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Cahyanti N, Syukur S, Purwati E, Fitria Y, Rahmadani I, Subekti DT. Molecular analysis and geographic distribution of the recent Indonesian rabies virus. Vet World 2023; 16:2479-2487. [PMID: 38328351 PMCID: PMC10844793 DOI: 10.14202/vetworld.2023.2479-2487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 11/17/2023] [Indexed: 02/09/2024] Open
Abstract
Background and Aim Some Indonesian islands, including Sumatra, Kalimantan, Sulawesi, Java, and East Nusa Tenggara, have endemic rabies. Rabies outbreaks in Bali began from 2008 to 2011 and continue to occur sporadically. This study aimed to study the molecular analysis and geographical distribution of Indonesian rabies virus (RABV) from 2016 to 2021 and compare to previous periods. Materials and Methods Virus isolates from 2016 to 2021 were extracted from dog brains and sequenced at the nucleoprotein gene locus. They were compared with data sequences available in the GenBank database. Indonesian RABV from the previous three periods (before 1989, 1997-2003, and 2008-2010) was extracted from the GenBank database. The genetic diversity in this study was based on the N gene of Indonesian RABV. Results Asian RABV, which is genetically close to the Indonesian virus, is a virus from China (ASIA-3 cluster) and from the Southeast Asia region, namely, virus isolates from Sarawak and Malaysia and some Cambodian isolates. Rabies virus, which was isolated from the Bali islands, was the new cluster first detected and published in Bali, Indonesia, in 2008, while RABV from West Sumatra Province, which was isolated from 2016 to 2021, was also considered a new cluster that is genetically distant from other clusters in Indonesia. Conclusion The RABV in Indonesia is divided into five clusters. The isolates from West Sumatra Province from 2016 to 2021 were a new cluster genetically distant from other Indonesian viruses.
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Affiliation(s)
- Nirma Cahyanti
- Biotechnology Program Postgraduate School, Andalas University, West Sumatra Province, Indonesia
| | - Sumaryati Syukur
- Faculty of Mathematics and Natural Sciences, Division of Chemistry, Department of Biotechnology, Andalas University, West Sumatra Province, Indonesia
| | - Endang Purwati
- Biotechnology Program Postgraduate School, Andalas University, West Sumatra Province, Indonesia
| | - Yul Fitria
- National Reference Laboratory for Animal Rabies - Animal Disease Investigation Center of Bukittinggi, Bukittinggi, Indonesia
| | - Ibenu Rahmadani
- National Reference Laboratory for Animal Rabies - Animal Disease Investigation Center of Bukittinggi, Bukittinggi, Indonesia
| | - Didik T. Subekti
- Center for Biomedical Research, Research Organization for Health, National Research and Innovation Agency, Cibinong Science Center, West Java Province, Indonesia
- Indonesian Research Center for Veterinary Science, Agency for Agricultural Research and Development, Indonesian Ministry of Agriculture, Bogor, West Java Province, Indonesia
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2
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Layan M, Müller NF, Dellicour S, De Maio N, Bourhy H, Cauchemez S, Baele G. Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations. Virus Evol 2023; 9:vead010. [PMID: 36860641 PMCID: PMC9969415 DOI: 10.1093/ve/vead010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/06/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023] Open
Abstract
Bayesian phylogeographic inference is a powerful tool in molecular epidemiological studies, which enables reconstruction of the origin and subsequent geographic spread of pathogens. Such inference is, however, potentially affected by geographic sampling bias. Here, we investigated the impact of sampling bias on the spatiotemporal reconstruction of viral epidemics using Bayesian discrete phylogeographic models and explored different operational strategies to mitigate this impact. We considered the continuous-time Markov chain (CTMC) model and two structured coalescent approximations (Bayesian structured coalescent approximation [BASTA] and marginal approximation of the structured coalescent [MASCOT]). For each approach, we compared the estimated and simulated spatiotemporal histories in biased and unbiased conditions based on the simulated epidemics of rabies virus (RABV) in dogs in Morocco. While the reconstructed spatiotemporal histories were impacted by sampling bias for the three approaches, BASTA and MASCOT reconstructions were also biased when employing unbiased samples. Increasing the number of analyzed genomes led to more robust estimates at low sampling bias for the CTMC model. Alternative sampling strategies that maximize the spatiotemporal coverage greatly improved the inference at intermediate sampling bias for the CTMC model, and to a lesser extent, for BASTA and MASCOT. In contrast, allowing for time-varying population sizes in MASCOT resulted in robust inference. We further applied these approaches to two empirical datasets: a RABV dataset from the Philippines and a SARS-CoV-2 dataset describing its early spread across the world. In conclusion, sampling biases are ubiquitous in phylogeographic analyses but may be accommodated by increasing the sample size, balancing spatial and temporal composition in the samples, and informing structured coalescent models with reliable case count data.
