infected wild boar within 10‐km radii from a pig farm and the occurrence of CSF outbreaks on neighboring farms. Conversely, the probability of virus introduction was assumed to decrease in response to on‐farm biosecurity measures being implemented on each farm. The implementation of biosecurity measures on the farms and farm attributes were obtained through a questionnaire survey. Analyses were performed on each farm under the weekly situations where infected wild boar were both absent and present in the vicinity using a binomial generalized linear model. On farms where infected wild boar were not present around farms, daily washing and disinfecting of work clothing in pig houses was identified as the main measure to reduce the risk of CSF introduction into farms. On farms with infected wild boar in the vicinity, the absence of public roads on the farm and preventing wildlife intrusion into the areas where pig carcasses were stored were demonstrated to be effective in preventing CSF introduction. Based on the assumption that strict and comprehensive biosecurity measures are required to prevent CSF introduction, the implementation of these potentially effective measures is worth being prioritized.

Time changes of customer behavior on accommodation reservation: a case study of Japan
Koichi Ito; Shunsuke Kanemitsu; Ryusuke Kimura; Ryosuke Omori
Japan Journal of Industrial and Applied Mathematics, Springer Science and Business Media LLC, 28 Nov. 2023, [Peer-reviewed], [Last author, Corresponding author]
Scientific journal, Abstract

The forecasting of demand or cancellations is highly important for efficient revenue management in the hotel industry. Previous studies have mainly focused on the accuracy of the prediction of reservation number or cancellation rate on a specific accommodation or hotel chain; therefore, the application of the prediction to different accommodations or under the behavioral change of customers in response to natural or human events is difficult without the re-estimation of the prediction model. Information of the customer behavioral trend on the accommodation reservations is necessary for the construction of a general forecasting model. In this study, we focus on one of the general trends of customer behavior, that is, the reservation timing and the time changes of the cancellation probability using the big data of the reservation records provided by an online trip agency in Japan. We showed that the reservation timing and cancellation probability can be decomposed by five and six exponential functions of the days until the stay and the days from the reservations. We also showed that the significant factors influencing the time changing patterns are the guest numbers per room for both reservation and cancellation, composition of guests in terms of the number and gender of guests, and the stay length for reservation. These findings imply that the customer behavior during accommodation reservation could be categorized into multiple motivational factors toward reservations or cancellations. Our results contribute to the construction of a general forecasting model on the accommodation reservations.

Assessing Access to Digital Services in Health Care–Underserved Communities in the United States: A Cross-Sectional Study
Diego F. Cuadros; Claudia M. Moreno; F.DeWolfe Miller; Ryosuke Omori; Neil J. MacKinnon
Mayo Clinic Proceedings: Digital Health, 1, 3, 217, 225, Elsevier BV, Sep. 2023, [Peer-reviewed]
Scientific journal

Impact of healthcare capacity disparities on the COVID-19 vaccination coverage in the United States: A cross-sectional study
Diego F. Cuadros; Juan D. Gutierrez; Claudia M. Moreno; Santiago Escobar; F. DeWolfe Miller; Godfrey Musuka; Ryosuke Omori; Phillip Coule; Neil J. MacKinnon
The Lancet Regional Health - Americas, 18, 100409, 100409, Elsevier BV, Feb. 2023, [Peer-reviewed]
Scientific journal

Shedding of rubella virus in postsymptomatic individuals; viral RNA load is a potential indicator to estimate candidate patients excreting infectious rubella virus
Daiki Kanbayashi; Takako Kurata; Atsushi Kaida; Hideyuki Kubo; Seiji P Yamamoto; Kazutaka Egawa; Yuki Hirai; Kazuma Okada; Yuko Kaida; Ryo Ikemori; Takahiro Yumisashi; Ayami Ito; Takeshi Saito; Yoshihiko Yamaji; Yuka Nishino; Ryosuke Omori; Haruyo Mori; Kazushi Motomura; Kazuyoshi Ikuta
Journal of Clinical Virology, 160, 105377, 105377, Elsevier BV, Jan. 2023, [Peer-reviewed], [International Magazine]
English, Scientific journal, BACKGROUND: Since the first isolation of rubella virus (RuV) in 1962, comprehensive data regarding the quantitative evaluation of RuV shedding remain unavailable. In this study, we evaluated the shedding of viral RNA and infectious virus in patients with acute RuV infection. STUDY DESIGN: We analyzed 767 specimens, including serum/plasma, peripheral blood mononuclear cells (PBMCs), throat swabs, and urine, obtained from 251 patients with rubella. The viral RNA load and the presence of infectious RuV were determined using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and virus isolation. RESULTS: Virus excretion peaked 0-2 days after rash onset and decreased over time. The median viral RNA load dropped to an undetectable level on day 3 after rash onset in serum/plasma, day 2 in PBMCs, days 10-13 in throat swabs, and days 6-7 in urine. Infectious virus could be isolated for up to day 2 after rash onset in serum/plasma, day 1 in PBMCs, days 8-9 in throat swabs, and days 4-5 in urine. The minimum viral RNA load that allowed virus isolation was 961 copies/mL in serum/plasma, 784 copies/mL in PBMCs, 650 copies/mL in throat swabs, and 304 copies/mL in urine. A higher viral RNA load indicated a higher likelihood of the presence of infectious virus. CONCLUSION: These findings would contribute to improve algorithms for rubella surveillance and diagnosis. In addition, this study indicates that the results of RT-qPCR enable efficient rubella control by estimating candidate patients excreting infectious virus, which could help prevent viral transmission at an early stage and eliminate rubella ultimately.

Future behaviours decision-making regarding travel avoidance during COVID-19 outbreaks
Koichi Ito; Shunsuke Kanemitsu; Ryusuke Kimura; Ryosuke Omori
Scientific Reports, 12, 1, Springer Science and Business Media LLC, 17 Nov. 2022, [Peer-reviewed], [Last author, Corresponding author]
English, Scientific journal, Abstract

Human behavioural changes are poorly understood, and this limitation has been a serious obstacle to epidemic forecasting. It is generally understood that people change their respective behaviours to reduce the risk of infection in response to the status of an epidemic or government interventions. We must first identify the factors that lead to such decision-making to predict these changes. However, due to an absence of a method to observe decision-making for future behaviour, understanding the behavioural responses to disease is limited. Here, we show that accommodation reservation data could reveal the decision-making process that underpins behavioural changes, travel avoidance, for reducing the risk of COVID-19 infections. We found that the motivation to avoid travel with respect to only short-term future behaviours dynamically varied and was associated with the outbreak status and/or the interventions of the government. Our developed method can quantitatively measure and predict a large-scale population’s behaviour to determine the future risk of COVID-19 infections. These findings enable us to better understand behavioural changes in response to disease spread, and thus, contribute to the development of reliable long-term forecasting of disease spread.

