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Hunsawong T, Buddhari D, Rungrojcharoenkit K, Suthangkornkul R, Mongkolsirichaikul D, Lohachanakul J, Tayong K, Sirikajornpan K, Rodpradit P, Poolpanichupatam Y, Klungthong C, Utennam D, Kaewhiran S, Cotrone TS, Fernandez S, Jones AR. Anti-Arbovirus Antibodies Cross-React With Severe Acute Respiratory Syndrome Coronavirus 2. Microbiol Spectr 2022; 10:e0263922. [PMID: 36445096 PMCID: PMC9769545 DOI: 10.1128/spectrum.02639-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is found in regions where dengue (DENV) and chikungunya (CHIKV) viruses are endemic. Any serological cross-reactivity between DENV, CHIKV, and SARS-CoV-2 is significant as it could lead to misdiagnosis, increased severity, or cross-protection. This study examined the potential cross-reactivity of anti-DENV and CHIKV antibodies with SARS-CoV-2 using acute and convalescent-phase samples collected before the SARS-CoV-2 pandemic. These included healthy, normal human (NHS, n = 6), CHIKV-positive (n = 14 pairs acute and convalescent), primary DENV-positive (n = 20 pairs), secondary DENV-positive (n = 20 pairs), and other febrile illnesses sera (n = 23 pairs). Samples were tested using an in-house SARS-CoV-2 and a EUROIMMUN IgA and IgG ELISAs. All NHS samples were negative, whereas 3.6% CHIKV, 21.7% primary DENV, 15.7% secondary DENV, and 10.8% febrile diseases sera resulted as anti-SARS-CoV-2 antibody positive. The EUROIMMUN ELISA using spike 1 as the antigen detected more positives among the primary DENV infections than the in-house ELISA using spike 1-receptor binding domain (RBD) protein. Among ELISA-positive samples, four had detectable neutralizing antibodies against SARS-CoV-2 reporter virus particles yet none had detectable neutralizing antibodies against the live Wuhan strain of SARS-CoV-2. These data demonstrated the SARS-CoV-2 diagnostic cross-reactivity, but not neutralizing antibody cross-reactivity, among dengue seropositive cases. IMPORTANCE SARS-CoV-2 continues to cause significant morbidity globally, including in areas where DENV and CHIKV are endemic. Reports using rapid diagnostic and ELISAs have demonstrated that serological cross-reactivity between DENV and SARS-CoV-2 can occur. Furthermore, it has been observed that convalescent DENV patients are at a lower risk of developing COVID-19. This phenomenon can interfere with the accuracy of serological testing and clinical management of both DENV and COVID-19 patients. In this study, the cross-reactivity of primary/secondary anti-DENV, CHIKV, and other febrile illness antibodies with SARS-CoV-2 using two ELISAs has been shown. Among ELISA-positive samples, four had detectable levels of neutralizing antibodies against SARS-CoV-2 reporter virus particles. However, none had detectable neutralizing antibodies against the live Wuhan strain of SARS-CoV-2. These data demonstrated SARS-CoV-2 diagnostic cross-reactivity, but not neutralizing antibody cross-reactivity, among dengue seropositive cases. The data discussed here provide information regarding diagnosis and may help guide appropriate public health interventions.
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Affiliation(s)
- Taweewun Hunsawong
- Department of Virology, US Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Darunee Buddhari
- Department of Virology, US Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Kamonthip Rungrojcharoenkit
- Department of Virology, US Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Rungarun Suthangkornkul
- Department of Virology, US Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Duangrat Mongkolsirichaikul
- Department of Virology, US Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Jindarat Lohachanakul
- Department of Virology, US Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Kedsara Tayong
- Department of Virology, US Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Kanittha Sirikajornpan
- Department of Virology, US Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Prinyada Rodpradit
- Department of Virology, US Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Yongyuth Poolpanichupatam
- Department of Virology, US Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Chonticha Klungthong
- Department of Virology, US Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Darunee Utennam
- Research Division, Royal Thai Army, Armed Force Research Institute of Medical Sciences, Bangkok, Thailand
| | | | - Thomas S. Cotrone
- Department of Virology, US Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stefan Fernandez
- Department of Virology, US Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Anthony R. Jones
- Department of Virology, US Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
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Myint KSA, Mawuntu AHP, Haryanto S, Imran D, Dian S, Dewi YP, Ganiem AR, Anggreani R, Iskandar MM, Bernadus JBB, Maharani K, Susanto D, Estiasari R, Dewi H, Kristiani A, Gaghiwu L, Johar E, Yudhaputri FA, Antonjaya U, Ledermann JP, van Crevel R, Hamers RL, Powers AM. Neurological Disease Associated with Chikungunya in Indonesia. Am J Trop Med Hyg 2022; 107:291-295. [PMID: 35895435 PMCID: PMC9393428 DOI: 10.4269/ajtmh.22-0050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 04/04/2022] [Indexed: 11/07/2022] Open
Abstract
Chikungunya virus (CHIKV) is recognized but rarely considered as a cause of central nervous system infection in endemic areas. A total of 244 patients with acute meningoencephalitis in Indonesia were retrospectively tested to identify whether any CHIKV infection was associated with neurological manifestations, especially in provinces known for CHIKV endemicity. Cerebrospinal fluid (CSF) and blood specimens were tested using CHIKV-specific real-time reverse transcription polymerase chain reaction and IgM ELISA, alongside a panel of neurotropic viruses. We report four cases of suspected or confirmed CHIKV-associated neurological disease, including CHIKV RNA detection in CSF of one patient and in acute serum of another, and CHIKV IgM in CSF of three patients and in serum of a fourth. In conclusion, CHIKV should be considered as a cause of neurologic disease in endemic areas and especially during outbreaks, in addition to the more common arboviral diseases such as dengue and Japanese encephalitis viruses.