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Affiliation(s)
| | | | | | | | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université Paris Cité, 25-28 rue du Docteur Roux, Paris 75014, France,WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, Université Paris Cité, 28 rue du Docteur Roux, Paris 75724, France
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3
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Guzman FD, Iwamoto Y, Saito N, Salva EP, Dimaano EM, Nishizono A, Suzuki M, Oloko O, Ariyoshi K, Smith C, Parry CM, Solante RM. Clinical, epidemiological, and spatial features of human rabies cases in Metro Manila, the Philippines from 2006 to 2015. PLoS Negl Trop Dis 2022; 16:e0010595. [PMID: 35852994 PMCID: PMC9295989 DOI: 10.1371/journal.pntd.0010595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 06/18/2022] [Indexed: 11/18/2022] Open
Abstract
Rabies remains a public health problem in the Philippines despite the widespread provision of rabies vaccines and rabies immunoglobulin (RIG) as post-exposure prophylaxis (PEP). Detailed descriptions of recent human rabies cases in the Philippines are scarce. This study aimed to describe the clinical, epidemiological, and spatial features of human rabies cases between January 1, 2006, and December 31, 2015. We conducted a retrospective hospital-based case record review of all patients admitted to one referral hospital in Manila who received a clinical diagnosis of rabies. During the 10-year study period there were 575 patients (average 57.5 cases per year, range 57 to 119) with a final diagnosis of rabies. Most patients were male (n = 404, 70.3%) and aged ≥ 20 years (n = 433, 75.3%). Patients mostly came from the National Capital Region (n = 160, 28.0%) and the adjacent Regions III (n = 197, 34.4%) and IV-A (n = 168, 29.4%). Case mapping and heatmaps showed that human rabies cases were continuously observed in similar areas throughout the study period. Most patients had hydrophobia (n = 444, 95.5%) and/or aerophobia (n = 432, 93.3%). The leading causative animals were dogs (n = 421, 96.3%) and cats (n = 16, 3.7%). Among 437 patients with animal exposure history, only 42 (9.6%) had been administered at least one rabies vaccine. Two patients (0.5%), young children bitten on their face, had received and a full course of rabies vaccine. Human rabies patients were continuously admitted to the hospital, with no notable decline over the study period. The geographical area in which human rabies cases commonly occurred also did not change. Few patients received PEP and there were two suspected cases of PEP failure. The retrospective design of this study was a limitation; thus, prospective studies are required. Rabies remains a public health problem in the Philippines despite improvements in the availability of rabies vaccines and rabies immunoglobulin (RIG) as post-exposure prophylaxis (PEP). The incidence of rabies is highest in Metro Manila and surrounding areas. We reviewed the records of all human rabies patients admitted to the national infectious disease hospital in Manila between 2006 and 2015. This hospital treats most cases in this area. During the 10-year study period, human rabies cases were continuously admitted to the hospital, with no notable decline in numbers by year. Most patients were adult men bitten by domestic dogs. The geographical areas in which cases commonly occurred during the 10-year period also did not change over time. Only 9.6% of patients had received at least one dose of a rabies vaccine as PEP. Although the risk of PEP failure is reported to be almost zero, we identified two suspected cases of PEP failure. The retrospective design of this study was a limitation, and the exact details of PEP were not reliably available. As human rabies death is a significant public health concern, the circumstances of each case should be prospectively investigated. Further research is required to understand how to reduce the number of rabies cases.
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Affiliation(s)
| | - Yuta Iwamoto
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Nobuo Saito
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Japan
- * E-mail:
| | | | | | - Akira Nishizono
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Japan
| | - Motoi Suzuki
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Oladeji Oloko
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Koya Ariyoshi
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Chris Smith
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Christopher M. Parry
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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4
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Bouslama Z, Kharmachi H, Basdouri N, Ben Salem J, Ben Maiez S, Handous M, Saadi M, Ghram A, Turki I. Molecular Epidemiology of Rabies in Wild Canidae in Tunisia. Viruses 2021; 13:v13122473. [PMID: 34960742 PMCID: PMC8703460 DOI: 10.3390/v13122473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 12/25/2022] Open
Abstract
Rabies is a viral zoonosis that is transmissible to humans via domestic and wild animals. There are two epidemiological cycles for rabies, the urban and the sylvatic cycles. In an attempt to study the epidemiological role of wild canidae in rabies transmission, the present study aimed to analyze the genetic characteristics of virus isolates and confirm prior suggestions that rabies is maintained through a dog reservoir in Tunisia. Virus strains isolated from wild canidae were subject to viral sequencing, and Bayesian phylogenetic analysis was performed using Beast2 software. Essentially, the virus strains isolated from wild canidae belonged to the Africa-1 clade, which clearly diverges from fox-related strains. Our study also demonstrated that genetic characteristics of the virus isolates were not as distinct as could be expected if a wild reservoir had already existed. On the contrary, the geographic landscape is responsible for the genetic diversity of the virus. The landscape itself could have also acted as a natural barrier to the spread of the virus.
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Affiliation(s)
- Zied Bouslama
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
- Faculty of Sciences, Université Tunis El Manar, Tunis 2092, Tunisia
- Correspondence:
| | - Habib Kharmachi
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
| | - Nourhene Basdouri
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
| | - Jihen Ben Salem
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
| | - Samia Ben Maiez
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
| | - Mariem Handous
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
| | - Mohamed Saadi
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
| | - Abdeljalil Ghram
- Laboratory of Epidemiology and Veterinary Microbiology, LR 16 IPT 03, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 2092, Tunisia;
| | - Imed Turki
- Service des Maladies Contagieuses, Ecole Nationale de Médecine Vétérinaire-Sidi Thabet, Université Manouba, Sidi Thabet 2020, Tunisia;
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5
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Nahata KD, Bollen N, Gill MS, Layan M, Bourhy H, Dellicour S, Baele G. On the Use of Phylogeographic Inference to Infer the Dispersal History of Rabies Virus: A Review Study. Viruses 2021; 13:v13081628. [PMID: 34452492 PMCID: PMC8402743 DOI: 10.3390/v13081628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 12/28/2022] Open
Abstract
Rabies is a neglected zoonotic disease which is caused by negative strand RNA-viruses belonging to the genus Lyssavirus. Within this genus, rabies viruses circulate in a diverse set of mammalian reservoir hosts, is present worldwide, and is almost always fatal in non-vaccinated humans. Approximately 59,000 people are still estimated to die from rabies each year, leading to a global initiative to work towards the goal of zero human deaths from dog-mediated rabies by 2030, requiring scientific efforts from different research fields. The past decade has seen a much increased use of phylogeographic and phylodynamic analyses to study the evolution and spread of rabies virus. We here review published studies in these research areas, making a distinction between the geographic resolution associated with the available sequence data. We pay special attention to environmental factors that these studies found to be relevant to the spread of rabies virus. Importantly, we highlight a knowledge gap in terms of applying these methods when all required data were available but not fully exploited. We conclude with an overview of recent methodological developments that have yet to be applied in phylogeographic and phylodynamic analyses of rabies virus.
