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Furuse Y. Characteristics of retracted research papers before and during the COVID-19 pandemic. Front Med (Lausanne) 2024; 10:1288014. [PMID: 38269323 PMCID: PMC10806159 DOI: 10.3389/fmed.2023.1288014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 12/15/2023] [Indexed: 01/26/2024] Open
Abstract
Objectives During the COVID-19 pandemic, a large number of research papers were published, and some of them were retracted. The present study aims to reveal the characteristics of retracted papers before and during the pandemic. Methods The study investigated 24,542,394 publications from 1999 to 2022 and analyzed the profiles of retracted papers from the perspectives of year, disease category, country, and journal. Results Retraction rates were generally increasing at least until 2019, and were the highest for "Neoplasms." The number of publications for "Infections" and "Respiratory Tract Diseases" dramatically rose during the COVID-19 pandemic; however, the retraction rates in the two categories or of COVID-19-related papers were not especially high compared to other diseases. The association with retraction was strongest for China in most disease categories, whereas for COVID-19 papers, other countries showed higher retraction rates than China. In recent years, retracted papers have become less likely to be published in high-impact journals. Conclusion The COVID-19 pandemic does not seem to affect the retractions of research papers much. We should keep monitoring retractions and analyze the effects of pandemics for better science.
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Affiliation(s)
- Yuki Furuse
- Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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2
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Ko YK, Furuse Y, Otani K, Yamauchi M, Ninomiya K, Saito M, Imamura T, Cook AR, Ahiko T, Fujii S, Mori Y, Suzuki E, Yamada K, Ashino Y, Yamashita H, Kato Y, Mizuta K, Suzuki M, Oshitani H. Time-varying overdispersion of SARS-CoV-2 transmission during the periods when different variants of concern were circulating in Japan. Sci Rep 2023; 13:13230. [PMID: 37580339 PMCID: PMC10425347 DOI: 10.1038/s41598-023-38007-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/30/2023] [Indexed: 08/16/2023] Open
Abstract
Japan has implemented a cluster-based approach for coronavirus disease 2019 (COVID-19) from the pandemic's beginning based on the transmission heterogeneity (overdispersion) of severe acute respiratory coronavirus 2 (SARS-CoV-2). However, studies analyzing overdispersion of transmission among new variants of concerns (VOCs), especially for Omicron, were limited. Thus, we aimed to clarify how the transmission heterogeneity has changed with the emergence of VOCs (Alpha, Delta, and Omicron) using detailed contact tracing data in Yamagata Prefecture, Japan. We estimated the time-varying dispersion parameter ([Formula: see text]) by fitting a negative binomial distribution for each transmission generation. Our results showed that even after the emergence of VOCs, there was transmission heterogeneity of SARS-CoV-2, with changes in [Formula: see text] during each wave. Continuous monitoring of transmission dynamics is vital for implementing appropriate measures. However, a feasible and sustainable epidemiological analysis system should be established to make this possible.
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Affiliation(s)
- Yura K Ko
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
| | - Yuki Furuse
- Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kanako Otani
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Kota Ninomiya
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
| | - Takeaki Imamura
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
| | - Alex R Cook
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Tadayuki Ahiko
- Division of Health and Welfare Planning, Yamagata Prefectural Government, Yamagata, Japan
| | | | | | | | | | | | | | - Yuichi Kato
- Yamagata City Institute of Public Health, Yamagata, Japan
| | - Katsumi Mizuta
- Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Motoi Suzuki
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan.
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3
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Furuse Y. Estimation of excess cardiovascular deaths after COVID-19 in 2020. J Infect 2023; 87:e5-e7. [PMID: 37100175 PMCID: PMC10125210 DOI: 10.1016/j.jinf.2023.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/11/2023] [Accepted: 04/21/2023] [Indexed: 04/28/2023]
Affiliation(s)
- Yuki Furuse
- Department of Medical Virology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.
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4
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Sato T, Umeda M, Sato S, Michitsuji T, Shimizu T, Koga T, Furuse Y, Kawakami A. Increase in the number of new cases of ANCA-associated vasculitis in the COVID-19 vaccine era. Clin Immunol 2023:109656. [PMID: 37263519 DOI: 10.1016/j.clim.2023.109656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/03/2023]
Abstract
Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is an autoimmune vasculitis characterized by the production of antibodies against ANCA, with unclear pathogenesis. With the ongoing COVID-19 pandemic, COVID-19 mRNA vaccination has been available in Japan since February 2021. Although autoimmune symptoms have been reported after COVID-19 vaccinations, there have been no clinical investigations regarding the relationship between COVID-19 mRNA vaccines and the pathogenesis of AAV. Thus, the present study aimed to investigate whether the administration of COVID-19 mRNA vaccines affects the development of AAV. The study identified patients with new-onset AAV who were MPO-ANCA or PR3-ANCA positive and met the entry criteria of the AAV EMA classification algorithm. The study compared the number of new AAV cases per year before and after the start of the COVID-19 mRNA vaccine program in Japan. The study found that the annual number of new cases of AAV in Japan's Nagasaki Prefecture increased by approximately 1.5-fold since the COVID-19 vaccine program was initiated, suggesting a possible link between the COVID-19 mRNA vaccines and the development of AAV. Although the study provides insight into the clinical evaluation and management of autoimmune symptoms following COVID-19 vaccination, further investigation of the possible association between COVID-19 mRNA vaccines and the pathogenesis of AAV is required.
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Affiliation(s)
- Tomohito Sato
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Masataka Umeda
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan; Research Unit for Preventive and Clinical Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.
| | - Shuntaro Sato
- Clinical Research Center, Nagasaki University Hospital, Nagasaki, Japan
| | - Toru Michitsuji
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Toshimasa Shimizu
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan; Clinical Research Center, Nagasaki University Hospital, Nagasaki, Japan
| | - Tomohiro Koga
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yuki Furuse
- Department of Medical Virology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Atsushi Kawakami
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan; Research Unit for Preventive and Clinical Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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5
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Furuse Y. Cartography of SARS-CoV-2 variants based on the susceptibility to therapeutic monoclonal antibodies. J Med Virol 2023; 95:e28275. [PMID: 36326059 PMCID: PMC9877944 DOI: 10.1002/jmv.28275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/18/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
A comprehensive picture of a phenotypic relationship among severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has been poorly studied. Here, this study presents cartography showing how the wild-type strain of SARS-CoV-2 and 14 variants are alike or different from the perspective of the susceptibility to 12 therapeutic monoclonal antibodies. The Alpha variant is close to the wild-type strain, whereas the Beta, Gamma, and Delta variants diverge from the wild-type. The map highlights the very unique property of the Omicron variant. Interestingly, sublineages of the Omicron variants, BA.1, BA.2, and BA.4/5, differ substantially in the cartography.
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Affiliation(s)
- Yuki Furuse
- Nagasaki University Graduate School of Biomedical SciencesNagasakiJapan,Medical Education Development CenterNagasaki University HospitalNagasakiJapan,Institute for Frontier Life and Medical SciencesKyoto UniversityKyotoJapan,Hakubi Center for Advanced ResearchKyoto UniversityKyotoJapan
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6
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Yamayoshi S, Iwatsuki-Horimoto K, Okuda M, Ujie M, Yasuhara A, Murakami J, Duong C, Hamabata T, Ito M, Chiba S, Kobayashi R, Takahashi S, Mitamura K, Hagihara M, Shibata A, Uwamino Y, Hasegawa N, Ebina T, Izumi A, Kato H, Nakajima H, Sugaya N, Seki Y, Iqbal A, Kamimaki I, Yamazaki M, Kawaoka Y, Furuse Y. Age-Stratified Seroprevalence of SARS-CoV-2 Antibodies before and during the Vaccination Era, Japan, February 2020–March 2022. Emerg Infect Dis 2022; 28:2198-2205. [PMID: 36198306 PMCID: PMC9622230 DOI: 10.3201/eid2811.221127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Japan has reported a relatively small number of COVID-19 cases. Because not all infected persons receive diagnostic tests for COVID-19, the reported number must be lower than the actual number of infections. We assessed SARS-CoV-2 seroprevalence by analyzing >60,000 samples collected in Japan (Tokyo Metropolitan Area and Hokkaido Prefecture) during February 2020–March 2022. The results showed that ≈3.8% of the population had become seropositive by January 2021. The seroprevalence increased with the administration of vaccinations; however, among the elderly, seroprevalence was not as high as the vaccination rate. Among children, who were not eligible for vaccination, infection was spread during the epidemic waves caused by the SARS-CoV-2 Delta and Omicron variants. Nevertheless, seroprevalence for unvaccinated children <5 years of age was as low as 10% as of March 2022. Our study underscores the low incidence of SARS-CoV-2 infection in Japan and the effects of vaccination on immunity at the population level.
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7
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Olayinka AT, Elimian K, Ipadeola O, Dan-Nwafor C, Gibson J, Ochu C, Furuse Y, Iniobong A, Akano A, Enenche L, Onoja M, Uzoho C, Ugbogulu N, Makava F, Arinze C, Namara G, Muwanguzi E, Jan K, Ukponu W, Okwor T, Anueyiagu C, Saleh M, Ahumibe A, Eneh C, Ilori E, Mba N, Ihekweazu C. Analysis of sociodemographic and clinical factors associated with Lassa fever disease and mortality in Nigeria. PLOS Glob Public Health 2022; 2:e0000191. [PMID: 36962735 PMCID: PMC10022364 DOI: 10.1371/journal.pgph.0000191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/19/2022] [Indexed: 11/18/2022]
Abstract
Over past decades, there has been increasing geographical spread of Lassa fever (LF) cases across Nigeria and other countries in West Africa. This increase has been associated with significant morbidity and mortality despite increasing focus on the disease by both local and international scientists. Many of these studies on LF have been limited to few specialised centres in the country. This study was done to identify sociodemographic and clinical predictors of LF disease and related deaths across Nigeria. We analysed retrospective surveillance data on suspected LF cases collected during January-June 2018 and 2019. Multivariable logistic regression analyses were used to identify the factors independently associated with laboratory-confirmed LF diagnosis, and with LF-related deaths. There were confirmed 815 of 1991 suspected LF cases with complete records during this period. Of these, 724/815 confirmed cases had known clinical outcomes, of whom 100 died. LF confirmation was associated with presentation of gastrointestinal tract (aOR 3.47, 95% CI: 2.79-4.32), ear, nose and throat (aOR 2.73, 95% CI: 1.80-4.15), general systemic (aOR 2.12, 95% CI: 1.65-2.70) and chest/respiratory (aOR 1.71, 95% CI: 1.28-2.29) symptoms. Other factors were being male (aOR 1.32, 95% CI: 1.06-1.63), doing business/trading (aOR 2.16, 95% CI: 1.47-3.16) and farming (aOR 1.73, 95% CI: 1.12-2.68). Factors associated with LF mortality were a one-year increase in age (aOR 1.03, 95% CI: 1.01-1.04), bleeding (aOR 2.07, 95% CI: 1.07-4.00), and central nervous manifestations (aOR 5.02, 95% CI: 3.12-10.16). Diverse factors were associated with both LF disease and related death. A closer look at patterns of clinical variables would be helpful to support early detection and management of cases. The findings would also be useful for planning preparedness and response interventions against LF in the country and region.