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Affiliation(s)
| | - Arthur H. P. Mawuntu
- Faculty of Medicine, Universitas Sam Ratulangi, R.D. Kandou Hospital, Manado, Indonesia
| | - Sotianingsih Haryanto
- Raden Mattaher Hospital, Jambi, Indonesia
- Faculty of Medicine and Health Sciences, Universitas Jambi, Jambi, Indonesia
| | - Darma Imran
- Faculty of Medicine Universitas Indonesia, Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Sofiati Dian
- Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Yora P. Dewi
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Ahmad R. Ganiem
- Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Riane Anggreani
- Faculty of Medicine, Universitas Sam Ratulangi, R.D. Kandou Hospital, Manado, Indonesia
| | - Mirna M. Iskandar
- Raden Mattaher Hospital, Jambi, Indonesia
- Faculty of Medicine and Health Sciences, Universitas Jambi, Jambi, Indonesia
| | - Janno B. B. Bernadus
- Faculty of Medicine, Universitas Sam Ratulangi, R.D. Kandou Hospital, Manado, Indonesia
| | - Kartika Maharani
- Faculty of Medicine Universitas Indonesia, Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - David Susanto
- Faculty of Medicine, Universitas Sam Ratulangi, R.D. Kandou Hospital, Manado, Indonesia
| | - Riwanti Estiasari
- Faculty of Medicine Universitas Indonesia, Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Hasna Dewi
- Faculty of Medicine and Health Sciences, Universitas Jambi, Jambi, Indonesia
| | | | - Lidia Gaghiwu
- Faculty of Medicine, Universitas Sam Ratulangi, R.D. Kandou Hospital, Manado, Indonesia
| | - Edison Johar
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | - Ungke Antonjaya
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia
| | | | - Reinout van Crevel
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Raph L. Hamers
- Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Ann M. Powers
- Centers for Disease Control and Prevention, Fort Collins, Colorado
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Santoso MS, Haryanto S, Rulian F, Hayati RF, Kristiani A, Kartika R, Yohan B, Hibberd ML, Sasmono RT. Continuous Circulation of Chikungunya Virus during COVID-19 Pandemic in Jambi, Sumatra, Indonesia. Trop Med Infect Dis 2022; 7:tropicalmed7060091. [PMID: 35736970 PMCID: PMC9231073 DOI: 10.3390/tropicalmed7060091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/23/2022] [Accepted: 05/26/2022] [Indexed: 12/10/2022] Open
Abstract
Chikungunya fever is a self-limiting viral illness that is caused by the chikungunya virus (CHIKV). CHIKV is found in multiple provinces of Indonesia, with clustered local outbreaks. This case series investigates a local chikungunya outbreak during the COVID-19 pandemic, involving two virologically confirmed chikungunya cases found in Jambi, Sumatra, Indonesia in 2021 and the contact tracing of 65 people from the same neighborhood (one of which was also virologically confirmed with CHIKV). The two original cases were symptomatic with classic signs of chikungunya fever, while the CHIKV-positive neighbor was asymptomatic. Out of the 65 participants, chikungunya IgM was detected in seven (10.8%) people while chikungunya IgG was detected in six (9.2%) using capture ELISA. Dengue IgG was detected by rapid test in three (4.6%) of the participants, showcasing a history of dengue virus (DENV) infection along with the circulation of CHIKV in the area. A phylogenetic analysis demonstrates a close evolutionary relationship between all three 2021 Jambi CHIKV isolates and the 2015–2016 isolates from Jambi. This case series showcases the endemicity and persistent circulation of CHIKV in Jambi, leaving the area vulnerable to eminent outbreaks of chikungunya fever and doubling the burden of disease during the COVID-19 pandemic. Health staff training for case detection and notification, as well as an integrated vector surveillance should continue to be implemented to provide an early warning indicator of possible chikungunya outbreaks.
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Affiliation(s)
- Marsha Sinditia Santoso
- Eijkman Institute for Molecular Biology, National Agency for Research and Innovation, Jakarta 10430, Indonesia; (M.S.S.); (R.F.H.); (B.Y.)
| | | | - Fadil Rulian
- Raden Mattaher Hospital, Jambi 36361, Indonesia; (S.H.); (F.R.)
| | - Rahma F. Hayati
- Eijkman Institute for Molecular Biology, National Agency for Research and Innovation, Jakarta 10430, Indonesia; (M.S.S.); (R.F.H.); (B.Y.)
| | | | - Rini Kartika
- Jambi City Health Office, Jambi 36128, Indonesia;
| | - Benediktus Yohan
- Eijkman Institute for Molecular Biology, National Agency for Research and Innovation, Jakarta 10430, Indonesia; (M.S.S.); (R.F.H.); (B.Y.)
| | - Martin L. Hibberd
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK;
| | - R. Tedjo Sasmono
- Eijkman Institute for Molecular Biology, National Agency for Research and Innovation, Jakarta 10430, Indonesia; (M.S.S.); (R.F.H.); (B.Y.)
- Correspondence:
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Harapan H, Michie A, Ernst T, Panta K, Mudatsir M, Yohan B, Haryanto S, McCarthy S, Sasmono RT, Imrie A. Co-Circulation of Chikungunya and Multiple DENV Serotypes and Genotypes, Western Indonesia 2015-2016. Viruses 2022; 14:99. [PMID: 35062303 PMCID: PMC8779054 DOI: 10.3390/v14010099] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/31/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
Dengue is a mosquito-borne disease of public health concern affecting tropical and subtropical countries, including Indonesia. Although studies on dengue epidemiology have been undertaken in Indonesia, data are lacking in many areas of the country. The aim of this study was to determine dengue virus (DENV) and chikungunya virus (CHIKV) molecular epidemiology in western regions of the Indonesian archipelago. A one-year prospective study was conducted in Aceh and Jambi in 2015 and 2016, respectively, where patients with dengue-like illness were enrolled. Of 205 patients recruited, 29 and 27 were confirmed with dengue in Aceh and Jambi, respectively, and three from Jambi were confirmed with chikungunya. DENV-1 was the predominant serotype identified in Aceh while DENV-2 was predominant in Jambi. All DENV-1 and DENV-2 from both regions were classified as Genotype I and Cosmopolitan genotype, respectively, and all DENV-3 viruses from Jambi were Genotype I. Some viruses, in particular DENV-1, displayed a distinct lineage distribution, where two DENV-1 lineages from Aceh were more closely related to viruses from China instead of Jambi highlighting the role of travel and flight patterns on DENV transmission in the region. DENV-2 from both Aceh and Jambi and DENV-3 from Jambi were all closely related to Indonesian local strains. All three CHIKV belonged to Asian genotype and clustered closely with Indonesian CHIKV strains including those previously circulating in Jambi in 2015, confirming continuous and sustainable transmission of CHIKV in the region. The study results emphasize the importance of continuous epidemiological surveillance of arboviruses in Indonesia and simultaneous testing for CHIKV among dengue-suspected patients.
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Affiliation(s)
- Harapan Harapan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia; (H.H.); (M.M.)
- Tropical Disease Centre, School of Medicine, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia
- Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6009, Australia; (A.M.); (T.E.); (K.P.); (S.M.)
| | - Alice Michie
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6009, Australia; (A.M.); (T.E.); (K.P.); (S.M.)
| | - Timo Ernst
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6009, Australia; (A.M.); (T.E.); (K.P.); (S.M.)
| | - Kritu Panta
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6009, Australia; (A.M.); (T.E.); (K.P.); (S.M.)
| | - Mudatsir Mudatsir
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia; (H.H.); (M.M.)
- Tropical Disease Centre, School of Medicine, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia
- Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia
| | - Benediktus Yohan
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia; (B.Y.); (R.T.S.)
| | - Sotianingsih Haryanto
- Faculty of Medicine and Health Science, Universitas Jambi, Jambi 36361, Indonesia;
- Raden Mattaher Hospital, Jambi 36361, Indonesia
| | - Suzi McCarthy
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6009, Australia; (A.M.); (T.E.); (K.P.); (S.M.)
