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Wulandari S, Nuryastuti T, Oktoviani FN, Daniwijaya MEW, Supriyati E, Arguni E, Hartono, Wibawa T. The association between high mobility group box 1 (HMGB1) and Interleukin-18 (IL-18) serum concentrations in COVID-19 inpatients. Heliyon 2024; 10:e26619. [PMID: 38434314 PMCID: PMC10907672 DOI: 10.1016/j.heliyon.2024.e26619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/05/2024] [Accepted: 02/16/2024] [Indexed: 03/05/2024] Open
Abstract
Background High mobility group box 1 (HMGB1) and interleukin-18 (IL-18) are involved in various non-coronavirus disease pathogenesis and are reported as potential biomarkers for coronavirus disease (COVID-19). However, their association with COVID-19 pathogenesis has not yet been explored. Aim This study aimed to investigate the association between HMGB1 and IL-18 concentrations in the sera of COVID-19 patients versus non-COVID-19 patients. Material and methods We used stored serum samples obtained from 30 COVID-19 patients and 30 non-COVID-19 patients. We collected data on age, gender, treatment status, principal diagnosis, and comorbidity from patient medical records. HMGB1 and IL-18 concentrations were analyzed in the serum by enzyme-linked immunosorbent assay (ELISA). The swab samples' RT-PCR cycle threshold (CT) values were obtained from the laboratory database. Results HMGB1 concentrations were increased in the COVID-19 inpatients and non-COVID-19 inpatients compared to non-COVID-19 outpatients (COVID-19 inpatients vs. non-COVID-19 outpatients: 151.33 (90.27-192.38) vs. 80.75 (54.16-128.72) ng/ml; p = 0.0316; non-COVID-19 inpatients vs. non-COVID-19 outpatients: 152.66 (104.04-288.51) vs. 80.75 (54.16-128.72) ng/ml; p = 0.0199). IL-18 concentrations were also higher in the COVID-19 inpatients and non-COVID-19 inpatients compared to non-COVID-19 outpatients (COVID-19 inpatients vs. non-COVID-19 outpatients: 620.00 (461.50-849.6) vs. 403.10 (372.70-556.90) pg/ml; p = 0.0376; non-COVID-19 inpatients vs. non-COVID-19 outpatients: 835.70 (558.30-1602.00) vs. 403.10 (372.70-556.90) pg/ml; p = 0.0026). Moreover, HMGB1 was associated with IL-18 concentrations in the sera of COVID-19 inpatients (p = 0.0337; r = 0.5500). Conclusion The association of HMGB1 and IL-18 in COVID-19 might indicate the potential for a dangerous cycle leading to a cytokine storm to occur.
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Affiliation(s)
- Sri Wulandari
- Doctorate Program of Medicine and Health Science, Faculty of Medicine Public Health and Nursing Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Physiology, Faculty of Medicine, Universitas Sebelas Maret, Surakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine Public Health and Nursing Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Farida Nur Oktoviani
- Department of Microbiology, Faculty of Medicine Public Health and Nursing Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Endah Supriyati
- Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hartono
- Department of Physiology, Faculty of Medicine, Universitas Sebelas Maret, Surakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine Public Health and Nursing Universitas Gadjah Mada, Yogyakarta, Indonesia
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Hakim MS, Gunadi, Rahayu A, Wibawa H, Eryvinka LS, Supriyati E, Vujira KA, Iskandar K, Afiahayati, Daniwijaya EW, Oktoviani FN, Annisa L, Utami FDT, Amadeus VC, Nurhidayah SS, Leksono TP, Halim FV, Arguni E, Nuryastuti T, Wibawa T. Sequence analysis of the Spike, RNA-dependent RNA polymerase, and protease genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia. Virus Genes 2024:10.1007/s11262-023-02048-1. [PMID: 38244104 DOI: 10.1007/s11262-023-02048-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 12/22/2023] [Indexed: 01/22/2024]
Abstract
During the Covid-19 pandemic, the resurgence of SARS-CoV-2 was due to the development of novel variants of concern (VOC). Thus, genomic surveillance is essential to monitor continuing evolution of SARS-CoV-2 and to track the emergence of novel variants. In this study, we performed phylogenetic, mutation, and selection pressure analyses of the Spike, nsp12, nsp3, and nsp5 genes of SARS-CoV-2 isolates circulating in Yogyakarta and Central Java provinces, Indonesia from May 2021 to February 2022. Various bioinformatics tools were employed to investigate the evolutionary dynamics of distinct SARS-CoV-2 isolates. During the study period, 213 and 139 isolates of Omicron and Delta variants were identified, respectively. Particularly in the Spike gene, mutations were significantly more abundant in Omicron than in Delta variants. Consistently, in all of four genes studied, the substitution rates of Omicron were higher than that of Delta variants, especially in the Spike and nsp12 genes. In addition, selective pressure analysis revealed several sites that were positively selected in particular genes, implying that these sites were functionally essential for virus evolution. In conclusion, our study demonstrated a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia.
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Affiliation(s)
- Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Gunadi
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ayu Rahayu
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hendra Wibawa
- Disease Investigation Center Wates, Directorate General of Livestok Services, Ministry of Agriculture, Yogyakarta, Indonesia
| | - Laudria Stella Eryvinka
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Khanza Adzkia Vujira
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Kristy Iskandar
- Department of Child Health and Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Afiahayati
- Department of Computer Science and Electronics, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edwin Widyanto Daniwijaya
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Farida Nur Oktoviani
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Luthvia Annisa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Fadila Dyah Trie Utami
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Verrell Christopher Amadeus
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Setiani Silvy Nurhidayah
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tiara Putri Leksono
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Fiqih Vidiantoro Halim
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Gunadi, Hakim MS, Wibawa H, Vujira KA, Puspitarani DA, Supriyati E, Trisnawati I, Iskandar K, Khair RE, Afiahayati, Siswanto, Puspadewi Y, Irianingsih SH, Nugrahaningsih DAA, Eryvinka LS, Utami FDT, Devana EM, Aditama L, Kinasih NCP, Hediningsih Y, Ananda NR, Marcellus, Arguni E, Nuryastuti T, Wibawa T. Prognostic factors for the outcomes of COVID-19 patients infected with SARS-CoV-2 Omicron and Delta variants. BMC Med Genomics 2023; 16:205. [PMID: 37644458 PMCID: PMC10464379 DOI: 10.1186/s12920-023-01637-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 Omicron variant has replaced the previously dominant Delta variant because of high transmissibility. However, studies on the impact of the Omicron variant on the severity of COVID-19 are still limited in developing countries. Our study aimed to determine the prognostic factors for the outcomes of patients infected with SARS-CoV-2 Omicron and Delta variants, including age, sex, comorbidities, and smoking. METHODS In this retrospective cross-sectional study, we involved 352 patients with COVID-19 from Yogyakarta and Central Java provinces, Indonesia, from May 2021 to February 2022, consisting of 164 males and 188 females. We included all patients with the PCR's Ct value of less than 30 for further whole-genome sequencing. RESULTS Ct value and mean age of COVID-19 patients were not significantly different between both groups (p = 0.146 and 0.273, respectively). Patients infected with Omicron (n = 139) and Delta (n = 213) variants showed similar hospitalization (p = 0.396) and mortality rates (p = 0.565). Multivariate analysis of both groups showed that older age (≥ 65 years) had a higher risk for hospitalization (OR = 3.86 [95% CI = 1.29-11.5]; p = 0.015) and fatalities (OR = 3.91 [95% CI = 1.35-11.42]; p = 0.012). In both groups, patients with cardiovascular disease had a higher risk for hospitalization (OR = 5.36 [95% CI = 1.08-26.52]; p = 0.039), whereas patients with diabetes revealed a higher risk for fatalities (OR = 9.47 [95% CI = 3.23-27.01]; p = < 0.001). CONCLUSIONS Our study shows that patients infected with Omicron and Delta variants reveal similar clinical outcomes, including hospitalization and mortality. Our findings further confirm that older age, cardiovascular disease, and diabetes are substantial prognostic factors for the outcomes of COVID-19 patients. Our findings imply that COVID-19 patients with older age, cardiovascular disease, or diabetes should be treated comprehensively and cautiously to prevent further morbidity and mortality. Furthermore, incomplete data on vaccination status hampered us from analyzing further its impact on hospitalization and mortality in our patients.
