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Last Updated :2024/10/29

Researcher Profile and Settings

Master

Affiliation (Master)

  • International Institute for Zoonosis Control　Division of Bioinformatics

Affiliation (Master)

  • International Institute for Zoonosis Control　Division of Bioinformatics

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Profile and Settings

Degree

  • Ph.D

Profile and Settings

  • Profile

    My research interest is mathematical modelling of infectious diseases and its application for controlling infectious diseases. Especially, I am interested in
    i) complex interactions between epidemics of different pathogens, i.e., immune cross-reactivity, non-specific immunity etc.
    ii) the effect of exogenous factors to the epidemic, i.e., the seasonality of epidemics etc.
    iii) the transmission process of infectious diseases on the realistic networks.
    iV) the co-evolution of host and pathogen.

  • Name (Japanese)

    Omori

  • Name (Kana)

    Ryosuke

  • Name

    201101005760901146

Achievement

Research Interests

  • 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   

Research Areas

  • Life sciences / Evolutionary biology / 数理生物学
  • Life sciences / Hygiene and public health (non-laboratory)
  • Life sciences / Hygiene and public health (laboratory)
  • Life sciences / Healthcare management, medical sociology

Research Experience

  • 2020/04 - Today Hokkaido University Research Center for Zoonosis Control Associate Professor
  • 2018/10 - Today Editorial board member of Journal of Biological Systems
  • 2017/02 - Today Editorial board member of Scientific Reports
  • 2020/07 - 2023/05 沖縄県 疫学・統計解析委員
  • 2018/07 - 2020/03 Research Center for Zoonosis Control, Hokkaido University Division of Bioinformatics Specially Appointed Associate Professor
  • 2015/10 - 2019/03 JST PRESTO researcher
  • 2014/07 - 2018/06 Research Center for Zoonosis Control, Hokkaido Univeristy Division of Bioinformatics Assistant Professor
  • 2013/05 - 2014/07 Weill Cornell Medical College in Qatar Infectious Disease Epidemiology Group Post-doctoral associate
  • 2012/04 - 2013/04 The University of Hong Kong Post-doctoral fellow
  • 2009/04 - 2012/03 日本学術振興会 特別研究員 DC1
  • 2009/04 - 2012/03 Kyushu University Graduate School of Systems Life Sciences Ph.D student
  • 2007/04 - 2012/03 九州大学理学研究院 数理生物学研究室
  • 2010/04 - 2011/03 The University of Edinburgh Visiting PhD. student

Awards

  • 2022/03 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－ 
    受賞者: 大森亮介;松山亮太;降幡充;笠井久会
  • 2021/03 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 
    受賞者: 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

Published Papers

  • Yoshihiro Takayama, Yusuke Shimakawa, Ryota Matsuyama, Gerardo Chowell, Ryosuke Omori, Tetsuharu Nagamoto, Taro Yamamoto, Kenji Mizumoto
    Emerging Infectious Diseases 30 (11) 1080-6040 2024/11 [Refereed]
  • 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 1877-959X 2024/11 [Refereed]
  • Ryota Matsuyama, Nobuhide Kido, Ryosuke Omori
    International Journal for Parasitology: Parasites and Wildlife 101010 - 101010 2213-2244 2024/10 [Refereed][Not invited]
     
    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.

  • 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 1344-6304 2024/09/30 [Refereed]
  • Houssein H. Ayoub, Milan Tomy, Hiam Chemaitelly, Ryosuke Omori, Kent Buse, Nicola Low, Sarah Hawkes, Laith J. Abu-Raddad
    Epidemics 48 100785 - 100785 1755-4365 2024/09 [Refereed]
  • Diego F. Cuadros, Xi Chen, Jingjing Li, Ryosuke Omori, Godfrey Musuka
    Pathogens 13 (8) 685 - 685 2024/08/14 [Refereed]
     
    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.
  • Yoshihiro Takayama, Yining S. Xu, Yusuke Shimakawa, Gerardo Chowell, Masahiro Kozuka, Ryosuke Omori, Ryota Matsuyama, Taro Yamamoto, Kenji Mizumoto
    BMC Infectious Diseases 24 (1) 2024/05/30 [Refereed]
     
    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.
  • Ryosuke Omori, Hiam Chemaitelly, Laith J. Abu-Raddad
    Frontiers in Public Health 12 2024/04/02 [Refereed][Not invited]
     
    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.
  • Ryosuke Omori, Teruyoshi Hagino, Puttirungroj Pattama, Kenichi Ozaki, Ikuo Hirono
    Aquaculture 582 740548 - 740548 0044-8486 2024/03 [Refereed]
  • Ryosuke Omori, Koichi Ito, Shunsuke Kanemitsu, Ryusuke Kimura, Yoh Iwasa
    Journal of Theoretical Biology 111795 - 111795 0022-5193 2024/03 [Refereed]
  • 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 0022-538X 2024/02/07 [Refereed]
     
    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.
  • Makoto Ukita, Ryota Matsuyama, Norikazu Isoda, Ryosuke Omori, Takehisa Yamamoto, Kohei Makita
    Transboundary and Emerging Diseases 2024 (1) 1865-1674 2024/01 [Refereed][Not invited]
     
    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.
  • Koichi Ito, Shunsuke Kanemitsu, Ryusuke Kimura, Ryosuke Omori
    Japan Journal of Industrial and Applied Mathematics 0916-7005 2023/11/28 [Refereed]
     
    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.
  • Diego F. Cuadros, Claudia M. Moreno, F.DeWolfe Miller, Ryosuke Omori, Neil J. MacKinnon
    Mayo Clinic Proceedings: Digital Health 1 (3) 217 - 225 2949-7612 2023/09 [Refereed][Not invited]
  • 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 2667-193X 2023/02 [Refereed]
  • 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 1386-6532 2023/01 [Refereed]
     
    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.
  • Koichi Ito, Shunsuke Kanemitsu, Ryusuke Kimura, Ryosuke Omori
    Scientific Reports 12 (1) 2022/11/17 [Refereed]
     
    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.
  • Ryota Matsuyama, Takehisa Yamamoto, Yoko Hayama, Ryosuke Omori
    PLOS Computational Biology 18 (10) e1010510 - e1010510 2022/10/06 [Refereed][Not invited]
     
    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.
  • 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 2352-3018 2022/07 [Refereed]
  • Ryosuke Omori, Ryota Matsuyama, Yukihiko Nakata, Mitsuru Furihata, Hisae Kasai
    Aquaculture 554 738165 - 738165 0044-8486 2022/03 [Refereed]
  • Ryota Matsuyama, Takehisa Yamamoto, Yoko Hayama, Ryosuke Omori
    Frontiers in Veterinary Science 8 2021/12/15 [Refereed][Not invited]
     
    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.
  • 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 0923-2508 2021/07 [Refereed]
     
    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.
  • 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 2021/06/11 [Refereed]
     