- Pathwest Laboratory Medicine, Nedlands, WA 6009, Australia
| | - R. Tedjo Sasmono
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia; (B.Y.); (R.T.S.)
| | - Allison Imrie
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6009, Australia; (A.M.); (T.E.); (K.P.); (S.M.)
- Pathwest Laboratory Medicine, Nedlands, WA 6009, Australia
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Clinical and virological characteristics of patients during the outbreak of chikungunya in Thiruvananthapuram, Kerala, India, 2019–2020. JOURNAL OF CLINICAL VIROLOGY PLUS 2021. [DOI: 10.1016/j.jcvp.2021.100043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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Chaudhary S, Jain J, Kumar R, Shrinet J, Weaver SC, Auguste AJ, Sunil S. Chikungunya virus molecular evolution in India since its re-emergence in 2005. Virus Evol 2021; 7:veab074. [PMID: 34754512 PMCID: PMC8570154 DOI: 10.1093/ve/veab074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 07/20/2021] [Accepted: 08/25/2021] [Indexed: 11/13/2022] Open
Abstract
Chikungunya virus (CHIKV), an alphavirus of the Togaviridae family, is among the most medically significant mosquito-borne viruses, capable of causing major epidemics of febrile disease and severe, chronic arthritis. Identifying viral mutations is crucial for understanding virus evolution and evaluating those genetic determinants that directly impact pathogenesis and transmissibility. The present study was undertaken to expand on past CHIKV evolutionary studies through robust genome-scale phylogenetic analysis to better understand CHIKV genetic diversity and evolutionary dynamics since its reintroduction into India in 2005. We sequenced the complete genomes of fifty clinical isolates collected between 2010 and 2016 from two geographic locations, Delhi and Mumbai. We then analysed them along with 753 genomes available on the Virus Pathogen Database and Analysis Resource sampled over fifteen years (2005-20) from a range of locations across the globe and identified novel genetic variants present in samples from this study. Our analyses show evidence of frequent reintroduction of the virus into India and that the most recent CHIKV outbreak shares a common ancestor as recently as 2006.
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Affiliation(s)
| | - Jaspreet Jain
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | | | - Jatin Shrinet
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Scott C Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Albert J Auguste
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Sujatha Sunil
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
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Molecular epidemiology of dengue in North Kalimantan, a province with the highest incidence rates in Indonesia in 2019. INFECTION GENETICS AND EVOLUTION 2021; 95:105036. [PMID: 34411743 DOI: 10.1016/j.meegid.2021.105036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/27/2021] [Accepted: 08/09/2021] [Indexed: 11/20/2022]
Abstract
OBJECTIVES Dengue is endemic to Indonesia, a country that has largely varied geographical and demographic conditions across different regions. In 2019, dengue epidemic occurred in North Kalimantan province and recorded as the highest incidence rate in Indonesia. This study aims to investigate the molecular epidemiology of dengue during outbreak in the province and compare the epidemiological characteristics between two cities/towns in North Kalimantan, namely Malinau, an inland town surrounded by a dense rainforest, and Tarakan, an island city. METHODS A cross sectional study was conducted between September 2018 and July 2019. Dengue-like illness patients were recruited in hospitals and tested for dengue NS1 and IgG/IgM. Serological prevalence was measured using IgG ELISA, dengue virus (DENV) serotyping was conducted using RT-PCR and Envelope gene sequencing was performed to infer the virus origins and phylogeny. Clinical, demographical, and diagnostics data were also recorded and analyzed. RESULTS We recruited 523 patients, 261 from Malinau and 262 from Tarakan. Among them, 349 patients were confirmed dengue. Cases in Malinau had a higher proportion of confirmed dengue (82.0%) compared to those in Tarakan (51.5%). Cases in Malinau were more likely to be dengue hemorrhagic fever with more severe hematological features compared to those in Tarakan. All four DENV serotypes were detected in both cities, the most prevalent serotype being DENV-2. The genetic characteristics of the viruses in the two towns was similar except for DENV-3. No sylvatic DENV was detected as well as alphaviruses and non-dengue flaviviruses during the outbreak. CONCLUSIONS The molecular epidemiology of dengue in North Kalimantan revealed the similar virological characteristics but different clinical and demographic aspects in Malinau and Tarakan. The distinct dengue dynamics between different regions of Indonesia is prominent and this knowledge will be important for understanding future patterns of DENV transmission in the region.
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Dhenni R, Yohan B, Alisjahbana B, Lucanus A, Riswari SF, Megawati D, Haryanto S, Gampamole D, Hayati RF, Sari K, Witari NPD, Myint KSA, Sasmono RT. Comparative cytokine profiling identifies common and unique serum cytokine responses in acute chikungunya and dengue virus infection. BMC Infect Dis 2021; 21:639. [PMID: 34215212 PMCID: PMC8254284 DOI: 10.1186/s12879-021-06339-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 06/18/2021] [Indexed: 01/09/2023] Open
Abstract
Background Infection by chikungunya (CHIKV) and dengue virus (DENV) can cause a wide spectrum of clinical features, many of which are undifferentiated. Cytokines, which broadly also include chemokines and growth factors, have been shown to play a role in protective immunity as well as DENV and CHIKV pathogenesis. However, differences in cytokine response to both viruses remain poorly understood, especially in patients from countries where both viruses are endemic. Our study is therefore aimed to provide a comparative profiling of cytokine response induced by acute DENV and CHIKV infections in patients with similar disease stages and in experimental in vitro infections. Methods By using multiplex immunoassay, we compared host cytokine profiles between acute CHIKV and DENV infections by analysing serum cytokine levels of IL-1α, IL-4, IL-5, IL-8, IL-13, RANTES, MCP-3, eotaxin, PDGF-AB/BB, and FGF-2 from the sera of acute chikungunya and dengue fever patients. We further investigated the cytokine profile responses using experimental in vitro CHIKV and DENV infections of peripheral blood mononuclear cells (PBMCs). Results We found that both CHIKV and DENV-infected patients had an upregulated level of IL-8 and IL-4, with the highest IL-4 level observed in DENV-2 infected patients. Higher IL-8 level was also correlated with lower platelet count in dengue patients. IL-13 and MCP-3 downregulation was observed only in chikungunya patients, while conversely PDGF-AB/BB and FGF-2 downregulation was unique in dengue patients. Age-associated differential expression of IL-13, MCP-3, and IL-5 was also observed, while distinct kinetics of IL-4, IL-8, and FGF-2 expression between CHIKV and DENV-infected patients were identified. Furthermore, the unique pattern of IL-8, IL-13 and MCP-3, but not IL-4 expression was also recapitulated using experimental in vitro infection in PBMCs. Conclusions Taken together, our study identified common cytokine response profile characterized by upregulation of IL-8 and IL-4 between CHIKV and DENV infection. Downregulation of IL-13 and MCP-3 was identified as a unique cytokine response profile of acute CHIKV infection, while distinct downregulation of PDGF-AB/BB and FGF-2 characterized the response from acute DENV infection. Our study provides an important overview of the host cytokine responses between CHIKV and DENV infection, which is important to further understand the mechanism and pathology of these diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06339-6.