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Affiliation(s)
- Gunadi
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hendra Wibawa
- Directorate General, and Livestock Services, Disease Investigation Center Wates (Balai Besar Veteriner Wates), Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Khanza Adzkia Vujira
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dyah Ayu Puspitarani
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ika Trisnawati
- Pulmonology Division, Department of Internal Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Kristy Iskandar
- Department of Child Health/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Riat El Khair
- Department of Clinical Pathology and Laboratory Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, 55281, Indonesia
| | - Afiahayati
- Department of Computer Science and Electronics Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Siswanto
- Department of Physiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Yunika Puspadewi
- Department of Child Health/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Sri Handayani Irianingsih
- Directorate General, and Livestock Services, Disease Investigation Center Wates (Balai Besar Veteriner Wates), Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Dwi Aris Agung Nugrahaningsih
- Department of Pharmacology and Therapy/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Laudria Stella Eryvinka
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Fadila Dyah Trie Utami
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edita Mayda Devana
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Lanang Aditama
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Nathania Christi Putri Kinasih
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Yekti Hediningsih
- Balai Laboratorium Kesehatan dan Pengujian Alat Kesehatan, Central Java, Semarang, Indonesia
| | - Nur Rahmi Ananda
- Pulmonology Division, Department of Internal Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Marcellus
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Gazali FM, Wijayanti N, Hakim MS, Supriyati E, Arguni E, Daniwijaya MEW, Nuryastuti T, Nuhamunada M, Nabilla R, Haryana SM, Wibawa T. The high mutation rate at the D614G hotspot-furin cleavage site region increases the priming efficiency of the Spike protein by furin protease: analysis of Indonesian SARS-CoV-2 G614 variants obtained during the early COVID-19 pandemic. Virusdisease 2023:1-10. [PMID: 37363361 PMCID: PMC10231289 DOI: 10.1007/s13337-023-00827-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/08/2023] [Indexed: 06/28/2023] Open
Abstract
D614G mutation plays a significant role in the transmissibility of SARS-CoV-2. Identification of other mutations related to D614G mutation within the Spike protein is pivotal as they might contribute to the pathogenicity of SARS-CoV-2. This study aims to analyze the mutation rate of furin cleavage site (FCS) region of Indonesian origin SARS-CoV-2 and to predict the effect of mutation against Spike priming efficiency by furin. A total of 375 sequences of Indonesian isolates obtained during the early pandemic were used for mutation analysis. Mutation analysis includes mutation pattern, variability, frequency of mutation, amino acid conservation, and mutation rate. The effect of mutation against Spike priming efficiency by furin protease from eight sequences with mutation in the FCS region was analyzed by protein-protein docking. We showed that mutations related to the G614 variant were increasing through time, in contrast to the D614 variant. The FCS region at the position 675-692 contained the most variable (66.67%) as well as the highest mutation frequency (85.92%) and has been observed to be the hotspot mutations linked to the D614G mutation. The D614G hotspot-FCS region (residue 600-700) had the highest amino acid change per site (20.8%) as well as the highest mutation rate as 1.34 × 10-2 substitution per site per year (95% CI 1.79 × 10-3-2.74 × 10-2), compared with other Spike protein regions. Mutations in the FCS region were the most common mutation found after the D614G mutation. These mutations were predicted to increase the Spike priming efficiency by furin. Thus, this study elucidates the importance of D614G mutation to other mutations located in the FCS region and their significance to Spike priming efficiency by furin. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-023-00827-w.
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Affiliation(s)
- Faris Muhammad Gazali
- Master Program in Biotechnology, Postgraduate School, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Nastiti Wijayanti
- Animal Physiology Laboratory, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre for Tropical Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Matin Nuhamunada
- Biotechnology Laboratory, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Rahma Nabilla
- Graduate Program in Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Sofia Mubarika Haryana
- Department of Histology and Cell Biology, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Murni IK, Oktaria V, Handley A, McCarthy DT, Donato CM, Nuryastuti T, Supriyati E, Putri DAD, Sari HM, Laksono IS, Thobari JA, Bines JE. The feasibility of SARS-CoV-2 surveillance using wastewater and environmental sampling in Indonesia. PLoS One 2022; 17:e0274793. [PMID: 36240187 PMCID: PMC9565423 DOI: 10.1371/journal.pone.0274793] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/05/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Wastewater-based epidemiology (WBE) surveillance as an early warning system (EWS) for monitoring community transmission of SARS-CoV-2 in low- and middle-income country (LMIC) settings, where diagnostic testing capacity is limited, needs further exploration. We explored the feasibility to conduct a WBE surveillance in Indonesia, one of the global epicenters of the COVID-19 pandemic in the middle of 2021, with the fourth largest population in the world where sewer and non-sewered sewage systems are implemented. The feasibility and resource capacity to collect samples on a weekly or fortnightly basis with grab and/or passive sampling methods, as well as to conduct qualitative and quantitative identification of SARS-CoV-2 ribonucleic acid (RNA) using real-time RT-PCR (RT-qPCR) testing of environmental samples were explored. MATERIALS AND METHODS We initiated a routine surveillance of wastewater and environmental sampling at three predetermined districts in Special Region of Yogyakarta Province. Water samples were collected from central and community wastewater treatment plants (WWTPs), including manholes flowing to the central WWTP, and additional soil samples were collected for the near source tracking (NST) locations (i.e., public spaces where people congregate). RESULTS We began collecting samples in the Delta wave of the COVID-19 pandemic in Indonesia in July 2021. From a 10-week period, 54% (296/544) of wastewater and environmental samples were positive for SARS-CoV-2 RNA. The sample positivity rate decreased in proportion with the reported incidence of COVID-19 clinical cases in the community. The highest positivity rate of 77% in week 1, was obtained for samples collected in July 2021 and decreased to 25% in week 10 by the end of September 2021. CONCLUSION A WBE surveillance system for SARS-CoV-2 in Indonesia is feasible to monitor the community burden of infections. Future studies testing the potential of WBE and EWS for signaling early outbreaks of SARS-CoV-2 transmissions in this setting are required.
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Affiliation(s)
- Indah K. Murni
- Faculty of Medicine, Center for Child Health–Pediatric Research Office, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Faculty of Medicine, Child Health Department, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- * E-mail: (IKM); (VO)
| | - Vicka Oktaria
- Faculty of Medicine, Center for Child Health–Pediatric Research Office, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Faculty of Medicine, Department of Biostatistics, Epidemiology and Population Health, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- * E-mail: (IKM); (VO)
| | - Amanda Handley
- Enteric Diseases Group, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Medicines Development for Global Health, Southbank, Victoria, Australia
| | - David T. McCarthy
- Department of Civil Engineering, Environmental and Public Health Microbiology Lab (EPHM Lab), Monash University, Clayton, Victoria, Australia
| | - Celeste M. Donato
- Enteric Diseases Group, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Titik Nuryastuti
- Faculty of Medicine, Department of Microbiology, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Faculty of Medicine, Center for Tropical Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dwi Astuti Dharma Putri
- Faculty of Medicine, Center for Child Health–Pediatric Research Office, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hendri Marinda Sari
- Faculty of Medicine, Center for Child Health–Pediatric Research Office, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ida Safitri Laksono
- Faculty of Medicine, Center for Child Health–Pediatric Research Office, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Faculty of Medicine, Child Health Department, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Jarir At Thobari
- Faculty of Medicine, Center for Child Health–Pediatric Research Office, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Julie E. Bines
- Enteric Diseases Group, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Department of Gastroenterology and Clinical Nutrition, Royal Children’s Hospital Melbourne, Parkville, Victoria, Australia
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6
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Arguni E, Indriani C, Rahayu A, Supriyati E, Yohan B, Hayati RF, Wardana S, Tantowijoyo W, Anshari MR, Rahayu E, Ahmad RA, Utarini A, Simmons CP, Sasmono RT. Dengue virus population genetics in Yogyakarta, Indonesia prior to city-wide Wolbachia deployment. Infect Genet Evol 2022; 102:105308. [PMID: 35644356 DOI: 10.1016/j.meegid.2022.105308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/29/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
Dengue has been endemic in Yogyakarta, Indonesia for decades. Here, we report the dengue epidemiology, entomology, and virology in Yogyakarta in 2016-2017, prior to the commencement of the Applying Wolbachia to Eliminate Dengue (AWED) randomized trial. Dengue epidemiological data were compiled and blood samples from dengue-suspected patients were tested for dengue virus (DENV). Ae. aegypti mosquito samples were caught from the field using BG-Sentinel traps and tested for the presence of DENV infection. Sequencing of the DENV E gene was used to determine the phylogeny and genotypes of circulating DENV. Within the last decade, the 2016-2017 dengue incidence was considered very high. Among the 649 plasma samples collected between March 2016-February 2017; and 36,910 mosquito samples collected between December 2016-May 2017, a total of 197 and 38 samples were DENV-positive by qRT-PCR, respectively. All four DENV serotypes were detected, with DENV-3 (n = 88; 44.67%) and DENV-1 (n = 87; 44.16%) as the predominant serotype, followed by DENV-4 (n = 12; 6.09%) and DENV-2 (n = 10; 5.08%). The Yogyakarta DENV-1 isolates were classified into Genotype I and IV, while DENV-2, DENV-3, and DENV-4 isolates were classified into the Cosmopolitan genotype, Genotype I, and Genotype II, respectively. Yogyakarta DENV isolates were closely related to Indonesian strains from neighboring Javanese cities, consistent with the endemic circulation of DENV on this highly populous island. Our study provides comprehensive baseline information on the DENV population genetic characteristics in Yogyakarta, which are useful as baseline data for the AWED trial and the future DENV surveillance in the city in the presence of a Wolbachia-infected Ae. aegypti population.