Measuring impact of vaccination among wildlife: The case of bait vaccine campaigns for classical swine fever epidemic among wild boar in Japan
Ryota Matsuyama; Takehisa Yamamoto; Yoko Hayama; Ryosuke Omori
PLOS Computational Biology, 18, 10, e1010510, e1010510, Public Library of Science (PLoS), 06 Oct. 2022, [Peer-reviewed], [Last author, Corresponding author]
Scientific journal, Understanding the impact of vaccination in a host population is essential to control infectious diseases. However, the impact of bait vaccination against wildlife diseases is difficult to evaluate. The vaccination history of host animals is generally not observable in wildlife, and it is difficult to distinguish immunity by vaccination from that caused by disease infection. For these reasons, the impact of bait vaccination against classical swine fever (CSF) in wild boar inhabiting Japan has not been evaluated accurately. In this study, we aimed to estimate the impact of the bait vaccination campaign by modelling the dynamics of CSF and the vaccination process among a Japanese wild boar population. The model was designed to estimate the impact of bait vaccination despite lack of data regarding the demography and movement of wild boar. Using our model, we solved the theoretical relationship between the impact of vaccination, the time-series change in the proportion of infected wild boar, and that of immunised wild boar. Using this derived relationship, the increase in antibody prevalence against CSF because of vaccine campaigns in 2019 was estimated to be 12.1 percentage points (95% confidence interval: 7.8–16.5). Referring to previous reports on the basic reproduction number (R₀) of CSF in wild boar living outside Japan, the amount of vaccine distribution required for CSF elimination by reducing the effective reproduction number under unity was also estimated. An approximate 1.6 (when R₀ = 1.5, target vaccination coverage is 33.3% of total population) to 2.9 (when R₀ = 2.5, target vaccination coverage is 60.0% of total population) times larger amount of vaccine distribution would be required than the total amount of vaccine distribution in four vaccination campaigns in 2019.

HIV incidence and impact of interventions among female sex workers and their clients in the Middle East and north Africa: a modelling study
Hiam Chemaitelly; Houssein H Ayoub; Ryosuke Omori; Shereen El Feki; Joumana G Hermez; Helen A Weiss; Laith J Abu-Raddad
The Lancet HIV, 9, 7, e496, e505, Elsevier BV, Jul. 2022, [Peer-reviewed]
Scientific journal

Estimating the comprehensive overview of Oncorhynchus masou virus disease outbreak in Rainbow trout using mortality data: Coupling data on experimental infection and field observation by mathematical modeling
Ryosuke Omori; Ryota Matsuyama; Yukihiko Nakata; Mitsuru Furihata; Hisae Kasai
Aquaculture, 554, 738165, 738165, Elsevier BV, Mar. 2022, [Peer-reviewed], [Lead author, Corresponding author]
Scientific journal

Estimation of the Lethality Rate, Recovery Rate, and Case Fatality Ratio of Classical Swine Fever in Japanese Wild Boar: An Analysis of the Epidemics From September 2018 to March 2019
Ryota Matsuyama; Takehisa Yamamoto; Yoko Hayama; Ryosuke Omori
Frontiers in Veterinary Science, 8, Frontiers Media SA, 15 Dec. 2021, [Peer-reviewed], [Last author, Corresponding author]
Scientific journal, Understanding the morbidity and lethality of diseases is necessary to evaluate the effectiveness of countermeasure against the epidemics (e.g., vaccination). To estimate them, detailed data on host population dynamics are required; however, estimating the population size for wildlife is often difficult. We aimed to elucidate the morbidity and lethality of classical swine fever (CSF) currently highly prevalent in the wild boar population in Japan. To this end, we estimated lethality rate, recovery rate, and case fatality ratio (CFR) of CSF without detailed data on the population estimates of wild boar. A mathematical model was constructed to describe the CSF dynamics and population dynamics of wild boar. We fitted the model to the (i) results of the reverse transcription polymerase chain reaction (RT-PCR) test for the CSFV gene and the (ii) results of the enzyme-linked immunosorbent assay (ELISA) test for the antibody against CSFV in sampled wild boar. In the 280 wild boar sampled from September 2018 to March 2019 in the major CSF-affected area in Japan, the lethality rate and recovery rate of CSF per week were estimated as 0.165 (95% confidence interval: 0.081–0.250) and 0.004 (0–0.009), respectively. While the estimate of lethality rate of CSF was similar with the estimates in previous studies, the recovery rate was lower than those reported previously. CFR was estimated as 0.959 (0.904–0.981) using our estimate of recovery rate. This study is the first to estimate lethality rate of CSF from the dynamics of CSF epidemics in the wild boar population. Since the value of CFR is sensitive to the value of recovery rate, the accuracy in the estimate of recovery rate is a key for the accurate estimation of CFR. A long-term transmission experiment of moderately virulent strains may lead to more accurate estimation of the recovery rate and CFR of CSF.

Usefulness of a 3D-printing air sampler for capturing live airborne bacteria and exploring the environmental factors that can influence bacterial dynamics
Saaya Mori; Sakura Ishiguro; Satoru Miyazaki; Torahiko Okubo; Ryosuke Omori; Ayako Kai; Kyohei Sugiyama; Airi Kawashiro; Masato Sumi; Jeewan Thapa; Shinji Nakamura; Chietsugu Katoh; Hiroyuki Yamaguchi
Research in Microbiology, 172, 6, 103864, 103864, Elsevier BV, Jul. 2021, [Peer-reviewed], [International Magazine]
English, Scientific journal, We created a handmade 3D-printed air sampler to effectively collect live airborne bacteria, and determined which environmental factors influenced the bacteria. Bacterial colony forming units (CFUs) in the air samples (n = 37) were monitored by recording the environmental changes occurring over time, then determining the presence/absence of correlations among such changes. The bacterial CFUs changed sharply and were significantly correlated with the DNA concentrations, indicating that the captured bacteria made up most of the airborne bacteria. Spearman's rank correlation analysis revealed significant correlations between the bacterial CFU values and some environmental factors (humidity, wind speed, insolation, and 24-h rainfall). Similarly the significant associations of CFU with humidity and wind speed were also found by multiple regression analysis with box-cox transformation. Among our panel of airborne bacteria (952 strains), 70 strains were identified as soil-derived Bacillus via the production of Escherichia coli- and Staphylococcus aureus-growth inhibiting antibiotics and by 16S rDNA typing. Soil-derived protozoa were also isolated from the air samples. We conclude that the airborne bacteria mainly derived from soil can alter in number according to environmental changes. Our sampler, which was created by easy-to-customize 3D printing, is a useful device for understanding the dynamics of live airborne bacteria.

Immunization Coverage and Antibody Retention against Rabies in Domestic Dogs in Lusaka District, Zambia
Chiho Kaneko; Michihito Sasaki; Ryosuke Omori; Ryo Nakao; Chikako Kataoka-Nakamura; Ladslav Moonga; Joseph Ndebe; Walter Muleya; Edgar Simulundu; Bernard M. Hang’ombe; George Dautu; Masahiro Kajihara; Akina Mori-Kajihara; Yongjin Qiu; Naoto Ito; Herman M. Chambaro; Chihiro Sugimoto; Hideaki Higashi; Ayato Takada; Hirofumi Sawa; Aaron S. Mweene; Norikazu Isoda
Pathogens, 10, 6, 738, 738, MDPI AG, 11 Jun. 2021, [Peer-reviewed], [International Magazine]
English, Scientific journal, Rabies remains endemic in Zambia. Despite conducting canine vaccinations in Lusaka district, the vaccination coverage and actual seropositivity in the dog population in Lusaka district are rarely evaluated. This study estimated the seropositivity-based immunization coverage in the owned dog population in Lusaka district using the expanded program on immunization cluster survey method. The time-series trend of neutralizing antibodies against rabies in vaccinated dogs was also evaluated. Of 366 dogs in 200 dog-owning households in Lusaka district, blood samples were collected successfully from 251 dogs. In the sampled dogs, 42.2% (106/251) had an antibody titer ≥0.5 IU/mL. When the 115 dogs whose blood was not collected were assumed to be seronegative, the minimum immunization coverage in Lusaka district’s owned dog population was estimated at 29.0% (95% confidence interval: 22.4–35.5). It was also found that a single vaccination with certified vaccines is capable of inducing protective levels of antibodies. In contrast, higher antibody titers were observed in multiple-vaccinated dogs than in single-vaccinated dogs, coupled with the observation of a decline in antibody titer over time. These results suggest the importance of continuous booster immunization to maintain herd immunity and provide useful information to plan mass vaccination against rabies in Zambia.