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Affiliation(s)
- Kanika D. Nahata
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
- Correspondence:
| | - Nena Bollen
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
| | - Mandev S. Gill
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
| | - Maylis Layan
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Sorbonne Université, UMR2000, CNRS, 75015 Paris, France;
| | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, 75015 Paris, France;
- WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, 75015 Paris, France
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
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Bacus MG, Buenaventura SGC, Mamites AMC, Elizagaque HG, Labrador CC, Delfin FC, Eng MNJ, Lagare AP, Marquez GN, Murao LAE. Genome-based local dynamics of canine rabies virus epidemiology, transmission, and evolution in Davao City, Philippines, 2018-2019. INFECTION GENETICS AND EVOLUTION 2021; 92:104868. [PMID: 33878454 DOI: 10.1016/j.meegid.2021.104868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 04/01/2021] [Accepted: 04/13/2021] [Indexed: 11/19/2022]
Abstract
Rabies is a fatal zoonotic and neglected tropical disease caused by the rabies virus (RABV) and is associated with neuronal dysfunction and death, with dogs as the predominant carrier. The Philippines plans to eradicate rabies by 2022, but this is challenged with sub-optimal coverage of vaccination programs coupled with sustained transmission chains, making it unable to eradicate the disease. We investigated the dynamics of canine rabies in the highly urbanized Davao City of the Philippines and its neighboring localities by assessing genetic relationships, transmission patterns, selection pressure, and recombination events using the whole genome sequence of 49 RABV cases from June 2018 to May 2019, majority of which (46%) were from the district of Talomo, Davao City. Although phylogeographic clustering was observed, local variants also exhibited genetic sub-lineages. Phylogenetic and spatial transmission analysis provided evidence for intra- and inter-city transmission predominantly through the Talomo district of Davao City. Around 84% of the cases were owned dogs, but the genetic similiarity of RABVs from stray and owned dogs further alluded to the role of the former as transmission vectors. The high rate of improper vaccination among the affected dogs (80%) was also a likely contributor to transmission. The RABV population under Investigation is generally under strong purifying selection with no evidence of vaccine evasion due to the genetic homogeneity of viruses from vaccinated and improperly vaccinated dogs. However, some homologous recombination (HR) events were identified along the G and L genes, also predominantly associated with viruses from Talomo. The complementary findings on epidemiology, transmission, and recombination for Talomo suggest that high incidence areas can be seeds for virus dispersal and evolution. We recommend further Investigations on the possibility of HR in future large-scale genome studies. Finally, districts associated with these phenomena can be targeted for evidence-based local strategies that can help break RABV transmission chains and prevent emergence of novel strains in Davao City.
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Affiliation(s)
- Michael G Bacus
- Philippine Genome Center Mindanao, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines
| | - Sheryl Grace C Buenaventura
- Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines
| | - Allan Michael C Mamites
- Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines
| | - Hannah G Elizagaque
- Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines
| | - Christian C Labrador
- Philippine Genome Center Mindanao, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines
| | - Frederick C Delfin
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Ma Noreen J Eng
- Davao City Veterinary Office, Pichon St., Davao City, Philippines
| | - Arlene P Lagare
- Davao City Veterinary Office, Pichon St., Davao City, Philippines
| | - Gloria N Marquez
- Davao City Veterinary Office, Pichon St., Davao City, Philippines
| | - Lyre Anni E Murao
- Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines; Philippine Genome Center Mindanao, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines.
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7
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Kimitsuki K, Saito N, Yamada K, Park CH, Inoue S, Suzuki M, Saito-Obata M, Kamiya Y, Manalo DL, Demetria CS, Mananggit MR, Quiambao BP, Nishizono A. Evaluation of the diagnostic accuracy of lateral flow devices as a tool to diagnose rabies in post-mortem animals. PLoS Negl Trop Dis 2020; 14:e0008844. [PMID: 33151941 PMCID: PMC7671516 DOI: 10.1371/journal.pntd.0008844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/17/2020] [Accepted: 09/28/2020] [Indexed: 11/19/2022] Open
Abstract
Implementation of lateral flow devices (LFDs) for rabies antigen detection is expected to improve surveillance through the efficient detection of rabid animals in resource-limited settings; however, the use of LFDs for diagnosis remains controversial because some commercially available kits show low sensitivity. Therefore, we compared the diagnostic efficacy of three LFDs (ADTEC, Bionote, and Elabscience kits) paralleled with the direct fluorescent antibody test (dFAT) using fresh samples and investigated the diagnostic accuracies. To do so, we evaluated rabies-suspected samples submitted to the Regional Animal Disease Diagnostic Laboratory III, Philippines. Furthermore, we conducted real-time RT-PCR and sequencing to measure the accuracy of field laboratory diagnosis. The total number of animals submitted during this study period was 184 cases, including negative control samples. Of these, 53.9% (84 cases) were positive in the dFAT. Dogs were the most common rabies-suspected animal (n = 135). The sensitivities of the ADTEC and Bionote kits were 0.88 (74 cases) and 0.95 (80 cases), respectively. The specificity of both kits was 1.00 (100 cases). Furthermore, the sensitivity and specificity of the ADTEC kit after directly homogenizing the samples in assay buffer without dilution in phosphate-buffered saline (ADTEC kit DM) were 0.94 (79 cases) and 1.00 (100 cases), respectively. By contrast, there were no positive results using the Elabscience kit among all dFAT-positive samples. The sensitivity and specificity of LFDs make these tests highly feasible if properly used. Therefore, LFD tests can be used to strengthen the surveillance of rabies-infected animals in endemic and resource-limited settings.