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Affiliation(s)
- Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Citra Indriani
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; Department of Biostatistics, Epidemiology and Population Health, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ayu Rahayu
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Rahma F Hayati
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Satrio Wardana
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Warsito Tantowijoyo
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Muhammad Ridwan Anshari
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endang Rahayu
- Disease Control Department, Yogyakarta District Health Office, Yogyakarta, Indonesia
| | - Riris Andono Ahmad
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; Department of Biostatistics, Epidemiology and Population Health, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Adi Utarini
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; Department of Health Policy and Management, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Cameron P Simmons
- World Mosquito Program, Institute of Vector Borne Disease, Monash University, Clayton, Victoria 3800, Australia
| | - R Tedjo Sasmono
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
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7
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Arguni E, Supriyati E, Hakim MS, Daniwijaya EW, Makrufardi F, Rahayu A, Rovik A, Saraswati U, Oktoviani FN, Prastiwi N, Nuryastuti T, Wibawa T, Haryana SM. Co-infection of SARS-CoV-2 with other viral respiratory pathogens in Yogyakarta, Indonesia: A cross-sectional study. Ann Med Surg (Lond) 2022; 77:103676. [PMID: 35531428 PMCID: PMC9055379 DOI: 10.1016/j.amsu.2022.103676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 11/05/2022] Open
Abstract
Background Growing evidence shows that viral co-infection is found repeatedly in patients with Coronavirus Disease–2019 (COVID-19). This is the first report of SARS-CoV-2 co-infection with viral respiratory pathogens in Indonesia. Methods Over a one month period of April to May 2020, SARS-CoV-2 positive nasopharyngeal swabs in our COVID-19 referral laboratory in Yogyakarta, Indonesia, were tested for viral respiratory pathogens by real-time, reverse transcription polymerase chain reaction (RT-PCR). Proportion of co-infection reported in percentage. Results Fifty-nine samples were positive for other viral respiratory pathogens among a total of 125 samples. Influenza A virus was detected in 32 samples, Influenza B in 16 samples, Human metapneumovirus in 1 sample, and adenovirus in 10 samples. We did not detect any co-infection with respiratory syncytial virus. Nine (7.2%) patients had co-infection with more than two viruses. Conclusion Viral co-infection with SARS-CoV-2 is common. These results will provide a helpful reference for diagnosis and clinical treatment of patients with COVID-19. Viral co-infection with SARS-CoV-2 is common. Co-infection by two viral respiratory pathogens is prevalent. Pandemic transmission control may also impact in other viral respiratory infections. Early identification of co-infection is necessary, given differences in treatment. Simple laboratory diagnosis algorithm may be applied to screen viral co-infection.
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8
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Tantowijoyo W, Tanamas SK, Nurhayati I, Setyawan S, Budiwati N, Fitriana I, Ernesia I, Wardana DS, Supriyati E, Arguni E, Meitika Y, Prabowo E, Andari B, Green BR, Hodgson L, Rancès E, Ryan PA, O’Neill SL, Anders KL, Ansari MR, Indriani C, Ahmad RA, Utarini A, Simmons CP. Aedes aegypti abundance and insecticide resistance profiles in the Applying Wolbachia to Eliminate Dengue trial. PLoS Negl Trop Dis 2022; 16:e0010284. [PMID: 35442957 PMCID: PMC9060332 DOI: 10.1371/journal.pntd.0010284] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 05/02/2022] [Accepted: 02/27/2022] [Indexed: 11/21/2022] Open
Abstract
The Applying Wolbachia to Eliminate Dengue (AWED) trial was a parallel cluster randomised trial that demonstrated Wolbachia (wMel) introgression into Ae. aegypti populations reduced dengue incidence. In this predefined substudy, we compared between treatment arms, the relative abundance of Ae. aegypti and Ae. albopictus before, during and after wMel-introgression. Between March 2015 and March 2020, 60,084 BG trap collections yielded 478,254 Ae. aegypti and 17,623 Ae. albopictus. Between treatment arms there was no measurable difference in Ae. aegypti relative abundance before or after wMel-deployments, with a count ratio of 0.96 (95% CI 0.76, 1.21) and 1.00 (95% CI 0.85, 1.17) respectively. More Ae. aegypti were caught per trap per week in the wMel-intervention arm compared to the control arm during wMel deployments (count ratio 1.23 (95% CI 1.03, 1.46)). Between treatment arms there was no measurable difference in the Ae. albopictus population size before, during or after wMel-deployment (overall count ratio 1.10 (95% CI 0.89, 1.35)). We also compared insecticide resistance phenotypes of Ae. aegypti in the first and second years after wMel-deployments. Ae. aegypti field populations from wMel-treated and untreated arms were similarly resistant to malathion (0.8%), permethrin (1.25%) and cyfluthrin (0.15%) in year 1 and year 2 of the trial. In summary, we found no between-arm differences in the relative abundance of Ae. aegypti or Ae. albopictus prior to or after wMel introgression, and no between-arm difference in Ae. aegypti insecticide resistance phenotypes. These data suggest neither Aedes abundance, nor insecticide resistance, confounded the epidemiological outcomes of the AWED trial. Dengue is a mosquito-borne viral disease and a major public health problem in the tropical and subtropical world. It is caused by any of the four dengue virus serotypes. In a previously published randomised clinical trial, called the AWED trial, we demonstrated that releases of Aedes aegypti mosquitoes infected with the insect bacterium Wolbachia can reduce the case incidence of dengue by 77%. In this current study, we compared the abundance of Ae. aegypti mosquitoes in the neighbourhoods where Wolbachia-infected mosquitoes were released versus the untreated neighbourhoods. This was important to do so that scientists could understand the mechanism for how Wolbachia releases reduced dengue incidence. Between March 2015 and March 2020, we did not observe any differences in Ae. aegypti abundance before or after Wolbachia-deployments in the AWED trial area. There was also no difference in the abundance of the related mosquito, Ae. albopictus, before, during or after wMel-deployment. We also compared insecticide resistance characteristics amongst Ae. aegypti in the first and second years after Wolbachia -deployments and found no difference between mosquitoes from Wolbachia-treated and untreated neighbourhoods. These data suggest neither Aedes abundance, nor insecticide resistance, were confounding sources to the epidemiological outcomes of the AWED trial.