Age-dependent association between SARS-CoV-2 cases reported by passive surveillance and viral load in wastewater
Ryosuke Omori; Fuminari Miura; Masaaki Kitajima
Science of The Total Environment, 792, 148442, 148442, Jun. 2021, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal

Potent priming by inactivated whole influenza virus particle vaccines is linked to viral RNA uptake into antigen presenting cells
Masashi Shingai; Naoki Nomura; Toshiki Sekiya; Marumi Ohno; Daisuke Fujikura; Chimuka Handabile; Ryosuke Omori; Yuki Ohara; Tomohiro Nishimura; Masafumi Endo; Kazuhiko Kimachi; Ryotarou Mitsumata; Tomio Ikeda; Hiroki Kitayama; Hironori Hatanaka; Tomoyoshi Sobue; Fumihito Muro; Saori Suzuki; Cong Thanh Nguyen; Hirohito Ishigaki; Misako Nakayama; Yuya Mori; Yasushi Itoh; Marios Koutsakos; Brendon Y Chua; Katherine Kedzierska; Lorena E Brown; David C Jackson; Kazumasa Ogasawara; Yoichiro Kino; Hiroshi Kida
Vaccine, 39, 29, 3940, 3951, Elsevier BV, Jun. 2021, [Peer-reviewed]
Scientific journal

Estimation of the Actual Incidence of Coronavirus Disease (COVID-19) in Emergent Hotspots: The Example of Hokkaido, Japan during February–March 2020
Andrei R. Akhmetzhanov; Kenji Mizumoto; Sung-Mok Jung; Natalie M. Linton; Ryosuke Omori; Hiroshi Nishiura
Journal of Clinical Medicine, 10, 11, 2392, 2392, MDPI AG, 28 May 2021, [Peer-reviewed], [International Magazine]
English, Scientific journal, Following the first report of the coronavirus disease 2019 (COVID-19) in Sapporo city, Hokkaido Prefecture, Japan, on 14 February 2020, a surge of cases was observed in Hokkaido during February and March. As of 6 March, 90 cases were diagnosed in Hokkaido. Unfortunately, many infected persons may not have been recognized due to having mild or no symptoms during the initial months of the outbreak. We therefore aimed to predict the actual number of COVID-19 cases in (i) Hokkaido Prefecture and (ii) Sapporo city using data on cases diagnosed outside these areas. Two statistical frameworks involving a balance equation and an extrapolated linear regression model with a negative binomial link were used for deriving both estimates, respectively. The estimated cumulative incidence in Hokkaido as of 27 February was 2,297 cases (95% confidence interval (CI): 382–7091) based on data on travelers outbound from Hokkaido. The cumulative incidence in Sapporo city as of 28 February was estimated at 2233 cases (95% CI: 0–4893) based on the count of confirmed cases within Hokkaido. Both approaches resulted in similar estimates, indicating a higher incidence of infections in Hokkaido than were detected by the surveillance system. This quantification of the gap between detected and estimated cases helped to inform the public health response at the beginning of the pandemic and provided insight into the possible scope of undetected transmission for future assessments.

Updating the influenza virus library at Hokkaido University -It's potential for the use of pandemic vaccine strain candidates and diagnosis
Naoki Nomura; Keita Matsuno; Masashi Shingai; Marumi Ohno; Toshiki Sekiya; Ryosuke Omori; Yoshihiro Sakoda; Robert G. Webster; Hiroshi Kida
Virology, 557, 55, 61, Elsevier BV, May 2021, [Peer-reviewed]
Scientific journal

Analytic characterization of the herpes simplex virus type 2 epidemic in the United States, 1950-2050
Houssein H Ayoub; Ibtihel Amara; Susanne F Awad; Ryosuke Omori; Hiam Chemaitelly; Laith J Abu-Raddad
Open Forum Infectious Diseases, 8, 7, ofab218, Oxford University Press (OUP), 29 Apr. 2021, [Peer-reviewed]
Scientific journal,


We analytically characterized the past, present, and future levels and trends of the national herpes simplex virus type 2 (HSV-2) epidemic in the United States.





A population-level mathematical model was constructed to describe HSV-2 transmission dynamics and was fitted to the data series of the National Health and Nutrition Examination Surveys.





Over 1950-2050, antibody prevalence (seroprevalence) increased rapidly from 1960, peaking at 19.9% in 1983 in those aged 15-49, before reversing course to decline to 13.2% by 2020 and 8.5% by 2050. Incidence rate peaked in 1971 at 11.9 per 1,000 person-years, before declining by 59% by 2020 and 70% by 2050. Annual number of new infections peaked at 1,033,000 in 1978, before declining to 667,000 by 2020 and 600,000 by 2050. Women were disproportionately affected, averaging 75% higher seroprevalence, 95% higher incidence rate, and 71% higher annual number of infections. In 2020, 78% of infections were acquired by those 15-34 year-olds.





The epidemic has undergone a major transition over a century, with the greatest impact in those 15-34 year-olds. In addition to 47 million prevalent infections in 2020, high incidence will persist over the next three decades, adding >600,000 new infections every year.

Domestic dog demographics and estimates of canine vaccination coverage in a rural area of Zambia for the elimination of rabies
Chiho Kaneko; Ryosuke Omori; Michihito Sasaki; Chikako Kataoka-Nakamura; Edgar Simulundu; Walter Muleya; Ladslav Moonga; Joseph Ndebe; Bernard M. Hang’ombe; George Dautu; Yongjin Qiu; Ryo Nakao; Masahiro Kajihara; Akina Mori-Kajihara; Herman M. Chambaro; Hideaki Higashi; Chihiro Sugimoto; Hirofumi Sawa; Aaron S. Mweene; Ayato Takada; Norikazu Isoda
PLOS Neglected Tropical Diseases, 15, 4, e0009222, e0009222, Public Library of Science (PLoS), 28 Apr. 2021, [Peer-reviewed], [International Magazine]
English, Scientific journal,

An estimated 75% or more of the human rabies cases in Africa occur in rural settings, which underscores the importance of rabies control in these areas. Understanding dog demographics can help design strategies for rabies control and plan and conduct canine mass vaccination campaigns effectively in African countries.





A cross-sectional survey was conducted to investigate domestic dog demographics in Kalambabakali, in the rural Mazabuka District of Zambia. The population of ownerless dogs and the total achievable vaccination coverage among the total dog population was estimated using the capture-recapture-based Bayesian model by conducting a canine mass vaccination campaign. This study revealed that 29% of the domestic dog population was under one year old, and 57.7% of those were under three months old and thus were not eligible for the canine rabies vaccination in Zambia. The population growth was estimated at 15% per annum based on the cross-sectional household survey. The population of ownerless dogs was estimated to be small, with an ownerless-to-owned-dog ratio of 0.01–0.06 in the target zones. The achieved overall vaccination coverage from the first mass vaccination was estimated 19.8–51.6%. This low coverage was principally attributed to the owners’ lack of information, unavailability, and dog-handling difficulties. The follow-up mass vaccination campaign achieved an overall coverage of 54.8–76.2%.





This paper indicates the potential for controlling canine rabies through mass vaccination in rural Zambia. Rabies education and responsible dog ownership are required to achieve high and sustainable vaccination coverage. Our findings also propose including puppies below three months old in the target population for rabies vaccination and emphasize that securing an annual enforcement of canine mass vaccination that reaches 70% coverage in the dog population is necessary to maintain protective herd immunity.