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Affiliation(s)
- Rama Dhenni
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | | | - Anton Lucanus
- School of Anatomy, Physiology and Human Biology, University of Western Australia, Perth, Australia
| | | | - Dewi Megawati
- Faculty of Medicine and Health Sciences, Warmadewa University, Denpasar, Bali, Indonesia
| | | | | | - Rahma F Hayati
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Kartika Sari
- Faculty of Medicine and Health Sciences, Warmadewa University, Denpasar, Bali, Indonesia
| | - Ni Putu Diah Witari
- Faculty of Medicine and Health Sciences, Warmadewa University, Denpasar, Bali, Indonesia
| | | | - R Tedjo Sasmono
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
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Abdullah N, Ahemad N, Aliazis K, Khairat JE, Lee TC, Abdul Ahmad SA, Adnan NAA, Macha NO, Hassan SS. The Putative Roles and Functions of Indel, Repetition and Duplication Events in Alphavirus Non-Structural Protein 3 Hypervariable Domain (nsP3 HVD) in Evolution, Viability and Re-Emergence. Viruses 2021; 13:v13061021. [PMID: 34071712 PMCID: PMC8228767 DOI: 10.3390/v13061021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 11/23/2022] Open
Abstract
Alphavirus non-structural proteins 1–4 (nsP1, nsP2, nsP3, and nsP4) are known to be crucial for alphavirus RNA replication and translation. To date, nsP3 has been demonstrated to mediate many virus–host protein–protein interactions in several fundamental alphavirus mechanisms, particularly during the early stages of replication. However, the molecular pathways and proteins networks underlying these mechanisms remain poorly described. This is due to the low genetic sequence homology of the nsP3 protein among the alphavirus species, especially at its 3′ C-terminal domain, the hypervariable domain (HVD). Moreover, the nsP3 HVD is almost or completely intrinsically disordered and has a poor ability to form secondary structures. Evolution in the nsP3 HVD region allows the alphavirus to adapt to vertebrate and insect hosts. This review focuses on the putative roles and functions of indel, repetition, and duplication events that have occurred in the alphavirus nsP3 HVD, including characterization of the differences and their implications for specificity in the context of virus–host interactions in fundamental alphavirus mechanisms, which have thus directly facilitated the evolution, adaptation, viability, and re-emergence of these viruses.
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Affiliation(s)
- Nurshariza Abdullah
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia; (N.A.); (N.A.A.A.); (N.O.M.)
| | - Nafees Ahemad
- School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia;
- Infectious Diseases and Health Cluster, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia
| | - Konstantinos Aliazis
- Institute of Immunology and Immunotherapy, Centre for Liver and Gastrointestinal Research, University of Birmingham, Birmingham B15 2TT, UK;
| | - Jasmine Elanie Khairat
- Institute of Biological Sciences, Faculty of Science, University Malaya, Kuala Lumpur 50603, Malaysia;
| | - Thong Chuan Lee
- Faculty of Industrial Sciences & Technology, University Malaysia Pahang, Lebuhraya Tun Razak, Gambang, Kuantan 26300, Pahang, Malaysia;
| | - Siti Aisyah Abdul Ahmad
- Immunogenetic Unit, Allergy and Immunology Research Center, Institute for Medical Research, Ministry of Health Malaysia, Shah Alam 40170, Selangor, Malaysia;
| | - Nur Amelia Azreen Adnan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia; (N.A.); (N.A.A.A.); (N.O.M.)
| | - Nur Omar Macha
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia; (N.A.); (N.A.A.A.); (N.O.M.)
| | - Sharifah Syed Hassan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia; (N.A.); (N.A.A.A.); (N.O.M.)
- Infectious Diseases and Health Cluster, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia
- Correspondence: ; Tel.: +60-3-5514-6340
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10
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[6]-Gingerol Inhibits Chikungunya Virus Infection by Suppressing Viral Replication. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6623400. [PMID: 33855075 PMCID: PMC8019639 DOI: 10.1155/2021/6623400] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/22/2021] [Accepted: 03/10/2021] [Indexed: 11/18/2022]
Abstract
Chikungunya (CHIK) is a reemerging arboviral disease caused by chikungunya virus (CHIKV) infection. The disease is clinically hallmarked by prolonged debilitating joint pain. Currently, there is no specific antiviral medication nor commercial vaccine available for treatment of the disease, which makes the discovery or development of specific anti-CHIKV compounds a priority. Ginger (Zingiber officinale Roscoe) is widely known for its various health benefits. The compound [6]-gingerol is the main active ingredient found in ginger. This study sought to determine the potential of [6]-gingerol antiviral activity against CHIKV infection using in vitro human hepatocyte HepG2 cells. The antiviral activity mechanism was investigated using direct virucidal and four indirect (pre-, post-, full-, and prevention) treatment assays. [6]-Gingerol showed weak virucidal activity but significant indirect antiviral activity against CHIKV through post- and full treatment with IC50 of 0.038 mM and 0.031 mM, respectively, without showing cell cytotoxicity. The results indicated that [6]-gingerol inhibits CHIKV infection through suppression of viral replication. Together, this study confirms the potential use of [6]-gingerol for CHIK antiviral compound.