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Affiliation(s)
- Warsito Tantowijoyo
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Stephanie K. Tanamas
- World Mosquito Program, Institute of Vector-borne Disease, Monash University, Clayton, Australia
| | - Indah Nurhayati
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Sigit Setyawan
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Nida Budiwati
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Iva Fitriana
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Inggrid Ernesia
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dwi Satria Wardana
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Yeti Meitika
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Equatori Prabowo
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Bekti Andari
- World Mosquito Program, Institute of Vector-borne Disease, Monash University, Clayton, Australia
| | - Benjamin R. Green
- World Mosquito Program, Institute of Vector-borne Disease, Monash University, Clayton, Australia
| | - Lauren Hodgson
- World Mosquito Program, Institute of Vector-borne Disease, Monash University, Clayton, Australia
| | - Edwige Rancès
- World Mosquito Program, Institute of Vector-borne Disease, Monash University, Clayton, Australia
| | - Peter A. Ryan
- World Mosquito Program, Institute of Vector-borne Disease, Monash University, Clayton, Australia
| | - Scott L. O’Neill
- World Mosquito Program, Institute of Vector-borne Disease, Monash University, Clayton, Australia
| | - Katherine L. Anders
- World Mosquito Program, Institute of Vector-borne Disease, Monash University, Clayton, Australia
| | - M. Ridwan Ansari
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Citra Indriani
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Biostatistics, Epidemiology and Public Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Riris Andono Ahmad
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Biostatistics, Epidemiology and Public Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Adi Utarini
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Health Policy and Management, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Cameron P. Simmons
- World Mosquito Program, Institute of Vector-borne Disease, Monash University, Clayton, Australia
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- * E-mail:
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9
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Wijayanti N, Gazali FM, Supriyati E, Hakim MS, Arguni E, Daniwijaya MEW, Nuryastuti T, Nuhamunada M, Nabilla R, Haryana SM, Wibawa T. Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. Int Microbiol 2022; 25:531-540. [PMID: 35165816 PMCID: PMC8853438 DOI: 10.1007/s10123-022-00239-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/21/2022] [Accepted: 02/03/2022] [Indexed: 01/20/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new virus responsible for the COVID-19 pandemic. The emergence of the new SARS-CoV-2 has been attributed to the possibility of evolutionary dynamics in the furin cleavage site (FCS) region. This study aimed to analyze the sequence of the FCS region in the spike protein of SARS-CoV-2 isolates that circulated in the Special Region of Yogyakarta and Central Java provinces in Indonesia. The RNA solution extracted from nasopharyngeal swab samples of confirmed COVID-19 patients were used and subjected to cDNA synthesis, PCR amplification, sequencing, and analysis of the FCS region. The sequence data from GISAID were also retrieved for further genome analysis. This study included 52 FCS region sequences. Several mutations were identified in the FCS region, i.e., D614G, Q675H, Q677H, S680P, and silent mutation in 235.57 C > T. The most important mutation in the FCS region is D614G. This finding indicated the G614 variant was circulating from May 2020 in those two provinces. Eventually, the G614 variant totally replaced the D614 variant from September 2020. All Indonesian SARS-CoV-2 isolates during this study and those deposited in GISAID showed the formation of five clade clusters from the FCS region, in which the D614 variant is in one specific cluster, and the G614 variant is dispersed into four clusters. The data indicated there is evolutionary advantage of the D614G mutation in the FCS region of the spike protein of SARS-CoV-2 circulating in the Special Region of Yogyakarta and Central Java provinces in Indonesia.
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Affiliation(s)
- Nastiti Wijayanti
- Animal Physiology Laboratory, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Faris Muhammad Gazali
- Master Program in Biotechnology, Postgraduate School, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Jl. Farmako, Sekip Utara, Yogyakarta, 55281, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Marselinus Edwin Widyanto Daniwijaya
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Jl. Farmako, Sekip Utara, Yogyakarta, 55281, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Jl. Farmako, Sekip Utara, Yogyakarta, 55281, Indonesia
| | - Matin Nuhamunada
- Biotechnology Laboratory, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Rahma Nabilla
- Graduate Program in Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Sofia Mubarika Haryana
- Department of Histology and Cell Biology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Jl. Farmako, Sekip Utara, Yogyakarta, 55281, Indonesia.
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10
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Gunadi, Hakim MS, Wibawa H, Marcellus, Setiawaty V, Slamet, Trisnawati I, Supriyati E, El Khair R, Iskandar K, Afiahayati, Siswanto, Irene, Anggorowati N, Daniwijaya EW, Nugrahaningsih DAA, Puspadewi Y, Puspitarani DA, Tania I, Vujira KA, Ardlyamustaqim MB, Gabriela GC, Eryvinka LS, Nirmala BC, Geometri ET, Darutama AA, Kuswandani AA, Lestari, Irianingsih SH, Khoiriyah S, Lestari I, Ananda NR, Arguni E, Nuryastuti T, Wibawa T. Is the Infection of the SARS-CoV-2 Delta Variant Associated With the Outcomes of COVID-19 Patients? Front Med (Lausanne) 2021; 8:780611. [PMID: 34957154 PMCID: PMC8695874 DOI: 10.3389/fmed.2021.780611] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) Delta variant (B.1.617.2) has been responsible for the current increase in Coronavirus disease 2019 (COVID-19) infectivity rate worldwide. We compared the impact of the Delta variant and non-Delta variant on the COVID-19 outcomes in patients from Yogyakarta and Central Java provinces, Indonesia. Methods: In this cross-sectional study, we ascertained 161 patients, 69 with the Delta variant and 92 with the non-Delta variant. The Illumina MiSeq next-generation sequencer was used to perform the whole-genome sequences of SARS-CoV-2. Results: The mean age of patients with the Delta variant and the non-Delta variant was 27.3 ± 20.0 and 43.0 ± 20.9 (p = 3 × 10-6). The patients with Delta variant consisted of 23 males and 46 females, while the patients with the non-Delta variant involved 56 males and 36 females (p = 0.001). The Ct value of the Delta variant (18.4 ± 2.9) was significantly lower than that of the non-Delta variant (19.5 ± 3.8) (p = 0.043). There was no significant difference in the hospitalization and mortality of patients with Delta and non-Delta variants (p = 0.80 and 0.29, respectively). None of the prognostic factors were associated with the hospitalization, except diabetes with an OR of 3.6 (95% CI = 1.02-12.5; p = 0.036). Moreover, the patients with the following factors have been associated with higher mortality rate than the patients without the factors: age ≥65 years, obesity, diabetes, hypertension, and cardiovascular disease with the OR of 11 (95% CI = 3.4-36; p = 8 × 10-5), 27 (95% CI = 6.1-118; p = 1 × 10-5), 15.6 (95% CI = 5.3-46; p = 6 × 10-7), 12 (95% CI = 4-35.3; p = 1.2 × 10-5), and 6.8 (95% CI = 2.1-22.1; p = 0.003), respectively. Multivariate analysis showed that age ≥65 years, obesity, diabetes, and hypertension were the strong prognostic factors for the mortality of COVID-19 patients with the OR of 3.6 (95% CI = 0.58-21.9; p = 0.028), 16.6 (95% CI = 2.5-107.1; p = 0.003), 5.5 (95% CI = 1.3-23.7; p = 0.021), and 5.8 (95% CI = 1.02-32.8; p = 0.047), respectively. Conclusions: We show that the patients infected by the SARS-CoV-2 Delta variant have a lower Ct value than the patients infected by the non-Delta variant, implying that the Delta variant has a higher viral load, which might cause a more transmissible virus among humans. However, the Delta variant does not affect the COVID-19 outcomes in our patients. Our study also confirms that older age and comorbidity increase the mortality rate of patients with COVID-19.