    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.
  • Ryosuke Omori, Fuminari Miura, Masaaki Kitajima
    Science of The Total Environment 792 148442 - 148442 0048-9697 2021/06 [Refereed]
     
    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 in the symptomatic ratio of SARS-CoV-2 infections, here, we aimed to estimate i) an age-dependent association between the number of reported cases and viral load in wastewater and ii) the time lag between these time series. The viral load in wastewater was modeled as a combination of contributions from virus shedding by different age groups, incorporating the delay, and fitted with daily case count data collected from the Massachusetts Department of Public Health and SARS-CoV-2 RNA concentration in wastewater recorded by the Massachusetts Water Resources Authority. The estimated lag between the time series of viral loads in wastewater and of reported cases was 10.8 (95% confidence interval: 10.2-11.6) and 8.8 (8.4-9.1) days for the northern and southern areas of the wastewater treatment plant, respectively. The estimated contribution rate of a reported case to the viral load in wastewater in the 0-19 yr age group was 0.38 (0.35-0.41) and 0.40 (0.37-0.43) for the northern and southern areas, and that in the 80+ yr age group was 0.67 (0.65-0.69) and 0.51 (0.49-0.52) for the northern and southern areas, respectively. The estimated lag between these time series suggested the predictability of reported cases 10 days later using viral loads in wastewater. The contribution of a reported case in passive surveillance to the viral load in wastewater differed by age, suggesting a large variation in viral shedding kinetics among age groups. (c) 2021 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http:// creativecommons.org/licenses/by-nc-nd/4.0/).
  • 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 0264-410X 2021/06 [Refereed]
     
    Current detergent or ether-disrupted split vaccines (SVs) for influenza do not always induce adequate immune responses, especially in young children. This contrasts with the whole virus particle vaccines (WPVs) originally used against influenza that were immunogenic in both adults and children but were replaced by SV in the 1970s due to concerns with reactogenicity. In this study, we re-evaluated the immunogenicity of WPV and SV, prepared from the same batch of purified influenza virus, in cynomolgus macaques and confirmed that WPV is superior to SV in priming potency. In addition, we compared the ability of WPV and SV to induce innate immune responses, including the maturation of dendritic cells (DCs) in vitro. WPV stimulated greater production of inflammatory cytokines and type-I interferon in immune cells from mice and macaques compared to SV. Since these innate responses are likely triggered by the activation of pattern recognition receptors (PRRs) by viral RNA, the quantity and quality of viral RNA in each vaccine were assessed. Although the quantity of viral RNA was similar in the two vaccines, the amount of viral RNA of a length that can be recognized by PRRs was over 100-fold greater in WPV than in SV. More importantly, 1000-fold more viral RNA was delivered to DCs by WPV than by SV when exposed to preparations containing the same amount of HA protein. Furthermore, WPV induced up-regulation of the DC maturation marker CD86 on murine DCs, while SV did not. The present results suggest that the activation of antigen-presenting DCs, by PRR-recognizable viral RNA contained in WPV is responsible for the effective priming potency of WPV observed in naïve mice and macaques. WPV is thus recommended as an alternative option for seasonal influenza vaccines, especially for children.
  • Andrei R. Akhmetzhanov, Kenji Mizumoto, Sung-Mok Jung, Natalie M. Linton, Ryosuke Omori, Hiroshi Nishiura
    Journal of Clinical Medicine 10 (11) 2392 - 2392 2021/05/28 [Refereed]
     
    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.
  • Naoki Nomura, Keita Matsuno, Masashi Shingai, Marumi Ohno, Toshiki Sekiya, Ryosuke Omori, Yoshihiro Sakoda, Robert G. Webster, Hiroshi Kida
    Virology 557 55 - 61 0042-6822 2021/05 [Refereed]
  • Houssein H Ayoub, Ibtihel Amara, Susanne F Awad, Ryosuke Omori, Hiam Chemaitelly, Laith J Abu-Raddad
    Open Forum Infectious Diseases 8 (7) ofab218  2021/04/29 [Refereed][Not invited]
     
    Abstract Background 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. Methods 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. Results 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. Conclusions 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.
  • 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 2021/04/28 [Refereed][Not invited]
     
    Background 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. Methodology/Principal findings 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%. Conclusions/Significance 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.
  • 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 2021/01/27 [Refereed]
     
    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.
  • Fuminari Miura, Masaaki Kitajima, Ryosuke Omori
    Science of The Total Environment 769 144549 - 144549 0048-9697 2021/01 [Refereed]
     
    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.
  • Ryosuke Omori, Ryota Matsuyama, Yukihiko Nakata
    Scientific Reports 10 (1) 16642 - 16642 2020/12 [Refereed]
     
    Abstract 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.
  • 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 1344-6304 2020/06 [Refereed][Not invited]
  • Ryosuke Omori, Kenji Mizumoto, Hiroshi Nishiura
    International Journal of Infectious Diseases 96 673 - 675 1201-9712 2020/05 [Refereed][Not invited]
  • Ryosuke Omori, Kenji Mizumoto, Gerardo Chowell
    International Journal of Infectious Diseases 94 116 - 118 1201-9712 2020/05 [Refereed][Not invited]
  • Wessam Mohamed, Kimihito Ito, Ryosuke Omori
    Frontiers in Microbiology 10 2765  2019/12 [Refereed][Not invited]
  • Yukihiko Nakata, Ryosuke Omori
    Journal of Biological Dynamics 13 (1) 567 - 585 2019/08 [Refereed][Not invited]
  • Susanne F. Awad, Soha R. Dargham, Ryosuke Omori, Fiona Pearson, Julia Critchley, Laith J. Abu-Raddad
    Scientific Reports 9 8494  2019/06 [Refereed][Not invited]
  • Hiam Chemaitelly, Nico Nagelkerke, Ryosuke Omori, Laith J. Abu-Raddad
    PLOS ONE 14 (6) e0214151  2019/06 [Refereed][Not invited]
  • 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 2019/05 [Refereed][Not invited]
     
    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.
  • Bashir Salim, Abdullah D. Alanazi, Ryosuke Omori, Mohamed S. Alyousif, Ibrahim O. Alanazi, Ken Katakura, Ryo Nakao
    Acta Tropica 193 (2019) 78 - 83 0001-706X 2019/05 [Refereed][Not invited]
  • 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 2019/02/06 [Refereed][Not invited]
     
