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Wibawa H, Wibowo PE, Supriyadi A, Lestari L, Silaban J, Fuadi AA, Fiqri AJ, Handayani RW, Irianingsih SH, Fahmia Z, Mulyawan H, Idris S, Zainuddin N. Highly Pathogenic Avian Influenza A(H5N1) Virus Clade 2.3.4.4b in Domestic Ducks, Indonesia, 2022. Emerg Infect Dis 2024; 30:586-590. [PMID: 38407163 PMCID: PMC10902521 DOI: 10.3201/eid3003.230973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Abstract
Highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b viruses were isolated from domestic ducks in South Kalimantan, Indonesia, during April 2022. The viruses were genetically similar to those detected in East Asia during 2021-2022. Molecular surveillance of wild birds is needed to detect potential pandemic threats from avian influenza virus.
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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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4
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Zainuddin N, Susila EB, Wibawa H, Daulay RSD, Wijayanti PE, Fitriani D, Hidayati DN, Idris S, Wadsworth J, Polo N, Hicks HM, Mioulet V, Knowles NJ, King DP. Genome Sequence of a Foot-and-Mouth Disease Virus Detected in Indonesia in 2022. Microbiol Resour Announc 2023; 12:e0108122. [PMID: 36622181 PMCID: PMC9933659 DOI: 10.1128/mra.01081-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/08/2022] [Indexed: 01/10/2023] Open
Abstract
During 2022, outbreaks of foot-and-mouth disease (FMD) were reported across the islands of Indonesia, a country that had previously maintained an FMD-free (without vaccination) status since 1990. This report describes the near-complete genome sequence of a representative FMD virus collected from these cases belonging to the O/ME-SA/Ind-2001e lineage.
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Affiliation(s)
- Nuryani Zainuddin
- Directorate General of Livestock and Animal Health Services, Ministry of Agriculture of Indonesia, Jakarta, Indonesia
| | - Edy Budi Susila
- Pusat Veteriner Farma, National Center for Veterinary Biologics, Surabaya, Indonesia
| | - Hendra Wibawa
- Balai Besar Veteriner Wates, Disease Investigation Center, Wates, Yogyakarta, Indonesia
| | | | | | - Dini Fitriani
- Pusat Veteriner Farma, National Center for Veterinary Biologics, Surabaya, Indonesia
| | - Dewi Noor Hidayati
- Pusat Veteriner Farma, National Center for Veterinary Biologics, Surabaya, Indonesia
| | - Syafrison Idris
- Directorate General of Livestock and Animal Health Services, Ministry of Agriculture of Indonesia, Jakarta, Indonesia
| | | | - Noemi Polo
- The Pirbright Institute, Pirbright, United Kingdom
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5
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Brookes VJ, Wismandanu O, Sudarnika E, Roby JA, Hayes L, Ward MP, Basri C, Wibawa H, Davis J, Indrawan D, Manyweathers J, Nugroho WS, Windria S, Hernandez-Jover M. A scoping review of live wildlife trade in markets worldwide. Sci Total Environ 2022; 819:153043. [PMID: 35032529 DOI: 10.1016/j.scitotenv.2022.153043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Wet markets sell fresh food and are a global phenomenon. They are important for food security in many regions worldwide but have come under scrutiny due to their potential role in the emergence of infectious diseases. The sale of live wildlife has been highlighted as a particular risk, and the World Health Organisation has called for the banning of live, wild-caught mammalian species in markets unless risk assessment and effective regulations are in place. Following PRISMA guidelines, we conducted a global scoping review of peer-reviewed information about the sale of live, terrestrial wildlife in markets that are likely to sell fresh food, and collated data about the characteristics of such markets, activities involving live wildlife, the species sold, their purpose, and animal, human, and environmental health risks that were identified. Of the 56 peer-reviewed records within scope, only 25% (n = 14) focussed on disease risks; the rest focused on the impact of wildlife sale on conservation. Although there were some global patterns (for example, the types of markets and purpose of sale of wildlife), there was wide diversity and huge epistemic uncertainty in all aspects associated with live, terrestrial wildlife sale in markets such that the feasibility of accurate assessment of the risk of emerging infectious disease associated with live wildlife trade in markets is currently limited. Given the value of both wet markets and wildlife trade and the need to support food affordability and accessibility, conservation, public health, and the social and economic aspects of livelihoods of often vulnerable people, there are major information gaps that need to be addressed to develop evidence-based policy in this environment. This review identifies these gaps and provides a foundation from which information for risk assessments can be collected.