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Affiliation(s)
- Gunadi
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hendra Wibawa
- Disease Investigation Center, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Marcellus
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Vivi Setiawaty
- National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Slamet
- National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Ika Trisnawati
- Pulmonology Division, Department of Internal Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Riat El Khair
- Department of Clinical Pathology and Laboratory Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Kristy Iskandar
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Afiahayati
- Department of Computer Science and Electronics Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Siswanto
- Department of Physiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Irene
- Balai Besar Teknik Kesehatan Lingkungan dan Pengendalian Penyakit, Yogyakarta, Indonesia
| | - Nungki Anggorowati
- Department of Anatomical Pathology/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edwin Widyanto Daniwijaya
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dwi Aris Agung Nugrahaningsih
- Department of Pharmacology and Therapy/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Yunika Puspadewi
- Department of Clinical Pathology and Laboratory Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Dyah Ayu Puspitarani
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Irene Tania
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Khanza Adzkia Vujira
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Muhammad Buston Ardlyamustaqim
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Gita Christy Gabriela
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Laudria Stella Eryvinka
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Bunga Citta Nirmala
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Esensi Tarian Geometri
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Abirafdi Amajida Darutama
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Anisa Adityarini Kuswandani
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Lestari
- Disease Investigation Center, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | | | | | | | - Nur Rahmi Ananda
- Pulmonology Division, Department of Internal Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Gunadi, Hakim MS, Wibawa H, Marcellus, Trisnawati I, Supriyati E, Afiahayati, Khair RE, Iskandar K, Siswanto, Irene, Anggorowati N, Daniwijaya EW, Nugrahaningsih DAA, Puspadewi Y, Simanjaya S, Puspitarani DA, Hanifin HF, Setiawan AA, Tania I, Amalia CS, Artayasa IPA, Rachman H, Mulyawan H, Ananda NR, Arguni E, Nuryastuti T, Wibawa T. Association between prognostic factors and the outcomes of patients infected with SARS-CoV-2 harboring multiple spike protein mutations. Sci Rep 2021; 11:21352. [PMID: 34725366 PMCID: PMC8560824 DOI: 10.1038/s41598-021-00459-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/05/2021] [Indexed: 12/16/2022] Open
Abstract
The outcome of SARS-CoV-2 infection is determined by multiple factors, including the viral, host genetics, age, and comorbidities. This study investigated the association between prognostic factors and disease outcomes of patients infected by SARS-CoV-2 with multiple S protein mutations. Fifty-one COVID-19 patients were recruited in this study. Whole-genome sequencing of 170 full-genomes of SARS-CoV-2 was conducted with the Illumina MiSeq sequencer. Most patients (47%) had mild symptoms of COVID-19 followed by moderate (19.6%), no symptoms (13.7%), severe (4%), and critical (2%). Mortality was found in 13.7% of the COVID-19 patients. There was a significant difference between the age of hospitalized patients (53.4 ± 18 years) and the age of non-hospitalized patients (34.6 ± 19) (p = 0.001). The patients' hospitalization was strongly associated with hypertension, diabetes, and anticoagulant and were strongly significant with the OR of 17 (95% CI 2-144; p = 0.001), 4.47 (95% CI 1.07-18.58; p = 0.039), and 27.97 (95% CI 1.54-507.13; p = 0.02), respectively; while the patients' mortality was significantly correlated with patients' age, anticoagulant, steroid, and diabetes, with OR of 8.44 (95% CI 1.5-47.49; p = 0.016), 46.8 (95% CI 4.63-472.77; p = 0.001), 15.75 (95% CI 2-123.86; p = 0.009), and 8.5 (95% CI 1.43-50.66; p = 0.019), respectively. This study found the clade: L (2%), GH (84.3%), GR (11.7%), and O (2%). Besides the D614G mutation, we found L5F (18.8%), V213A (18.8%), and S689R (8.3%). No significant association between multiple S protein mutations and the patients' hospitalization or mortality. Multivariate analysis revealed that hypertension and anticoagulant were the significant factors influencing the hospitalization and mortality of patients with COVID-19 with an OR of 17.06 (95% CI 2.02-144.36; p = 0.009) and 46.8 (95% CI 4.63-472.77; p = 0.001), respectively. Moreover, the multiple S protein mutations almost reached a strong association with patients' hospitalization (p = 0.07). We concluded that hypertension and anticoagulant therapy have a significant impact on COVID-19 outcomes. This study also suggests that multiple S protein mutations may impact the COVID-19 outcomes. This further emphasized the significance of monitoring SARS-CoV-2 variants through genomic surveillance, particularly those that may impact the COVID-19 outcomes.
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Affiliation(s)
- Gunadi
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Jl. Kesehatan No. 1, Yogyakarta, 55281, Indonesia.
| | - Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hendra Wibawa
- Disease Investigation Center, Wates, Yogyakarta, Indonesia
| | - Marcellus
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ika Trisnawati
- Pulmonology Division, Department of Internal Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Afiahayati
- Department of Computer Science and Electronics Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Riat El Khair
- Department of Clinical Pathology and Laboratory Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, 55281, Indonesia
| | - Kristy Iskandar
- Department of Child Health/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Siswanto
- Department of Physiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Irene
- Balai Besar Teknik Kesehatan Lingkungan Dan Pengendalian Penyakit, Yogyakarta, Yogyakarta, Indonesia
| | - Nungki Anggorowati
- Department of Anatomical Pathology/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edwin Widyanto Daniwijaya
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Dwi Aris Agung Nugrahaningsih
- Department of Pharmacology and Therapy/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Yunika Puspadewi
- Department of Clinical Pathology and Laboratory Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, 55281, Indonesia
| | - Susan Simanjaya
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dyah Ayu Puspitarani
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hana Fauzyyah Hanifin
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Alvina Alexandra Setiawan
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Irene Tania
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Cita Shafira Amalia
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - I Putu Aditio Artayasa
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Haries Rachman
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Nur Rahmi Ananda
- Pulmonology Division, Department of Internal Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Gazali FM, Nuhamunada M, Nabilla R, Supriyati E, Hakim MS, Arguni E, Daniwijaya EW, Nuryastuti T, Haryana SM, Wibawa T, Wijayanti N. Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. Heliyon 2021; 7:e07936. [PMID: 34514180 PMCID: PMC8420086 DOI: 10.1016/j.heliyon.2021.e07936] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/03/2021] [Accepted: 09/02/2021] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES Monitoring the spread of the G614 in specific locations is critical as this variant is highly transmissible and can trigger the emergence of other mutations. Therefore, a rapid and accurate method that can reliably detect the D614G mutation will be beneficial. This study aims to analyze the potential use of the two-step Reverse Transcriptase quantitative polymerase chain reaction - high resolution melting analysis (RT-qPCR-HRM) to detect a specific mutation in the SARS-CoV-2 genome. METHODS Six SARS-CoV-2 RNA samples were synthesized into cDNA and analyzed with the qPCR-HRM method in order to detect the D614G mutation in Spike protein of SARS-CoV-2. The primers are designed to target the specific Spike region containing the D614G mutation. The qPCR-HRM analysis was conducted simultaneously, and the identification of the SARS-CoV-2 variant was confirmed by conventional PCR and Sanger sequencing methods. RESULTS The results showed that the melting temperature (Tm) of the D614 variant was 79.39 ± 0.03 °C, which was slightly lower than the Tm of the G614 variant (79.62 ± 0.015 °C). The results of the HRM analysis, visualized by the normalized melting curve and the difference curve were able to discriminate the D614 and G614 variant samples. All samples were identified as G614 variants by qPCR-HRM assay, which was subsequently confirmed by Sanger sequencing. CONCLUSIONS This study demonstrated a sensitive method that can identify the D614G mutation by a simple two-step RT-qPCR-HRM assay procedure analysis, which can be useful for active surveillance of the transmission of a specific mutation.