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Affiliation(s)
| | - Kelly Elimian
- Nigeria Centre for Disease Control, Abuja, FCT, Nigeria
| | | | | | - Jack Gibson
- University of Nottingham, Nottingham, United Kingdom
| | - Chinwe Ochu
- Nigeria Centre for Disease Control, Abuja, FCT, Nigeria
| | - Yuki Furuse
- World Health Organisation, Abuja, FCT, Nigeria
| | | | - Adejoke Akano
- Nigeria Centre for Disease Control, Abuja, FCT, Nigeria
| | - Lorna Enenche
- Nigeria Centre for Disease Control, Abuja, FCT, Nigeria
| | - Michael Onoja
- Nigeria Centre for Disease Control, Abuja, FCT, Nigeria
| | | | - Nkem Ugbogulu
- Nigeria Centre for Disease Control, Abuja, FCT, Nigeria
| | - Favour Makava
- Nigeria Centre for Disease Control, Abuja, FCT, Nigeria
| | | | | | | | - Kamji Jan
- Nigeria Centre for Disease Control, Abuja, FCT, Nigeria
| | - Winifred Ukponu
- Georgetown University Centre for Global Health Practice and Impact, Abuja, Nigeria
| | - Tochi Okwor
- Nigeria Centre for Disease Control, Abuja, FCT, Nigeria
| | | | - Muhammad Saleh
- Centers for Disease Prevention and Control, Abuja, Nigeria
| | | | - Chibuzo Eneh
- Nigeria Centre for Disease Control, Abuja, FCT, Nigeria
| | - Elsie Ilori
- Nigeria Centre for Disease Control, Abuja, FCT, Nigeria
| | - Nwando Mba
- Nigeria Centre for Disease Control, Abuja, FCT, Nigeria
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8
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Furuse Y. [Comprehensive understanding of viral diseases by field, molecular, and theoretical studies]. Uirusu 2022; 72:87-92. [PMID: 37899235 DOI: 10.2222/jsv.72.87] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
Viral diseases are responsible for substantial morbidity and mortality and continue to be of great concern. To ensure better control of viral infections, I have been tackling the issue as a medical doctor, an academic researcher, and a public health officer. Especially, I have studied respiratory viruses, such as the influenza virus, from the perspectives of molecular virology, theoretical modeling, and field epidemiology. RNA biology and its involvement with viral life-cycle and pathogenicity are central topics of molecular study, while mathematical models of transmission dynamics and phylogenetics are major components of theoretical research. As a field epidemiologist, I work with public health authorities during viral disease outbreaks. I was deployed to West Africa for viral hemorrhagic fever outbreak responses as a WHO consultant, and I have served the Japanese Government as an advisor for COVID-19 countermeasures. I would like to integrate various approaches from clinical medicine to epidemiology, theoretical modeling, evolutionary biology, genetics, and molecular biology in my research. In that way, we could gain a more comprehensive understanding of viral diseases. I hope these findings will help ease the disease burden of viral infections around the world.
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Affiliation(s)
- Yuki Furuse
- Nagasaki University Graduate School of Biomedical Sciences/Nagasaki University Hospital Medical Education Development Center
- Institute for Frontier Life and Medical Sciences/Hakubi Center for Advanced Research, Kyoto University
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9
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Ko YK, Furuse Y, Ninomiya K, Otani K, Akaba H, Miyahara R, Imamura T, Imamura T, Cook AR, Saito M, Suzuki M, Oshitani H. Secondary transmission of SARS-CoV-2 during the first two waves in Japan: Demographic characteristics and overdispersion. Int J Infect Dis 2022; 116:365-373. [PMID: 35066162 PMCID: PMC8772065 DOI: 10.1016/j.ijid.2022.01.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 12/04/2022] Open
Abstract
Objectives Super-spreading events caused by overdispersed secondary transmission are crucial in the transmission of COVID-19. However, the exact level of overdispersion, demographics, and other factors associated with secondary transmission remain elusive. In this study, we aimed to elucidate the frequency and patterns of secondary transmission of SARS-CoV-2 in Japan. Methods We analyzed 16,471 cases between January 2020 and August 2020. We generated the number of secondary cases distribution and estimated the dispersion parameter (k) by fitting the negative binomial distribution in each phase. The frequencies of the secondary transmission were compared by demographic and clinical characteristics, calculating the odds ratio using logistic regression models. Results We observed that 76.7% of the primary cases did not generate secondary cases with an estimated dispersion parameter k of 0.23. The demographic patterns of primary-secondary cases differed between phases, with 20–69 years being the predominant age group. There were higher proportions of secondary transmissions among older individuals, symptomatic patients, and patients with 2 days or more between onset and confirmation. Conclusions The study showed the estimation of the frequency of secondary transmission of SARS-CoV-2 and the characteristics of people who generated the secondary transmission.
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Affiliation(s)
- Yura K Ko
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo, Japan; Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, Japan 980-8575.
| | - Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, 53 kawaramachi, Shogoin, Sakyo-ku, Kyoto, Japan; Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki, Japan.
| | - Kota Ninomiya
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; National Institute of Public Health, 2-3-6 Minami, Wako-shi, Saitama 351-0197 Japan.
| | - Kanako Otani
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo, Japan.
| | - Hiroki Akaba
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, Japan 980-8575.
| | - Reiko Miyahara
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo, Japan.
| | - Tadatsugu Imamura
- Japan International Cooperation Agency, 5-25 Niban-cho, Chiyoda-ku, Tokyo 102-8012, Japan; Center for Postgraduate Education and Training, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, Japan.
| | - Takeaki Imamura
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, Japan 980-8575.
| | - Alex R Cook
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, 12 Science Drive 2, #10-01, Singapore.
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, Japan 980-8575.
| | - Motoi Suzuki
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo, Japan.
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, Japan 980-8575.
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10
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Furuse Y. Simulation study reveals factors that affect the predominance of SARS-CoV-2 novel variant. Virol J 2021; 18:253. [PMID: 34930336 PMCID: PMC8685792 DOI: 10.1186/s12985-021-01726-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 12/09/2021] [Indexed: 11/17/2022] Open
Abstract
The novel variants of the SARS-CoV-2 are a great global concern for the ongoing COVID-19 pandemic. However, how the novel variants predominate and replace existing strains remains elusive. In this study, I simulated the infection spread to investigate what kinds of viral, immunological, and epidemiological factors affect the predominance of SARS-CoV-2 novel variants. The results showed that the increase of the transmissibility of the novel variant substantially enhanced the predominance probability. In addition, the increasing trend of the infection spread, the large case number of the epidemic, and the ability of immune escape of the novel variant increased the predominance probability. A small number of cases and a decreasing trend of an entire epidemic, including not only the novel variant but also earlier strains, are especially important to reduce the chance of the predominance of the novel variant and delay the process. Good control of the COVID-19 epidemic could make the disease burden small and sequester the spread of the SARS-CoV-2 novel variants.
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Affiliation(s)
- Yuki Furuse
- Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
- Medical Education Development Center, Nagasaki University Hospital, 1-7-1 Sakamoto, Nagasaki, 852-8501, Japan.
- Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan.
- Hakubi Center for Advanced Research, Kyoto University, Yoshida Honmachi, Sakyo-ku, Kyoto, 606-8501, Japan.
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11
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Abstract
Background COVID-19 continues to impose significant morbidity and mortality in Japan even after implementing the vaccination program. It would remain elusive if restrictions for its mitigation were to be lifted or relaxed in the future. Methods A simulation study that explored possible vaccination coverage scenarios and changes in the intensity of nonpharmaceutical intervention restrictions was performed to assess the impact of COVID-19 based on death count. Results Assuming the basic reproduction number of circulating viruses was 5.0, vaccines could prevent 90% of infections and 95% of deaths, and the vaccination coverage rate was high (75%, 80%, and 90% in people aged 12-39 years, 40-59 years, ≥60 years, respectively), approximately 50 000 deaths would occur over 150 days in Japan if all restrictions were lifted. Most deaths would occur among older adults, even if their vaccination coverage was assumed to be especially high. A low vaccination coverage scenario (45%, 60%, and 80% in people aged 12-39 years, 40-59 years, ≥60 years, respectively) would require periodic implementation of strict measures even if the modified lifestyle observed in 2020 was sustained and vaccines were very effective. Some restrictions could be relaxed under high vaccination coverage. However, in the worst-case scenario where vaccines had decreased efficacy, as we have observed for the Delta variant, and people lived a relaxed lifestyle, our simulation suggests that even high vaccination coverage would occasionally require strict measures. Conclusions We should carefully explore a manageable degree of restrictions and their relaxation. We will have to keep bracing for occasional surges of COVID-19 infection, which could lead to strict measures, such as those under a state of emergency. Such strategies are essential even after a wide rollout of vaccination.
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Affiliation(s)
- Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan.,Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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12
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Nwafor CD, Ilori E, Olayinka A, Ochu C, Olorundare R, Edeh E, Okwor T, Oyebanji O, Namukose E, Ukponu W, Olugbile M, Adekanye U, Chandra N, Bolt H, Namara G, Ipadeola O, Furuse Y, Woldetsadik S, Akano A, Iniobong A, Amedu M, Anueyiagu C, Bakare L, Ahumibe A, Joseph G, Eneh C, Saleh M, Dhamari N, Okoli I, Kachalla M, Okea R, Okenyi C, Makava F, Makwe C, Ugbogulu N, Fonkeng F, Aniaku E, Agogo E, Mba N, Aruna O, Nguku P, Ihekweazu C. The One Health approach to incident management of the 2019 Lassa fever outbreak response in Nigeria. One Health 2021; 13:100346. [PMID: 34820499 PMCID: PMC8600060 DOI: 10.1016/j.onehlt.2021.100346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 11/07/2021] [Accepted: 11/07/2021] [Indexed: 11/18/2022] Open
Abstract
Globally, effective emergency response to disease outbreaks is usually affected by weak coordination. However, coordination using an incident management system (IMS) in line with a One Health approach involving human, environment, and animal health with collaborations between government and non-governmental agencies result in improved response outcome for zoonotic diseases such as Lassa fever (LF). We provide an overview of the 2019 LF outbreak response in Nigeria using the IMS and One Health approach. The response was coordinated via ten Emergency Operation Centre (EOC) response pillars. Cardinal response activities included activation of EOC, development of an incident action plan, deployment of One Health rapid response teams to support affected states, mid-outbreak review and after-action review meetings. Between 1st January and 29th December 2019, of the 5057 people tested for LF, 833 were confirmed positive from 23 States, across 86 Local Government Areas. Of the 833 confirmed cases, 650 (78%) were from hotspot States of Edo (36%), Ondo (26%) and Ebonyi (16%). Those in the age-group 21–40 years (47%) were mostly affected, with a male to female ratio of 1:1. Twenty healthcare workers were affected. Two LF naïve states Kebbi and Zamfara, reported confirmed cases for the first time during this period. The outbreak peaked earlier in the year compared to previous years, and the emergency phase of the outbreak was declared over by epidemiological week 17 based on low national threshold composite indicators over a period of six consecutive weeks. Multisectoral and multidisciplinary strategic One Health EOC coordination at all levels facilitated the swift containment of Nigeria's large LF outbreak in 2019. It is therefore imperative to embrace One Health approach embedded within the EOC to holistically address the increasing LF incidence in Nigeria.