Genetic Diversity of African Trypanosomes in Tsetse Flies and Cattle From the Kafue Ecosystem
Yukiko Nakamura; Kyoko Hayashida; Victoire Delesalle; Yongjin Qiu; Ryosuke Omori; Martin Simuunza; Chihiro Sugimoto; Boniface Namangala; Junya Yamagishi
Frontiers in Veterinary Science, 8, 599815, 599815, Frontiers Media SA, 27 Jan. 2021, [Peer-reviewed], [International Magazine]
English, Scientific journal, We clarified the genetic diversity of Trypanosoma spp. within the Kafue ecosystem, using PCR targeting the internal transcribed spacer 1 and the cathepsin L-like cysteine protease (CatL) sequences. The overall prevalence of Trypanosoma spp. in cattle and tsetse flies was 12.65 and 26.85%, respectively. Cattle positive for Trypanosoma vivax had a significantly lower packed cell volume, suggesting that T. vivax is the dominant Trypanosoma spp. causing anemia in this area. Among the 12 operational taxonomic units (OTUs) of T. vivax CatL sequences detected, one was from a known T. vivax lineage, two OTUs were from known T. vivax-like lineages, and nine OTUs were considered novel T. vivax-like lineages. These findings support previous reports that indicated the extensive diversity of T. vivax-like lineages. The findings also indicate that combining CatL PCR with next generation sequencing is useful in assessing Trypanosoma spp. diversity, especially for T. vivax and T. vivax-like lineages. In addition, the 5.42% prevalence of Trypanosoma brucei rhodesiense found in cattle raises concern in the community and requires careful monitoring of human African trypanosomiasis.

Duration of SARS-CoV-2 viral shedding in faeces as a parameter for wastewater-based epidemiology: Re-analysis of patient data using a shedding dynamics model
Fuminari Miura; Masaaki Kitajima; Ryosuke Omori
Science of The Total Environment, 769, 144549, 144549, Elsevier BV, Jan. 2021, [Peer-reviewed], [International Magazine]
English, Scientific journal, Wastewater-based epidemiology (WBE) is one of the most promising approaches to effectively monitor the spread of COVID-19. The virus concentration in faeces and its temporal variations are essential information for WBE. While some clinical studies have reported SARS-CoV-2 concentrations in faeces, the value varies amongst patients and changes over time. The present study aimed to examine how the temporal variations in the concentration of virus in faeces affect the monitoring of disease incidence. We reanalysed the experimental findings of clinical studies to estimate the duration of virus shedding and the faecal virus concentration. Available experimental data as of 23 October 2020 were collected. The viral shedding kinetics was modelled, and the dynamic model was fitted to the collected data by a Bayesian framework. Using posterior distributions, the duration of viral shedding and the concentration of virus copies in faeces over time were computed. We estimated the median concentration of SARS-CoV-2 in faeces as 3.4 (95% CrI: 0.24-6.5) log copies per gram-faeces over the shedding period, and our model implied that the duration of viral shedding was 26.0 days (95% CrI: 21.7-34.9), given the current standard quantification limit (Ct = 40). With simulated incidences, our results also indicated that a one-week delay between symptom onset and wastewater sampling increased the estimation of incidence by a factor of 17.2 (i.e., 101.24 times higher). Our results demonstrated that the temporal variation in virus concentration in faeces affects microbial monitoring systems such as WBE. The present study also implied the need for adjusting the estimates of virus concentration in faeces by incorporating the kinetics of unobserved concentrations. The method used in this study is easily implemented in further simulations; therefore, the results of this study might contribute to enhancing disease surveillance and risk assessments that require quantities of virus to be excreted into the environment.

The age distribution of mortality from novel coronavirus disease (COVID-19) suggests no large difference of susceptibility by age
Ryosuke Omori; Ryota Matsuyama; Yukihiko Nakata
Scientific Reports, 10, 1, 16642, 16642, Springer Science and Business Media LLC, Dec. 2020, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
English, Scientific journal,
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 reported data, including the effect of change in contact patterns during the epidemics of COVID-19, and the fraction of symptomatic infections. Our study revealed that if the mortality rate or the fraction of symptomatic infections among all COVID-19 cases does not depend on age, then unrealistically different age-dependencies of susceptibilities against COVID-19 infections between Italy, Japan, and Spain are required to explain the similar age distribution of mortality but different basic reproduction numbers (R₀). Variation of susceptibility by age itself cannot explain the robust age distribution in mortality by COVID-19 infections in those three countries, however it does suggest that the age-dependencies of (i) the mortality rate and (ii) the fraction of symptomatic infections among all COVID-19 cases determine the age distribution of mortality by COVID-19.

Cluster-Based Approach to Coronavirus Disease 2019 (COVID-19) Response in Japan, from February to April 2020
Oshitani H; the Experts Members of The; National COVID; Cluster Task force; at; Ministry of Health; Labour; Welfare, Japan
Japanese Journal of Infectious Diseases, 73, 6, 491, 493, Editorial Committee of Japanese Journal of Infectious Diseases, National Institute of Infectious Dis, Jun. 2020, [Peer-reviewed]
Scientific journal

Ascertainment rate of novel coronavirus disease (COVID-19) in Japan
Ryosuke Omori; Kenji Mizumoto; Hiroshi Nishiura
International Journal of Infectious Diseases, 96, 673, 675, Elsevier BV, May 2020, [Peer-reviewed], [Lead author]
Scientific journal

Changes in testing rates could mask the novel coronavirus disease (COVID-19) growth rate
Ryosuke Omori; Kenji Mizumoto; Gerardo Chowell
International Journal of Infectious Diseases, 94, 116, 118, Elsevier BV, May 2020, [Peer-reviewed], [Lead author, Corresponding author], ［Internationally co-authored］
English, Scientific journal

Estimating Transmission Potential of H5N1 Viruses among Humans in Egypt Using Phylogeny, Genetic Distance and Sampling Time Interval
Wessam Mohamed; Kimihito Ito; Ryosuke Omori
Frontiers in Microbiology, 10, 2765, Dec. 2019, [Peer-reviewed]

Epidemic dynamics with time-varying susceptibility due to repeated infections
Yukihiko Nakata; Ryosuke Omori
Journal of Biological Dynamics, 13, 1, 567, 585, Aug. 2019, [Peer-reviewed], [Lead author]

Analytical Exploration of Potential Pathways by which Diabetes Mellitus Impacts Tuberculosis Epidemiology
Susanne F. Awad; Soha R. Dargham; Ryosuke Omori; Fiona Pearson; Julia Critchley; Laith J. Abu-Raddad
Scientific Reports, 9, 8494, Jun. 2019, [Peer-reviewed]
English, Scientific journal

Characterizing herpes simplex virus type 1 and type 2 seroprevalence declines and epidemiological association in the United States
Hiam Chemaitelly; Nico Nagelkerke; Ryosuke Omori; Laith J. Abu-Raddad
PLOS ONE, 14, 6, e0214151, Jun. 2019, [Peer-reviewed]

The intercellular expression of type-XVII collagen, laminin-332, and integrin-β1 promote contact following during the collective invasion of a cancer cell population
Yuji Kumagai; Junko Nio-Kobayashi; Sumire Ishida-Ishihara; Hiromi Tachibana; Ryosuke Omori; Atsushi Enomoto; Seiichiro Ishihara; Hisashi Haga
Biochemical and Biophysical Research Communications, 514, 4, 1115, 1121, May 2019, [Peer-reviewed], [International Magazine]
English, Scientific journal, Cancer cells can invade as a population in various cancer tissues. This phenomenon is called collective invasion, which is associated with the metastatic potential and prognosis of cancer patients. The collectiveness of cancer cells is necessary for collective invasion. However, the mechanism underlying the generation of collectiveness by cancer cells is not well known. In this study, the phenomenon of contact following, where neighboring cells move in the same direction via intercellular adhesion, was investigated. An experimental system was created to observe the two-dimensional invasion using a collagen gel overlay to study contact following in collective invasion. The role of integrin-β1, one of the major extracellular matrix (ECM) receptors, in contact following was examined through the experimental system. Integrin-β1 was localized to the intercellular site in squamous carcinoma cells. Moreover, the intercellular adhesion and contact following were suppressed by treatment of an integrin-β1 inhibitory antibody. ECM proteins such as laminin-332 and type-XVII collagen were also localized to the intercellular site and critical for contact following. Collectively, it was demonstrated that the activity of integrin-β1 and expression of ECM proteins in the intercellular site promote contact following in the collective invasion of a cancer cell population.