    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.
  • Simbotwe M, Fujikura D, Ohnuma M, Omori R, Furuta Y, Muuka GM, Hang'ombe BM, Higashi H
    PloS one 14 (1) e0211592  1932-6203 2019 [Refereed][Not invited]
  • Yukihiko Nakata, Ryosuke Omori
    Mathematical Biosciences and Engineering 16 (2) 813 - 830 2019/01 [Refereed][Not invited]
  • Houssein Ayoub, Hiam Chemaitelly, Ryosuke Omori, Laith Abu-Raddad
    International Journal of Infectious Diseases 75 60 - 66 2018/10 [Refereed][Not invited]
  • Takeshi Koyama, Ryosuke Omori, Keisuke Koyama, Yoshitaka Matsui, Masahito Sugimoto
    Theriogenology 119 (1) 225 - 232 2018/10 [Refereed][Not invited]
  • Manyando Simbotwe, Daisuke Fujikura, Miyuki Ohnuma, Ryosuke Omori, Yoshikazu Furuta, Geoffrey Munkombwe Muuka, Bernar, Mudenda Hang’ombe, Hideaki Higashi
    PloS one 13 (10) e0205986  1932-6203 2018/10 [Refereed][Not invited]
     
    In Zambia, anthrax outbreaks among cattle are reported on nearly an annual basis. Presently, there is a lack of serological assays and information to develop an anthrax management and control strategy. In this study, an indirect enzyme-linked immunosorbent assay (ELISA) based on recombinant protective antigen domain 1 (rPA-D1) of Bacillus anthracis was developed and used to detect anti-PA antibodies in cattle in Zambia. An antigen coating of 10 ng/well and a serum dilution of 1: 100 were determined to be the optimal rPA-D1 ELISA titration conditions. The intra-and inter-assay% coefficients of variation were less than 10% and 15%, respectively. The rPA-D1 ELISA could detect seroconversion in the cattle 1 month after anthrax vaccination. In a cross-sectional study conducted in the Western Province, Zambia, 187 serum samples from 8 herds of cattle were screened for anti-PA antibodies using the rPA-D1 ELISA. The seropositive rate of the serum samples was 8%, and the mean anti-PA antibody was 0.358 ELISA units. Additionally, we screened 131 cattle serum samples from Lusaka, which is a nonendemic area, and found no significant association between the antibody levels and sampling area (endemic versus nonendemic area). Conversely, significant differences were observed between the anti-PA antibody levels and herds, anti-PA antibody levels and vaccination status and anti-PA antibody levels and vaccination timing. Collectively, these findings suggest that the rPA-D1 ELISA is a useful tool for the detection of anti-PA antibodies in cattle in Zambia. The low proportion of seropositive sera indicates that there is inadequate cattle vaccination in the Western Province and, in addition to other epidemiological factors, this may precipitate the anthrax outbreak recurrence.
  • Ryosuke Omori, Hiam Chemaitelly, Christian L. Althaus, Laith J. Abu-Raddad
    Sexually Transmitted Infections 95 115 - 121 2018/09 [Refereed][Not invited]
  • Lara Khadra, Manale Harfouche, Ryosuke Omori, Guido Schwarzer, Hiam Chemaitelly, Laith J. Abu-Raddad
    Clinical Infectious Diseases 68 (5) 757 - 772 2018/07 [Refereed][Not invited]
  • Jednipit Borthong, Ryosuke Omori, Chihiro Sugimoto, Orasa Suthienkul, Ryo Nakao, Kimihito Ito
    Frontiers in Microbiology 9 1272  1664-302X 2018/06/19 [Refereed][Not invited]
     
    Metagenomic analysis has become a powerful tool to analyze bacterial communities in environmental samples. However, the detection of a specific bacterial species using metagenomic analysis remains difficult due to false positive detections of sequences shared between different bacterial species. In this study, 16S rRNA amplicon and shotgun metagenomic analyses were conducted on samples collected along a stream and ponds in the campus of Hokkaido University. We compared different database search methods for bacterial detection by focusing on Legionella pneumophila. In this study, we used L. pneumophila-specific nested PCR as a gold standard to evaluate the results of the metagenomic analysis. Comparison with the results from L. pneumophila-specific nested PCR indicated that a blastn search of shotgun reads against the NCBI-NT database led to false positive results and had problems with specificity. We also found that a blastn search of shotgun reads against a database of the catalase-peroxidase (katB) gene detected L. pneumophila with the highest area under the receiver operating characteristic curve among the tested search methods indicating that a blastn search against the katB gene database had better diagnostic ability than searches against other databases. Our results suggest that sequence searches targeting long genes specifically associated with the bacterial species of interest is a prerequisite to detecting the bacterial species in environmental samples using metagenomic analyses. Metagenomic analysis has become a powerful tool to analyze bacterial communities in environmental samples. However, the detection of a specific bacterial species using metagenomic analysis remains difficult due to false positive detections of sequences shared between different bacterial species. In this study, 16S rRNA amplicon and shotgun metagenomic analyses were conducted on samples collected along a stream and ponds in the campus of Hokkaido University. We compared different database search methods for bacterial detection by focusing on Legionella pneumophila. In this study, we used L. pneumophila-specific nested PCR as a gold standard to evaluate the results of the metagenomic analysis. Comparison with the results from L. pneumophila-specific nested PCR indicated that a blastn search of shotgun reads against the NCBI-NT database led to false positive results and had problems with specificity. We also found that a blastn search of shotgun reads against a database of the catalase-peroxidase (katB) gene detected L. pneumophila with the highest area under the receiver operating characteristic curve among the tested search methods indicating that a blastn search against the katB gene database had better diagnostic ability than searches against other databases. Our results suggest that sequence searches targeting long genes specifically associated with the bacterial species of interest is a prerequisite to detecting the bacterial species in environmental samples using metagenomic analyses.
  • Silva P. Kouyoumjian, Marieke Heijnen, Karima Chaabna, Ghina R. Mumtaz, Ryosuke Omori, Peter Vickerman, Laith J. Abu-Raddad
    AIDS 32 (10) 1343 - 1352 1473-5571 2018/06/19 [Refereed][Not invited]
     
    Background: Our objective was to assess the population-level association between herpes simplex virus 2 (HSV-2) and HIV prevalence. Methods: Reports of HSV-2 and HIV prevalence were systematically reviewed and synthesized following PRISMA guidelines. Spearman rank correlation () was used to assess correlations. Risk ratios (RR HSV-2/HIV) and odds ratios (OR HSV-2/HIV) were used to assess HSV-2/HIV epidemiologic overlap. DerSimonian-Laird random-effects meta-Analyses were conducted. Results: In total, 939 matched HSV-2/HIV prevalence measures were identified from 77 countries. HSV-2 prevalence was consistently higher than HIV prevalence. Strong HSV-2/HIV prevalence association was found for all data ( = 0.6, P < 0.001), all data excluding people who inject drugs (PWID) and children ( = 0.7, P < 0.001), female sex workers ( = 0.5, P < 0.001), and MSM ( = 0.7, P < 0.001). No association was found for PWID ( = 0.2, P = 0.222) and children ( = 0.3, P = 0.082). A threshold effect was apparent where HIV prevalence was limited at HSV-2 prevalence less than 20%, but grew steadily with HSV-2 prevalence for HSV-2 prevalence greater than 20%. The overall pooled mean RR HSV-2/HIV was 5.0 (95% CI 4.7-5.3) and OR HSV-2/HIV was 9.0 (95% CI 8.4-9.7). The RR HSV-2/HIV and OR HSV-2/HIV showed similar patterns that conveyed inferences about HSV-2 and HIV epidemiology. Conclusion: HSV-2 and HIV prevalence are strongly associated. HSV-2 prevalence can be used as a proxy 'biomarker' of HIV epidemic potential, acting as a 'temperature scale' of the intensity of sexual risk behavior that drive HIV transmission. HSV-2 prevalence can be used to identify populations and/or sexual networks at high-risk of future HIV expansion, and help prioritization, optimization, and resource allocation of cost-effective prevention interventions.
  • Jun Moriwaki, Ryosuke Omori, Michito Shimozuru, Hifumi Tsuruga, Tsutomu Mano, Toshio Tsubota
    Japanese Journal of Veterinary Research 66 (2) 71 - 81 0047-1917 2018/05/01 [Refereed][Not invited]
     