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Affiliation(s)
| | - Elsie Ilori
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | | | - Chinwe Ochu
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | | | - Edwin Edeh
- World Health Organisation, Abuja, Nigeria
| | - Tochi Okwor
- Nigeria Centre for Disease Control, Abuja, Nigeria.,World Health Organisation, Abuja, Nigeria
| | | | | | | | | | - Usman Adekanye
- Nigeria Ministry of Defense, Health Implementation Program, Nigeria
| | | | - Hikaru Bolt
- UK Public Health Rapid Support Team, London, United Kingdom
| | | | | | | | | | | | | | | | | | - Lawal Bakare
- Nigeria Centre for Disease Control, Abuja, Nigeria.,World Health Organisation, Abuja, Nigeria
| | | | | | - Chibuzo Eneh
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | | | | | - Ihekerenma Okoli
- Federal Ministry of Agriculture and Rural Development, Abuja, Nigeria
| | - Mairo Kachalla
- Federal Ministry of Agriculture and Rural Development, Abuja, Nigeria
| | - Rita Okea
- Federal Ministry of Environment, Abuja, Nigeria
| | | | | | | | | | | | | | | | - Nwando Mba
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Olusola Aruna
- Public Health England, International Health Regulations (IHR) Strengthening Project, Abuja, Nigeria
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13
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Imamura T, Ko YK, Furuse Y, Imamura T, Jindai K, Miyahara R, Sando E, Yasuda I, Tsuchiya N, Saito M, Suzuki M, Oshitani H. Epidemiological factors associated with COVID-19 clusters in medical and social welfare facilities. Jpn J Infect Dis 2021; 75:281-287. [PMID: 34719529 DOI: 10.7883/yoken.jjid.2021.288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Characteristics of COVID-19 clusters in medical and social welfare facilities, and factors associated with cluster size are still not fully understood. We reviewed COVID-19 cases identified from January 15 to April 30 of 2020 in Japan, and analyzed factors associated with cluster size in medical and social welfare facilities. In the study, COVID-19 clusters were identified in 56 medical and 34 social welfare facilities. Numbers of cases in those facilities reached their peaks after the peak of general population. Duration of occurrence of new cases in clusters showed a positive correlation with the number of cases in both types of facilities (rho = 0.44, p < 0.001; and rho = 0.69, p < 0.001, respectively). However, number of days between the first case in the prefecture and the onset of clusters showed a negative correlation with the number of cases only in clusters in social welfare facilities (rho = -0.4, p = 0.004). Our results suggested that COVID-19 cases in those facilities were prevalent in the latter phase of the community transmissions, although the underlying mechanisms for such trend could be different between medical and social welfare facilities.
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Affiliation(s)
- Tadatsugu Imamura
- Japan International Cooperation Agency, Japan.,Center for Postgraduate Education and Training, National Center for Child Health and Development, Japan
| | - Yura K Ko
- Department of Virology, Tohoku University Graduate School of Medicine, Japan.,Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Japan
| | - Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
| | - Takeaki Imamura
- Department of Virology, Tohoku University Graduate School of Medicine, Japan
| | - Kazuaki Jindai
- Department of Healthcare Epidemiology, Kyoto University, Japan
| | - Reiko Miyahara
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Japan.,Medical Genome Science Project, National Center for Global Health and Medicine, Japan
| | - Eiichiro Sando
- Department of General Internal Medicine & Clinical Infectious Diseases, Fukushima Medical University, Japan
| | - Ikkoh Yasuda
- Department of General Internal Medicine & Clinical Infectious Diseases, Fukushima Medical University, Japan
| | - Naho Tsuchiya
- Yamato-Clinic, Japan.,Tohoku Medical Megabank Organization, Tohoku University, Japan
| | | | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Japan
| | - Motoi Suzuki
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Japan
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Japan
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14
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Furuse Y. RNA Modifications in Genomic RNA of Influenza A Virus and the Relationship between RNA Modifications and Viral Infection. Int J Mol Sci 2021; 22:ijms22179127. [PMID: 34502037 PMCID: PMC8431438 DOI: 10.3390/ijms22179127] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/23/2021] [Accepted: 08/23/2021] [Indexed: 02/07/2023] Open
Abstract
Recent studies about the transcriptome-wide presence of RNA modifications have revealed their importance in many cellular functions. Nevertheless, information about RNA modifications in viral RNA is scarce, especially for negative-strand RNA viruses. Here we provide a catalog of RNA modifications including m1A, ac4C, m7G, inosine, and pseudouridine on RNA derived from an influenza A virus infected into A549 cells, as studied by RNA immunoprecipitation followed by deep-sequencing. Possible regions with RNA modifications were found in the negative-strand segments of viral genomic RNA. In addition, our analyses of previously published data revealed that the expression levels of the host factors for RNA modifications were affected by an infection with influenza A virus, and some of the host factors likely have a proviral effect. RNA modification is a novel aspect of host-virus interactions leading to the discovery of previously unrecognized viral pathogenicity mechanisms and has the potential to aid the development of novel antivirals.
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Affiliation(s)
- Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan;
- Hakubi Center for Advanced Research, Kyoto University, Kyoto 606-8501, Japan
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15
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Furuse Y, Ko YK, Ninomiya K, Suzuki M, Oshitani H. Relationship of Test Positivity Rates with COVID-19 Epidemic Dynamics. Int J Environ Res Public Health 2021; 18:4655. [PMID: 33925665 PMCID: PMC8125747 DOI: 10.3390/ijerph18094655] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 12/23/2022]
Abstract
Detection and isolation of infected people are believed to play an important role in the control of the COVID-19 pandemic. Some countries conduct large-scale screenings for testing, whereas others test mainly people with high prior probability of infection such as showing severe symptoms and/or having an epidemiological link with a known or suspected case or cluster of cases. However, what a good testing strategy is and whether the difference in testing strategy shows a meaningful, measurable impact on the COVID-19 epidemic remain unknown. Here, we showed that patterns of association between effective reproduction number (Rt) and test positivity rate can illuminate differences in testing situation among different areas, using global and local data from Japan. This association can also evaluate the adequacy of current testing systems and what information is captured in COVID-19 surveillance. The differences in testing systems alone cannot predict the results of epidemic containment efforts. Furthermore, monitoring test positivity rates and severe case proportions among the nonelderly can predict imminent case count increases. Monitoring test positivity rates in conjunction with the concurrent Rt could be useful to assess and strengthen public health management and testing systems and deepen understanding of COVID-19 epidemic dynamics.
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Affiliation(s)
- Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yura K. Ko
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan; (Y.K.K.); (H.O.)
- National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (K.N.); (M.S.)
| | - Kota Ninomiya
- National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (K.N.); (M.S.)
- National Institute of Public Health, Wako 351-0197, Japan
| | - Motoi Suzuki
- National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (K.N.); (M.S.)
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan; (Y.K.K.); (H.O.)
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16
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Miyahara R, Tsuchiya N, Yasuda I, Ko YK, Furuse Y, Sando E, Nagata S, Imamura T, Saito M, Morimoto K, Imamura T, Shobugawa Y, Nishiura H, Suzuki M, Oshitani H. Familial Clusters of Coronavirus Disease in 10 Prefectures, Japan, February-May 2020. Emerg Infect Dis 2021; 27:915-918. [PMID: 33622475 PMCID: PMC7920650 DOI: 10.3201/eid2703.203882] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The overall coronavirus disease secondary attack rate (SAR) in family members was 19.0% in 10 prefectures of Japan during February 22–May 31, 2020. The SAR was lower for primary cases diagnosed early, within 2 days after symptom onset. The SAR of asymptomatic primary cases was 11.8%.
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17
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Furuse Y. [Epidemiology of Viral Hemorrhagic Fever in Africa]. Uirusu 2021; 71:11-18. [PMID: 35526990 DOI: 10.2222/jsv.71.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A variety of viral hemorrhagic fevers such as Ebola virus disease exist in Africa and impose a great threat in public health due to their high fatality. It is considered to be difficult to eradicate the etiological agents of viral hemorrhagic fever because they have non-human natural hosts. Therefore, the importance of public health measures remains high in addition to the urgent need for the development of medicines for treatment and prevention. Furthermore, public health measures directly lead to the accumulation of epidemiological knowledge about the diseases. As an infectious disease consultant for the World Health Organization, I have been involved with public health activities including the development of clinical guidelines, the establishment of laboratory diagnostic systems, the training for infection, prevention and control, the planning of budget for outbreak response, and the analysis of epidemiological data. On the last point, I reported the situation of Ebola virus disease outbreak in Liberia, 2014-2015 and Lassa fever outbreak in Nigeria, 2018-2019 describing the risk factors, morbidity, and mortality of the diseases.
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Affiliation(s)
- Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University
- Hakubi Center for Advanced Research, Kyoto University
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18
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Imamura T, Saito M, Ko YK, Imamura T, Otani K, Akaba H, Ninomiya K, Furuse Y, Miyahara R, Sando E, Yasuda I, Tsuchiya N, Suzuki M, Oshitani H. Roles of Children and Adolescents in COVID-19 Transmission in the Community: A Retrospective Analysis of Nationwide Data in Japan. Front Pediatr 2021; 9:705882. [PMID: 34447727 PMCID: PMC8382948 DOI: 10.3389/fped.2021.705882] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/08/2021] [Indexed: 12/24/2022] Open
Abstract
Background: Roles of children and adolescents in spreading coronavirus disease 2019 (COVID-19) in the community is not fully understood. Methods: We analyzed the data of 7,758 children and adolescents with COVID-19 and characteristics of secondary transmission generated by these cases using case information published by local governments. Ratio of pediatric and adolescent cases generating secondary transmission was calculated for various social settings. Results: The incidence of COVID-19 was 24.8 cases per 105 population aged between 0 and 9 years, and 59.2 among those aged between 10 and 19 years, which was lower than that among individuals of all age groups (79.6 per 105 population) between January 15 and October 31, 2020. The proportion of cases generating secondary cases was 8.3% among infants and young children in nursery schools and kindergartens, 16% among children and adolescents attending primary schools, 34% among those attending junior high schools, 43% among those attending high schools, 31% among those attending professional training colleges, and 24% in those attending universities. Households were the most common setting for secondary transmission. Conclusion: The risk of generating secondary cases might be limited among pediatric and adolescent cases with COVID-19, especially in settings outside households. Effectiveness of traditional mitigation measures (e.g., school closures) to suppress COVID-19 transmissions should be carefully evaluated.