Potential role of dogs as sentinels and reservoirs for piroplasms infecting equine and cattle in Riyadh City, Saudi Arabia
Bashir Salim; Abdullah D. Alanazi; Ryosuke Omori; Mohamed S. Alyousif; Ibrahim O. Alanazi; Ken Katakura; Ryo Nakao
Acta Tropica, 193, 2019, 78, 83, Elsevier BV, May 2019, [Peer-reviewed]
Scientific journal

Diversity of spotted fever group rickettsiae and their association with host ticks in Japan.
May June Thu; Yongjin Qiu; Keita Matsuno; Masahiro Kajihara; Akina Mori-Kajihara; Ryosuke Omori; Naota Monma; Kazuki Chiba; Junji Seto; Mutsuyo Gokuden; Masako Andoh; Hideo Oosako; Ken Katakura; Ayato Takada; Chihiro Sugimoto; Norikazu Isoda; Ryo Nakao
Scientific reports, 9, 1, 1500, 1500, 06 Feb. 2019, [Peer-reviewed], [International Magazine]
English, Scientific journal, Spotted fever group (SFG) rickettsiae are obligate intracellular Gram-negative bacteria mainly associated with ticks. In Japan, several hundred cases of Japanese spotted fever, caused by Rickettsia japonica, are reported annually. Other Rickettsia species are also known to exist in ixodid ticks; however, their phylogenetic position and pathogenic potential are poorly understood. We conducted a nationwide cross-sectional survey on questing ticks to understand the overall diversity of SFG rickettsiae in Japan. Out of 2,189 individuals (19 tick species in 4 genera), 373 (17.0%) samples were positive for Rickettsia spp. as ascertained by real-time PCR amplification of the citrate synthase gene (gltA). Conventional PCR and sequencing analyses of gltA indicated the presence of 15 different genotypes of SFG rickettsiae. Based on the analysis of five additional genes, we characterised five Rickettsia species; R. asiatica, R. helvetica, R. monacensis (formerly reported as Rickettsia sp. In56 in Japan), R. tamurae, and Candidatus R. tarasevichiae and several unclassified SFG rickettsiae. We also found a strong association between rickettsial genotypes and their host tick species, while there was little association between rickettsial genotypes and their geographical origins. These observations suggested that most of the SFG rickettsiae have a limited host range and are maintained in certain tick species in the natural environment.

Correction: Development and application of a Bacillus anthracis protective antigen domain-1 in-house ELISA for the detection of anti-protective antigen antibodies in cattle in Zambia.
Simbotwe M; Fujikura D; Ohnuma M; Omori R; Furuta Y; Muuka GM; Hang'ombe BM; Higashi H
PloS one, 14, 1, e0211592, 2019, [Peer-reviewed]
English

The change of susceptibility following infection can induce failure to predict outbreak potential by $\mathcal{R}_{0}
Yukihiko Nakata; Ryosuke Omori
Mathematical Biosciences and Engineering, 16, 2, 813, 830, Jan. 2019, [Peer-reviewed]
English

Hepatitis C virus infection spontaneous clearance: Has it been underestimated?
Houssein Ayoub; Hiam Chemaitelly; Ryosuke Omori; Laith Abu-Raddad
International Journal of Infectious Diseases, 75, 60, 66, Oct. 2018, [Peer-reviewed]

Optimization of diagnostic methods and criteria of endometritis for various postpartum days to evaluate infertility in dairy cows
Takeshi Koyama; Ryosuke Omori; Keisuke Koyama; Yoshitaka Matsui; Masahito Sugimoto
Theriogenology, 119, 1, 225, 232, Oct. 2018, [Peer-reviewed]

Development and application of a Bacillus anthracis protective antigen domain-1 in-house ELISA for the detection of anti-protective antigen antibodies in cattle in Zambia
Manyando Simbotwe; Daisuke Fujikura; Miyuki Ohnuma; Ryosuke Omori; Yoshikazu Furuta; Geoffrey Munkombwe Muuka, Bernar; Mudenda Hang’ombe; Hideaki Higashi
PloS one, 13, 10, e0205986, Oct. 2018, [Peer-reviewed]
English, Scientific journal

Does infection with Chlamydia trachomatis induce long-lasting partial immunity? Insights from mathematical modelling
Ryosuke Omori; Hiam Chemaitelly; Christian L. Althaus; Laith J. Abu-Raddad
Sexually Transmitted Infections, 95, 115, 121, Sep. 2018, [Peer-reviewed], [Lead author, Corresponding author]
English

The epidemiology of herpes simplex virus type 1 in Asia: systematic review, meta-analyses, and meta-regressions
Lara Khadra; Manale Harfouche; Ryosuke Omori; Guido Schwarzer; Hiam Chemaitelly; Laith J. Abu-Raddad
Clinical Infectious Diseases, 68, 5, 757, 772, Jul. 2018, [Peer-reviewed]
English

Comparison of database search methods for the detection of Legionella pneumophila in water samples using metagenomic analysis
Jednipit Borthong; Ryosuke Omori; Chihiro Sugimoto; Orasa Suthienkul; Ryo Nakao; Kimihito Ito
Frontiers in Microbiology, 9, 1272, Frontiers Media S.A., 19 Jun. 2018, [Peer-reviewed]
English, Scientific journal

Global population-level association between herpes simplex virus 2 prevalence and HIV prevalence
Silva P. Kouyoumjian; Marieke Heijnen; Karima Chaabna; Ghina R. Mumtaz; Ryosuke Omori; Peter Vickerman; Laith J. Abu-Raddad
AIDS, 32, 10, 1343, 1352, Lippincott Williams and Wilkins, 19 Jun. 2018, [Peer-reviewed]
English, Scientific journal

Evaluation of body condition using body mass and chest girth in brown bears of Hokkaido, Japan (Ursus arctos yesoensis)
Jun Moriwaki; Ryosuke Omori; Michito Shimozuru; Hifumi Tsuruga; Tsutomu Mano; Toshio Tsubota
Japanese Journal of Veterinary Research, 66, 2, 71, 81, Hokkaido University, 01 May 2018, [Peer-reviewed]
English, Scientific journal

Can machines learn respiratory virus epidemiology?: A comparative study of likelihood-free methods for the estimation of epidemiological dynamics
Heidi L. Tessmer; Kimihito Ito; Ryosuke Omori
Frontiers in Microbiology, 9, 343, Frontiers Media S.A., 02 Mar. 2018, [Peer-reviewed], [Last author, Corresponding author]
English, Scientific journal

High transmissibility of norovirus among infants and school children during the 2016/17 season in Osaka, Japan
Naomi Sakon; Jun Komano; Heidi L. Tessmer; Ryosuke Omori
Eurosurveillance, 23, 6, 18-00029, European Centre for Disease Prevention and Control (ECDC), 08 Feb. 2018, [Peer-reviewed], [Last author, Corresponding author]
English, Scientific journal