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Affiliation(s)
- V J Brookes
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; Graham Centre for Agricultural Innovation (NSW Dept. of Primary Industries and Charles Sturt University), Charles Sturt University, Wagga Wagga, NSW 2678, Australia; Sydney School of Veterinary Science, The University of Sydney, Camden 2570, Australia.
| | - O Wismandanu
- Veterinary Medicine Study Program, Faculty of Medicine, Padjadjaran University, Indonesia
| | - E Sudarnika
- Faculty of Veterinary Medicine, IPB (Institut Pertanian Bogor) University, Indonesia
| | - J A Roby
- Graham Centre for Agricultural Innovation (NSW Dept. of Primary Industries and Charles Sturt University), Charles Sturt University, Wagga Wagga, NSW 2678, Australia; School of Dentistry and Medical Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - L Hayes
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; Graham Centre for Agricultural Innovation (NSW Dept. of Primary Industries and Charles Sturt University), Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - M P Ward
- Sydney School of Veterinary Science, The University of Sydney, Camden 2570, Australia
| | - C Basri
- Faculty of Veterinary Medicine, IPB (Institut Pertanian Bogor) University, Indonesia
| | - H Wibawa
- Disease Investigation Centre Wates, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture of Indonesia, Indonesia
| | - J Davis
- Australian Department of Agriculture, Water and the Environment, Canberra, Australia
| | - D Indrawan
- School of Business, IPB (Institut Pertanian Bogor) University, Indonesia
| | - J Manyweathers
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; Graham Centre for Agricultural Innovation (NSW Dept. of Primary Industries and Charles Sturt University), Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - W S Nugroho
- Faculty of Veterinary Medicine, Universitas Gadjah Mada, Indonesia
| | - S Windria
- Department of Biomedical Sciences, Division of Microbiology, Veterinary Medicine Study Program, Faculty of Medicine, Padjadjaran University, Indonesia
| | - M Hernandez-Jover
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; Graham Centre for Agricultural Innovation (NSW Dept. of Primary Industries and Charles Sturt University), Charles Sturt University, Wagga Wagga, NSW 2678, Australia
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6
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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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7
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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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Apriliana U, Wibawa H, Ruhiat E, Untari T, Indarjulianto S. Isolation and identification of avirulent strains of Bacillus anthracis from environmental samples in Central Java, Indonesia. Int J One Health 2021. [DOI: 10.14202/ijoh.2021.204-211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: Anthrax is a non-contagious infectious disease caused by Bacillus anthracis. The bacteria form spores that are resistant to extreme conditions and can contaminate the environment for decades. This study aimed to detect and characterize B. anthracis found in endemic areas of anthrax in Yogyakarta and Central Java province, Indonesia.
Materials and Methods: Soil samples were collected from Gunungkidul regency, Yogyakarta province (n=315) and Boyolali regency, Central Java province (n=100). Additional soil samples (n=10) and straw samples (n=5) were obtained from Pati regency, Central Java province. The isolation and identification of B. anthracis were performed using conventional methods: Morphology of bacteria colony in solid media, Gram staining, capsule staining, spores staining, and motility test. Isolates were further identified using polymerase chain reaction (PCR) against Ba813, lef (pXO1), and capC (pXO2) gene. An avirulent vaccine strain of B. anthracis (strain 34F2) was used as a control.
Results: Only four samples grew on blood agar with a ground-glass appearance, white-gray colony (Gunungkidul and avirulent strain) or yellowish (Boyolali and Pati). All were Gram-positive, presented chains, square-ended rods, spores, and were then identified as B. anthracis. Boyolali, Pati, and avirulent strain isolates had slightly different characteristics, including the growth of non-mucoid in the bicarbonate agar medium, and their uncapsulated form. The PCR showed two Gunungkidul isolates which amplified three genes, including Ba813, lef, and capC. Contrarily, the other isolates did not amplify the capC gene.
Conclusion: Gunungkidul isolates were identified as virulent strains of B. anthracis while Boyolali and Pati isolates were proposed as avirulent strains. This is the first report of isolation and identification of avirulent strains of B. anthracis in Central Java, Indonesia.