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Affiliation(s)
- Tadatsugu Imamura
- Japan International Cooperation Agency, Tokyo, Japan.,Center for Postgraduate Education and Training, National Center for Child Health and Development, Tokyo, Japan
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yura K Ko
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takeaki Imamura
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kanako Otani
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroki Akaba
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kota Ninomiya
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Reiko Miyahara
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan.,Medical Genome Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Eiichiro Sando
- Department of General Internal Medicine and Clinical Infectious Diseases, Fukushima Medical University, Fukushima, Japan.,Department of General Internal Medicine and Infectious Diseases, Kita-Fukushima Medical Center, Fukushima, Japan
| | - Ikkoh Yasuda
- Department of General Internal Medicine and Clinical Infectious Diseases, Fukushima Medical University, Fukushima, Japan
| | - Naho Tsuchiya
- Yamato-Clinic, Tome, Japan.,Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | | | - Motoi Suzuki
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
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19
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Abstract
Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), tremendous efforts have been made to sequence the viral genome from samples collected throughout the world. Here, we evaluate how various countries have performed in sequencing from the perspectives of “fraction”, “timeliness”, and “openness”. We found that high proportions of samples were sequenced in the UK, the USA, Australia, and Iceland; sequencing was performed promptly in Iceland, the Netherlands, and the Democratic Republic of the Congo; and data were shared timely from the Netherlands, the USA, Iceland, and the UK. Although many developing countries have high numbers of SARS-CoV-2 infected cases but few published sequences, we observed good performance on sequencing efforts for some low- and middle-income countries. Further strengthening of the sequencing capacity at a global level would help in the fight against not only the current pandemic but also future outbreaks of viral diseases.
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Affiliation(s)
- Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan; Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan.
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20
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Furuse Y. Risk at mass-gathering events and the usefulness of complementary events during COVID-19 pandemic. J Infect 2020; 82:e20-e21. [PMID: 33271175 PMCID: PMC9190236 DOI: 10.1016/j.jinf.2020.11.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 11/28/2020] [Indexed: 01/12/2023]
Affiliation(s)
- Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.
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21
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Ipadeola O, Furuse Y, de Gooyer T, Dan-Nwafor C, Namara G, Ilori E, Ihekweazu C. Determination of the emergency phase for response against endemic disease outbreak: A case of Lassa fever outbreak in Nigeria. J Glob Health 2020; 10:020353. [PMID: 33110549 PMCID: PMC7568005 DOI: 10.7189/jogh.10.020353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
| | - Yuki Furuse
- World Health Organization, Abuja, Nigeria.,Kyoto University, Kyoto, Japan
| | - Tanyth de Gooyer
- World Health Organization, Abuja, Nigeria.,Victorian Department of Health and Human Services, Melbourne, Australia
| | | | | | - Elsie Ilori
- Nigeria Centre for Disease Control, Abuja, Nigeria
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22
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a worldwide pandemic. Many projections concerning the outbreak, such as the estimated number of cases and deaths in upcoming months, have been made available. However, what happens to the virus after the pandemic subsides has not been fully explored. In this article, we discuss the ways that past and present human viruses have emerged via zoonotic transmission, the mechanisms that they have acquired the ability for effective transmission among humans, the process to sustain a chain of transmission to coexist with humans, and the factors important for complete containment leading to eradication of viruses. These aspects of viral disease may provide clues for the future path that SARS-CoV-2 might take in relation to human infection.
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Affiliation(s)
- Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
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23
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Furuse Y, Tamaki R, Suzuki A, Kamigaki T, Okamoto M, Saito-Obata M, Nakagawa E, Saito M, Segubre-Mercado E, Tallo V, Lupisan S, Oshitani H. Epidemiological and clinical characteristics of children with acute respiratory viral infections in the Philippines: a prospective cohort study. Clin Microbiol Infect 2020; 27:1037.e9-1037.e14. [PMID: 32950713 DOI: 10.1016/j.cmi.2020.09.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/31/2020] [Accepted: 09/10/2020] [Indexed: 10/23/2022]
Abstract
OBJECTIVES Viral acute respiratory infection (ARI) remains a major global health problem, especially among children in low- and middle-income countries. The study was conducted to reveal aetiological significance of respiratory viruses among both non-hospitalized and hospitalized children. METHODS A cohort study of children with ARI at the household, primary healthcare facility, and hospital levels was conducted alongside a hospital-based study including non-cohort children from 2014 to 2016 in the Philippines. The ARI cases were recorded at households and healthcare facilities, and a clinical investigation was performed. Nasopharyngeal swabs were collected from the symptomatic children and tested for respiratory viruses via polymerase chain reaction. Then, the association between healthcare facility utilization and viral detection was investigated. RESULTS Overall, 18,514 ARI cases were enrolled in the cohort study, and samples were collected from 4735 of these cases. The hospital-based study detected 648 ARI cases, all of which were sampled. Rhinovirus (22.2%; 1052/4735) was most frequently detected followed by respiratory syncytial virus (12.0%; 566/4735). Enterovirus (adjusted odds ratio, 1.8; 95% confidence interval, 1.1-2.8), human metapneumovirus (2.1, 1.4-3.2), rhinovirus (2.1, 1.8-2.6), and respiratory syncytial virus (1.6, 1.2-1.9) were significantly more prevalent in the ARI cases at healthcare facilities than in those in households. Of all ARI cases, 0.6% required hospitalization while 1.8% were hospitalized among the respiratory syncytial virus-positive cases (3.8, 3.0-4.9). CONCLUSIONS We determined the prevalence of respiratory viruses among children with ARIs at the household, primary healthcare facility, and hospital levels and the association with clinical characteristics. In particular, we discovered a significant disease burden and impact of respiratory syncytial virus infections as well as a considerable aetiological implication of rhinovirus infections.
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Affiliation(s)
- Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan; Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan.
| | - Raita Tamaki
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Akira Suzuki
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Taro Kamigaki
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Michiko Okamoto
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mariko Saito-Obata
- RITM-Tohoku Collaborating Research Center on Emerging and Reemerging Infectious Diseases, Muntinlupa, Philippines
| | - Emiko Nakagawa
- RITM-Tohoku Collaborating Research Center on Emerging and Reemerging Infectious Diseases, Muntinlupa, Philippines
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Veronica Tallo
- Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Socorro Lupisan
- Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
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24
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Dan-Nwafor CC, Furuse Y, Ilori EA, Ipadeola O, Akabike KO, Ahumibe A, Ukponu W, Bakare L, Okwor TJ, Joseph G, Mba NG, Akano A, Olayinka AT, Okoli I, Okea RA, Makava F, Ugbogulu N, Oladele S, Namara G, Muwanguzi EN, Naidoo D, Mutbam SK, Okudo I, Woldetsadik SF, Lasuba CL, Ihekweazu C. Measures to control protracted large Lassa fever outbreak in Nigeria, 1 January to 28 April 2019. ACTA ACUST UNITED AC 2020; 24. [PMID: 31115314 PMCID: PMC6530254 DOI: 10.2807/1560-7917.es.2019.24.20.1900272] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Lassa fever cases have increased in Nigeria since 2016 with the highest number, 633 cases, reported in 2018. From 1 January to 28 April 2019, 554 laboratory-confirmed cases including 124 deaths were reported in 21 states in Nigeria. A public health emergency was declared on 22 January by the Nigeria Centre for Disease Control. We describe the various outbreak responses that have been implemented, including establishment of emergency thresholds and guidelines for case management.
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Affiliation(s)
- Chioma C Dan-Nwafor
- These authors contributed equally to this work.,Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,World Health Organization, Abuja, Nigeria.,These authors contributed equally to this work
| | | | - Oladipupo Ipadeola
- United States Centers for Disease Control and Prevention, Abuja, Nigeria
| | | | | | - Winifred Ukponu
- Georgetown University, Washington DC, United States of America
| | - Lawal Bakare
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | | | | | - Nwando G Mba
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | | | | | - Ihekerenma Okoli
- Federal Ministry of Agriculture and Rural Development, Abuja, Nigeria
| | - Rita A Okea
- Federal Ministry of Environment, Abuja, Nigeria
| | - Favour Makava
- Maryland Global Initiatives Corporation, Abuja, Nigeria
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25
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Furuse Y, Oshitani H. Association between Numbers of "Imported Cases" and "Reported Cases in a Source Country" of COVID-19: January to April 2020 in Japan. J Infect 2020; 81:e153-e154. [PMID: 32522454 PMCID: PMC7833536 DOI: 10.1016/j.jinf.2020.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 11/25/2022]
Affiliation(s)
- Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawaracho, Sakyo-ku, Kyoto, Japan; Hakubi Center for Advanced Research, Kyoto University, Yoshida Honmachi, Sakyo-ku, Kyoto, Japan.
| | - Hitoshi Oshitani
- Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan.
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26
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Furuse Y, Sando E, Tsuchiya N, Miyahara R, Yasuda I, Ko YK, Saito M, Morimoto K, Imamura T, Shobugawa Y, Nagata S, Jindai K, Imamura T, Sunagawa T, Suzuki M, Nishiura H, Oshitani H. Clusters of Coronavirus Disease in Communities, Japan, January-April 2020. Emerg Infect Dis 2020; 26. [PMID: 32521222 PMCID: PMC7454082 DOI: 10.3201/eid2609.202272] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We analyzed 3,184 cases of coronavirus disease in Japan and identified 61 case-clusters in healthcare and other care facilities, restaurants and bars, workplaces, and music events. We also identified 22 probable primary case-patients for the clusters; most were 20–39 years of age and presymptomatic or asymptomatic at virus transmission.