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Affiliation(s)
- Kazunori Kimitsuki
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Nobuo Saito
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Kentaro Yamada
- Laboratory of Veterinary Public Health, Department of Veterinary Medical Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, Japan
| | - Chun-Ho Park
- Department of Veterinary Pathology, School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - Satoshi Inoue
- National Institute of Infectious Disease, Tokyo, Japan
| | - Motoi Suzuki
- National Institute of Infectious Disease, Tokyo, Japan
| | | | - Yasuhiko Kamiya
- School of Tropical Medicine & Global Health, Nagasaki University, Nagasaki, Nagasaki, Japan
| | - Daria L. Manalo
- Research Institute for Tropical Medicine, Muntinlupa City, Metro Manila, Philippines
| | - Catalino S. Demetria
- Research Institute for Tropical Medicine, Muntinlupa City, Metro Manila, Philippines
| | - Milagros R. Mananggit
- Regional Animal Disease Diagnostic Laboratory, Department of Agriculture Field Office III, San Fernando, Pampanga, Philippines
| | - Beatriz P. Quiambao
- Research Institute for Tropical Medicine, Muntinlupa City, Metro Manila, Philippines
| | - Akira Nishizono
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Oita, Japan
- * E-mail:
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8
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Spatio-temporal evolution of canine rabies in Tunisia, 2011-2016. Prev Vet Med 2020; 185:105195. [PMID: 33212333 DOI: 10.1016/j.prevetmed.2020.105195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 10/05/2020] [Accepted: 10/27/2020] [Indexed: 11/22/2022]
Abstract
Tunisia is an endemic country for dog mediated rabies. An increase in canine rabies cases during the last decade has been suspected. Since no studies have been conducted on rabies spatial distribution, the present work was focused on spatiotemporal evolution of rabies in Tunisia during the 2011-2016 period with a special focus on the reservoir species. Data collected concerned suspected dogs that originate from the whole country. Surveillance indicators such as positive fractions and number of suspected dogs received at the laboratory have been calculated. Spatiotemporal hotspots were then mapped, spatial and spatio-temporal analysis were carried out using discrete Poisson spatial model and space-time permutation models available in SaTScan9 software. The study revealed that an actual increase in canine rabies incidence occurred in Tunisia since 2012. Spatial and spatio-temporal analysis identified clusters centered in the North and in the Center East of the country. Spatio-temporal clusters were non overlapping, indicating that this spatial distribution is not fixed through time. A large heterogeneity in surveillance indicators such as number of suspected dogs was associated to the distance to the laboratory or to insufficient coordination between governorates.
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9
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Brunker K, Jaswant G, Thumbi S, Lushasi K, Lugelo A, Czupryna AM, Ade F, Wambura G, Chuchu V, Steenson R, Ngeleja C, Bautista C, Manalo DL, Gomez MRR, Chu MYJV, Miranda ME, Kamat M, Rysava K, Espineda J, Silo EAV, Aringo AM, Bernales RP, Adonay FF, Tildesley MJ, Marston DA, Jennings DL, Fooks AR, Zhu W, Meredith LW, Hill SC, Poplawski R, Gifford RJ, Singer JB, Maturi M, Mwatondo A, Biek R, Hampson K. Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes. Wellcome Open Res 2020; 5:3. [PMID: 32090172 PMCID: PMC7001756 DOI: 10.12688/wellcomeopenres.15518.2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2020] [Indexed: 12/19/2022] Open
Abstract
Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.
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Affiliation(s)
- Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Gurdeep Jaswant
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- University of Nairobi Institute of Tropical and Infectious Diseases (UNITID), Nairobi, Kenya
| | - S.M. Thumbi
- University of Nairobi Institute of Tropical and Infectious Diseases (UNITID), Nairobi, Kenya
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | | | - Ahmed Lugelo
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Anna M. Czupryna
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Fred Ade
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Gati Wambura
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Veronicah Chuchu
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Rachel Steenson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Chanasa Ngeleja
- Tanzania Veterinary Laboratory Agency, Ministry of Livestock and Fisheries Development, Dar es Salaam, Tanzania
| | - Criselda Bautista
- Research Institute for Tropical Medicine (RITM), Manilla, Philippines
| | - Daria L. Manalo
- Research Institute for Tropical Medicine (RITM), Manilla, Philippines
| | | | | | - Mary Elizabeth Miranda
- Research Institute for Tropical Medicine (RITM), Manilla, Philippines
- Field Epidemiology Training Program Alumni Foundation (FETPAFI), Manilla, Philippines
| | - Maya Kamat
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Kristyna Rysava
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematical Institute, University of Warwick, Coventry, UK
| | - Jason Espineda
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Eva Angelica V. Silo
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Ariane Mae Aringo
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Rona P. Bernales
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Florencio F. Adonay
- Albay Veterinary Office, Provincial Government of Albay, Albay Farmers' Bounty Village, Cabangan, Camalig, Albay, Philippines
| | - Michael J. Tildesley
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematical Institute, University of Warwick, Coventry, UK
| | - Denise A. Marston
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK
| | - Daisy L. Jennings
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK
| | - Anthony R. Fooks
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK
- Institute of Infection and Global Health,, University of Liverpool, Liverpool, UK
| | - Wenlong Zhu
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | | | - Radoslaw Poplawski
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
- Advanced Research Computing, University of Birmingham, Birmingham, B15 2TT, UK
| | - Robert J. Gifford
- MRC-University of Glasgow Centre for Virus Research (CVR), University of Glasgow, Glasgow, UK
| | - Joshua B. Singer
- MRC-University of Glasgow Centre for Virus Research (CVR), University of Glasgow, Glasgow, UK
| | - Mathew Maturi
- Zoonotic Disease Unit, Ministry of Health, Ministry of Agriculture, Livestock and Fisheries, Nairobi, Kenya
| | - Athman Mwatondo
- Zoonotic Disease Unit, Ministry of Health, Ministry of Agriculture, Livestock and Fisheries, Nairobi, Kenya
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Katie Hampson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, G12 8QQ, UK
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10
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Brunker K, Jaswant G, Thumbi S, Lushasi K, Lugelo A, Czupryna AM, Ade F, Wambura G, Chuchu V, Steenson R, Ngeleja C, Bautista C, Manalo DL, Gomez MRR, Chu MYJV, Miranda ME, Kamat M, Rysava K, Espineda J, Silo EAV, Aringo AM, Bernales RP, Adonay FF, Tildesley MJ, Marston DA, Jennings DL, Fooks AR, Zhu W, Meredith LW, Hill SC, Poplawski R, Gifford RJ, Singer JB, Maturi M, Mwatondo A, Biek R, Hampson K. Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes. Wellcome Open Res 2020; 5:3. [PMID: 32090172 PMCID: PMC7001756 DOI: 10.12688/wellcomeopenres.15518.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2019] [Indexed: 08/27/2023] Open
Abstract
Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.