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Affiliation(s)
- Ully Apriliana
- Disease Investigation Center Wates, Jalan Raya Jogja-Wates Km 27 Po Box 18, Wates, Yogyakarta, 55602, Indonesia; Department of Internal Medicine, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Jl. Fauna 2, Karangmalang, Yogyakarta, 55281, Indonesia
| | - Hendra Wibawa
- Disease Investigation Center Wates, Jalan Raya Jogja-Wates Km 27 Po Box 18, Wates, Yogyakarta, 55602, Indonesia
| | - Endang Ruhiat
- Disease Investigation Center Wates, Jalan Raya Jogja-Wates Km 27 Po Box 18, Wates, Yogyakarta, 55602, Indonesia
| | - Tri Untari
- Department of Internal Medicine , Faculty of Veterinary Medicine, Universitas Gadjah Mada, Jl. Fauna 2, Karangmalang, Yogyakarta, 55281, Indonesia
| | - Soedarmanto Indarjulianto
- Department of Internal Medicine , Faculty of Veterinary Medicine, Universitas Gadjah Mada, Jl. Fauna 2, Karangmalang, Yogyakarta, 55281, Indonesia
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Mutisari D, Muflihanah M, Wibawa H, Hendrawati F, Putra HH, Sulistyo KP, Ahmad A, Sjahril R, Mubin RH, Sari DK, Massi MN. Phylogenetic analysis of HPAI H5N1 virus from duck swab specimens in Indonesia. J Adv Vet Anim Res 2021; 8:346-354. [PMID: 34395607 PMCID: PMC8280988 DOI: 10.5455/javar.2021.h521] [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: 03/30/2021] [Revised: 06/08/2021] [Accepted: 06/20/2021] [Indexed: 11/04/2022] Open
Abstract
Objective: A phylogenetic study was carried out on the avian influenza virus (AIV) isolated from a disease outbreak in Sidenreng Rappang Regency, South Sulawesi, Indonesia, in 2018. Material and Methods: Oropharyngeal swabs and organ samples were obtained from ducks that showed clinical symptoms: torticollis, fascial edema, neurological disorders, the corneas appear cloudy, and death occurs less than 1 day after symptoms appear. In this study, isolate A/duck/Sidenreng Rappang/07180110-11/2018 from duck was sequenced and characterized. Results: It was found that each gene segment of the virus has the highest nucleotide homology to the Indonesian highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.2.1c. Multiple alignments of the sample Hemagglutinin (HA) gene with the avian influenza references virus showed that the pattern of amino acid arrangement in the cleavage site PQRERRRK-RGLF is the characteristic of the HPAI virus. In addition, the HA gene contained Q222 (glutamine) and G224 (glycine), signifying a high affinity to avian receptor binding specificity (SA α2,3 Gal). Furthermore, there was no genetic reassortment of this virus based on the phylogenetic analysis of HA, NA, PB1, PB2, PA, NP, M, and NS genes. Conclusion: The HPAI H5N1 clade 2.3.2.1c virus was identified in duck farms in South Sulawesi, Indonesia.