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27
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Furuse Y, Ko YK, Saito M, Shobugawa Y, Jindai K, Saito T, Nishiura H, Sunagawa T, Suzuki M, Oshitani H. Epidemiology of COVID-19 Outbreak in Japan, from January-March 2020. Jpn J Infect Dis 2020; 73:391-393. [PMID: 32350228 DOI: 10.7883/yoken.jjid.2020.271] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | - Motoi Suzuki
- National Institute of Infectious Diseases, Japan
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28
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Ilori EA, Furuse Y, Ipadeola OB, Dan-Nwafor CC, Abubakar A, Womi-Eteng OE, Ogbaini-Emovon E, Okogbenin S, Unigwe U, Ogah E, Ayodeji O, Abejegah C, Liasu AA, Musa EO, Woldetsadik SF, Lasuba CLP, Alemu W, Ihekweazu C. Epidemiologic and Clinical Features of Lassa Fever Outbreak in Nigeria, January 1-May 6, 2018. Emerg Infect Dis 2019; 25:1066-1074. [PMID: 31107222 PMCID: PMC6537738 DOI: 10.3201/eid2506.181035] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The outbreak, which resulted in 423 confirmed cases and 106 deaths, was the largest recorded Lassa fever outbreak. Lassa fever (LF) is endemic to Nigeria, where the disease causes substantial rates of illness and death. In this article, we report an analysis of the epidemiologic and clinical aspects of the LF outbreak that occurred in Nigeria during January 1–May 6, 2018. A total of 1,893 cases were reported; 423 were laboratory-confirmed cases, among which 106 deaths were recorded (case-fatality rate 25.1%). Among all confirmed cases, 37 occurred in healthcare workers. The secondary attack rate among 5,001 contacts was 0.56%. Most (80.6%) confirmed cases were reported from 3 states (Edo, Ondo, and Ebonyi). Fatal outcomes were significantly associated with being elderly; no administration of ribavirin; and the presence of a cough, hemorrhaging, and unconsciousness. The findings in this study should lead to further LF research and provide guidance to those preparing to respond to future outbreaks.
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Affiliation(s)
- Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
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Furuse Y, Tamaki R, Okamoto M, Saito-Obata M, Suzuki A, Saito M, Imamura T, Khandaker I, Dapat I, Ueno F, Alday PP, Tan AG, Inobaya MT, Segubre-Mercado E, Tallo V, Lupisan S, Oshitani H. Association Between Preceding Viral Respiratory Infection and Subsequent Respiratory Illnesses Among Children: A Prospective Cohort Study in the Philippines. J Infect Dis 2019; 219:197-205. [PMID: 30189092 PMCID: PMC6306022 DOI: 10.1093/infdis/jiy515] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/23/2018] [Indexed: 11/30/2022] Open
Abstract
Background Acute respiratory infection (ARI) is of great concern in public health. It remains unclear whether viral infections can affect the host’s susceptibility to subsequent ARIs. Methods A prospective cohort study on ARIs of children below 5 years old was conducted in the Philippines from 2014 to 2016. The respiratory symptoms were recorded daily, and nasopharyngeal swabs were collected at both household and health facilities. The specimens were tested for respiratory viruses. We then determined whether viral etiology was associated with the severity of the present ARI and whether previous viral infections was associated with subsequent ARIs. Results A total of 3851 children and 16337 ARI episodes were enrolled and recorded, respectively. Samples were collected from 24% of all ARI episodes; collection rate at the healthcare facilities was 95%. Enterovirus D68, rhinovirus species C, and respiratory syncytial virus were significantly associated with severe ARIs. The risk for subsequent ARIs was significantly enhanced after infections with adenovirus, influenza A virus, parainfluenza virus type 4, and rhinovirus species C. Conclusions This study revealed that viral etiology plays a significant role in the severity of the present ARI and that viral infection affects the host’s susceptibility to subsequent ARIs.
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Affiliation(s)
- Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, Japan.,Hakubi Center for Advanced Research, Kyoto University, Japan.,Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan
| | - Raita Tamaki
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Michiko Okamoto
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mariko Saito-Obata
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan.,RITM-Tohoku Collaborating Research Center on Emerging and Reemerging Infectious Diseases, Muntinlupa, Philippines
| | - Akira Suzuki
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tadatsugu Imamura
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Irona Khandaker
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Isolde Dapat
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Fumihiko Ueno
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Alvin Gue Tan
- Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | | | | | - Veronica Tallo
- Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Socorro Lupisan
- Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
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Furuse Y, Chaimongkol N, Okamoto M, Oshitani H. Evolutionary and Functional Diversity of the 5' Untranslated Region of Enterovirus D68: Increased Activity of the Internal Ribosome Entry Site of Viral Strains during the 2010s. Viruses 2019; 11:v11070626. [PMID: 31288421 PMCID: PMC6669567 DOI: 10.3390/v11070626] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 12/14/2022] Open
Abstract
The 5′ untranslated region (UTR) of the RNA genomes of enteroviruses possesses an internal ribosome entry site (IRES) that directs translation of the mRNA by binding to ribosomes. Infection with enterovirus D68 causes respiratory symptoms and is sometimes associated with neurological disorders. The number of reports of the viral infection and neurological disorders has increased in 2010s, although the reason behind this phenomenon remains unelucidated. In this study, we investigated the evolutionary and functional diversity of the 5′ UTR of recently circulating strains of the virus. Genomic sequences of 374 viral strains were acquired and subjected to phylogenetic analysis. The IRES activity of the viruses was measured using a luciferase reporter assay. We found a highly conserved sequence in the 5′ UTR and also identified the location of variable sites in the predicted RNA secondary structure. IRES activities differed among the strains in some cell lines, including neuronal and respiratory cells, and were especially high in strains of a major lineage from the recent surge. The effect of mutations in the 5′ UTR should be studied further in the future for better understanding of viral pathogenesis.
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Affiliation(s)
- Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawaracho, Sakyo-ku, Kyoto 606-8507, Japan.
- Hakubi Center for Advanced Research, Kyoto University, Yoshidahonmachi, Sakyo-ku, Kyoto 606-8501, Japan.
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan.
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki aza Aoba, Aoba-ku, Sendai 980-8578, Japan.
| | - Natthawan Chaimongkol
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan
| | - Michiko Okamoto
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan
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Furuse Y. Analysis of research intensity on infectious disease by disease burden reveals which infectious diseases are neglected by researchers. Proc Natl Acad Sci U S A 2019; 116:478-483. [PMID: 30598444 PMCID: PMC6329976 DOI: 10.1073/pnas.1814484116] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Infectious diseases are associated with considerable morbidity and mortality worldwide. Although human, financial, substantial, and time resources are limited, it is unknown whether such resources are used effectively in research to manage diseases. The correlation between the disability-adjusted life years to represent disease burden and number of publications as a surrogate for research activity was investigated to measure burden-adjusted research intensity for 52 infectious diseases at global and country levels. There was significantly low research intensity for paratyphoid fever and high intensity for influenza, HIV/acquired immunodeficiency syndrome, hepatitis C, and tuberculosis considering their disease burden. We identified the infectious diseases that have received the most attention from researchers and those that have been relatively disregarded. Interestingly, not all so-called neglected tropical diseases were subject to low burden-adjusted research intensity. Analysis of the intensity of infectious disease research at a country level revealed characteristic patterns. These findings provided a basis for further discussion of the more appropriate allocation of resources for research into infectious diseases.
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Affiliation(s)
- Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, 606-8507 Kyoto, Japan;
- Hakubi Center for Advanced Research, Kyoto University, 606-8501 Kyoto, Japan
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Matsuzaki Y, Sugawara K, Furuse Y, Shimotai Y, Hongo S, Mizuta K, Nishimura H. Neutralizing Epitopes and Residues Mediating the Potential Antigenic Drift of the Hemagglutinin-Esterase Protein of Influenza C Virus. Viruses 2018; 10:E417. [PMID: 30096880 PMCID: PMC6116000 DOI: 10.3390/v10080417] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/07/2018] [Accepted: 08/08/2018] [Indexed: 12/22/2022] Open
Abstract
We mapped the hemagglutinin-esterase (HE) antigenic epitopes of the influenza C virus on the three-dimensional (3D) structure of the HE glycoprotein using 246 escape mutants that were selected by a panel of nine anti-HE monoclonal antibodies (MAbs), including seven of the C/Ann Arbor/1/50 virus and two of the C/Yamagata/15/2004 virus. The frequency of variant selection in the presence of anti-HE MAbs was very low, with frequencies ranging from 10-4.62 to 10-7.58 for the C/Ann Arbor/1/50 virus and from 10-7.11 to 10-9.25 for the C/Yamagata/15/2004 virus. Sequencing of mutant HE genes revealed 25 amino acid substitutions at 16 positions in three antigenic sites: A-1, A-2, and A-3, and a newly designated Y-1 site. In the 3D structure, the A-1 site was widely located around the receptor-binding site, the A-2 site was near the receptor-destroying enzyme site, and the Y-1 site was located in the loop on the topside of HE. The hemagglutination inhibition reactions of the MAbs with influenza C viruses, circulating between 1947 and 2016, were consistent with the antigenic-site amino acid changes. We also found some amino acid variations in the antigenic site of recently circulating strains with antigenic changes, suggesting that viruses that have the potential to alter antigenicity continue to circulate in humans.
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Affiliation(s)
- Yoko Matsuzaki
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan.
| | - Kanetsu Sugawara
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan.
| | - Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan.
- Hakubi Center for Advanced Research, Kyoto University, Kyoto 606-8501, Japan.
| | - Yoshitaka Shimotai
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan.
| | - Seiji Hongo
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan.
| | - Katsumi Mizuta
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata 990-0031, Japan.
| | - Hidekazu Nishimura
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai 983-8520, Japan.
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Furuse Y. Multiple or Single Duplication Events Leading to the Emergence of a Novel Genotype of Respiratory Syncytial Virus. J Infect Dis 2018; 217:2008-2010. [PMID: 29562336 DOI: 10.1093/infdis/jiy154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
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Malasao R, Furuse Y, Okamoto M, Dapat C, Saito M, Saito-Obata M, Tamaki R, Segubre-Mercado E, Lupisan S, Oshitani H. Complete Genome Sequences of 13 Human Respiratory Syncytial Virus Subgroup A Strains of Genotypes NA1 and ON1 Isolated in the Philippines. Genome Announc 2018; 6:e00151-18. [PMID: 29519842 PMCID: PMC5843736 DOI: 10.1128/genomea.00151-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 02/13/2018] [Indexed: 11/20/2022]
Abstract
Complete genome sequences of 13 human respiratory syncytial virus strains were determined from samples obtained from children hospitalized in the Philippines between 2012 and 2013 because of acute respiratory infection. We identified amino acid polymorphisms between the NA1 and ON1 genotypes in the P, G, F, and L proteins.