    Chest girth and body mass of 3,576 brown bears (Ursus arctos yesoensis) harvested for conflict management in Hokkaido, Japan during 1991-2012 were used to establish methods to assess body condition and to compare the body condition of bears by sex, month, year, and reproductive status. The body mass was estimated based on the chest girth in cases with no measurements of the bear body mass. Using the measured and estimated body mass, a growth curve by age was demonstrated to ascertain the mean asymptotical body mass (245 kg for males, 114 kg for females) and ages at 95% asymptotic body mass (14.2 years for males, 7.1 years for females). The body condition value of bears was evaluated as body mass difference (kg) between the individual body mass and the standard body mass as estimated from the growth curve. Body condition value changed seasonally with a low in summer and the highest in the autumnal hyperphagic period. Female body condition value was higher than the males during September. Fluctuation in annual body condition value was found for females however, there was no difference between solitary adult females and females with offspring (cubs, yearlings, or offspring of unknown age). No significant fluctuation was found for males. Our body condition evaluation method using chest girth and body mass of brown bears is useful to elucidate different trends across sex, year, and season.
  • Heidi L. Tessmer, Kimihito Ito, Ryosuke Omori
    Frontiers in Microbiology 9 343  1664-302X 2018/03/02 [Refereed][Not invited]
     
    To estimate and predict the transmission dynamics of respiratory viruses, the estimation of the basic reproduction number, R0, is essential. Recently, approximate Bayesian computation methods have been used as likelihood free methods to estimate epidemiological model parameters, particularly R0. In this paper, we explore various machine learning approaches, the multi-layer perceptron, convolutional neural network, and long-short term memory, to learn and estimate the parameters. Further, we compare the accuracy of the estimates and time requirements for machine learning and the approximate Bayesian computation methods on both simulated and real-world epidemiological data from outbreaks of influenza A(H1N1)pdm09, mumps, and measles. We find that the machine learning approaches can be verified and tested faster than the approximate Bayesian computation method, but that the approximate Bayesian computation method is more robust across different datasets.
  • Naomi Sakon, Jun Komano, Heidi L. Tessmer, Ryosuke Omori
    Eurosurveillance 23 (6) 18-00029  1560-7917 2018/02/08 [Refereed][Not invited]
     
    The number of person-to-person transmitted norovirus cases (n = 4,712) in school children in Osaka, Japan, during 2016/17 was the largest since 2012/13. Norovirus outbreaks were reported by 101 schools including 53 nursery schools (1,927 cases), 18 kindergartens (1,086 cases) and 30 elementary schools (1,699 cases). The dominant genotype among outbreaks was GII.P16-GII.2 (57.4% 58/101), followed by GII.P2-GII.2 (8.9% 9/101) and GII.P7-GII.6 (5.9% 6/101). GII.4 was not detected despite dominance in previous years.
  • 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 1865-1682 2018/02/01 [Refereed][Not invited]
     
    Bovine viral diarrhoea virus (BVDV) infection in cattle can result in growth retardation, reduced milk production, reproductive disorders and death. Persistently infected animals are the primary source of infection. In Hokkaido, Japan, all cattle entering shared pastures in summer are vaccinated before movement for disease control. Additionally, these cattle may be tested for BVDV and culled if positive. However, the effectiveness of this control strategy aiming to reduce the number of BVDV-infected animals has not been assessed. The aim of this study was to evaluate the effectiveness of various test-and-cull and/or vaccination strategies on BVDV control in dairy farms in two districts of Hokkaido, Nemuro and Hiyama. A stochastic model was developed to compare the different control strategies over a 10-year period. The model was individual-based and simulated disease dynamics both within and between herds. Parameters included in the model were obtained from the literature, the Hokkaido government and the Japanese Ministry of Agriculture, Forestry and Fisheries. Nine different scenarios were compared as follows: no control, test-and-cull strategies based on antigen testing of either calves or only cattle entering common pastures, vaccination of all adult cattle or only cattle entering shared pastures and combinations thereof. The results indicate that current strategies for BVDV control in Hokkaido slightly reduced the number of BVDV-infected animals however, alternative strategies such as testing all calves and culling any positives or vaccinating all susceptible adult animals dramatically reduced those. To our knowledge, this is the first report regarding the comparison of the effectiveness between the current strategies in Hokkaido and the alternative strategies for BVDV control measures.
  • Ryosuke Omori, Nico Nagelkerke, Laith J. Abu-Raddad
    Sexually Transmitted Infections 94 372 - 376 1472-3263 2017/12/04 [Refereed][Not invited]
     
    Objectives: To investigate whether observational studies of HIV and herpes simplex virus type 2 (HSV-2) infections have the capacity to assess the HIV/HSV-2 epidemiological synergy. Methods: An individual-based Monte Carlo model was used to simulate HIV/HSV-2 epidemics in two scenarios: no HIV/HSV-2 biological interaction and HSV-2 seropositivity enhancing HIV acquisition. Cross-sectional observational studies were simulated by sampling individuals from the population to assess resulting crude and adjusted ORs of the HIV/HSV-2 association. Meta-analyses were conducted to estimate the pooled mean ORs. Impact of under-reporting of sexual behaviour and miscapture of high-risk individuals was assessed through sensitivity analyses. Results: Assuming no HIV/HSV-2 biological interaction, the crude HIV/HSV-2 OR ranged between 1.38 and 9.93, with a pooled mean of 6.45 (95% CI 5.81 to 7.17). Adjustment for the number of sexual partners over last year, over lifetime and for both partner numbers simultaneously reduced the mean OR to 5.45 (95% CI 4.90 to 6.06), 3.70 (95% CI 3.32 to 4.12) and 3.54 (95% CI 3.17 to 3.94), respectively. Assuming HIV/HSV-2 biological interaction, the crude OR ranged between 3.44 and 9.95, with a pooled mean of 8.05 (95% CI 7.14 to 9.07). The adjustments reduced the mean OR to 7.00 (95% CI 6.21 to 7.90), 3.76 (95% CI 3.32 to 4.25) and 3.68 (95% CI 3.25 to 4.17), respectively. Under-reporting of partners reduced the confounder-adjustment effects. Miscapture of high-risk individuals considerably lowered the estimated ORs. Conclusions: 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.
  • Kiyeon Kim, Ryosuke Omori, Kimihito Ito
    EPIDEMICS 21 21 - 29 1755-4365 2017/12 [Refereed][Not invited]
     