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Affiliation(s)
- Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Gurdeep Jaswant
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- University of Nairobi Institute of Tropical and Infectious Diseases (UNITID), Nairobi, Kenya
| | - S.M. Thumbi
- University of Nairobi Institute of Tropical and Infectious Diseases (UNITID), Nairobi, Kenya
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | | | - Ahmed Lugelo
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Anna M. Czupryna
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Fred Ade
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Gati Wambura
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Veronicah Chuchu
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Rachel Steenson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Chanasa Ngeleja
- Tanzania Veterinary Laboratory Agency, Ministry of Livestock and Fisheries Development, Dar es Salaam, Tanzania
| | - Criselda Bautista
- Research Institute for Tropical Medicine (RITM), Manilla, Philippines
| | - Daria L. Manalo
- Research Institute for Tropical Medicine (RITM), Manilla, Philippines
| | | | | | - Mary Elizabeth Miranda
- Research Institute for Tropical Medicine (RITM), Manilla, Philippines
- Field Epidemiology Training Program Alumni Foundation (FETPAFI), Manilla, Philippines
| | - Maya Kamat
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Kristyna Rysava
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematical Institute, University of Warwick, Coventry, UK
| | - Jason Espineda
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Eva Angelica V. Silo
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Ariane Mae Aringo
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Rona P. Bernales
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Florencio F. Adonay
- Albay Veterinary Office, Provincial Government of Albay, Albay Farmers' Bounty Village, Cabangan, Camalig, Albay, Philippines
| | - Michael J. Tildesley
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematical Institute, University of Warwick, Coventry, UK
| | - Denise A. Marston
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK
| | - Daisy L. Jennings
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK
| | - Anthony R. Fooks
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK
- Institute of Infection and Global Health,, University of Liverpool, Liverpool, UK
| | - Wenlong Zhu
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | | | - Radoslaw Poplawski
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
- Advanced Research Computing, University of Birmingham, Birmingham, B15 2TT, UK
| | - Robert J. Gifford
- MRC-University of Glasgow Centre for Virus Research (CVR), University of Glasgow, Glasgow, UK
| | - Joshua B. Singer
- MRC-University of Glasgow Centre for Virus Research (CVR), University of Glasgow, Glasgow, UK
| | - Mathew Maturi
- Zoonotic Disease Unit, Ministry of Health, Ministry of Agriculture, Livestock and Fisheries, Nairobi, Kenya
| | - Athman Mwatondo
- Zoonotic Disease Unit, Ministry of Health, Ministry of Agriculture, Livestock and Fisheries, Nairobi, Kenya
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Katie Hampson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, G12 8QQ, UK
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11
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Deviatkin AA, Lukashev AN, Poleshchuk EM, Dedkov VG, Tkachev SE, Sidorov GN, Karganova GG, Galkina IV, Shchelkanov MY, Shipulin GA. The phylodynamics of the rabies virus in the Russian Federation. PLoS One 2017; 12:e0171855. [PMID: 28225771 PMCID: PMC5321407 DOI: 10.1371/journal.pone.0171855] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/26/2017] [Indexed: 12/25/2022] Open
Abstract
Near complete rabies virus N gene sequences (1,110 nt) were determined for 82 isolates obtained from different regions of Russia between 2008 and 2016. These sequences were analyzed together with 108 representative GenBank sequences from 1977-2016 using the Bayesian coalescent approach. The timing of the major evolutionary events was estimated. Most of the isolates represented the steppe rabies virus group C, which was found over a vast geographic region from Central Russia to Mongolia and split into three groups (C0-C2) with discrete geographic prevalence. A single strain of the steppe rabies virus lineage was isolated in the far eastern part of Russia (Primorsky Krai), likely as a result of a recent anthropogenic introduction. For the first time the polar rabies virus group A2, previously reported in Alaska, was described in the northern part of European Russia and at the Franz Josef Land. Phylogenetic analysis suggested that all currently circulating rabies virus groups in the Russian Federation were introduced within the few last centuries, with most of the groups spreading in the 20th century. The dating of evolutionary events was highly concordant with the historical epidemiological data.