Evaluation of bovine viral diarrhoea virus control strategies in dairy herds in Hokkaido, Japan, using stochastic modelling
S. Sekiguchi; P. Presi; R. Omori; K. Staerk; M. Schuppers; N. Isoda; Y. Yoshikawa; T. Umemura; H. Nakayama; Y. Fujii; Y. Sakoda
Transboundary and Emerging Diseases, 65, 1, e135, e144, Blackwell Publishing Ltd, 01 Feb. 2018, [Peer-reviewed]
English, Scientific journal

HIV and herpes simplex virus type 2 epidemiological synergy: Misguided observational evidence? A modelling study
Ryosuke Omori; Nico Nagelkerke; Laith J. Abu-Raddad
Sexually Transmitted Infections, 94, 372, 376, BMJ Publishing Group, 04 Dec. 2017, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal

Inferring epidemiological dynamics of infectious diseases using Tajima's D statistic on nucleotide sequences of pathogens
Kiyeon Kim; Ryosuke Omori; Kimihito Ito
EPIDEMICS, 21, 21, 29, Dec. 2017, [Peer-reviewed]
English, Scientific journal

Modelling infectious diseases with relapse: a case study of HSV-2
Jinliang Wang; Xiaoqing Yu; Heidi L. Tessmer; Toshikazu Kuniya; Ryosuke Omori
THEORETICAL BIOLOGY AND MEDICAL MODELLING, 14, 13, Jul. 2017, [Peer-reviewed]
English, Scientific journal

Sexual network drivers of HIV and herpes simplex virus type 2 transmission
Ryosuke Omori; Laith J. Abu-Raddad
AIDS, 31, 12, 1721, 1732, Jul. 2017, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal

TAJIMA'S D AND SITE-SPECIFIC NUCLEOTIDE FREQUENCY IN A POPULATION DURING AN INFECTIOUS DISEASE OUTBREAK
Ryosuke Omori; Jianhong Wu
SIAM JOURNAL ON APPLIED MATHEMATICS, 77, 6, 2156, 2171, 2017, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal

Nonpaternity and Half-Siblingships as Objective Measures of Extramarital Sex: Mathematical Modeling and Simulations
Ryosuke Omori; Nico Nagelkerke; Laith J. Abu-Raddad
BIOMED RESEARCH INTERNATIONAL, 2017, 2017, 3564861, 2017, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal

Tracking the Evolution of Polymerase Genes of Influenza A Viruses during Interspecies Transmission between Avian and Swine Hosts
Nipawit Karnbunchob; Ryosuke Omori; Heidi L. Tessmer; Kimihito Ito
FRONTIERS IN MICROBIOLOGY, 7, 2118, Dec. 2016, [Peer-reviewed]
English, Scientific journal

Estimating the Lineage Dynamics of Human Influenza B Viruses
Mayumbo Nyirenda; Ryosuke Omori; Heidi L. Tessmer; Hiroki Arimura; Kimihito Ito
PLOS ONE, 11, 11, e0166107, Nov. 2016, [Peer-reviewed], [Corresponding author]
English, Scientific journal

Population sexual behavior and HIV prevalence in Sub-Saharan Africa: missing links?
Ryosuke Omori; Laith J. Abu-Raddad
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 44, 1, 3, Mar. 2016, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal

Host-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review
Kiyeon Kim; Ryosuke Omori; Keisuke Ueno; Sayaka Iida; Kimihito Ito
PLOS ONE, 11, 1, e0147021, Jan. 2016, [Peer-reviewed]
English, Scientific journal

The determinant of periodicity in Mycoplasma pneumoniae incidence: an insight from mathematical modelling
Ryosuke Omori; Yukihiko Nakata; Heidi L. Tessmer; Satowa Suzuki; Keigo Shibayama
SCIENTIFIC REPORTS, 5, 14473, Sep. 2015, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal

Dynamics of non-cohabiting sex partnering in sub-Saharan Africa: a modelling study with implications for HIV transmission
Ryosuke Omori; Hiam Chemaitelly; Laith J. Abu-Raddad
SEXUALLY TRANSMITTED INFECTIONS, 91, 6, 451, 457, Sep. 2015, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal

Timing of the emergence of new successful viral strains in seasonal influenza
Ryosuke Omori; Akira Sasaki
Journal of Theoretical Biology, 329, 21, 32, 38, Elsevier BV, Jul. 2013, [Peer-reviewed], [Lead author, Corresponding author]
Scientific journal

How Is Vaccine Effectiveness Scaled by the Transmission Dynamics of Interacting Pathogen Strains with Cross-Protective Immunity?
Ryosuke Omori; Benjamin J. Cowling; Hiroshi Nishiura
PLOS ONE, 7, 11, e50751, Nov. 2012, [Peer-reviewed], [Lead author]
English, Scientific journal

Incubation period as part of the case definition of severe respiratory illness caused by a novel coronavirus
H. Nishiura; K. Mizumoto; K. Ejima; Y. Zhong; B. J. Cowling; R. Omori
EUROSURVEILLANCE, 17, 42, 4, 7, Oct. 2012, [Peer-reviewed]
English, Scientific journal

Real-time Investigation of Measles Epidemics with Estimate of Vaccine Efficacy
Keisuke Ejima; Ryosuke Omori; Kazuyuki Aihara; Hiroshi Nishiura
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES, 8, 5, 620, 629, 2012, [Peer-reviewed]
English, Scientific journal

The Time Required to Estimate the Case Fatality Ratio of Influenza Using Only the Tip of an Iceberg: Joint Estimation of the Virulence and the Transmission Potential
Keisuke Ejima; Ryosuke Omori; Benjamin J. Cowling; Kazuyuki Aihara; Hiroshi Nishiura
COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE, 2012, 2012, 978901, 2012, [Peer-reviewed]
English, Scientific journal

Disrupting seasonality to control disease outbreaks: The case of koi herpes virus
Ryosuke Omori; Ben Adams
JOURNAL OF THEORETICAL BIOLOGY, 271, 1, 159, 165, Feb. 2011, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal

Theoretical basis to measure the impact of short-lasting control of an infectious disease on the epidemic peak
Ryosuke Omori; Hiroshi Nishiura
THEORETICAL BIOLOGY AND MEDICAL MODELLING, 8, 2, Jan. 2011, [Peer-reviewed], [Lead author]
English, Scientific journal

An Epidemiological Analysis of the Foot-and-Mouth Disease Epidemic in Miyazaki, Japan, 2010
H. Nishiura; R. Omori
TRANSBOUNDARY AND EMERGING DISEASES, 57, 6, 396, 403, Dec. 2010, [Peer-reviewed]
English, Scientific journal

Coexistence conditions for strains of influenza with immune cross-reaction
Ryosuke Omori; Ben Adams; Akira Sasaki
JOURNAL OF THEORETICAL BIOLOGY, 262, 1, 48, 57, Jan. 2010, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal

Estimatiing the dynamics of a raccoon dog population using animal rescue data
松山亮太; 木戸伸英; 大森亮介, 日本生態学会大会講演要旨(Web), 71st, 2024

Quantification of Within-Farm Vertical and Horizontal Transmission of Bovine Infectious Leukemia Virus Using Mother-Calf Pair Analysis
松本藤乃; 吉岡知輝; 小原潤子; 松山亮太; 蒔田浩平; 大森亮介, 獣医疫学雑誌, 28, 1, 2024

2酪農場の牛伝染性リンパ腫ウイルス年齢別解析による感染様式の検討
蒔田浩平; 松本藤乃; 小原潤子; 松山亮太; 大森亮介, 日本獣医学会学術集会講演要旨集, 167th, 2024

野生動物の死体調査記録を用いた野生動物集団の個体群動態と感染症流行動態の推定:和歌山県南部のホンドタヌキ個体群における疥癬の事例
松山亮太; 大森亮介; 加藤卓也; 立木靖之; 浅川満彦; 長雄一; 鈴木和男, 日本獣医学会学術集会講演要旨集, 167th, 2024