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Affiliation(s)
- Faris Muhammad Gazali
- Master Program in Biotechnology Study Program, Postgraduate School, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Matin Nuhamunada
- Biotechnology Laboratory, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Rahma Nabilla
- Graduate Program in Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Diagnostic Laboratory of World Mosquito Program (WMP), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edwin Widyanto Daniwijaya
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Sofia Mubarika Haryana
- Department of Histology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Nastiti Wijayanti
- Animal Physiology Laboratory, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
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13
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Utarini A, Indriani C, Ahmad RA, Tantowijoyo W, Arguni E, Ansari MR, Supriyati E, Wardana DS, Meitika Y, Ernesia I, Nurhayati I, Prabowo E, Andari B, Green BR, Hodgson L, Cutcher Z, Rancès E, Ryan PA, O'Neill SL, Dufault SM, Tanamas SK, Jewell NP, Anders KL, Simmons CP. Efficacy of Wolbachia-Infected Mosquito Deployments for the Control of Dengue. N Engl J Med 2021; 384:2177-2186. [PMID: 34107180 PMCID: PMC8103655 DOI: 10.1056/nejmoa2030243] [Citation(s) in RCA: 209] [Impact Index Per Article: 69.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Aedes aegypti mosquitoes infected with the wMel strain of Wolbachia pipientis are less susceptible than wild-type A. aegypti to dengue virus infection. METHODS We conducted a cluster-randomized trial involving releases of wMel-infected A. aegypti mosquitoes for the control of dengue in Yogyakarta, Indonesia. We randomly assigned 12 geographic clusters to receive deployments of wMel-infected A. aegypti (intervention clusters) and 12 clusters to receive no deployments (control clusters). All clusters practiced local mosquito-control measures as usual. A test-negative design was used to assess the efficacy of the intervention. Patients with acute undifferentiated fever who presented to local primary care clinics and were 3 to 45 years of age were recruited. Laboratory testing was used to identify participants who had virologically confirmed dengue (VCD) and those who were test-negative controls. The primary end point was symptomatic VCD of any severity caused by any dengue virus serotype. RESULTS After successful introgression of wMel into the intervention clusters, 8144 participants were enrolled; 3721 lived in intervention clusters, and 4423 lived in control clusters. In the intention-to-treat analysis, VCD occurred in 67 of 2905 participants (2.3%) in the intervention clusters and in 318 of 3401 (9.4%) in the control clusters (aggregate odds ratio for VCD, 0.23; 95% confidence interval [CI], 0.15 to 0.35; P = 0.004). The protective efficacy of the intervention was 77.1% (95% CI, 65.3 to 84.9) and was similar against the four dengue virus serotypes. The incidence of hospitalization for VCD was lower among participants who lived in intervention clusters (13 of 2905 participants [0.4%]) than among those who lived in control clusters (102 of 3401 [3.0%]) (protective efficacy, 86.2%; 95% CI, 66.2 to 94.3). CONCLUSIONS Introgression of wMel into A. aegypti populations was effective in reducing the incidence of symptomatic dengue and resulted in fewer hospitalizations for dengue among the participants. (Funded by the Tahija Foundation and others; AWED ClinicalTrials.gov number, NCT03055585; Indonesia Registry number, INA-A7OB6TW.).
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Affiliation(s)
- Adi Utarini
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Citra Indriani
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Riris A Ahmad
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Warsito Tantowijoyo
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Eggi Arguni
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - M Ridwan Ansari
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Endah Supriyati
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - D Satria Wardana
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Yeti Meitika
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Inggrid Ernesia
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Indah Nurhayati
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Equatori Prabowo
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Bekti Andari
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Benjamin R Green
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Lauren Hodgson
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Zoe Cutcher
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Edwige Rancès
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Peter A Ryan
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Scott L O'Neill
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Suzanne M Dufault
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Stephanie K Tanamas
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Nicholas P Jewell
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Katherine L Anders
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
| | - Cameron P Simmons
- From the World Mosquito Program Yogyakarta, Center for Tropical Medicine (A.U., C.I., R.A.A., W.T., E.A., M.R.A., E.S., D.S.W., Y.M., I.E., I.N., E.P.), the Department of Health Policy and Management (A.U.), the Department of Biostatistics, Epidemiology, and Public Health (C.I., R.A.A.), and the Department of Child Health (E.A.), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; the Department of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley (S.M.D., N.P.J.); the London School of Hygiene and Tropical Medicine, London (N.P.J.); Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam (C.P.S.); and the World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia (B.A., B.R.G., L.H., Z.C., E.R., P.A.R., S.L.O., S.M.D., S.K.T., K.L.A., C.P.S.)
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14
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Gunadi, Wibawa H, Hakim MS, Marcellus, Trisnawati I, Khair RE, Triasih R, Irene, Afiahayati, Iskandar K, Siswanto, Anggorowati N, Daniwijaya EW, Supriyati E, Nugrahaningsih DAA, Budiono E, Retnowulan H, Puspadewi Y, Puspitawati I, Sianipar O, Afandy D, Simanjaya S, Widitjiarso W, Puspitarani DA, Fahri F, Riawan U, Fauzi AR, Kalim AS, Ananda NR, Setyati A, Setyowireni D, Laksanawati IS, Arguni E, Nuryastuti T, Wibawa T. Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. BMC Med Genomics 2021; 14:144. [PMID: 34074255 PMCID: PMC8169432 DOI: 10.1186/s12920-021-00990-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/18/2021] [Indexed: 02/06/2023] Open
Abstract
Background Transmission within families and multiple spike protein mutations have been associated with the rapid transmission of SARS-CoV-2.
We aimed to: (1) describe full genome characterization of SARS-CoV-2 and correlate the sequences with epidemiological data within family clusters, and (2) conduct phylogenetic analysis of all samples from Yogyakarta and Central Java, Indonesia and other countries. Methods The study involved 17 patients with COVID-19, including two family clusters. We determined the full-genome sequences of SARS-CoV-2 using the Illumina MiSeq next-generation sequencer. Phylogenetic analysis was performed using a dataset of 142 full-genomes of SARS-CoV-2 from different regions. Results Ninety-four SNPs were detected throughout the open reading frame (ORF) of SARS-CoV-2 samples with 58% (54/94) of the nucleic acid changes resulting in amino acid mutations. About 94% (16/17) of the virus samples showed D614G on spike protein and 56% of these (9/16) showed other various amino acid mutations on this protein, including L5F, V83L, V213A, W258R, Q677H, and N811I. The virus samples from family cluster-1 (n = 3) belong to the same clade GH, in which two were collected from deceased patients, and the other from the survived patient. All samples from this family cluster revealed a combination of spike protein mutations of D614G and V213A. Virus samples from family cluster-2 (n = 3) also belonged to the clade GH and showed other spike protein mutations of L5F alongside the D614G mutation. Conclusions Our study is the first comprehensive report associating the full-genome sequences of SARS-CoV-2 with the epidemiological data within family clusters. Phylogenetic analysis revealed that the three viruses from family cluster-1 formed a monophyletic group, whereas viruses from family cluster-2 formed a polyphyletic group indicating there is the possibility of different sources of infection. This study highlights how the same spike protein mutations among members of the same family might show different disease outcomes. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-00990-3.
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Affiliation(s)
- Gunadi
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr, Sardjito Hospital, Jl. Kesehatan No. 1, Yogyakarta, 55281, Indonesia.
| | - Hendra Wibawa
- Disease Investigation Center Wates, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture, Yogyakarta, Indonesia
| | - Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Marcellus
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ika Trisnawati
- Pulmonology Division, Department of Internal Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr, Sardjito Hospital, Yogyakarta, Indonesia
| | - Riat El Khair
- Department of Clinical Pathology and Laboratory Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr, Sardjito Hospital, Yogyakarta, 55281, Indonesia
| | - Rina Triasih
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr, Sardjito Hospital, Yogyakarta, Indonesia
| | - Irene
- Balai Besar Teknik Kesehatan Lingkungan Dan Pengendalian Penyakit, Yogyakarta, Yogyakarta, Indonesia
| | - Afiahayati
- Department of Computer Science and Electronics Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Kristy Iskandar
- Department of Child Health/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Siswanto
- Department of Physiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Nungki Anggorowati
- Department of Anatomical Pathology/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edwin Widyanto Daniwijaya
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, UGM Academic Hospital, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dwi Aris Agung Nugrahaningsih
- Department of Pharmacology and Therapy/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eko Budiono
- Pulmonology Division, Department of Internal Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr, Sardjito Hospital, Yogyakarta, Indonesia
| | - Heni Retnowulan
- Pulmonology Division, Department of Internal Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr, Sardjito Hospital, Yogyakarta, Indonesia
| | - Yunika Puspadewi
- Department of Clinical Pathology and Laboratory Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr, Sardjito Hospital, Yogyakarta, 55281, Indonesia
| | - Ira Puspitawati
- Department of Clinical Pathology and Laboratory Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr, Sardjito Hospital, Yogyakarta, 55281, Indonesia
| | - Osman Sianipar
- Department of Clinical Pathology and Laboratory Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr, Sardjito Hospital, Yogyakarta, 55281, Indonesia
| | - Dwiki Afandy
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Susan Simanjaya
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - William Widitjiarso
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dyah Ayu Puspitarani
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Fadil Fahri
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Untung Riawan
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Aditya Rifqi Fauzi
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Alvin Santoso Kalim
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Nur Rahmi Ananda
- Pulmonology Division, Department of Internal Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr, Sardjito Hospital, Yogyakarta, Indonesia
| | - Amalia Setyati
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr, Sardjito Hospital, Yogyakarta, Indonesia
| | - Dwikisworo Setyowireni
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr, Sardjito Hospital, Yogyakarta, Indonesia
| | - Ida Safitri Laksanawati
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr, Sardjito Hospital, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr, Sardjito Hospital, Yogyakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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15
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Gunadi, Wibawa H, Marcellus, Hakim MS, Daniwijaya EW, Rizki LP, Supriyati E, Nugrahaningsih DAA, Afiahayati, Siswanto, Iskandar K, Anggorowati N, Kalim AS, Puspitarani DA, Athollah K, Arguni E, Nuryastuti T, Wibawa T. Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. PeerJ 2020; 8:e10575. [PMID: 33391880 PMCID: PMC7759132 DOI: 10.7717/peerj.10575] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/24/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Recently, SARS-CoV-2 virus with the D614G mutation has become a public concern due to rapid dissemination of this variant across many countries. Our study aims were (1) to report full-length genome sequences of SARS-CoV-2 collected from four COVID-19 patients in the Special Region of Yogyakarta and Central Java provinces, Indonesia; (2) to compare the clade distribution of full-length genome sequences from Indonesia (n = 60) from March to September 2020 and (3) to perform phylogenetic analysis of SARS-CoV-2 complete genomes from different countries, including Indonesia. METHODS Whole genome sequencing (WGS) was performed using next-generation sequencing (NGS) applied in the Illumina MiSeq instrument. Full-length virus genomes were annotated using the reference genome of hCoV-19/Wuhan/Hu-1/2019 (NC_045512.2) and then visualized in UGENE v. 1.30. For phylogenetic analysis, a dataset of 88 available SARS-CoV-2 complete genomes from different countries, including Indonesia, was retrieved from GISAID. RESULTS All patients were hospitalized with various severities of COVID-19. Phylogenetic analysis revealed that one and three virus samples belong to clade L and GH. These three clade GH virus samples (EPI_ISL_525492, EPI_ISL_516800 and EPI_ISL_516829) were not only located in a cluster with SARS-CoV-2 genomes from Asia but also those from Europe, whereas the clade L virus sample (EPI_ISL_516806) was located amongst SARS-CoV-2 genomes from Asia. Using full-length sequences available in the GISAID EpiCoV Database, 39 of 60 SARS-CoV-2 (65%) from Indonesia harbor the D614G mutation. CONCLUSION These findings indicate that SARS-CoV-2 with the D614G mutation appears to become the major circulating virus in Indonesia, concurrent with the COVID-19 situation worldwide.