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Affiliation(s)
- Andrei A. Deviatkin
- Federal Budget Institute of Science Central Research Institute for Epidemiology, Moscow, Russian Federation
- Federal Budget Institute Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russian Federation
- Research Institute of Occupational Health, Moscow, Russian Federation
| | - Alexander N. Lukashev
- Federal Budget Institute Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russian Federation
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
- RUDN University, Moscow, Russia
| | | | - Vladimir G. Dedkov
- Federal Budget Institute of Science Central Research Institute for Epidemiology, Moscow, Russian Federation
- Research Institute of Occupational Health, Moscow, Russian Federation
| | - Sergey E. Tkachev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), Novosibirsk, Russian Federation
| | - Gennadiy N. Sidorov
- Institute for Natural Foci Infections, Omsk, Russian Federation
- Omsk State Pedagogical University, Omsk, Russian Federation
| | - Galina G. Karganova
- Federal Budget Institute Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russian Federation
| | | | - Mikhail Yu. Shchelkanov
- Far Eastern Federal University, Vladivostok, Russian Federation
- Institute of Biology and Soil Science, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, Russian Federation
| | - German A. Shipulin
- Federal Budget Institute of Science Central Research Institute for Epidemiology, Moscow, Russian Federation
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12
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Cheng J, Qi X, Chen D, Xu X, Wang G, Dai Y, Cui D, Chen Q, Fan P, Ni L, Liu M, Zhu F, Yang M, Wang C, Li Y, Sun C, Wang Z. Epidemiology and transmission characteristics of human adenovirus type 7 caused acute respiratory disease outbreak in military trainees in East China. Am J Transl Res 2016; 8:2331-2342. [PMID: 27347341 PMCID: PMC4891446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/04/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Human adenovirus type 7 (HAdV7) is globally attracting great concern as its high morbidity and severity in respiratory diseases, especially in Asia. OBJECTIVE To investigate the clinical and epidemiologic characteristics of HAdV7 infection outbreak in East China. METHODS The clinical samples were collected from the patients of an ARD outbreak in East Chinafor the detection of causative pathogens by multiplex PCR. The molecular type of human adenovirus isolates were identified by sequencing and homologous comparison based on their hexon genes. The spatiotemporal dynamics of global HAdV7 was investigated using the phylogenetic and phylogeographic analyses. Total 67 referenced HAdV7 hexon sequences (>800 bp) from GenBank were selected for constructing the maximum likelihood tree by MEGA 5.1.0, grouped according to the tree topology for the further migration analysis by PAUP* 4.0 and MigraPhyla 1.0 b to understand the transmission patterns of HAdV7 in global epidemics. RESULTS The results showed HAdV7 as the causative pathogen in this outbreak, and the outbreak strains had the hexon sequences highly identical with the isolates in Shaanxi (2012). The origin of HAdV7 was inferred as California, meanwhile a total of 21 migration routes were acquired. HAdV7 in this outbreak was statistically proven dispersed from Shaanxi province (2012). CONCLUSIONS The analyses of epidemiology and transmission pattern of HAdV7 would not only enrich the molecular biological basic database but also provide theoretical basis for HAdV7 prevention and control strategy.
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Affiliation(s)
- Jun Cheng
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou, China
- Department of Clinical Laboratory Science, The 117th Hospital of PLAHangzhou,China
| | - Xiaoping Qi
- Department of Respiratory Medicine, The 117th Hospital of PLAHangzhou, China
| | - Dawei Chen
- Department of Respiratory Medicine, The 117th Hospital of PLAHangzhou, China
| | - Xujian Xu
- Department of Biotechnology, The University of TokyoTokyo, Japan
| | - Guozheng Wang
- Department of Clinical Laboratory Science, The 117th Hospital of PLAHangzhou,China
| | - Yuzhu Dai
- Department of Clinical Laboratory Science, The 117th Hospital of PLAHangzhou,China
| | - Dawei Cui
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou, China
| | - Qingyong Chen
- Department of Respiratory Medicine, The 117th Hospital of PLAHangzhou, China
| | - Ping Fan
- Department of Infectious Diseases, The 113rd Hospital of PLANingbo, China
| | - Liuda Ni
- Department of Infectious Diseases, The 85th Hospital of PLAShanghai, China
| | - Miao Liu
- Department of Radio Diagnosis and Imaging, The 117th Hospital of PLAHangzhou, China
| | - Feiyan Zhu
- Department of Infectious Diseases, The 117th Hospital of PLAHangzhou, China
| | - Mei Yang
- Department of Epidemiology and Infection Control, The 117th Hospital of PLAHangzhou, China
| | - Changjun Wang
- Institute of Military Medical Sciences of Nanjing Military CommandNanjing, China
| | - Yuexi Li
- Center for Disease Control and Prevention of Nanjing Military CommandNanjing, China
| | - Changgui Sun
- Department of Clinical Laboratory Science, The 117th Hospital of PLAHangzhou,China
| | - Zhongyong Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou, China
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13
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Tohma K, Saito M, Demetria CS, Manalo DL, Quiambao BP, Kamigaki T, Oshitani H. Molecular and mathematical modeling analyses of inter-island transmission of rabies into a previously rabies-free island in the Philippines. INFECTION GENETICS AND EVOLUTION 2015; 38:22-28. [PMID: 26656835 DOI: 10.1016/j.meegid.2015.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 11/14/2015] [Accepted: 12/01/2015] [Indexed: 10/22/2022]
Abstract
Rabies is endemic in the Philippines and dog bites are a major cause of rabies cases in humans. The rabies control program has not been successful in eliminating rabies because of low vaccination coverage among dogs. Therefore, more effective and feasible strategies for rabies control are urgently required in the country. To control rabies, it is very important to know if inter-island transmission can occur because rabies can become endemic once the virus is introduced in areas that previously had no reported cases. Our molecular epidemiological study suggests that inter-island transmission events can occur; therefore, we further investigated these inter-island transmission using phylogenetic and modeling approaches. We investigate inter-island transmission between Luzon and Tablas Islands in the Philippines. Phylogenetic analysis and mathematical modeling demonstrate that there was a time lag of several months to a year from rabies introduction to initial case detection, indicating the difficulties in recognizing the initial rabies introductory event. There had been no rabies cases reported in Tablas Island; however, transmission chain was sustained on this island after the introduction of rabies virus because of low vaccination coverage among dogs. Across the islands, a rabies control program should include control of inter-island dog transportation and rabies vaccination to avoid viral introduction from the outside and to break transmission chains after viral introduction. However, this program has not yet been completely implemented and transmission chains following inter-island virus transmission are still observed. Local government units try to control dog transport; however, it should be more strictly controlled, and a continuous rabies control program should be implemented to prevent rabies spread even in rabies-free areas.