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Affiliation(s)
- Rungnapa Malasao
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chang Mai, Thailand
| | - Yuki Furuse
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Michiko Okamoto
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Clyde Dapat
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mariko Saito-Obata
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
- RITM-Tohoku Collaborating Research Center on Emerging and Reemerging Infectious Diseases, Muntinlupa, Philippines
| | - Raita Tamaki
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Socorro Lupisan
- Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
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Furuse Y, Fallah M, Oshitani H, Kituyi L, Mahmoud N, Musa E, Gasasira A, Nyenswah T, Dahn B, Bawo L. Analysis of patient data from laboratories during the Ebola virus disease outbreak in Liberia, April 2014 to March 2015. PLoS Negl Trop Dis 2017; 11:e0005804. [PMID: 28732038 PMCID: PMC5540615 DOI: 10.1371/journal.pntd.0005804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/02/2017] [Accepted: 07/12/2017] [Indexed: 12/22/2022] Open
Abstract
An outbreak of Ebola virus disease (EVD) in Liberia began in March 2014 and ended in January 2016. Epidemiological information on the EVD cases was collected and managed nationally; however, collection and management of the data were challenging at the time because surveillance and reporting systems malfunctioned during the outbreak. EVD diagnostic laboratories, however, were able to register basic demographic and clinical information of patients more systematically. Here we present data on 16,370 laboratory samples that were tested between April 4, 2014 and March 29, 2015. A total of 10,536 traceable individuals were identified, of whom 3,897 were confirmed cases (positive for Ebola virus RNA). There were significant differences in sex, age, and place of residence between confirmed and suspected cases that tested negative for Ebola virus RNA. Age (young children and the elderly) and place of residence (rural areas) were the risk factors for death due to the disease. The case fatality rate of confirmed cases decreased from 80% to 63% during the study period. These findings may help support future investigations and lead to a fuller understanding of the outbreak in Liberia.
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Affiliation(s)
- Yuki Furuse
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
- * E-mail:
| | - Mosoka Fallah
- Ministry of Health and Social Welfare, Monrovia, Liberia
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ling Kituyi
- United Nations Office at Nairobi, Nairobi, Kenya
| | | | | | | | | | - Bernice Dahn
- Ministry of Health and Social Welfare, Monrovia, Liberia
| | - Luke Bawo
- Ministry of Health and Social Welfare, Monrovia, Liberia
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Furuse Y, Oshitani H. Global Transmission Dynamics of Measles in the Measles Elimination Era. Viruses 2017; 9:v9040082. [PMID: 28420160 PMCID: PMC5408688 DOI: 10.3390/v9040082] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/26/2017] [Accepted: 04/11/2017] [Indexed: 11/30/2022] Open
Abstract
Although there have been many epidemiological reports of the inter-country transmission of measles, systematic analysis of the global transmission dynamics of the measles virus (MV) is limited. In this study, we applied phylogeographic analysis to characterize the global transmission dynamics of the MV using large-scale genetic sequence data (obtained for 7456 sequences) from 115 countries between 1954 and 2015. These analyses reveal the spatial and temporal characteristics of global transmission of the virus, especially in Australia, China, India, Japan, the UK, and the USA in the period since 1990. The transmission is frequently observed, not only within the same region but also among distant and frequently visited areas. Frequencies of export from measles-endemic countries, such as China, India, and Japan are high but decreasing, while the frequencies from countries where measles is no longer endemic, such as Australia, the UK, and the USA, are low but slightly increasing. The world is heading toward measles eradication, but the disease is still transmitted regionally and globally. Our analysis reveals that countries wherein measles is endemic and those having eliminated the disease (apart from occasional outbreaks) both remain a source of global transmission in this measles elimination era. It is therefore crucial to maintain vigilance in efforts to monitor and eradicate measles globally.
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Affiliation(s)
- Yuki Furuse
- Tohoku University Graduate School of Medicine, 980-8575 Sendai, Japan.
| | - Hitoshi Oshitani
- Tohoku University Graduate School of Medicine, 980-8575 Sendai, Japan.
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Furuse Y, Matsuzaki Y, Nishimura H, Oshitani H. Analyses of Evolutionary Characteristics of the Hemagglutinin-Esterase Gene of Influenza C Virus during a Period of 68 Years Reveals Evolutionary Patterns Different from Influenza A and B Viruses. Viruses 2016; 8:E321. [PMID: 27898037 PMCID: PMC5192382 DOI: 10.3390/v8120321] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 11/08/2016] [Accepted: 11/21/2016] [Indexed: 12/13/2022] Open
Abstract
Infections with the influenza C virus causing respiratory symptoms are common, particularly among children. Since isolation and detection of the virus are rarely performed, compared with influenza A and B viruses, the small number of available sequences of the virus makes it difficult to analyze its evolutionary dynamics. Recently, we reported the full genome sequence of 102 strains of the virus. Here, we exploited the data to elucidate the evolutionary characteristics and phylodynamics of the virus compared with influenza A and B viruses. Along with our data, we obtained public sequence data of the hemagglutinin-esterase gene of the virus; the dataset consists of 218 unique sequences of the virus collected from 14 countries between 1947 and 2014. Informatics analyses revealed that (1) multiple lineages have been circulating globally; (2) there have been weak and infrequent selective bottlenecks; (3) the evolutionary rate is low because of weak positive selection and a low capability to induce mutations; and (4) there is no significant positive selection although a few mutations affecting its antigenicity have been induced. The unique evolutionary dynamics of the influenza C virus must be shaped by multiple factors, including virological, immunological, and epidemiological characteristics.
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Affiliation(s)
- Yuki Furuse
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai 9808575, Japan.
| | - Yoko Matsuzaki
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata 9909585, Japan.
| | - Hidekazu Nishimura
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai 9838520, Japan.
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai 9808575, Japan.
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Matsuzaki Y, Sugawara K, Furuse Y, Shimotai Y, Hongo S, Oshitani H, Mizuta K, Nishimura H. Genetic Lineage and Reassortment of Influenza C Viruses Circulating between 1947 and 2014. J Virol 2016; 90:8251-65. [PMID: 27384661 PMCID: PMC5008092 DOI: 10.1128/jvi.00969-16] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 06/28/2016] [Indexed: 11/20/2022] Open
Abstract
Since influenza C virus was first isolated in 1947, the virus has been only occasionally isolated by cell culture; there are only four strains for which complete genome sequences are registered. Here, we analyzed a total of 106 complete genomes, ranging from the first isolate from 1947 to recent isolates from 2014, to determine the genetic lineages of influenza C virus, the reassortment events, and the rates of nucleotide substitution. The results showed that there are six lineages, named C/Taylor, C/Mississippi, C/Aichi, C/Yamagata, C/Kanagawa, and C/Sao Paulo. They contain both antigenic and genetic lineages of the hemagglutinin-esterase (HE) gene, and the internal genes PB2, PB1, P3, NP, M, and NS are divided into two major lineages, a C/Mississippi/80-related lineage and a C/Yamagata/81-related lineage. Reassortment events were found over the entire period of 68 years. Several outbreaks of influenza C virus between 1990 and 2014 in Japan consisted of reassortant viruses, suggesting that the genomic constellation is related to influenza C virus epidemics. The nucleotide sequences were highly homologous to each other. The minimum percent identity between viruses ranged from 91.1% for the HE gene to 96.1% for the M gene, and the rate of nucleotide substitution for the HE gene was the highest, at 5.20 × 10(-4) substitutions/site/year. These results indicate that reassortment is an important factor that increases the genetic diversity of influenza C virus, resulting in its ability to prevail in humans. IMPORTANCE Influenza C virus is a pathogen that causes acute respiratory illness in children and results in hospitalization of infants. We previously demonstrated (Y. Matsuzaki et al., J Clin Virol 61:87-93, 2014, http://dx.doi.org/10.1016/j.jcv.2014.06.017) that periodic epidemics of this virus occurred in Japan between 1996 and 2014 and that replacement of the dominant antigenic group occurred every several years as a result of selection by herd immunity. However, the antigenicity of the HE glycoprotein is highly stable, and antigenic drift has not occurred for at least 30 years. Here, we analyzed a total of 106 complete genomes spanning 68 years for the first time, and we found that influenza C viruses are circulating worldwide while undergoing reassortment as well as selection by herd immunity, resulting in an increased ability to prevail in humans. The results presented in this study contribute to the understanding of the evolution, including reassortment events, underlying influenza C virus epidemics.
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Affiliation(s)
- Yoko Matsuzaki
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Kanetsu Sugawara
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Yuki Furuse
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshitaka Shimotai
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Seiji Hongo
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Katsumi Mizuta
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Hidekazu Nishimura
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Miyagi, Japan
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Furuse Y, Oshitani H. Mechanisms of replacement of circulating viruses by seasonal and pandemic influenza A viruses. Int J Infect Dis 2016; 51:6-14. [PMID: 27569827 DOI: 10.1016/j.ijid.2016.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 08/10/2016] [Accepted: 08/21/2016] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND Seasonal influenza causes annual epidemics by the accumulation of antigenic changes. Pandemic influenza occurs through a major antigenic change of the influenza A virus, which can originate from other hosts. Although new antigenic variants of the influenza A virus replace formerly circulating seasonal and pandemic viruses, replacement mechanisms remain poorly understood. METHODS A stochastic individual-based SEIR (susceptible-exposed-infectious-recovered) model with two viral strains (formerly circulating old strain and newly emerged strain) was developed for simulations to elucidate the replacement mechanisms. RESULTS Factors and conditions of virus and host populations affecting the replacement were identified. Replacement is more likely to occur in tropical regions than temperate regions. The magnitude of the ongoing epidemic by the old strain, herd immunity against the old strain, and timing of appearance of the new strain are not that important for replacement. It is probable that the frequency of replacement by a pandemic virus is higher than a seasonal virus because of the high initial susceptibility and high basic reproductive number of the pandemic virus. CONCLUSIONS The findings of this study on replacement mechanisms could lead to a better understanding of virus transmission dynamics and may possibly be helpful in establishing an effective strategy to mitigate the impact of seasonal and pandemic influenza.
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Affiliation(s)
- Yuki Furuse
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan.