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Affiliation(s)
- Gunadi
- Pediatric Surgery Division, Department of Surgery, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hendra Wibawa
- Disease Investigation Center Wates, Yogyakarta, Ministry of Agriculture, Indonesia
| | - Marcellus
- Pediatric Surgery Division, Department of Surgery, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edwin Widyanto Daniwijaya
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Ludhang Pradipta Rizki
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dwi Aris Agung Nugrahaningsih
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Afiahayati
- Department of Computer Science and Electronics, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Siswanto
- Department of Physiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Kristy Iskandar
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Nungki Anggorowati
- Department of Anatomical Pathology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Alvin Santoso Kalim
- Pediatric Surgery Division, Department of Surgery, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dyah Ayu Puspitarani
- Pediatric Surgery Division, Department of Surgery, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Kemala Athollah
- Pediatric Surgery Division, Department of Surgery, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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16
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Indriani C, Tantowijoyo W, Rancès E, Andari B, Prabowo E, Yusdi D, Ansari MR, Wardana DS, Supriyati E, Nurhayati I, Ernesia I, Setyawan S, Fitriana I, Arguni E, Amelia Y, Ahmad RA, Jewell NP, Dufault SM, Ryan PA, Green BR, McAdam TF, O'Neill SL, Tanamas SK, Simmons CP, Anders KL, Utarini A. Reduced dengue incidence following deployments of Wolbachia-infected Aedes aegypti in Yogyakarta, Indonesia: a quasi-experimental trial using controlled interrupted time series analysis. Gates Open Res 2020; 4:50. [PMID: 32803130 PMCID: PMC7403856 DOI: 10.12688/gatesopenres.13122.1] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2020] [Indexed: 12/20/2022] Open
Abstract
Background: Ae. aegypti mosquitoes stably transfected with the intracellular bacterium Wolbachia pipientis ( wMel strain) have been deployed for biocontrol of dengue and related arboviral diseases in multiple countries. Field releases in northern Australia have previously demonstrated near elimination of local dengue transmission from Wolbachia-treated communities, and pilot studies in Indonesia have demonstrated the feasibility and acceptability of the method. We conducted a quasi-experimental trial to evaluate the impact of scaled Wolbachia releases on dengue incidence in an endemic setting in Indonesia. Methods: In Yogyakarta City, Indonesia, following extensive community engagement, wMel Wolbachia-carrying mosquitoes were released every two weeks for 13-15 rounds over seven months in 2016-17, in a contiguous 5 km 2 area (population 65,000). A 3 km 2 area (population 34,000) on the opposite side of the city was selected a priori as an untreated control area. Passive surveillance data on notified hospitalised dengue patients was used to evaluate the epidemiological impact of Wolbachia deployments, using controlled interrupted time-series analysis. Results: Rapid and sustained introgression of wMel Wolbachia into local Ae. aegypti populations was achieved. Thirty-four dengue cases were notified from the intervention area and 53 from the control area (incidence 26 vs 79 per 100,000 person-years) during 24 months following Wolbachia deployment. This corresponded in the regression model to a 73% reduction in dengue incidence (95% confidence interval 49%,86%) associated with the Wolbachia intervention. Exploratory analysis including 6 months additional post-intervention observations showed a small strengthening of this effect (30 vs 115 per 100,000 person-years; 76% reduction in incidence, 95%CI 60%,86%). Conclusions: We demonstrate a significant reduction in dengue incidence following successful introgression of Wolbachia into local Ae. aegypti populations in an endemic setting in Indonesia. These findings are consistent with previous field trials in northern Australia, and support the effectiveness of this novel approach for dengue control.
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Affiliation(s)
- Citra Indriani
- Centre of Tropical Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Epidemiology Biostatistics and Public Health, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Warsito Tantowijoyo
- Centre of Tropical Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edwige Rancès
- Institute of Vector Borne Disease, Monash University, Melbourne, Australia
| | - Bekti Andari
- Centre of Tropical Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Equatori Prabowo
- Centre of Tropical Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dedik Yusdi
- Centre of Tropical Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Muhammad Ridwan Ansari
- Centre of Tropical Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dwi Satria Wardana
- Centre of Tropical Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre of Tropical Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Indah Nurhayati
- Centre of Tropical Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Inggrid Ernesia
- Centre of Tropical Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Sigit Setyawan
- Centre of Tropical Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Iva Fitriana
- Centre of Tropical Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Centre of Tropical Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Paediatrics, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Riris Andono Ahmad
- Centre of Tropical Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Epidemiology Biostatistics and Public Health, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Nicholas P. Jewell
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, USA
- Centre for Statistical Methodology, London School of Hygiene & Tropical Medicine, London, UK
| | - Suzanne M. Dufault
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, USA
| | - Peter A. Ryan
- Institute of Vector Borne Disease, Monash University, Melbourne, Australia
| | - Benjamin R. Green
- Institute of Vector Borne Disease, Monash University, Melbourne, Australia
| | - Thomas F. McAdam
- Institute of Vector Borne Disease, Monash University, Melbourne, Australia
| | - Scott L. O'Neill
- Institute of Vector Borne Disease, Monash University, Melbourne, Australia
| | | | - Cameron P. Simmons
- Institute of Vector Borne Disease, Monash University, Melbourne, Australia
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | - Adi Utarini
- Centre of Tropical Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Health Policy and Management, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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17
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Tantowijoyo W, Andari B, Arguni E, Budiwati N, Nurhayati I, Fitriana I, Ernesia I, Daniwijaya EW, Supriyati E, Yusdiana DH, Victorius M, Wardana DS, Ardiansyah H, Ahmad RA, Ryan PA, Simmons CP, Hoffmann AA, Rancès E, Turley AP, Johnson P, Utarini A, O’Neill SL. Stable establishment of wMel Wolbachia in Aedes aegypti populations in Yogyakarta, Indonesia. PLoS Negl Trop Dis 2020; 14:e0008157. [PMID: 32302295 PMCID: PMC7190183 DOI: 10.1371/journal.pntd.0008157] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/29/2020] [Accepted: 02/20/2020] [Indexed: 01/23/2023] Open
Abstract
The successful establishment of the wMel strain of Wolbachia for the control of arbovirus transmission by Aedes aegypti has been proposed and is being implemented in a number of countries. Here we describe the successful establishment of the wMel strain of Wolbachia in four sites in Yogyakarta, Indonesia. We demonstrate that Wolbachia can be successfully introgressed after transient releases of wMel-infected eggs or adult mosquitoes. We demonstrate that the approach is acceptable to communities and that Wolbachia maintains itself in the mosquito population once deployed. Finally, our data show that spreading rates of Wolbachia in the Indonesian setting are slow which may reflect more limited dispersal of Aedes aegypti than seen in other sites such as Cairns, Australia. We show that the wMel strain of Wolbachia can be deployed successfully into mosquito populations in an area of intense dengue transmission in Yogyakarta, Indonesia. Deployment was achieved through either the release of eggs or adult mosquitoes with full community support. This represents the successful first step toward a large trial to evaluate the use of Wolbachia in Indonesia to disrupt transmission of arboviruses such as dengue, Zika and chikungunya.