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Affiliation(s)
- Kentaro Tohma
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.
| | - Mariko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan; Tohoku-RITM Collaborative Research Center on Emerging and Re-emerging Infectious Diseases, Muntinlupa City, Metro Manila, Philippines.
| | - Catalino S Demetria
- Research Institute for Tropical Medicine (RITM), Muntinlupa City, Metro Manila, Philippines.
| | - Daria L Manalo
- Research Institute for Tropical Medicine (RITM), Muntinlupa City, Metro Manila, Philippines.
| | - Beatriz P Quiambao
- Research Institute for Tropical Medicine (RITM), Muntinlupa City, Metro Manila, Philippines.
| | - Taro Kamigaki
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan; Tohoku-RITM Collaborative Research Center on Emerging and Re-emerging Infectious Diseases, Muntinlupa City, Metro Manila, Philippines.
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan; Tohoku-RITM Collaborative Research Center on Emerging and Re-emerging Infectious Diseases, Muntinlupa City, Metro Manila, Philippines.
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14
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Tsai KJ, Hsu WC, Chuang WC, Chang JC, Tu YC, Tsai HJ, Liu HF, Wang FI, Lee SH. Emergence of a sylvatic enzootic formosan ferret badger-associated rabies in Taiwan and the geographical separation of two phylogenetic groups of rabies viruses. Vet Microbiol 2015; 182:28-34. [PMID: 26711025 DOI: 10.1016/j.vetmic.2015.10.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 09/17/2015] [Accepted: 10/28/2015] [Indexed: 11/16/2022]
Abstract
Taiwan had been declared rabies-free in humans and domestic animals for five decades until July 2013, when surprisingly, three Formosan ferret badgers (FB) were diagnosed with rabies. Since then, a variety of wild carnivores and other wildlife species have been found dead, neurologically ill, or exhibiting aggressive behaviors around the island. To determine the affected animal species, geographic areas, and environments, animal bodies were examined for rabies by direct fluorescent antibody test (FAT). The viral genomes from the brains of selected rabid animals were sequenced for the phylogeny of rabies viruses (RABV). Out of a total of 1016 wild carnivores, 276/831 (33.2%) Formosan FBs were FAT positive, with occasional biting incidents in 1 dog and suspected spillover in 1 house shrew. All other animals tested, including dogs, cats, bats, mice, house shrews, and squirrels, were rabies-negative. The rabies was badger-associated and confined to nine counties/cities in sylvatic environments. Phylogeny of nucleoprotein and glycoprotein genes from 59 Formosan FB-associated RABV revealed them to be clustered in two distinct groups, TWI and TWII, consistent with the geographic segregation into western and eastern Taiwan provided by the Central Mountain Range and into northern rabies-free and central-southern rabies-affected regions by a river bisecting western Taiwan. The unique features of geographic and genetic segregation, sylvatic enzooticity, and FB-association of RABV suggest a logical strategy for the control of rabies in this nation.
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Affiliation(s)
- K J Tsai
- Animal Health Research Institute, No.376, Chung-Cheng Rd., Tamsui District, New Taipei City 25158, Taiwan
| | - W C Hsu
- Animal Health Research Institute, No.376, Chung-Cheng Rd., Tamsui District, New Taipei City 25158, Taiwan
| | - W C Chuang
- Animal Health Research Institute, No.376, Chung-Cheng Rd., Tamsui District, New Taipei City 25158, Taiwan
| | - J C Chang
- Animal Health Research Institute, No.376, Chung-Cheng Rd., Tamsui District, New Taipei City 25158, Taiwan
| | - Y C Tu
- Animal Health Research Institute, No.376, Chung-Cheng Rd., Tamsui District, New Taipei City 25158, Taiwan
| | - H J Tsai
- Animal Health Research Institute, No.376, Chung-Cheng Rd., Tamsui District, New Taipei City 25158, Taiwan; School of Veterinary Medicine, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei City, 10617, Taiwan
| | - H F Liu
- Department of Medical Research, Mackay Memorial Hospital, No.45, Minsheng Rd., Tamsui District, New Taipei City 25160, Taiwan
| | - F I Wang
- School of Veterinary Medicine, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei City, 10617, Taiwan
| | - S H Lee
- Animal Drugs Inspection Branch, Animal Health Research Institute, No.21, Qiding, Zhunan Township, Miaoli County 35054, Taiwan.
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15
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Rabies Virus Infection in Ferret Badgers (Melogale moschata subaurantiaca) in Taiwan: A Retrospective Study. J Wildl Dis 2015; 51:923-8. [PMID: 26267459 DOI: 10.7589/2015-04-090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Fifteen ferret badgers (Melogale moschata subaurantiaca), collected 2010-13 and stored frozen, were submitted for rabies diagnosis by direct fluorescent antibody test and reverse transcription PCR. We detected seven positive animal samples, including some from 2010, which indicated that the ferret badger population in Taiwan had been affected by rabies prior to 2010.