沖縄県の高齢者介護施設における新型コロナウイルス感染症発生規模に関連する要因
許以寧; 高山義浩; 高山義浩; 高山義浩; 大森亮介; 大森亮介; 松山亮太; 松山亮太; 水本憲治; 水本憲治, 日本公衆衛生学会総会抄録集(CD-ROM), 83rd, 2024

ダニ媒介性ウイルスの感染リスクに影響する生態学的要因:北海道におけるアライグマとエゾウイルスについて
伊藤萌林; 南川未来; 伊藤萌林; 南川未来; コウバ アナスタシア; 沼田栄花; 伊藤哲治; 野中成晃; 中尾亮; 大森亮介; 尾針由真; 下鶴倫人; 坪田敏男; 松野啓太; 佐鹿万里子, 日本獣医学会学術集会講演要旨集, 167th, 2024

風疹患者におけるウイルスRNAと感染性ウイルスの排出について
上林 大起; 倉田 貴子; 改田 厚; 久保 英幸; 山元 誠司; 江川 和孝; 平井 有紀; 岡田 和真; 改田 祐子; 池森 亮; 弓指 孝博; 森 治代; 本村 和嗣; 山地 良彦; 西野 裕香; 伊藤 文美; 齊藤 武志; 大森 亮介; 生田 和良, 病原微生物検出情報月報, 44, 4, 51, 53, Apr. 2023
国立健康危機管理研究機構国立感染症研究所感染症サーベイランス研究部, Japanese

風疹患者におけるウイルスRNAと感染性ウイルスの排出について
上林 大起; 倉田 貴子; 改田 厚; 久保 英幸; 山元 誠司; 江川 和孝; 平井 有紀; 岡田 和真; 改田 祐子; 池森 亮; 弓指 孝博; 森 治代; 本村 和嗣; 山地 良彦; 西野 裕香; 伊藤 文美; 齊藤 武志; 大森 亮介; 生田 和良, 病原微生物検出情報月報, 44, 4, 51, 53, Apr. 2023
国立感染症研究所, Japanese

疫学的アプローチによる牛伝染性リンパ腫発症感受性牛と抵抗牛の識別
吉岡知輝; 小原潤子; 大森亮介; 松山亮太; 蒔田浩平, 日本獣医学会学術集会講演要旨集, 166th, 2023

Development of a method to estimate the impact of disease epidemic on wildlife populations using animal rescue data
松山亮太; 木戸伸英; 大森亮介, 日本野生動物医学会大会・講演要旨集, 29th, 2023

Ascertainment and biased testing rates in surveillance of emerging infectious diseases
Ryosuke Omori, Mathematical Modelling, Simulations, and AI for Emergent Pandemic Diseases, 251, 259, Jan. 2023, [Invited], [Lead author, Corresponding author]
Elsevier

Applications, Prospects and Problems in Mathematical Modelling
Ryosuke OMORI, Journal of Veterinary Epidemiology, 26, 2, 88, 89, 20 Dec. 2022, [Invited]
Japan Society of Veterinary Epidemiology

The Obstacle for the Epidemiological Analysis of Fish Disease in Aquaculture and its Solution-Application of Mathematical Model for Coupling Experiment and Field Observations-
大森亮介; 松山亮太; 降幡充; 笠井久会, 獣医疫学雑誌, 26, 1, 2022

養殖下での魚病疫学解析における問題点と数理モデルの活用による解決
大森亮介; 松山亮太; 降幡充; 笠井久会, 日本魚病学会大会プログラムおよび講演要旨, 2022, 2022

養豚場における豚熱発生に対する効果的な農場衛生対策の検討
浮田真琴; 松山亮太; 磯田典和; 大森亮介; 山本健久; 蒔田浩平, 日本獣医学会学術集会講演要旨集, 165th (CD-ROM), 2022

MSM向けHIV・性感染症検査キャンペーン(2020年度実績報告)
川畑 拓也; 阪野 文哉; 渡邊 大; 塩野 徳史; 福村 沙織; 朝来 駿一; 澤田 暁宏; 西岡 弘晶; 荒川 創一; 大森 亮介; 駒野 淳; 森 治代; 本村 和嗣, 日本エイズ学会誌, 23, 4, 387, 387, Nov. 2021
(一社)日本エイズ学会, Japanese

Estimation of Mortality Rate, Recovery Rate, and Case Fatality Ratio in Japanese Wild Boars in the Early Phase of Classical Swine Fever Epidemic
松山亮太; 大森亮介, 獣医疫学雑誌, 25, 1, 2021

Wastewater surveillance for COVID-19 and disease control: a perspective from mathematical epidemiology
三浦郁修; 三浦郁修; 大森亮介; 北島正章; 渡辺幸三, 日本水環境学会年会講演集, 55th, 2021

新型コロナウイルス感染症に対する感受性の年齢依存性の考察
大森亮介; 松山亮太; 中田行彦, 日本応用数理学会年会講演予稿集(CD-ROM), 2020, 2020

Age specificity of cases and attack rate of novel coronavirus disease (COVID-19)
Kenji Mizumoto; Ryosuke Omori; Hiroshi Nishiura, 2020

Reply to Brijwal et al
Lara Khadr; Manale Harfouche; Ryosuke Omori; Guido Schwarzer; Hiam Chemaitelly; Laith J. Abu-Raddad, Clinical Infectious Diseases, 68, 10, 1784, 01 May 2019
Oxford University Press, English, Report scientific journal

数理モデルによる感染症流行制御の検証
大森 亮介, システム/制御/情報, 59, 12, 458, 464, Dec. 2015, [Invited]
Japanese, Introduction scientific journal

Delay equation formulation for an epidemic model with waning immunity: An application to mycoplasma pneumoniae
Yukihiko Nakata; Ryosuke Omori, IFAC-PapersOnLine, 28, 18, 132, 135, 01 Nov. 2015, [Peer-reviewed]
English

Symptomatic treatment approach does not appear to be effective in controlling Chlamydia trachomatis transmission Read More: http://www.qscience.com/doi/abs/10.5339/qfarf.2013.BIOP-010
Ryosuke Omori, 2013, [Peer-reviewed]
English, Introduction international proceedings

Estimation of Basic Reproduction Number R0 using a Recurrent Neural Network
Heidi Tessmer; Ryosuke Omori
NIPS 2016 Workshop on Machine Learning for Health, 2016
2016

Timing of emergence and epidemic peak of novel influenza strains
Ryosuke Omori
Jun. 2010, English, Public discourse
Centre for Mathematical Sciences, Wilberforce Road, Cambridge., [Invited], [International presentation]