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan
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Kadji FMN, Okamoto M, Furuse Y, Tamaki R, Suzuki A, Lirio I, Dapat C, Malasao R, Saito M, Pedrera-Rico GAG, Tallo V, Lupisan S, Saito M, Oshitani H. Differences in viral load among human respiratory syncytial virus genotypes in hospitalized children with severe acute respiratory infections in the Philippines. Virol J 2016; 13:113. [PMID: 27350282 PMCID: PMC4924256 DOI: 10.1186/s12985-016-0565-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 06/17/2016] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Human respiratory syncytial virus (HRSV) is a leading viral etiologic agent of pediatric lower respiratory infections, including bronchiolitis and pneumonia. Two antigenic subgroups, HRSV-A and B, each contain several genotypes. While viral load may vary among HRSV genotypes and affect the clinical course of disease, data are scarce regarding the actual differences among genotypes. Therefore, this study estimated and compared viral load among NA1 and ON1 genotypes of HRSV-A and BA9 of HRSV-B. ON1 is a newly emerged genotype with a 72-nucleotide duplication in the G gene as observed previously with BA genotypes in HRSV-B. FINDINGS Children <5 years of age with an initial diagnosis of severe or very severe pneumonia at a hospital in the Philippines from September 2012 to December 2013 were enrolled. HRSV genotypes were determined and the viral load measured from nasopharyngeal swabs (NPS). The viral load of HRSV genotype NA1 were significantly higher than those of ON1 and BA9. Regression analysis showed that both genotype NA1 and younger age were significantly associated with high HRSV viral load. CONCLUSIONS The viral load of NA1 was higher than that of ON1 and BA9 in NPS samples. HRSV genotypes may be associated with HRSV viral load. The reasons and clinical impacts of these differences in viral load among HRSV genotypes require further evaluation.
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Affiliation(s)
| | - Michiko Okamoto
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yuki Furuse
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Raita Tamaki
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Akira Suzuki
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Irene Lirio
- Tohoku-RITM Collaborating Research Center on Emerging and Reemerging Diseases, Muntinlupa City, the Philippines
| | - Clyde Dapat
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Mariko Saito
- Tohoku-RITM Collaborating Research Center on Emerging and Reemerging Diseases, Muntinlupa City, the Philippines
| | | | - Veronica Tallo
- Research Institute for Tropical Medicine, Muntinlupa City, the Philippines
| | - Socorro Lupisan
- Research Institute for Tropical Medicine, Muntinlupa City, the Philippines
| | - Mayuko Saito
- Tohoku University Graduate School of Medicine, Sendai, Japan.
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Furuse Y, Odagiri T, Tamaki R, Kamigaki T, Otomaru H, Opinion J, Santo A, Dolina-Lacaba D, Daya E, Okamoto M, Saito-Obata M, Inobaya M, Tan A, Tallo V, Lupisan S, Suzuki A, Oshitani H. Local persistence and global dissemination play a significant role in the circulation of influenza B viruses in Leyte Island, Philippines. Virology 2016; 492:21-4. [PMID: 26896931 DOI: 10.1016/j.virol.2016.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 01/31/2016] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
Abstract
The local and global transmission dynamics of influenza B virus is not completely understood mainly because of limited epidemiological and sequence data for influenza B virus. Here we report epidemiological and molecular characteristics of influenza B viruses from 2010 to 2013 in Leyte Island, Philippines. Phylogenetic analyses showed global dissemination of the virus among both neighboring and distant areas. The analyses also suggest that southeast Asia is not a distributor of influenza B virus and can introduce the virus from other areas. Furthermore, we found evidence on the local persistence of the virus over years in the Philippines. Taken together, both local persistence and global dissemination play a significant role in the circulation of influenza B virus.
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Affiliation(s)
- Yuki Furuse
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Odagiri
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Raita Tamaki
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Taro Kamigaki
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hirono Otomaru
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Jamie Opinion
- Tacloban City Health Office, Tacloban City, Philippines
| | | | | | - Edgard Daya
- Leyte Provincial Health Office, Palo, Philippines
| | - Michiko Okamoto
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mariko Saito-Obata
- Tohoku-RITM Research Center for Emerging and Reemerging Infectious Diseases, Muntinlupa City, Philippines
| | | | - Alvin Tan
- Research Institute for Tropical Medicine, Muntinlupa City, Philippines
| | - Veronica Tallo
- Research Institute for Tropical Medicine, Muntinlupa City, Philippines
| | - Socorro Lupisan
- Research Institute for Tropical Medicine, Muntinlupa City, Philippines
| | - Akira Suzuki
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai, Japan
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan.
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Furuse Y, Okamoto M, Oshitani H. Conservation of nucleotide sequences for molecular diagnosis of Middle East respiratory syndrome coronavirus, 2015. Int J Infect Dis 2015; 40:25-7. [PMID: 26432410 PMCID: PMC7110737 DOI: 10.1016/j.ijid.2015.09.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/21/2015] [Accepted: 09/22/2015] [Indexed: 12/24/2022] Open
Abstract
Protocols for the laboratory diagnosis of Middle East respiratory syndrome coronavirus (MERS-CoV) were developed in 2012. Nucleotide sequences of the viruses detected between 2012 and 2015 were analyzed. Mismatches between the sequences of primers/probes and viruses were found. Such mismatches could lead to a lower sensitivity of the assay.
Infection due to the Middle East respiratory syndrome coronavirus (MERS-CoV) is widespread. The present study was performed to assess the protocols used for the molecular diagnosis of MERS-CoV by analyzing the nucleotide sequences of viruses detected between 2012 and 2015, including sequences from the large outbreak in eastern Asia in 2015. Although the diagnostic protocols were established only 2 years ago, mismatches between the sequences of primers/probes and viruses were found for several of the assays. Such mismatches could lead to a lower sensitivity of the assay, thereby leading to false-negative diagnosis. A slight modification in the primer design is suggested. Protocols for the molecular diagnosis of viral infections should be reviewed regularly after they are established, particularly for viruses that pose a great threat to public health such as MERS-CoV.
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Affiliation(s)
- Yuki Furuse
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan.
| | - Michiko Okamoto
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan
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Liu X, Yamamoto D, Saito M, Imagawa T, Ablola A, Tandoc AO, Segubre-Mercado E, Lupisan SP, Okamoto M, Furuse Y, Saito M, Oshitani H. Molecular detection and characterization of sapovirus in hospitalized children with acute gastroenteritis in the Philippines. J Clin Virol 2015; 68:83-8. [PMID: 26071343 DOI: 10.1016/j.jcv.2015.05.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 04/06/2015] [Accepted: 05/04/2015] [Indexed: 11/30/2022]
Abstract
BACKGROUND Human sapovirus (SaV) is a causative agent of acute gastroenteritis. Recently, SaV detection has been increasing worldwide due to the emerging SaV genotype I.2. However, SaV infection has not been reported in the Philippines. OBJECTIVES To evaluate the prevalence and genetic diversity of SaV in hospitalized children aged less than 5 years with acute gastroenteritis. STUDY DESIGN Stool samples were collected from children with acute gastroenteritis at three hospitals in the Philippines from June 2012 to August 2013. SaV was detected by reverse transcription real-time PCR, and the polymerase and capsid gene sequences were analyzed. Full genome sequencing and recombination analysis were performed on possible recombinant viruses. RESULTS SaV was detected in 7.0% of the tested stool samples (29/417). In 10 SaV-positive cases, other viruses were also detected, including rotavirus (n=6), norovirus (n=2), and human astrovirus (n=2). Four known SaV genotypes (GI.1 [7], GI.2 [2], GII.1 [12], and GV [2]) and one novel recombinant (n=3) were identified by polymerase and capsid gene sequence analysis. Full genome sequencing revealed that the 5' nontranslated region (NTR) and nonstructural protein region of the novel recombinant were closely related to the GII.1 Bristol/98/UK variant, whereas the structural protein region and 3' NTR were closely related to the GII.4 Kumamoto6/Mar2003/JPN variant. DISCUSSION AND CONCLUSIONS SaV was regularly detected in hospitalized children due to acute gastroenteritis during the study period. A novel recombinant, SaV GII.1/GII.4, was identified in three cases at two different study sites.
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Affiliation(s)
- Xiaofang Liu
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Dai Yamamoto
- Department of Pediatrics, Kushiro city General Hospital, 1-12 Shunkodai, Kushiro, Hokkaido 085-0822, Japan
| | - Mariko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan; Tohoku-RITM Collaborating Research Center on Emerging and Re-emerging Infectious Diseases, FCC, Alabang, Muntinlupa 1781, Philippines
| | - Toshifumi Imagawa
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Adrianne Ablola
- Molecular Biology Laboratory, Research Institute for Tropical Medicine (RITM), FCC, Alabang, Muntinlupa 1781, Philippines
| | - Amado O Tandoc
- Department of Virology, Research Institute for Tropical Medicine (RITM), FCC, Alabang, Muntinlupa 1781, Philippines
| | - Edelwisa Segubre-Mercado
- Molecular Biology Laboratory, Research Institute for Tropical Medicine (RITM), FCC, Alabang, Muntinlupa 1781, Philippines
| | - Socorro P Lupisan
- Research Institute for Tropical Medicine (RITM), FCC, Alabang, Muntinlupa 1781, Philippines
| | - Michiko Okamoto
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Yuki Furuse
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan.
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
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Galit SRL, Otsuka N, Furuse Y, Almonia DJV, Sombrero LT, Capeding RZ, Lupisan SP, Saito M, Oshitani H, Hiramatsu Y, Shibayama K, Kamachi K. Molecular epidemiology of Bordetella pertussis in the Philippines in 2012-2014. Int J Infect Dis 2015; 35:24-6. [PMID: 25861926 DOI: 10.1016/j.ijid.2015.04.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/16/2015] [Accepted: 04/01/2015] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVES The present study was designed to determine the genotypes of circulating Bordetella pertussis in the Philippines by direct molecular typing of clinical specimens. METHODS Nasopharyngeal swabs (NPSs) were collected from 50 children hospitalized with pertussis in three hospitals during 2012-2014. Multilocus variable-number tandem repeat analysis (MLVA) was performed on the DNA extracts from NPSs. B. pertussis virulence-associated allelic genes (ptxA, prn, and fim3) and the pertussis toxin promoter, ptxP, were also investigated by DNA sequence-based typing. RESULTS Twenty-six DNA extracts yielded a complete MLVA profile, which were sorted into 10 MLVA types. MLVA type 34 (MT34), which is rare in Australia, Europe, Japan, and the USA, was the predominant strain (50%). Seven MTs (MT29, MT32, MT33, and MT283-286, total 42%) were single-locus variants of MT34, while two (MT141 and MT287, total 8%) were double-locus variants of MT34. All MTs had the combination of virulence-associated allelic genes, ptxP1-ptxA1-prn1-fim3A. CONCLUSIONS The B. pertussis population in the Philippines comprises genetically related strains. These strains are markedly different from those found in patients from other countries where acellular pertussis vaccines are used. The differences in vaccine types between these other countries and the Philippines, where the whole-cell vaccine is still used, may select for distinct populations of B. pertussis.