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16
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Abstract
Tohoku University Graduate School of Medicine has established the Tohoku-RITM Collaborative Research Center on Emerging and Re-emerging Diseases at Research Institute for Tropical Medicine (RITM) in the Philippines in 2008. Our aim of the center is to conduct operational researches, which can contribute to control of infectious diseases in the Philippines. Therefore most of our researches in the Philippines are being conducted in the fields. Main research themes include severe acute respiratory infections in children, influenza disease burden study, molecular epidemiology of rabies, and viral etiology of acute diarrhea. The study on severe acute respiratory infections in children in Leyte Island has recruited hospitalized cases with severe pneumonia. We showed that enterovirus 68 was one of important causative agents in severe pneumonia cases. We also conducted other analyses including molecular epidemiology of respiratory syncytial virus (RSV) and pathogenesis of human rhinoviruses (HRV). Based on these studies, we initiated more comprehensive researches in the Philippines since 2010.
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17
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Chiou HY, Hsieh CH, Jeng CR, Chan FT, Wang HY, Pang VF. Molecular characterization of cryptically circulating rabies virus from ferret badgers, Taiwan. Emerg Infect Dis 2014; 20:790-8. [PMID: 24751120 PMCID: PMC4012806 DOI: 10.3201/eid2005.131389] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
After the last reported cases of rabies in a human in 1959 and a nonhuman animal in 1961, Taiwan was considered free from rabies. However, during 2012-2013, an outbreak occurred among ferret badgers in Taiwan. To examine the origin of this virus strain, we sequenced 3 complete genomes and acquired multiple rabies virus (RABV) nucleoprotein and glycoprotein sequences. Phylogeographic analyses demonstrated that the RABV affecting the Taiwan ferret badgers (RABV-TWFB) is a distinct lineage within the group of lineages from Asia and that it has been differentiated from its closest lineages, China I (including isolates from Chinese ferret badgers) and the Philippines, 158-210 years ago. The most recent common ancestor of RABV-TWFB originated 91-113 years ago. Our findings indicate that RABV could be cryptically circulating in the environment. An understanding of the underlying mechanism might shed light on the complex interaction between RABV and its host.
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Tohma K, Saito M, Kamigaki T, Tuason LT, Demetria CS, Orbina JRC, Manalo DL, Miranda ME, Noguchi A, Inoue S, Suzuki A, Quiambao BP, Oshitani H. Phylogeographic analysis of rabies viruses in the Philippines. INFECTION GENETICS AND EVOLUTION 2014; 23:86-94. [PMID: 24512808 DOI: 10.1016/j.meegid.2014.01.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 01/14/2014] [Accepted: 01/22/2014] [Indexed: 01/12/2023]
Abstract
Rabies still remains a public health threat in the Philippines. A significant number of human rabies cases, about 200-300 cases annually, have been reported, and the country needs an effective strategy for rabies control. To develop an effective control strategy, it is important to understand the transmission patterns of the rabies viruses. We conducted phylogenetic analyses by considering the temporal and spatial evolution of rabies viruses to reveal the transmission dynamics in the Philippines. After evaluating the molecular clock and phylogeographic analysis, we estimated that the Philippine strains were introduced from China around the beginning of 20th century. Upon this introduction, the rabies viruses evolved within the Philippines to form three major clades, and there was no indication of introduction of other rabies viruses from any other country. However, within the Philippines, island-to-island migrations were observed. Since then, the rabies viruses have diffused and only evolved within each island group. The evolutionary pattern of these viruses was strongly shaped by geographical boundaries. The association index statistics demonstrated a strong spatial structure within the island group, indicating that the seas were a significant geographical barrier for viral dispersal. Strong spatial structure was also observed even at a regional level, and most of the viral migrations (79.7% of the total median number) in Luzon were observed between neighboring regions. Rabies viruses were genetically clustered at a regional level, and this strong spatial structure suggests a geographical clustering of transmission chains and the potential effectiveness of rabies control that targets geographical clustering. Dog vaccination campaigns have been conducted independently by local governments in the Philippines, but it could be more effective to implement a coordinated vaccination campaign among neighboring areas to eliminate geographically-clustered rabies transmission chains.
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Affiliation(s)
- Kentaro Tohma
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.
| | - Mariko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan; Tohoku-RITM Collaborative Research Center on Emerging and Re-emerging Infectious Diseases, Muntinlupa City, Metro Manila, Philippines.
| | - Taro Kamigaki
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan; Tohoku-RITM Collaborative Research Center on Emerging and Re-emerging Infectious Diseases, Muntinlupa City, Metro Manila, Philippines.
| | - Laarni T Tuason
- Research Institute for Tropical Medicine (RITM), Muntinlupa City, Metro Manila, Philippines.
| | - Catalino S Demetria
- Research Institute for Tropical Medicine (RITM), Muntinlupa City, Metro Manila, Philippines.
| | - Jun Ryan C Orbina
- Research Institute for Tropical Medicine (RITM), Muntinlupa City, Metro Manila, Philippines.
| | - Daria L Manalo
- Research Institute for Tropical Medicine (RITM), Muntinlupa City, Metro Manila, Philippines.
| | - Mary E Miranda
- Research Institute for Tropical Medicine (RITM), Muntinlupa City, Metro Manila, Philippines.
| | - Akira Noguchi
- National Institute of Infectious Diseases (NIID), Tokyo, Japan.
| | - Satoshi Inoue
- National Institute of Infectious Diseases (NIID), Tokyo, Japan.
| | - Akira Suzuki
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan; Tohoku-RITM Collaborative Research Center on Emerging and Re-emerging Infectious Diseases, Muntinlupa City, Metro Manila, Philippines.
| | - Beatriz P Quiambao
- Research Institute for Tropical Medicine (RITM), Muntinlupa City, Metro Manila, Philippines.
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan; Tohoku-RITM Collaborative Research Center on Emerging and Re-emerging Infectious Diseases, Muntinlupa City, Metro Manila, Philippines.
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