    The estimation of the basic reproduction number is essential to understand epidemic dynamics, and time series data of infected individuals are usually used for the estimation. However, such data are not always available. Methods to estimate the basic reproduction number using genealogy constructed from nucleotide sequences of pathogens have been proposed so far. Here, we propose a new method to estimate epidemiological parameters of outbreaks using the time series change of Tajima's D statistic on the nucleotide sequences of pathogens. To relate the time evolution of Tajima's D to the number of infected individuals, we constructed a parsimonious mathematical model describing both the transmission process of pathogens among hosts and the evolutionary process of the pathogens. As a case study we applied this method to the field data of nucleotide sequences of pandemic influenza A (H1N1) 2009 viruses collected in Argentina. The Tajima's D-based method estimated basic reproduction number to be 1.55 with 95% highest posterior density (HPD) between 1.31 and 2.05, and the date of epidemic peak to be 10th July with 95% HPD between 22nd June and 9th August. The estimated basic reproduction number was consistent with estimation by birth-death skyline plot and estimation using the time series of the number of infected individuals. These results suggested that Tajima's D statistic on nucleotide sequences of pathogens could be useful to estimate epidemiological parameters of outbreaks. (C) 2017 The Authors. Published by Elsevier B.V.
  • Jinliang Wang, Xiaoqing Yu, Heidi L. Tessmer, Toshikazu Kuniya, Ryosuke Omori
    THEORETICAL BIOLOGY AND MEDICAL MODELLING 14 (13) 1742-4682 2017/07 [Refereed][Not invited]
     
    Background: Herpes Simplex Virus Type 2 (HSV-2) is one of the most common sexually transmitted diseases. Although there is still no licensed vaccine for HSV-2, a theoretical investigation of the potential effects of a vaccine is considered important and has recently been conducted by several researchers. Although compartmental mathematical models were considered for each special case in the previous studies, as yet there are few global stability results. Results: In this paper, we formulate a multi-group SVIRI epidemic model for HSV-2, which enables us to consider the effects of vaccination, of waning vaccine immunity, and of infection relapse. Since the number of groups is arbitrary, our model can be applied to various structures such as risk, sex, and age group structures. For our model, we define the basic reproduction number R-0 and prove that if R-0 = 1, then the disease-free equilibrium is globally asymptotically stable, whereas if R-0 > 1, then the endemic equilibrium is so. Based on this global stability result, we estimate R-0 for HSV-2 by applying our model to the risk group structure and using US data from 2001 to 2014. Through sensitivity analysis, we find that R-0 is approximately in the range of 2-3. Moreover, using the estimated parameters, we discuss the optimal vaccination strategy for the eradication of HSV-2. Conclusions: Through discussion of the optimal vaccination strategy, we come to the following conclusions. (1) Improving vaccine efficacy is more effective than increasing the number of vaccines. (2) Although the transmission risk in female individuals is higher than that in male individuals, distributing the available vaccines almost equally between female and male individuals is more effective than concentrating them within the female population.
  • Ryosuke Omori, Laith J. Abu-Raddad
    AIDS 31 (12) 1721 - 1732 0269-9370 2017/07 [Refereed][Not invited]
     
    Objectives: HIV and herpes simplex virus type 2 (HSV-2) infections are sexually transmitted and propagate in sexual networks. Using mathematical modeling, we aimed to quantify effects of key network statistics on infection transmission, and extent to which HSV-2 prevalence can be a proxy of HIV prevalence. Design/methods: An individual-based simulation model was constructed to describe sex partnering and infection transmission, and was parameterized with representative natural history, transmission, and sexual behavior data. Correlations were assessed on model outcomes (HIV/HSV-2 prevalences) and multiple linear regressions were conducted to estimate adjusted associations and effect sizes. Results: HIV prevalence was one-third or less of HSV-2 prevalence. HIV and HSV-2 prevalences were associated with a Spearman's rank correlation coefficient of 0.64 (95% confidence interval: 0.58-0.69). Collinearities among network statistics were detected, most notably between concurrency versus mean and variance of number of partners. Controlling for confounding, unmarried mean/variance of number of partners (or alternatively concurrency) were the strongest predictors of HIV prevalence. Meanwhile, unmarried/married mean/variance of number of partners (or alternatively concurrency), and clustering coefficient were the strongest predictors of HSV-2 prevalence. HSV-2 prevalence was a strong predictor of HIV prevalence by proxying effects of network statistics. Conclusion: Network statistics produced similar and differential effects on HIV/HSV2 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. Copyright (C) 2017 The Author(s). Published by Wolters Kluwer Health, Inc.
  • Ryosuke Omori, Jianhong Wu
    SIAM JOURNAL ON APPLIED MATHEMATICS 77 (6) 2156 - 2171 0036-1399 2017 [Refereed][Not invited]
     
    Tajima's D measures the difference between two estimates of genetic diversity in a given set of nucleic acid sequences. Here we show how Tajima's D can be calculated/estimated by developing an inductive algorithm for calculating the site-specific nucleotide frequencies from a standard multistrain susceptible-infective-removed (SIR) model (both deterministic and stochastic). We show that these frequencies are fully determined by the mutation rate and the initial condition of the frequencies. We prove that the sign of Tajima's D is independent of the disease population dynamics and that the negative sign does not imply an expansion of the infected population in the deterministic model. Using individual-based simulations, we also show that dependence of Tajima's D on the disease transmission and evolution dynamics is a result of the stochasticity of those dynamics. The same is true for the dependence related to genetic diversity of a pathogen.
  • Ryosuke Omori, Nico Nagelkerke, Laith J. Abu-Raddad
    BIOMED RESEARCH INTERNATIONAL 2017 (2017) 3564861  2314-6133 2017 [Refereed][Not invited]
     