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Affiliation(s)
- Dewi Mutisari
- Master of Biomedical Sciences, Graduate School Hasanuddin University, Makassar, Indonesia.,Disease Investigation Center Maros, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture, Maros, Indonesia
| | - Muflihanah Muflihanah
- Disease Investigation Center Maros, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture, Maros, Indonesia
| | - Hendra Wibawa
- Disease Investigation Center Wates, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture, Yogyakarta, Indonesia
| | - Ferra Hendrawati
- Disease Investigation Center Maros, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture, Maros, Indonesia
| | - Hamdu Hamjaya Putra
- Disease Investigation Center Maros, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture, Maros, Indonesia
| | - Kartika Priscillia Sulistyo
- Disease Investigation Center Maros, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture, Maros, Indonesia
| | - Ahyar Ahmad
- Departement of Chemistry, Mathematics and Natural Science Faculty, Hasanuddin University, Makassar, Indonesia
| | - Rizalinda Sjahril
- Department of Microbiology, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
| | - Risna Halim Mubin
- Departement of Internal Medicine, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
| | - Dwi Kesuma Sari
- Veterinary Medicine Study Program, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
| | - Muhammad Nasrum Massi
- Department of Microbiology, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
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10
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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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Dharmawan R, Sumiarto B, Wibawa H, Pramastuti I, Sutiyarmo S, Poermadjaja B. Contact rate and risk factors of classical swine fever disease in commercial and smallholder pig farms, Karanganyar, Central Java, Indonesia. Vet World 2021; 14:758-763. [PMID: 33935424 PMCID: PMC8076451 DOI: 10.14202/vetworld.2021.758-763] [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: 06/02/2020] [Accepted: 02/09/2021] [Indexed: 11/16/2022] Open
Abstract
Background and Aim Classical swine fever (CSF) is one of the primary diseases in animals in Indonesia, particularly areas that supply pig meat to the country, such as Karanganyar district, Central Java. The government has tried to prevent and control the disease by vaccination, but it has not yet given effective results. Therefore, another attempt to prevent the recurrence of CSF cases is to apply biosecurity in pig farms by looking for risk factors associated with on-farm and off-farm contact. This study aims to determine the contact rate and investigate the risk factors associated with on-farm and off-farm contact in commercial and smallholder pig farms in Karanganyar, Central Java, Indonesia, in the context of controlling CSF disease. Materials and Methods This study used a cross-sectional study design in which the pig farm was designed as the observed epidemiological unit. The contact structure data were conducted by sampling using a two-stage random method. We selected Karanganyar district because it is the center of a pig farm in the Central Java Province and has many CSF cases in several years before. The study was conducted for more or less 1 month from August to September 2019. The contact data were collected from 37 smallholder farms and 27 commercial farms within interviews. Risk factors for contact with pigs were analyzed using logistic regression using theStatistix Program version 8.0.(www.statistix.com). Results In comparison to smallholder farms, commercial farms had 2.38 and 3.32 times higher contact rate in outside farms and inside farms, respectively. Two factors increased the risk for on-farm contacts including commercials type farm (p=0.0012; odds ratio [OR]=8.32) with contact rate of 1.24 times/day and the time interval of CSF vaccination for 1-3 months (p=0.0013; OR=8.43) with contact rate of 0.98 times/day, and three factors increased the risk for off-farm contacts including the commercial farm type (p=0.012; OR=4.88) with 1.50 contact/day, the time interval of CSF vaccination for 1-3 months (p=0.036; OR=3.83) with 1.30 contact/day, and farmers with experience in pig husbandry <5 years (p=0.075; OR=3.56) with 1.13 contact/day. Conclusion This study shows that commercial farms and short CSF vaccination intervals increased the risk of either off-farm or on-farm contacts. The contact structure of pig farms in Karanganyar district is similar to that in other areas in Indonesia. Reducing the risk of contacts either outside or inside the pig farms is essential to prevent disease transmission. Enhancing communication and education to pig farmers and surveillance is also necessary to prevent such diseases in pigs.
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Affiliation(s)
- Rama Dharmawan
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Gadjah Mada University, Yogyakarta, Indonesia.,Disease Investigation Center Wates, Yogyakarta 55651, Indonesia
| | - Bambang Sumiarto
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Gadjah Mada University, Yogyakarta, Indonesia
| | - Hendra Wibawa
- Disease Investigation Center Wates, Yogyakarta 55651, Indonesia
| | - Ira Pramastuti
- Disease Investigation Center Wates, Yogyakarta 55651, Indonesia
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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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Nurhayati, Wibawa H, Mahawan T, Zenal FC, Schoonman L, Pfeiffer CN, Stevenson M, Punyapornwithaya V. Herd-Level Risk Factors for Swine Influenza (H1N1) Seropositivity in West Java and Banten Provinces of Indonesia (2016-2017). Front Vet Sci 2020; 7:544279. [PMID: 33263010 PMCID: PMC7685993 DOI: 10.3389/fvets.2020.544279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/22/2020] [Indexed: 11/13/2022] Open
Abstract
Swine could play a role as a “mixing vessel” for avian and human influenza viruses and should, therefore, be thought of playing an intermediate role in the emergence of pandemic influenza strains. The aim of this study was to identify risk factors for Swine influenza virus (SIV) seropositivity at the farm level in West Java and Banten provinces, Indonesia. A total of 649 blood samples were collected from 175 pig farms, and at the time of sampling, a questionnaire about routine herd management was administered to participant herd managers. Swine influenza virus serological status for each of the sampled pigs was tested using the IDEXX ELISA-test (Maine, US). The apparent herd-level prevalence of SIV seropositivity was expressed as a true herd-level prevalence using the Rogan and Gladen method, modified to account for low and high prevalence herds using a Markov chain Monte Carlo Bayesian approach. The association between herd-level characteristics and SIV seropositivity status was assessed using binary logistic regression. The true prevalence of SIV seropositivity was 26% (95% CI = 20–33). The presence of animals apart from pigs on farm (odds ratio, OR = 2.51, 95% CI = 1.0–6.0), keeping breeding sows for <2 years (OR = 5.9, 95% Cl = 1.8–20), being <1 km from a poultry farm (OR = 2.4, 95% Cl = 1.0–5.7), and purchasing pigs only through pig collectors (OR = 11, 95% CI = 4.3–29) increased the risk of a herd being seropositive to SIV. Our results show that biosecurity to limit the introduction of SIV should be enhanced on farms located in areas of high pig and poultry farm density. While the role that pig collectors play in the transmission of SIV warrants further investigation, swine producers in West Java and Banten should be made aware of the enhanced risk of SIV associated with purchasing of replacements from collectors.