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11
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Stubbs SCB, Johar E, Yudhaputri FA, Yohan B, Santoso MS, Hayati RF, Denis D, Blacklaws BA, Powers AM, Sasmono RT, Myint KSA, Frost SDW. An investig-ation into the epidemiology of chikungunya virus across neglected regions of Indonesia. PLoS Negl Trop Dis 2020; 14:e0008934. [PMID: 33347450 PMCID: PMC7785224 DOI: 10.1371/journal.pntd.0008934] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 01/05/2021] [Accepted: 10/30/2020] [Indexed: 12/17/2022] Open
Abstract
Background Chikungunya virus (CHIKV) is an important emerging and re-emerging public health problem worldwide. In Indonesia, where the virus is endemic, epidemiological information from outside of the main islands of Java and Bali is limited. Methodology/Principal Findings Four hundred and seventy nine acutely febrile patients presenting between September 2017–2019 were recruited from three city hospitals situated in Ambon, Maluku; Banjarmasin, Kalimantan; and Batam, Batam Island as part of a multi-site observational study. CHIKV RNA was detected in a single serum sample while a separate sample was IgM positive. IgG seroprevalence was also low across all three sites, ranging from 1.4–3.2%. The single RT-PCR positive sample from this study and 24 archived samples collected during other recent outbreaks throughout Indonesia were subjected to complete coding region sequencing to assess the genetic diversity of Indonesian strains. Phylogenetic analysis revealed all to be of a single clade, which was distinct from CHIKV strains recently reported from neighbouring regions including the Philippines and the Pacific Islands. Conclusions/Significance Chikungunya virus strains from recent outbreaks across Indonesia all belong to a single clade. However, low-level seroprevalence and molecular detection of CHIKV across the three study sites appears to contrast with the generally high seroprevalences that have been reported for non-outbreak settings in Java and Bali, and may account for the relative lack of CHIKV epidemiological data from other regions of Indonesia. Outbreaks of chikungunya virus (CHIKV) are a common occurrence in Indonesia. However, limited data is available on CHIKV from regions outside of the main, central islands of Java and Bali. We recruited hospital patients from three cities located in the east (Ambon), west (Batam) and north (Banjarmasin) of the country, and screened their blood for evidence of CHIKV infection. Our results showed that CHIKV infections were relatively uncommon across patients from all three sites, suggesting that CHIKV transmission is currently relatively rare in these regions. Additional analysis of 25 recent Indonesian CHIKV genome sequences revealed that a new lineage of CHIKV has recently emerged in Indonesia. Several reports have highlighted Indonesia as a major source of imported CHIKV cases, suggesting that this new lineage has the potential to be introduced into neighbouring countries in the near future, with unknown consequences. Overall, our results indicate that additional CHIKV surveillance studies in Indonesia and Southeast Asia are needed in order to gain a clearer understanding of transmission routes and hot spots throughout the region.
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Affiliation(s)
- Samuel C. B. Stubbs
- University of Cambridge, Department of Veterinary Medicine, Cambridge, United Kingdom
- * E-mail: (SCBS); (KSAM)
| | - Edison Johar
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | | | | | | | | | - Barbara A. Blacklaws
- University of Cambridge, Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Ann M. Powers
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | | | - Khin Saw Aye Myint
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- * E-mail: (SCBS); (KSAM)
| | - Simon D. W. Frost
- University of Cambridge, Department of Veterinary Medicine, Cambridge, United Kingdom
- Microsoft Research, Redmond, Washington, United States of America
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12
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Sasmono RT, Santoso MS, Pamai YWB, Yohan B, Afida AM, Denis D, Hutagalung IA, Johar E, Hayati RF, Yudhaputri FA, Haryanto S, Stubbs SCB, Blacklaws BA, Myint KSA, Frost SDW. Distinct Dengue Disease Epidemiology, Clinical, and Diagnosis Features in Western, Central, and Eastern Regions of Indonesia, 2017-2019. Front Med (Lausanne) 2020; 7:582235. [PMID: 33335904 PMCID: PMC7737558 DOI: 10.3389/fmed.2020.582235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/22/2020] [Indexed: 01/06/2023] Open
Abstract
The people of Indonesia have been afflicted by dengue, a mosquito-borne viral disease, for over 5 decades. The country is the world's largest archipelago with diverse geographic, climatic, and demographic conditions that may impact the dynamics of disease transmissions. A dengue epidemiology study was launched by us to compare and understand the dynamics of dengue and other arboviral diseases in three cities representing western, central, and eastern Indonesia, namely, Batam, Banjarmasin, and Ambon, respectively. A total of 732 febrile patients were recruited with dengue-like illness during September 2017-2019 and an analysis of their demographic, clinical, and virological features was performed. The seasonal patterns of dengue-like illness were found to be different in the three regions. Among all patients, 271 (37.0%) were virologically confirmed dengue, while 152 (20.8%) patients were diagnosed with probable dengue, giving a total number of 423 (57.8%) dengue patients. Patients' age and clinical manifestations also differed between cities. Mostly, mild dengue fever was observed in Batam, while more severe cases were prominent in Ambon. While all dengue virus (DENV) serotypes were detected, distinct serotypes dominated in different locations: DENV-1 in Batam and Ambon, and DENV-3 in Banjarmasin. We also assessed the diagnostic features in the study sites, which revealed different patterns of diagnostic agreements, particularly in Ambon. To detect the possibility of infection with other arboviruses, further testing on 461 DENV RT-PCR-negative samples was performed using pan-flavivirus and -alphavirus RT-PCRs; however, only one chikungunya infection was detected in Ambon. A diverse dengue epidemiology in western, central, and eastern Indonesia was observed, which is likely to be influenced by local geographic, climatic, and demographic conditions, as well as differences in the quality of healthcare providers and facilities. Our study adds a new understanding on dengue epidemiology in Indonesia.
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Affiliation(s)
| | | | | | | | - Anna M Afida
- Dr. H. M. Ansari Saleh Hospital, Banjarmasin, Indonesia
| | | | | | - Edison Johar
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Rahma F Hayati
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | | | - Samuel C B Stubbs
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Barbara A Blacklaws
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Khin S A Myint
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Simon D W Frost
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom.,Microsoft Research, Redmond, WA, United States
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13
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Alkaff AH, Yohan B, Tambunan USF, Sasmono RT. Zika, chikungunya, and dengue viral infections in human peripheral blood mononuclear cells: cell susceptibility and gene expression. MEDICAL JOURNAL OF INDONESIA 2020. [DOI: 10.13181/mji.oa.193548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
BACKGROUND Infections of Zika (ZIKV), dengue (DENV), and chikungunya viruses (CHIKV) are presented with similar clinical symptoms; these often lead to misdiagnosis. Viremia levels and host immune responses may contribute to disease severity. This study was aimed to characterize the ability of ZIKV, CHIKV, and DENV to infect human peripheral blood mononuclear cells (PBMCs) and assess the expression of tumor necrosis factor (TNF)-α, interleukin (IL)-10, and interferon gamma-induced protein (IP)- 10 genes in response to the viral infections.
METHODS PBMCs were isolated from healthy donors using gradient centrifugation. Cells were infected with Indonesian isolates of ZIKV, CHIKV, and DENV for 48 hours. Plaque assays were performed to measure viable virus titers, while viral genomic RNA and the gene expression of TNF-α, IL-10, and IP-10 were determined using real-time quantitative reverse transcription-polymerase chain reaction.
RESULTS The susceptibility of PBMCs to ZIKV, CHIKV, and DENV infection was observed, and the viable virus titer and viral genome quantity were found to be significantly higher in ZIKV and CHIKV. All viruses induced the expression of immune-related proteins. The TNF-α gene was upregulated by all viruses to relatively similar levels. IL-10 expression was highest in response to ZIKV, followed by CHIKV. In contrast, IP-10 expression was highly upregulated in DENV-infected cells and only moderately expressed in ZIKV- and CHIKV-infected cells.
CONCLUSIONS ZIKV, CHIKV, and DENV clinical isolates infected PBMCs with different levels of virus infectivity. The gene expression of IL-10 was highly upregulated in ZIKV infection and IP-10 in DENV infection.