    Background. Understanding the epidemiology ofHIV and other sexually transmitted infections (STIs) requires knowledge of sexual behavior, but self-reported behavior has limitations. We explored the reliability and validity of nonpaternity and half-siblings ratios as biomarkers of current and past extramarital sex. Methods. An individual-basedMonteCarlo simulationmodel was constructed to describepartnering and conception inhumanpopulationswith a focus onSub-SaharanAfrica (SSA). Themodel was parameterized with representative biological, behavioral, and demographic data. Results. Nonpaternity and half-siblings ratios were strongly correlated with extramarital sex, with Pearson correlation coefficients (PCC) of 0.79 (95% CI: 0.71-0.86) and 0.77 (0.68-0.84), respectively. Age-specific nonpaternity ratios correlated with past extramarital sex at time of conception for different scenarios: for example, PCC, after smoothing by moving averages, was 0.75 (0.52-0.89) in a scenario of steadily decreasing nonmarital sex and 0.39 (0.01-0.73) in a scenario of transient drops in nonmarital sex. Simulations assuming self-reported levels of extramarital sex from Kenya yielded nonpaternity levels lower than global nonpaternity data, suggesting sizable underreporting of extramarital sex. Conclusions. Nonpaternity and half-siblings ratios are useful objective measures of extramarital sex that avoid limitations in self-reported sexual behavior.
  • Nipawit Karnbunchob, Ryosuke Omori, Heidi L. Tessmer, Kimihito Ito
    FRONTIERS IN MICROBIOLOGY 7 2118  1664-302X 2016/12 [Refereed][Not invited]
     
    Human influenza pandemics have historically been caused by reassortant influenza A viruses using genes from human and avian viruses. This genetic reassortment between human and avian viruses has been known to occur in swine during viral circulation, as swine are capable of circulating both avian and human viruses. Therefore, avian-to-swine transmission of viruses plays an important role in the emergence of new pandemic strains. The amino acids at several positions on PB2, PB1, and PA are known to determine the host range of influenza A viruses. In this paper, we track viral transmission between avian and swine to investigate the evolution on polymerase genes associated with their hosts. We traced viral transmissions between avian and swine hosts by using nucleotide sequences of avian viruses and swine viruses registered in the NCBI GenBank. Using BLAST and the reciprocal best hits technique, we found 32, 33, and 30 pairs of avian and swine nucleotide sequences that may be associated with avian-to-swine transmissions for PB2, PB1, and PA genes, respectively. Then, we examined the amino acid substitutions involved in these sporadic transmissions. On average, avian-to-swine transmission pairs had 5.47, 3.73, and 5.13 amino acid substitutions on PB2, PB1, and PA, respectively. However, amino acid substitutions were distributed over the positions, and few positions showed common substitutions in the multiple transmission events. Statistical tests on the number of repeated amino acid substitutions suggested that no specific positions on PB2 and PA may be required for avian viruses to infect swine. We also found that avian viruses that transmitted to swine tend to process I478V substitutions on PB2 before interspecies transmission events. Furthermore, most mutations occurred after the interspecies transmissions, possibly due to selective viral adaptation to swine.
  • Mayumbo Nyirenda, Ryosuke Omori, Heidi L. Tessmer, Hiroki Arimura, Kimihito Ito
    PLOS ONE 11 (11) e0166107  1932-6203 2016/11 [Refereed][Not invited]
     
    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 interference. Using this model we estimated the epidemiological and evolutional parameters with the time-series data of the lineage specific isolates in Japan from the 2010-2011 season to the 2014-2015 season. The basic reproduction number is similar between Victoria and Yamagata, with a minimum value during one year as 0.82 (95% highest posterior density (HPD): 0.77-0.87) for the Yamagata and 0.83 (95% HPD: 0.74-0.92) for Victoria, the amplitude of seasonal variation of the basic reproduction number is 0.77 (95% HPD: 0.66-0.87) for Yamagata and 1.05 (95% HPD: 0.89-1.02) for Victoria. The duration for which the acquired immunity is effective against infection by the Yamagata lineage is shorter than the acquired immunity for Victoria, 424.1days (95% HPD: 317.4-561.5days). The reduction rate of susceptibility due to immune cross-reaction is 0.51 (95% HPD: 0.084-0.92) for the immunity obtained from the infection with Yamagata against the infection with Victoria and 0.62 (95% HPD: 0.42-0.80) for the immunity obtained from the infection with Victoria against the infection with Yamagata. Using estimated parameters, we predicted the dominant lineage in 2015-2016 season. The accuracy of this prediction is 68.8% if the emergence timings of the two lineages are known and 61.4% if the emergence timings are unknown. Estimated seasonal variation of the lineage specific reproduction number can narrow down the range of emergence timing, with an accuracy of 64.6% if the emergence times are assumed to be the time at which the estimated reproduction number exceeds one.
  • Ryosuke Omori, Laith J. Abu-Raddad
    INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES 44 1 - 3 1201-9712 2016/03 [Refereed][Not invited]
     
    Objectives: Patterns of sexual partnering should shape HIV transmission in human populations. The objective of this study was to assess empirical associations between population casual sex behavior and HIV prevalence, and between different measures of casual sex behavior. Methods: An ecological study design was applied to nationally representative data, those of the Demographic and Health Surveys, in 25 countries of Sub-Saharan Africa. Spearman rank correlation was used to assess different correlations for males and females and their statistical significance. Results: Correlations between HIV prevalence and means and variances of the number of casual sex partners were positive, but small and statistically insignificant. The majority of correlations across means and variances of the number of casual sex partners were positive, large, and statistically significant. However, all correlations between the means, as well as variances, and the variance of unmarried females were weak and statistically insignificant. Conclusions: Population sexual behavior was not predictive of HIV prevalence across these countries. Nevertheless, the strong correlations across means and variances of sexual behavior suggest that self-reported sexual data are self-consistent and convey valid information content. Unmarried female behavior seemed puzzling, but could be playing an influential role in HIV transmission patterns. (C) 2016 The Authors. Published by Elsevier Ltd on behalf of International Society for Infectious Diseases.
  • Kiyeon Kim, Ryosuke Omori, Keisuke Ueno, Sayaka Iida, Kimihito Ito
    PLOS ONE 11 (1) e0147021  1932-6203 2016/01 [Refereed][Not invited]
     
    Understanding the evolutionary dynamics of influenza viruses is essential to control both avian and human influenza. Here, we analyze host-specific and segment-specific Tajima's D trends of influenza A virus through a systematic review using viral sequences registered in the National Center for Biotechnology Information. To avoid bias from viral population subdivision, viral sequences were stratified according to their sampling locations and sampling years. As a result, we obtained a total of 580 datasets each of which consists of nucleotide sequences of influenza A viruses isolated from a single population of hosts at a single sampling site within a single year. By analyzing nucleotide sequences in the datasets, we found that Tajima's D values of viral sequences were different depending on hosts and gene segments. Tajima's D values of viruses isolated from chicken and human samples showed negative, suggesting purifying selection or a rapid population growth of the viruses. The negative Tajima's D values in rapidly growing viral population were also observed in computer simulations. Tajima's D values of PB2, PB1, PA, NP, and M genes of the viruses circulating in wild mallards were close to zero, suggesting that these genes have undergone neutral selection in constant-sized population. On the other hand, Tajima's D values of HA and NA genes of these viruses were positive, indicating HA and NA have undergone balancing selection in wild mallards. Taken together, these results indicated the existence of unknown factors that maintain viral subtypes in wild mallards.
  • Ryosuke Omori, Yukihiko Nakata, Heidi L. Tessmer, Satowa Suzuki, Keigo Shibayama
    SCIENTIFIC REPORTS 5 14473  2045-2322 2015/09 [Refereed][Not invited]
     