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Affiliation(s)
| | - Nao Otsuka
- Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Yuki Furuse
- Department of Virology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | | | - Lydia T Sombrero
- Research Institute for Tropical Medicine (RITM), Metro Manila, Philippines
| | - Rosario Z Capeding
- Research Institute for Tropical Medicine (RITM), Metro Manila, Philippines
| | - Socorro P Lupisan
- Research Institute for Tropical Medicine (RITM), Metro Manila, Philippines
| | - Mariko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Miyagi, Japan; Tohoku-RITM Collaborating Research Center on Emerging and Reemerging Infectious Diseases, Metro Manila, Philippines
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Yukihiro Hiramatsu
- Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Kazunari Kamachi
- Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan.
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Roy CN, Khandaker I, Furuse Y, Oshitani H. Molecular characterization of full-length Tat in HIV-1 subtypes B and C. Bioinformation 2015; 11:151-60. [PMID: 25914449 PMCID: PMC4403036 DOI: 10.6026/97320630011151] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/02/2015] [Indexed: 12/13/2022] Open
Abstract
HIV-1Tat (trans-acting activator of transcription) plays essential roles in the replication through viral mRNA and genome transcription from the HIV-1 LTR promoter. However, Tat undergoes continuous amino acid substitutions. As a consequence, the virus escapes from host immunity indicating that genetic diversity of Tat protein in major HIV-1 subtypes is required to be continuously monitored. We analyzed available full-length HIV-1 sequences of subtypes B (n=493) and C (n=280) strains circulating worldwide. We observed 81% and 84% nucleotide sequence identities of HIV-1 Tat for subtypes B and C, respectively. Based on phylogenetic and mutation analyses, global diversity of subtype B was apparently higher compared to that of subtype C. Positively selected sites, such as positions Ser68 and Ser70 in both subtypes, were located in the Tat-transactivation responsive RNA (TAR) interaction domain. We also found positively selected sites in exon 2, such as positions Ser75, Pro77, Asp80, Pro81 and Ser87 for both subtypes. Our study provides useful information on the full-length HIV-1 Tat sequences in globally circulating strains.
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Affiliation(s)
- Chandra Nath Roy
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba-ku, Sendai city, Miyagi, Japan-9808575
| | - Irona Khandaker
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba-ku, Sendai city, Miyagi, Japan-9808575
| | - Yuki Furuse
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba-ku, Sendai city, Miyagi, Japan-9808575
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba-ku, Sendai city, Miyagi, Japan-9808575
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Liu X, Saito M, Sayama Y, Suzuki E, Malbas FF, Galang HO, Furuse Y, Saito M, Li T, Suzuki A, Oshitani H. Seroprevalence and molecular characteristics of hepatitis E virus in household-raised pig population in the Philippines. BMC Vet Res 2015; 11:11. [PMID: 25622684 PMCID: PMC4312430 DOI: 10.1186/s12917-015-0322-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 01/12/2015] [Indexed: 01/21/2023] Open
Abstract
Background Hepatitis E virus (HEV) infection is a significant public health concern in Asia, and swine is an important source of sporadic HEV infection in human. However, no epidemiological data are available regarding HEV infection among the swine or human population in the Philippines. To assess the HEV infection status among pigs in rural areas, we investigated the molecular characteristics and seroprevalence of HEV among household-raised pigs in San Jose, Tarlac Province, the Philippines. Result Serum and rectal swab samples were collected from 299 pigs aged 2–24 months from 155 households in four barangays (villages) between July 2010 and June 2011. Enzyme-linked immunosorbent assay (ELISA) revealed that 50.3% [95% confidence interval (CI) 44.5–56.2%] and 22.9% (95% CI 18.2–28.1%) of pigs tested positive for anti-HEV IgG and IgM, respectively. HEV RNA was detected in the feces of 22 pigs (7.4%, 95% CI 4.7–10.9%). A total of 103 households (66.5%, 95% CI 58.4–73.8%) had at least one pig that tested positive for anti-HEV IgG or IgM or HEV RNA. The prevalence of anti-HEV IgG and IgM in breeding pig (8–24 months) were higher than that in growing pigs (2–4 months) (p < 0.0001 and p = 0.008, respectively). HEV RNA was more frequently detected in 2–4-month-old pigs (9.2%, 95% CI 5.4–14.6%) than in ≥5-month-old pigs (4.8%, 95% CI 1.1–8.5%) without statistical significance (p = 0.142). HEV RNA showed 0–27.6% nucleotide difference at the partial ORF2 gene among the detected viruses, and a majority of them belonged to subtype 3a (20/22, 90.9%). Conclusion We found a high prevalence of HEV antibodies in the household-raised pig population in rural areas of the Philippines, which indicates the potential risk of HEV infection among local residents. Only genotype 3 of HEV was observed, and genetically diverse strains of HEV were found to be circulating in pigs in this study. Electronic supplementary material The online version of this article (doi:10.1186/s12917-015-0322-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaofang Liu
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan.
| | - Mariko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan. .,Tohoku-RITM Collaborating Research Center on Emerging and Reemerging Infectious Diseases, RITM compound, FCC, Alabang, Muntinlupa City, 1781, Philippines.
| | - Yusuke Sayama
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan.
| | - Ellie Suzuki
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan.
| | - Fedelino F Malbas
- Research Institute for Tropical Medicine, FCC, Alabang, Muntinlupa City, 1781, Philippines.
| | - Hazel O Galang
- Research Institute for Tropical Medicine, FCC, Alabang, Muntinlupa City, 1781, Philippines.
| | - Yuki Furuse
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan.
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan.
| | - Tiancheng Li
- Depatment of Virology II, National Institute of Infectious Diseases, 4-7-1Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan.
| | - Akira Suzuki
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan.
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan. .,Tohoku-RITM Collaborating Research Center on Emerging and Reemerging Infectious Diseases, RITM compound, FCC, Alabang, Muntinlupa City, 1781, Philippines.
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Moriichi A, Cho K, Furuse Y, Akimoto T, Kaneshi Y, Yamada T, Morikawa M, Yamada T, Minakami H. B-type natriuretic peptide levels are correlated with birth-weight discordance in monochorionic-diamniotic twins without twin-twin transfusion syndrome. J Perinatol 2013; 33:182-7. [PMID: 22791277 DOI: 10.1038/jp.2012.94] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVE To determine whether B-type natriuretic peptide (BNP) levels in umbilical cord blood (UCB) and amniotic fluid (AF) are correlated with birth-weight discordances in monochorionic-diamniotic twins. STUDY DESIGN The UCB-BNP and AF-BNP levels were determined at birth in 36 twin-pairs without twin-twin transfusion syndrome (TTTS). RESULT Both the UCB-BNP and the AF-BNP levels were significantly higher among twins with either a birth-weight discordance ≥20% (141.6 versus 52.9 pg ml(-1) for UCB-BNP, 38.0 versus 17.2 pg ml(-1) for AF-BNP) or cardiac dysfunction at birth (167.2 versus 56.3 pg ml(-1) for UCB-BNP, 34.9 versus 19.0 pg ml(-1) for AF-BNP), compared with neonates without the respective characteristics. The UCB-BNP and AF-BNP levels in both the larger and the smaller twins were significantly correlated with birth-weight discordance. CONCLUSION Cardiac dysfunction occurs in both larger and smaller co-twins with increasing birth-weight discordances, even in the absence of TTTS.
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Affiliation(s)
- A Moriichi
- Maternity and Perinatal Care Center, Hokkaido University Hospital, Sapporo, Japan.
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49
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Suzuki A, Lupisan S, Furuse Y, Fuji N, Saito M, Tamaki R, Galang H, Sombrero L, Mondoy M, Aniceto R, Olveda R, Oshitani H. Respiratory viruses from hospitalized children with severe pneumonia in the Philippines. BMC Infect Dis 2012; 12:267. [PMID: 23092190 PMCID: PMC3519714 DOI: 10.1186/1471-2334-12-267] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 10/18/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pneumonia remains a leading cause of child death in developing countries. The viruses in severe pneumonia remain poorly defined. METHODS The study was conducted at the Eastern Visayas Regional Medical Center in Tacloban City, Philippines from May 2008 to May 2009. Patients aged 8 days to 13 years old who were admitted to the Department of Pediatrics with severe pneumonia were enrolled for the study. Upon admission, polymerase chain reaction was performed using nasopharyngeal swabs and blood cultures to detect respiratory viruses and bacteria, respectively. RESULT Among the 819 patients enrolled, at least one virus was detected in 501 cases (61.2%). In addition, 423 cases were positive for a single virus while bacteria were detected in the blood culture sample of 31 cases. The most commonly detected viruses were human rhinoviruses (n = 189), including types A (n = 103), B (n = 17), and C (n = 69), and respiratory syncytial virus (RSV) (n = 165). Novel viruses such as human metapneumovirus, human coronavirus NL63, human bocavirus, and human polyomaviruses WU and KI were also detected. There were 70 deaths, and one or more viruses were detected in 35 (50%) of these cases. Positivity only for influenza A virus (OR = 4.3, 95% CI = 1.3-14.6) was significantly associated with fatal outcome. From the blood culture, Burkholderia cepacia group (n = 9), Streptococcus pneumoniae (n = 4), Staphylococcus aureus (n = 4), Haemophilus influenzae (n = 1), and Salmonella C1 (n = 1) were also isolated. CONCLUSION Viruses were commonly detected in children with severe pneumonia in the Philippines. Hence, viral etiologies should be considered while developing better effective strategies to reduce child pneumonia-related deaths in developing countries.
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Affiliation(s)
- Akira Suzuki
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan.
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Furuse Y, Oshitani H. Evolution of the influenza A virus untranslated regions. Infect Genet Evol 2011; 11:1150-4. [PMID: 21515407 DOI: 10.1016/j.meegid.2011.04.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 03/31/2011] [Accepted: 04/08/2011] [Indexed: 01/28/2023]
Abstract
In case of the influenza virus, untranslated regions are considered to possess plural functions. The specific packaging model suggests that each of eight segments contains a unique "packaging signal", situated within the untranslated region and coding regions at the 5' and 3' ends of the genomic RNA. In addition to packaging signal, UTRs play key roles in polyadenylation and signals for genomic replication. In the present study, we report the evolutionary characteristics of untranslated regions of influenza virus. We analyzed 574 sequences of the human influenza A (H3N2) virus. The sequence of the untranslated region is highly conserved. Our analysis produced several observations regarding the untranslated region: (1) it has an extremely low divergence; (2) its evolutionary speed is not associated with the protein(s) it encodes; (3) its evolutionary rate is smaller than that of the open reading frame. We revealed the evolutionary characteristics of the untranslated region; this is the first study on the non-coding region of the influenza virus from the perspective of evolutionary molecular biology. In the future, clarifying the detailed mechanisms of packaging as well as the function of the RNA sequence in the untranslated region will increase the understanding of viral life cycles and evolution.
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Affiliation(s)
- Yuki Furuse
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryou-machi Aoba-ku, Sendai 980-8575, Japan
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