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14
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Arif M, Tauran P, Kosasih H, Pelupessy NM, Sennang N, Mubin RH, Sudarmono P, Tjitra E, Murniati D, Alam A, Gasem MH, Aman AT, Lokida D, Hadi U, Parwati KTM, Lau CY, Neal A, Karyana M. Chikungunya in Indonesia: Epidemiology and diagnostic challenges. PLoS Negl Trop Dis 2020; 14:e0008355. [PMID: 32479497 PMCID: PMC7289446 DOI: 10.1371/journal.pntd.0008355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 06/11/2020] [Accepted: 05/04/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Chikungunya virus (CHIKV) is often overlooked as an etiology of fever in tropical and sub-tropical regions. Lack of diagnostic testing capacity in these areas combined with co-circulation of clinically similar pathogens such as dengue virus (DENV), hinders CHIKV diagnosis. To better address CHIKV in Indonesia, an improved understanding of epidemiology, clinical presentation, and diagnostic approaches is needed. METHODOLOGY/PRINCIPAL FINDINGS Acutely hospitalized febrile patients ≥1-year-old were enrolled in a multi-site observational cohort study conducted in Indonesia from 2013 to 2016. Demographic and clinical data were collected at enrollment; blood specimens were collected at enrollment, once during days 14 to 28, and three months after enrollment. Plasma samples negative for DENV by serology and/or molecular assays were screened for evidence of acute CHIKV infection (ACI) by serology and molecular assays. To address the co-infection of DENV and CHIKV, DENV cases were selected randomly to be screened for evidence of ACI. ACI was confirmed in 40/1,089 (3.7%) screened subjects, all of whom were DENV negative. All 40 cases initially received other diagnoses, most commonly dengue fever, typhoid fever, and leptospirosis. ACI was found at five of the seven study cities, though evidence of prior CHIKV exposure was observed in 25.2% to 45.9% of subjects across sites. All subjects were assessed during hospitalization as mildly or moderately ill, consistent with the Asian genotype of CHIKV. Subjects with ACI had clinical presentations that overlapped with other common syndromes, atypical manifestations of disease, or persistent or false-positive IgM against Salmonella Typhi. Two of the 40 cases were possibly secondary ACI. CONCLUSIONS/SIGNIFICANCE CHIKV remains an underdiagnosed acute febrile illness in Indonesia. Public health measures should support development of CHIKV diagnostic capacity. Improved access to point-of-care diagnostic tests and clinical training on presentations of ACI will facilitate appropriate case management such as avoiding unneccessary treatments or antibiotics, early response to control mosquito population and eventually reducing disease transmission.
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Affiliation(s)
- Mansyur Arif
- Faculty of Medicine, Universitas Hasanuddin/Dr. Wahidin Sudirohusodo Hospital, Makassar, Indonesia
| | - Patricia Tauran
- Faculty of Medicine, Universitas Hasanuddin/Dr. Wahidin Sudirohusodo Hospital, Makassar, Indonesia
| | - Herman Kosasih
- *Indonesia Research Partnership on Infectious Disease (INA-RESPOND), Jakarta, Indonesia
- * E-mail:
| | - Ninny Meutia Pelupessy
- Faculty of Medicine, Universitas Hasanuddin/Dr. Wahidin Sudirohusodo Hospital, Makassar, Indonesia
| | - Nurhayana Sennang
- Faculty of Medicine, Universitas Hasanuddin/Dr. Wahidin Sudirohusodo Hospital, Makassar, Indonesia
| | - Risna Halim Mubin
- Faculty of Medicine, Universitas Hasanuddin/Dr. Wahidin Sudirohusodo Hospital, Makassar, Indonesia
| | - Pratiwi Sudarmono
- Cipto Mangunkusumo Hospital, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Emiliana Tjitra
- National Institute of Health Research and Development (NIHRD), Ministry of Health, Jakarta, Indonesia
| | | | - Anggraini Alam
- Hasan Sadikin Hospital–Faculty of Medicine Universitas Padjadjaran, Bandung, Indonesia
| | | | - Abu Tholib Aman
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dewi Lokida
- Tangerang District Hospital, Tangerang, Indonesia
| | - Usman Hadi
- Dr. Soetomo Academic General Hospital–Faculty of Medicine Universitas Airlangga, Surabaya, Indonesia
| | | | - Chuen-Yen Lau
- National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, Maryland, United States of America
| | - Aaron Neal
- National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, Maryland, United States of America
| | - Muhammad Karyana
- *Indonesia Research Partnership on Infectious Disease (INA-RESPOND), Jakarta, Indonesia
- National Institute of Health Research and Development (NIHRD), Ministry of Health, Jakarta, Indonesia
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15
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Ciccozzi M, Lai A, Zehender G, Borsetti A, Cella E, Ciotti M, Sagnelli E, Sagnelli C, Angeletti S. The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review. J Med Virol 2019; 91:1707-1724. [PMID: 31243773 DOI: 10.1002/jmv.25526] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/24/2019] [Indexed: 12/16/2022]
Abstract
In the last decade, the phylogenetic approach is recurrent in molecular evolutionary analysis. On 12 May, 2019, about 2 296 213 papers are found, but typing "phylogeny" or "epidemiology AND phylogeny" only 199 804 and 20 133 are retrieved, respectively. Molecular epidemiology in infectious diseases is widely used to define the source of infection as so as the ancestral relationships of individuals sampled from a population. Coalescent theory and phylogeographic analysis have had scientific application in several, recent pandemic events, and nosocomial outbreaks. Hepatitis viruses and immunodeficiency virus (human immunodeficiency virus) have been largely studied. Phylogenetic analysis has been recently applied on Polyomaviruses so as in the more recent outbreaks due to different arboviruses type as Zika and chikungunya viruses discovering the source of infection and the geographic spread. Data on sequences isolated by the microorganism are essential to apply the phylogenetic tools and research in the field of infectious disease phylodinamics is growing up. There is the need to apply molecular phylogenetic and evolutionary methods in areas out of infectious diseases, as translational genomics and personalized medicine. Lastly, the application of these tools in vaccine strategy so as in antibiotic and antiviral researchers are encouraged.