    Until the early 1990s, 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 epidemiological interference between MP serotypes. We find that minor variation in the duration of immunity at the population level must be considered essential for the MP epidemic cycle because the MP cyclic incidence pattern did not replicate without it. Minor variation, in this case, is a less dispersed distribution for the duration of immunity than an exponential distribution. Various lengths of epidemic cycles, including cycles typically found in nature, e.g. three to five year cycles, were also observed when there was minor variance in the duration of immunity. The cyclic incidence pattern is robust even if there is epidemiological interference due to cross-immune protection, which is observed in the epidemiological data as negative correlation between epidemics per MP serotype.
  • Ryosuke Omori, Hiam Chemaitelly, Laith J. Abu-Raddad
    SEXUALLY TRANSMITTED INFECTIONS 91 (6) 451 - 457 1368-4973 2015/09 [Refereed][Not invited]
     
    Objective To develop an analytical understanding of non-cohabiting sex partnering in sub-Saharan Africa (SSA) using nationally representative sexual behaviour data. Method A non-homogenous Poisson stochastic process model was used to describe the dynamics of non-cohabiting sex. The model was applied to 25 countries in SSA and was fitted to Demographic and Health Survey data. The country-specific mean values and variances of the distributions of number of non-cohabiting partners were estimated. Results The model yielded overall robust fits to the empirical distributions stratified by marital status and sex. The median across all country-specific mean values was highest for unmarried men at 0.574 non-cohabiting partners over the last 12 months, followed by that of unmarried women at 0.337, married men at 0.192 and married women at 0.038. The median of variances was highest for unmarried men at 0.127, followed by married men at 0.057, unmarried women at 0.003 and married women at 0.000. The largest variability in mean values across countries was for unmarried men (0.103-1.206), and the largest variability in variances was among unmarried women (0.000-1.994). Conclusions 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 transmitted infections.
  • Ryosuke Omori, Akira Sasaki
    Journal of Theoretical Biology 329 (21) 32 - 38 0022-5193 2013/07 [Refereed][Not invited]
  • Ryosuke Omori, Benjamin J. Cowling, Hiroshi Nishiura
    PLOS ONE 7 (11) e50751  1932-6203 2012/11 [Refereed][Not invited]
     
    Background: Many novel vaccines can cover only a fraction of all antigenic types of a pathogen. Vaccine effectiveness (VE) in the presence of interactions between vaccine strains and others is complicated by the interacting transmission dynamics among all strains. The present study investigated how the VE estimates measured in the field, based on estimated odds ratio or relative risks, are scaled by vaccination coverage and the transmission dynamics in the presence of cross-protective immunity between two strains, i.e. vaccine and non-vaccine strains. Methodology/Principal Findings: Two different types of epidemiological models, i.e. with and without re-infection by the same antigenic type, were investigated. We computed the relative risk of infection and the odds ratio of vaccination, the latter of which has been measured by indirect cohort method as applied to vaccine effectiveness study of Streptococcus pneumoniae. The VE based on the relative risk was less sensitive to epidemiological dynamics such as cross-protective immunity and vaccination coverage than the VE calculated from the odds ratio, and this was especially the case for the model without re-infection. Vaccine-induced (cross-protective) immunity against a non-vaccine strain appeared to yield the highest impact on the VE estimate calculated from the odds ratio of vaccination. Conclusion: 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 unvaccinated individuals.
  • H. Nishiura, K. Mizumoto, K. Ejima, Y. Zhong, B. J. Cowling, R. Omori
    EUROSURVEILLANCE 17 (42) 4 - 7 1560-7917 2012/10 [Refereed][Not invited]
     
    Non-specific symptoms of acute respiratory viral infections make it difficult for many countries without ongoing transmission of a novel coronavirus to rule out other possibilities including influenza before isolating imported febrile individuals with a possible exposure history. The incubation period helps differential diagnosis, and up to two days is suggestive of influenza. It is worth including the incubation period in the case definition of novel coronavirus infection.
  • Keisuke Ejima, Ryosuke Omori, Kazuyuki Aihara, Hiroshi Nishiura
    INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES 8 (5) 620 - 629 1449-2288 2012 [Refereed][Not invited]
     
    As part of measles elimination effort, evaluation of the vaccination program and real-time assessment of the epidemic dynamics constitute two important tasks to improve and strengthen the control. The present study aimed to develop an epidemiological modeling method which can be applied to estimating the vaccine efficacy at an individual level while conducting the timely investigation of the epidemic. The multivariate renewal process model was employed to describe the temporal evolution of infection by vaccination history, jointly estimating the time-dependent reproduction number and the vaccine efficacy. Analyzing the enhanced surveillance data of measles in Aichi prefecture, Japan from 2007-08, the vaccine efficacy was estimated at 96.7% (95% confidence interval: 95.8, 97.4). Using an age structured model, the vaccine efficacy among those aged from 5-19 years was shown to be smaller than that among those from 0-4 years. The age-dependent vaccine efficacy estimate informs the age-groups to be targeted for revaccination. Because the estimation method can rest on readily available epidemiological data, the proposed model has a potential to be integrated with routine surveillance.
  • Keisuke Ejima, Ryosuke Omori, Benjamin J. Cowling, Kazuyuki Aihara, Hiroshi Nishiura
    COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2012 (2012) 978901  1748-670X 2012 [Refereed][Not invited]
     
    Estimating the case fatality ratio (CFR) of a novel strain of influenza virus during the early stage of the pandemic is one of key epidemiological tasks to be conducted as rapid research response. Past experience during the epidemics of severe acute respiratory syndrome (SARS) and influenza A (H1N1-2009) posed several technical challenges in estimating the CFR in real time. The present study aimed to develop a simple method to estimate the CFR based on readily available datasets, that is, confirmed cases and deaths, while addressing some of the known technical issues. To assess the reliability and validity of the proposed method, we examined the minimum length of time required for the assigned CFR to be included within the 95% confidence intervals and for the estimated CFR to be below a prespecified cut-off value by means of Monte Carlo simulations. Overall, the smaller the transmission potential was, the longer it took to compare the estimated CFR against the cut-off value. If policymaking and public health response have to be made based on the CFR estimate derived from the proposed method and readily available data, it should be noted that the successful estimation may take longer than a few months.
  • Ryosuke Omori, Ben Adams
    JOURNAL OF THEORETICAL BIOLOGY 271 (1) 159 - 165 0022-5193 2011/02 [Refereed][Not invited]
     