大学院共通授業科目（一般科目）：自然科学・応用科学, 2024年, 修士課程, 大学院共通科目

生物統計学特論, 2024年, 博士後期課程, 獣医学院

生物統計学特論, 2024年, 博士後期課程, 国際感染症学院

リスク分析学特論, 2024年, 博士後期課程, 国際感染症学院

情報科学特論, 2024年, 博士後期課程, 獣医学院

情報科学特論, 2024年, 博士後期課程, 国際感染症学院

感染症数理生物学特論, 2024年, 博士後期課程, 国際感染症学院

行動変容のビッグデータ解析による感染症流行予測の革新
科学研究費助成事業
01 Apr. 2022 - 31 Mar. 2027
大森 亮介
観光旅行といった長期的な計画のキャンセルは、旅行の直前だけでなく、計画立案以降の流行状況や介入の状況が関与していると考えられる。しかしながら、携帯電話の位置情報データだけでは、どの時点での流行状況や介入の状況が行動変容を促したのかは直接的にはわからない。そこで、旅行予約サイトにおける宿泊施設の予約の発生およびキャンセルのデータを解析した。旅行予約サイトのデータのような直接的に行動変容が抽出できるデータを数理モデルで解析した例は今までになく、世界で初めて詳細に行動変容を定量化することとなる。本年度は、宿泊施設の予約および予約のキャンセルの発生プロセスの数理モデルを構築した。宿泊施設の予約数は予約の発生によって増え、キャンセルによって減少する現象である。さらに、予約の発生およびキャンセルは流行の状況（行政の介入の状況と陽性者数）に応じて変化すると考える。宿泊施設の予約を指数関数の加法モデルとみなした数理モデルを構築し、旅行予約サイトにおける宿泊施設の予約の発生およびキャンセルのデータをフィッティングさせたところ、予約に関しては５個の、キャンセルに関しては６個の指数関数の和で表現することが最適であることが判明した。また、一部屋あたりの客数は予約とキャンセル両方に、シングル、家族といったゲストタイプと滞在期間が予約の発生ダイナミクスに大きな影響を与えていることが判明した。これらの解析により、コロナウイルス流行前の宿泊施設の予約およびキャンセルの発生を予測する基本の数理モデルの構築に成功した。
日本学術振興会, 基盤研究(B), 北海道大学, 23K24603

行動変容のビッグデータ解析による感染症流行予測の革新
科学研究費助成事業
01 Apr. 2022 - 31 Mar. 2027
大森 亮介
日本学術振興会, 基盤研究(B), 北海道大学, 22H03345

Establishment of real-time animal infectious disease mathematical modelling research platform by the analysis of past epidemics
Grants-in-Aid for Scientific Research
01 Apr. 2022 - 31 Mar. 2025
蒔田 浩平; 大森 亮介
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Rakuno Gakuen University, 22K05992

Understanding and application of microbiota in building environment: creation of pathogen control theory by temperature control
Grants-in-Aid for Scientific Research
30 Jul. 2020 - 31 Mar. 2024
山口 博之; 矢野 理香; 大森 亮介; 大久保 寅彦
消毒剤や抗菌剤に頼らない温度による新たな病原体制御理論を創成し、空間や高頻度接触面の温度を制御することで、感染予防へと応用を目指すために、2年目は以下の研究を実施しいくつかの成果を得た。
1. 乾燥表面の温度調節による大腸菌の生存性の制御に湿度変化が与える影響: 私達は乾燥面を37℃付近に温めることでその乾燥麺に塗抹した細菌の生存性が顕著に低下することを見いだした。その一方で環境温度は、熱を奪う空気中の水蒸気量すなわち湿度の影響も受ける。そこで恒温恒湿機を使用し，温度(25-37℃)と共に湿度(45-90%)が乾燥表面の大腸菌の生存性に与える影響を調査した。その結果湿度と大腸菌の生存率には逆相関関係(r=-0.241)があり，湿度が上がるほど生存率は有意に低下した(p=0.04)。このように、乾燥面での温度制御において湿度によるネガティブな効果は最小限であることを見いだした。
2. 温度制御手摺デバイス上での細菌の生存性の可視化法の開発: バイク用ハンドヒーターを改良し作成したデバイスの効果を振れ幅の大きい培養に頼らず正確かつ簡便に確認する方法を、無蛍光の透明テープとLIVE/DEAD染色による測定系とキーエンス画像解析ソフトを組み合わせることで実現した。具体的には、ヒーターより距離が離れるほど手摺上の生存菌数は有意に低下し、その効果は温度ヒートマップと一致した。
3. 土壌細菌の空間移動に環境要因の変化が及ぼす影響について: 新型コロナ感染症の影響で公共の閉鎖環境での採材ができなかったので、その代替えとして３Dプリンターを用いて空気中に浮遊する細菌を効率よく生け捕りにできるエアサンプラーを用いて北大農場にて実施した。その結果、環境因子(気圧、蒸気圧、湿度、風向き)が連動し変化することにより、空気中に巻き上げられ浮遊し移動することが明らかになった。
Japan Society for the Promotion of Science, Grant-in-Aid for Challenging Research (Pioneering), Hokkaido University, 20K20613

An analysis of the association between sexually transmitted diseases
Grants-in-Aid for Scientific Research
01 Apr. 2019 - 31 Mar. 2022
Omori Ryosuke
Associations between sexually transmitted infections are not understood well so far. Also, the outbreak risk of STIs are difficult to evaluate due to difficulty in measuring and quantifying the sexual network. In this project, we assessed these associations and quantifying STI epidemic potential using mathematical modeling. To this end, an individual-based mathematical model was constructed to describe sex partnering and STI concurrent transmission of HIV, herpes simplex virus type 2 (HSV-2), gonorrhea, chlamydia, and syphilis. Model parametrization was done using representative biological and behavioral data. Associations were assessed on model-simulated STI prevalences. Sexual networks affect STIs in variable ways, leading to rich dynamics and varying associations between STIs. The understanding of the prevalences of STIs can be predictive of that of another STI. Especially for HIV, prevalence of other STIs can be used as an objective biomarker for HIV outbreak potential.
Japan Society for the Promotion of Science, Grant-in-Aid for Early-Career Scientists, Hokkaido University, 19K20393

Simultaneous estimation of time-varying sexual contact network and prevalence of sexually transmitted infection from sexual behavior data
Grants-in-Aid for Scientific Research
01 Apr. 2015 - 31 Mar. 2018
Omori Ryosuke; Abu-Raddad Laith J.
A statistical model describing sexual partnering was established for estimation of sexual behavior at population level. The analysis of association between HIV prevalence and model parameters in the model described above showed no clear association, this suggests that the estimation of HIV prevalence from sexual behavior survey is difficult. Towards to evaluate efficacy of an alternative method, the estimation of HIV prevalence from the HSV-2 prevalence, the association of HIV and HSV-2 prevalences was explored. The result suggests the association depends on topology of sexual contact network.
Japan Society for the Promotion of Science, Grant-in-Aid for Young Scientists (B), Hokkaido University, 15K19217

ウイルスの抗原性と宿主免疫の共進化の理論的解析
科学研究費助成事業
2009 - 2011
大森 亮介
ウイルスの抗原性は多様な原因により決定され、温度などの環境要因からも大きく影響を受ける。これまでの進化学や理論疫学での感染症の研究では環境変動の感染症流行に与える影響を詳細に調べたものは少なく、宿主免疫の進化を考える上で、この環境要因による影響を考慮することは必要不可欠である。このため、環境要因の変化による感染症の流行をコイヘルペスウイルスを例に解析した。コイヘルペスは感染した個体の80%以上が死亡する非常に毒性の強い感染症で水産業界に多大な被害を与えた。また、コイヘルペスの流行には季節性がある事が知られており、これは感染が起きる水温の範囲が決まっている為である。この特性を利用し、感染が確認された後に水温を感染が起きない様な水温に人工的に変化させ、流行を抑制する治療法が考案された。この治療法を評価し最適な治療スケジュールを決定する為に、水温と感染率の関係性の実験データ(Yuasa et al. 2008)をもとに養殖場内の鯉の集団での感染を記述する数理モデルを構築し、解析を行った。コイヘルペスの流行の季節変動性は感染から発病までの期間、発病から死亡または回復するまでの期間の長さが水温によって変わる事に起因する(Yuasa et al. 2008)。また、水温を人工的に変える治療法は場合により治療を行っていない時よりも被害が増大することも明らかになった。ここから、感染症抑制の為の環境要因のコントロールは計画的かつ正確に行われる必要があることが示唆された。
日本学術振興会, 特別研究員奨励費, 九州大学, 09J01209