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Affiliation(s)
- Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, Roma, Italy
| | - Eleonora Cella
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Marco Ciotti
- Laboratory of Molecular Virology, Polyclinic Tor Vergata Foundation, Rome, Italy
| | - Evangelista Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Caterina Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
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16
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Harapan H, Michie A, Mudatsir M, Nusa R, Yohan B, Wagner AL, Sasmono RT, Imrie A. Chikungunya virus infection in Indonesia: a systematic review and evolutionary analysis. BMC Infect Dis 2019; 19:243. [PMID: 30866835 PMCID: PMC6417237 DOI: 10.1186/s12879-019-3857-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/27/2019] [Indexed: 11/13/2022] Open
Abstract
Background Despite the high number of chikungunya cases in Indonesia in recent years, comprehensive epidemiological data are lacking. The systematic review was undertaken to provide data on incidence, the seroprevalence of anti-Chikungunya virus (CHIKV) IgM and IgG antibodies, mortality, the genotypes of circulating CHIKV and travel-related cases of chikungunya in the country. In addition, a phylogenetic and evolutionary analysis of Indonesian CHIKV was conducted. Methods A systematic review was conducted to identify eligible studies from EMBASE, MEDLINE, PubMed and Web of Science as of October 16th 2017. Studies describing the incidence, seroprevalence of IgM and IgG, mortality, genotypes and travel-associated chikungunya were systematically reviewed. The maximum likelihood phylogenetic and evolutionary rate was estimated using Randomized Axelerated Maximum Likelihood (RAxML), and the Bayesian Markov chain Monte Carlo (MCMC) method identified the Time to Most Recent Common Ancestors (TMRCA) of Indonesian CHIKV. The systematic review was registered in the PROSPERO database (CRD42017078205). Results Chikungunya incidence ranged between 0.16-36.2 cases per 100,000 person-year. Overall, the median seroprevalence of anti-CHIKV IgM antibodies in both outbreak and non-outbreak scenarios was 13.3% (17.7 and 7.3% for outbreak and non-outbreak events, respectively). The median seroprevalence of IgG antibodies in both outbreak and non-outbreak settings was 18.5% (range 0.0–73.1%). There were 130 Indonesian CHIKV sequences available, of which 120 (92.3%) were of the Asian genotype and 10 (7.7%) belonged to the East/Central/South African (ECSA) genotype. The ECSA genotype was first isolated in Indonesia in 2008 and was continually sampled until 2011. All ECSA viruses sampled in Indonesia appear to be closely related to viruses that caused massive outbreaks in Southeast Asia countries during the same period. Massive nationwide chikungunya outbreaks in Indonesia were reported during 2009–2010 with a total of 137,655 cases. Our spatio-temporal, phylogenetic and evolutionary data suggest that these outbreaks were likely associated with the introduction of the ECSA genotype of CHIKV to Indonesia. Conclusions Although no deaths have been recorded, the seroprevalence of anti-CHIKV IgM and IgG in the Indonesian population have been relatively high in recent years following re-emergence in early 2001. There is sufficient evidence to suggest that the introduction of ECSA into Indonesia was likely associated with massive chikungunya outbreaks during 2009–2010. Electronic supplementary material The online version of this article (10.1186/s12879-019-3857-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Harapan Harapan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia. .,School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, 6009, Australia.
| | - Alice Michie
- School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, 6009, Australia
| | - Mudatsir Mudatsir
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia. .,Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Jl. T. Tanoeh Abe, Darussalam, Banda Aceh, 23111, Indonesia.
| | - Roy Nusa
- Vector Borne Disease Control, Research and Development Council, Ministry of Health of the Republic of Indonesia, Jakarta, Indonesia
| | | | | | | | - Allison Imrie
- School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, 6009, Australia. .,Pathwest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia.
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17
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Ball JD, Elbadry MA, Telisma T, White SK, Chavannes S, Anilis MG, Prosperi M, Cummings DAT, Lednicky JA, Morris JG, Beau de Rochars M. Clinical and Epidemiologic Patterns of Chikungunya Virus Infection and Coincident Arboviral Disease in a School Cohort in Haiti, 2014-2015. Clin Infect Dis 2019; 68:919-926. [PMID: 30184178 PMCID: PMC6399436 DOI: 10.1093/cid/ciy582] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/10/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Beginning in December 2013, an epidemic of chikungunya virus (CHIKV) infection spread across the Caribbean and into virtually all countries in the Western hemisphere, with >2.4 million cases reported through the end of 2017. METHODS We monitored a cohort of school children in rural Haiti from May 2014, through February 2015, for occurrence of acute undifferentiated febrile illness, with clinical and laboratory data available for 252 illness episodes. RESULTS Our findings document passage of the major CHIKV epidemic between May and July 2014, with 82 laboratory-confirmed cases. Subsequent peaks of febrile illness were found to incorporate smaller outbreaks of dengue virus serotypes 1 and 4 and Zika virus, with identification of additional infections with Mayaro virus, enterovirus D68, and coronavirus NL63. CHIKV and dengue virus serotype 1 infections were more common in older children, with a complaint of arthralgia serving as a significant predictor for infection with CHIKV (odds ratio, 16.2; 95% confidence interval, 8.0-34.4; positive predictive value, 66%; negative predictive value, 80%). CONCLUSIONS Viral/arboviral infections were characterized by a pattern of recurrent outbreaks and case clusters, with the CHIKV epidemic representing just one of several arboviral agents moving through the population. Although clinical presentations of these agents are similar, arthralgias are highly suggestive of CHIKV infection.
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Affiliation(s)
- Jacob D Ball
- Emerging Pathogens Institute, College of Public Health and Health Professions and College of Medicine
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine
| | - Maha A Elbadry
- Emerging Pathogens Institute, College of Public Health and Health Professions and College of Medicine
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville
| | - Taina Telisma
- Christianville School Clinic, Christianville Foundation, Gressier, Haiti
| | - Sarah K White
- Emerging Pathogens Institute, College of Public Health and Health Professions and College of Medicine
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville
| | - Sonese Chavannes
- Christianville School Clinic, Christianville Foundation, Gressier, Haiti
| | - Marie Gina Anilis
- Christianville School Clinic, Christianville Foundation, Gressier, Haiti
| | - Mattia Prosperi
- Emerging Pathogens Institute, College of Public Health and Health Professions and College of Medicine
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine
| | - Derek A T Cummings
- Emerging Pathogens Institute, College of Public Health and Health Professions and College of Medicine
- Department of Biology, College of Liberal Arts and Sciences
| | - John A Lednicky
- Emerging Pathogens Institute, College of Public Health and Health Professions and College of Medicine
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville
| | - J Glenn Morris
- Emerging Pathogens Institute, College of Public Health and Health Professions and College of Medicine
- Department of Medicine, College of Medicine
| | - Madsen Beau de Rochars
- Emerging Pathogens Institute, College of Public Health and Health Professions and College of Medicine
- Department of Health Services Research, Management, and Policy, College of Public Health and Health Professions, University of Florida, Gainesville