    Common carp accounts for a substantial proportion of global freshwater aquaculture production. Koi herpes virus (KHV), a highly virulent disease affecting carp that emerged in the late 1990s, is a serious threat to this industry. After a fish is infected with KHV, there is a temperature dependent delay before it becomes infectious, and a further delay before mortality. Consequently, KHV epidemiology is driven by seasonal changes in water temperature. Also, it has been proposed that outbreaks could be controlled by responsive management of water temperature in aquaculture setups. We use a mathematical model to analyse the effect of seasonal temperature cycles on KHV epidemiology, and the impact of attempting to control outbreaks by disrupting this cycle. We show that, although disease progression is fast in summer and slow in winter, total mortality over a 2-year period is similar for outbreaks that start in either season. However, for outbreaks that start in late autumn, mortality may be low and immunity high. A single bout of water temperature management can be an effective outbreak control strategy if it is started as soon as dead fish are detected and maintained for a long time. It can also be effective if the frequency of infectious fish is used as an indicator for the beginning of treatment. In this case, however, there is a risk that starting the treatment too soon will increase mortality relative to the case when no treatment is used. This counterproductive effect can be avoided if multiple bouts of temperature management are used. We conclude that disrupting normal seasonal patterns in water temperature can be an effective strategy for controlling koi herpes virus. Exploiting the seasonal patterns, possibly in combination with temperature management, can also induce widespread immunity to KHV in a cohort of fish. However, employing these methods successfully requires careful assessment to ensure that the treatment is started, and finished, at the correct time. (C) 2010 Elsevier Ltd. All rights reserved.
  • Ryosuke Omori, Hiroshi Nishiura
    THEORETICAL BIOLOGY AND MEDICAL MODELLING 8 (2) 1742-4682 2011/01 [Refereed][Not invited]
     
    Background: While many pandemic preparedness plans have promoted disease control effort to lower and delay an epidemic peak, analytical methods for determining the required control effort and making statistical inferences have yet to be sought. As a first step to address this issue, we present a theoretical basis on which to assess the impact of an early intervention on the epidemic peak, employing a simple epidemic model. Methods: We focus on estimating the impact of an early control effort (e. g. unsuccessful containment), assuming that the transmission rate abruptly increases when control is discontinued. We provide analytical expressions for magnitude and time of the epidemic peak, employing approximate logistic and logarithmic-form solutions for the latter. Empirical influenza data (H1N1-2009) in Japan are analyzed to estimate the effect of the summer holiday period in lowering and delaying the peak in 2009. Results: Our model estimates that the epidemic peak of the 2009 pandemic was delayed for 21 days due to summer holiday. Decline in peak appears to be a nonlinear function of control-associated reduction in the reproduction number. Peak delay is shown to critically depend on the fraction of initially immune individuals. Conclusions: The proposed modeling approaches offer methodological avenues to assess empirical data and to objectively estimate required control effort to lower and delay an epidemic peak. Analytical findings support a critical need to conduct population-wide serological survey as a prior requirement for estimating the time of peak.
  • H. Nishiura, R. Omori
    TRANSBOUNDARY AND EMERGING DISEASES 57 (6) 396 - 403 1865-1674 2010/12 [Refereed][Not invited]
     
    P>An epidemic of foot-and-mouth disease occurred in Miyazaki, Japan, beginning in late March 2010. Here, we document the descriptive epidemiological features and investigate the between-farm transmission dynamics. As of 10 July 2010, a total of 292 infected premises have been confirmed with a cumulative incidence for cattle and pig herds of 8.5% and 36.4%, respectively, for the whole of Miyazaki prefecture. Pig herds were more likely to be infected than cattle herds (odds ratio = 4.3 [95% confidence interval (CI): 3.2, 5.7]). Modelling analysis suggested that the relative susceptibility of a cattle herd is 4.2 times greater than a typical pig herd (95% CI: 3.9, 4.5), while the relative infectiousness of a pig herd is estimated to be 8.0 times higher than a cattle herd (95% CI: 5.0, 13.6). The epidemic peak occurred around mid-May, after which the incidence started to decline and the effective reproduction numbers from late May were mostly less than unity, although a vaccination programme in late May could have masked symptoms in infected animals. The infected premises were geographically confined to limited areas in Miyazaki, but sporadic long-distance transmissions were seen within the prefecture. Given that multiple outbreaks in Far East Asian countries have occurred since early 2010, continued monitoring and surveillance is deemed essential.
  • Ryosuke Omori, Ben Adams, Akira Sasaki
    JOURNAL OF THEORETICAL BIOLOGY 262 (1) 48 - 57 0022-5193 2010/01 [Refereed][Not invited]
     
    The accumulation of cross-immunity in the host population is an important factor driving the antigenic evolution of viruses such as influenza A. Mathematical models have shown that the strength of temporary non-specific cross-immunity and the basic reproductive number are both key determinants for evolutionary branching of the antigenic phenotype. Here we develop deterministic and stochastic versions of one such model. We examine how the time of emergence or introduction of a novel strain affects co-existence with existing strains and hence the initial establishment of a new evolutionary branch. We also clarify the roles of cross-immunity and the basic reproductive number in this process. We show that the basic reproductive number is important because it affects the frequency of infection, which influences the long term immune profile of the host population. The time at which a new strain appears relative to the epidemic peak of an existing strain is important because it determines the environment the emergent mutant experiences in terms of the short term immune profile of the host population. Strains are more likely to coexist, and hence to establish a new clade in the viral phylogeny, when there is a significant time overlap between their epidemics. It follows that the majority of antigenic drift in influenza is expected to occur in the earlier part of each transmission season and this is likely to be a key surveillance period for detecting emerging antigenic novelty. (C) 2009 Elsevier Ltd. All rights reserved.

MISC

Presentations

  • Estimation of Basic Reproduction Number R0 using a Recurrent Neural Network
    Heidi Tessmer, Ryosuke Omori
    NIPS 2016 Workshop on Machine Learning for Health  2016
  • Ryosuke Omori
    2010/06  Centre for Mathematical Sciences, Wilberforce Road, Cambridge.

Association Memberships

  • 獣医疫学会   日本疫学会   日本公衆衛生学会   日本性感染症学会   日本応用数理学会   日本数理生物学会   

Research Projects

  • 日本学術振興会：科学研究費助成事業
    Date (from‐to) : 2022/04 -2027/03 
    Author : 大森 亮介
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research
    Date (from‐to) : 2022/04 -2025/03 
    Author : 蒔田 浩平, 大森 亮介
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research
    Date (from‐to) : 2020/07 -2024/03 
    Author : 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：Grants-in-Aid for Scientific Research
    Date (from‐to) : 2019/04 -2022/03 
    Author : 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：Grants-in-Aid for Scientific Research
    Date (from‐to) : 2015/04 -2018/03 
    Author : 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.
  • 日本学術振興会：科学研究費助成事業
    Date (from‐to) : 2009 -2011 
    Author : 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。

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