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Affiliation(s)
- Warsito Tantowijoyo
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Bekti Andari
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Pediatrics, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Nida Budiwati
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Indah Nurhayati
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Iva Fitriana
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Inggrid Ernesia
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edwin W. Daniwijaya
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dedik H. Yusdiana
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Munasdi Victorius
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dwi S. Wardana
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hilmi Ardiansyah
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Riris Andono Ahmad
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Biostatistics, Epidemiology and Population Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Peter A. Ryan
- Institute of Vector-Borne Disease, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Cameron P. Simmons
- Institute of Vector-Borne Disease, Monash University, Clayton, Melbourne, Victoria, Australia
| | | | - Edwige Rancès
- Institute of Vector-Borne Disease, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Andrew P. Turley
- Institute of Vector-Borne Disease, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Petrina Johnson
- Institute of Vector-Borne Disease, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Adi Utarini
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Health Policy and Management, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Scott L. O’Neill
- Institute of Vector-Borne Disease, Monash University, Clayton, Melbourne, Victoria, Australia
- * E-mail:
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18
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Indriani C, Ahmad RA, Wiratama BS, Arguni E, Supriyati E, Sasmono RT, Kisworini FY, Ryan PA, O'Neill SL, Simmons CP, Utarini A, Anders KL. Baseline Characterization of Dengue Epidemiology in Yogyakarta City, Indonesia, before a Randomized Controlled Trial of Wolbachia for Arboviral Disease Control. Am J Trop Med Hyg 2019; 99:1299-1307. [PMID: 30226138 PMCID: PMC6221224 DOI: 10.4269/ajtmh.18-0315] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Dengue is endemic in Indonesia. Here, we describe the epidemiology of dengue in the city of Yogyakarta, Central Java, as a prelude to implementation of a cluster-randomized trial of Wolbachia for the biocontrol of arboviral transmission. Surveillance records from 2006 to 2016 demonstrate seasonal oscillations of dengue incidence with varying magnitude. Two lines of evidence demonstrate a high force of infection; the hospitalized case burden of patients diagnosed with dengue hemorrhagic fever or dengue shock syndrome over the last decade consisted predominantly of children/adolescents, and a serosurvey of 314 healthy children aged 1–10 years found 68% possessed dengue virus–neutralizing antibodies. Finally, a mobility survey indicated children aged 1–10 years, and particularly 1–5 year-olds, spent most of their daytime hours at home. These findings inform the design of clinical trials to measure the impact of novel vector control methods such as Wolbachia introgression into Aedes aegypti mosquitoes, by providing baseline data on disease incidence and identifying subpopulations for recruitment into prospective studies of dengue virus infection and disease. The mobility survey findings indicate that in cluster trials of interventions applied at the community level, young children can reasonably be expected to spend most of their exposure time, in epidemiological terms, within the treatment arm to which they were randomized.
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Affiliation(s)
- Citra Indriani
- Department of Epidemiology, Biostatistics and Population Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Riris A Ahmad
- Department of Epidemiology, Biostatistics and Population Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Bayu S Wiratama
- Department of Epidemiology, Biostatistics and Population Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Pediatrics, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | | | - Peter A Ryan
- Institute of Vector Borne Disease, Monash University, Melbourne, Australia
| | - Scott L O'Neill
- Institute of Vector Borne Disease, Monash University, Melbourne, Australia
| | - Cameron P Simmons
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Institute of Vector Borne Disease, Monash University, Melbourne, Australia
| | - Adi Utarini
- Department of Health Policy and Management, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Katherine L Anders
- Institute of Vector Borne Disease, Monash University, Melbourne, Australia
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19
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Rahayu A, Saraswati U, Supriyati E, Kumalawati DA, Hermantara R, Rovik A, Daniwijaya EW, Fitriana I, Setyawan S, Ahmad RA, Wardana DS, Indriani C, Utarini A, Tantowijoyo W, Arguni E. Prevalence and Distribution of Dengue Virus in Aedes aegypti in Yogyakarta City before Deployment of Wolbachia Infected Aedes aegypti. Int J Environ Res Public Health 2019; 16:ijerph16101742. [PMID: 31100967 PMCID: PMC6571630 DOI: 10.3390/ijerph16101742] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/06/2019] [Accepted: 05/12/2019] [Indexed: 12/17/2022]
Abstract
Indonesia is one of the countries where dengue infection is prevalent. In this study we measure the prevalence and distribution of dengue virus (DENV) DENV-infected Aedes aegypti in Yogyakarta City, Indonesia, during the wet season when high dengue transmission period occurred, as baseline data before implementation of a Wolbachia-infected Aedes aegypti trial for dengue control. We applied One-Step Multiplex Real Time PCR (RT-PCR) for the type-specific-detection of dengue viruses in field-caught adult Aedes aegypti mosquitoes. In a prospective field study conducted from December 2015 to May 2016, adult female Aedes aegypti were caught from selected areas in Yogyakarta City, and then screened by using RT-PCR. During the survey period, 36 (0.12%) mosquitoes from amongst 29,252 female mosquitoes were positive for a DENV type. In total, 22.20% of dengue-positive mosquitoes were DENV-1, 25% were DENV-2, 17% were DENV-3, but none were positive for DENV-4. This study has provided dengue virus infection prevalence in field-caught Aedes aegypti and its circulating serotype in Yogyakarta City before deployment of Wolbachia-infected Aedes aegypti.
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Affiliation(s)
- Ayu Rahayu
- Centre of Tropical Medicine, World Mosquito Program Yogyakarta, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
| | - Utari Saraswati
- Centre of Tropical Medicine, World Mosquito Program Yogyakarta, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
| | - Endah Supriyati
- Centre of Tropical Medicine, World Mosquito Program Yogyakarta, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
| | - Dian Aruni Kumalawati
- Centre of Tropical Medicine, World Mosquito Program Yogyakarta, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
| | - Rio Hermantara
- Centre of Tropical Medicine, World Mosquito Program Yogyakarta, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
| | - Anwar Rovik
- Centre of Tropical Medicine, World Mosquito Program Yogyakarta, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
| | - Edwin Widyanto Daniwijaya
- Centre of Tropical Medicine, World Mosquito Program Yogyakarta, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
| | - Iva Fitriana
- Centre of Tropical Medicine, World Mosquito Program Yogyakarta, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
| | - Sigit Setyawan
- Centre of Tropical Medicine, World Mosquito Program Yogyakarta, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
| | - Riris Andono Ahmad
- Centre of Tropical Medicine, World Mosquito Program Yogyakarta, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
- Department of Epidemiology, Biostatistics and Population Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
| | - Dwi Satria Wardana
- Centre of Tropical Medicine, World Mosquito Program Yogyakarta, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
| | - Citra Indriani
- Centre of Tropical Medicine, World Mosquito Program Yogyakarta, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
- Department of Epidemiology, Biostatistics and Population Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
| | - Adi Utarini
- Centre of Tropical Medicine, World Mosquito Program Yogyakarta, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
- Department of Health Policy and Management, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
| | - Warsito Tantowijoyo
- Centre of Tropical Medicine, World Mosquito Program Yogyakarta, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
| | - Eggi Arguni
- Centre of Tropical Medicine, World Mosquito Program Yogyakarta, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
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