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NAULITA TURNIP OKTAVIANI, FITRI HAYATI RAHMA, ALAWIYAH RIZKA, YOHAN BENEDIKTUS, DENIS DIONISIUS, BOWOLAKSONO ANOM, SOEBANDRIO AMIN, SASMONO RTEDJO. Growth Characteristics of Chikungunya Virus Isolate from Indonesia in Various Human Cell Lines in vitro. MICROBIOLOGY INDONESIA 2019. [DOI: 10.5454/mi.13.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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19
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Antivirus effectiveness of ivermectin on dengue virus type 2 in Aedes albopictus. PLoS Negl Trop Dis 2018; 12:e0006934. [PMID: 30452439 PMCID: PMC6277121 DOI: 10.1371/journal.pntd.0006934] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 12/03/2018] [Accepted: 10/18/2018] [Indexed: 12/27/2022] Open
Abstract
Background Dengue fever is the most rapidly spreading mosquito-borne viral disease over the past 50 years, with a 30-fold increase in global incidence. Dengue vector control is a key component for the dengue control strategy, since no absolutely effective vaccine or drug is available yet. However, the rapid rise and spread of mosquito insecticide resistance have become major threats to the efficiency of insecticide-based vector control activities. Thus, innovative vector control tools are badly needed. This study aims to confirm the antivirus effectiveness of ivermectin on dengue virus type 2 (DENV-2) in Aedes albopictus (Skuse, 1894), then to explore its potential use in the combating to the dengue epidemics. Methods Aedes albopictus were first infected with DENV-2 in human whole blood, and at the fourth day after infectious blood feeding, they were divided into eight groups. Seven of them were held for six days with access to 0, 2, 4, 8, 16, 32 and 64 ng/ml ivermectin, respectively, and the last one was set as a historical control group, which was stored at -80°C until being detected at the same time with the other groups. Each mosquito was detected using real-time fluorescent RT-PCR kit. DENV-2 RNA concentration (copies/ml) and infection rate in each group were compared. Results Both of quantitatively and qualitatively inhibiting effects of ivermectin have been detected in this study. Generally, DENV-2 replicated well in Aedes albopictus without ivermectin intervention, whose virus loads exhibited significantly higher when the mosquitoes were holding from 4 days to 10 days after infectious blood feeding. In contrast, with the treatment of ivermectin, the infection rate was reduced by as much as 49.63%. The regression equation between infection rates (Y2) and ivermectin concentration log2 values (X2) was obtained as Y2 = 91.41–7.21*X2 with R2 = 0.89. Conclusion Ivermectin can directly or indirectly inhibit DENV-2 multiplication in Aedes albopictus. Moreover, the actual concentration for application in zooprophylaxis needs to be confirmed in the further field trials. Dengue fever is one of neglected vector-borne tropical diseases with a 30-fold increase in global incidence recently. In 2012, World Health Organization set a goal to reduce dengue mortality by at least 50% by 2020. Being faced with more challenges in the dengue control programs, such as the increase of dengue outbreaks, lacking absolutely effective vaccine, rise of vector insecticide resistance and so on; innovative vector control tools are urgently needed for current control programs on dengue fever. To find a new avenue in vector control, we for the first time assessed the inhibiting effectiveness of ivermectin on dengue virus type 2 (DENV-2) inside Aedes mosquitoes. We found that about 80% Aedes albopictus mosquitoes were effectively infected with DENV-2 without treatment of ivermectin. But in the groups of ivermectin treatment, the infection rate of DENV-2 and the median of virus loads were significantly reduced by up to 49.63% and 99.99%, respectively. Both quantitatively and qualitatively inhibiting effects of ivermectin were detected. We found out that ivermectin was able to effectively inhibit the DENV-2 multiplication in Aedes albopictus, which may gave us a hint that using ivermectin in some control programs as a zooprophylaxis to block dengue epidemic through inhibiting DENV-2 in field Aedes mosquitoes.
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Zhang X, Huang Y, Wang M, Yang F, Wu C, Huang D, Xiong L, Wan C, Cheng J, Zhang R. Differences in genome characters and cell tropisms between two chikungunya isolates of Asian lineage and Indian Ocean lineage. Virol J 2018; 15:130. [PMID: 30126424 PMCID: PMC6102929 DOI: 10.1186/s12985-018-1024-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/16/2018] [Indexed: 12/17/2022] Open
Abstract
Background Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus within the family Togaviridae, which has attracted global attention due to its recent re-emergence. In one of our previous studies, we successfully isolated two CHIKV virus strains, SZ1050 and SZ1239, from the serum samples of two imported patients in 2010 and 2012, respectively. However, the differences in their genome characters and cell tropisms remain undefined. Methods We extracted the RNA of two CHIKV isolates and performed PCR to determine the sequence of the whole viral genomes. The genotypes were classified by phylogenetic analysis using the Mega 6.0 software. Furthermore, the cell tropisms of the two CHIKV isolates were evaluated in 13 cell lines. Results The lengths of the whole genomes for SZ1050 and SZ1239 were 11,844 nt and 12,000 nt, respectively. Phylogenetic analysis indicated that SZ1050 belonged to the Indian Ocean lineage (IOL), while SZ1239 was of the Asian lineage. Comparing to the prototype strain S27, a gap of 7 aa in the nsP3 gene and missing of one repeated sequence element (RSE) in the 3’ UTR were observed in SZ1239. The E1-A226V mutation was not detected in both strains. SZ1050 and SZ1239 could infect most of the evaluated mammalian epithelial cells. The K562 cells were permissive for both SZ1050 and SZ1239 while the U937 cells were refractory to both viruses. For Aedes cell lines C6/36 and Aag-2, both SZ1050 and SZ1239 were able to infect and replicate efficiently. Conclusions Compared to the prototype S27 virus, some deletions and mutations were found in the genomes of SZ1050 and SZ1239. Both viruses were susceptible to most evaluated epithelia or fibroblast cells and Aedes cell lines including C6/36 and Aag-2 in spite of marginal difference. Electronic supplementary material The online version of this article (10.1186/s12985-018-1024-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaomin Zhang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China.,School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yalan Huang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Miao Wang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Fan Yang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Chunli Wu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Dana Huang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Linghong Xiong
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Chengsong Wan
- School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515, China.
| | - Jinquan Cheng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China.
| | - Renli Zhang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China.
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Powers AM. Asymptomatic or Mild Febrile Cases of Madariaga: The Base of the Iceberg? Clin Infect Dis 2018; 67:622-623. [DOI: 10.1093/cid/ciy225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/06/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ann M Powers
- Arboviral Diseases Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado
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Complete Genome Sequences of Two Chikungunya Viruses Imported into China. GENOME ANNOUNCEMENTS 2018; 6:6/26/e00480-18. [PMID: 29954886 PMCID: PMC6025935 DOI: 10.1128/genomea.00480-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we isolated two chikungunya virus strains (SZ1050 and SZ1239) from patients infected with chikungunya virus who were returning to China from India and Indonesia, respectively. Strain SZ1050 was classed in the Indian Ocean lineage, and strain SZ1239 belonged to the Asian lineage. Here, we isolated two chikungunya virus strains (SZ1050 and SZ1239) from patients infected with chikungunya virus who were returning to China from India and Indonesia, respectively. Strain SZ1050 was classed in the Indian Ocean lineage, and strain SZ1239 belonged to the Asian lineage. No A226V mutation in the envelope protein E1 was found in either strain.
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