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Affiliation(s)
- Nurhayati
- Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand.,Directorate of Animal Health, Directorate General Livestock and Animal Health Services, Ministry of Agriculture, Jakarta, Indonesia
| | - Hendra Wibawa
- Disease Investigation Center Wates, Yogyakarta, Indonesia
| | - Trian Mahawan
- Disease Investigation Center Subang, West Java, Indonesia
| | - Farida Camallia Zenal
- Food and Agriculture Organization of the United Nations, Emergency Centre for Transboundary Animal Diseases, Jakarta, Indonesia
| | - Luuk Schoonman
- Food and Agriculture Organization of the United Nations, Emergency Centre for Transboundary Animal Diseases, Jakarta, Indonesia
| | - Caitlin Nicole Pfeiffer
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Mark Stevenson
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Veerasak Punyapornwithaya
- Veterinary Public Health and Food Safety Centre for Asia Pacific, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
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Yuyun I, Wibawa H, Setiaji G, Kusumastuti TA, Nugroho WS. Determining highly pathogenic H5 avian influenza clade 2.3.2.1c seroprevalence in ducks, Purbalingga, Central Java, Indonesia. Vet World 2020; 13:1138-1144. [PMID: 32801565 PMCID: PMC7396357 DOI: 10.14202/vetworld.2020.1138-1144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 11/19/2019] [Accepted: 04/22/2020] [Indexed: 12/24/2022] Open
Abstract
Background and Aim In Indonesia, highly pathogenic avian influenza (HPAI) H5N1 outbreaks in poultry are still reported. The disease causes a decrease in egg production and an increase in mortality; this has an impact on the economic losses of farmers. Several studies have considered that ducks play a role in the HPAI endemicity in the country; however, little is known about whether or not the type of duck farming is associated with HPAI H5 virus infection, particularly within clade 2.3.2.1c, which has been predominantly found in poultry since 2014. A cross-sectional study was conducted to determine the HPAI seroprevalence for H5 subtype clade 2.3.2.1c in laying ducks that are kept intensively and nomadically and to determine the associated risk factors. Materials and Methods Forty-nine duck farmers were randomly selected from ten sub-districts in Purbalingga District, Central Java, Indonesia; a cross-sectional study was implemented to collect field data. Based on an expected HPAI prevalence level of 10%, estimated accuracy of ± 5%, and 95% confidence interval (CI), the total sample size was calculated at 36 individuals. Samples must be multiplied by 7 to reduce bias; thus, 252 ducks were taken as samples in this study. Considering that the maintenance and duck handling were uniform and farmers complained that the effect of activity to take duck samples would reduce egg production, this study only took samples from 245 ducks (oropharyngeal swabs and serum). Those samples were taken from five birds on each farm. Hemagglutination inhibition tests examined the serum samples for HPAI H5 Clade 2.3.2.1c, and pool swab samples (five swabs in one viral media transport) were examined by real-time reverse transcription-polymerase chain reaction (qRT-PCR) test for influenza Type A and H5 subtype virus. Information regarding farm management was obtained using a questionnaire; face-to-face interviews were conducted with the duck farmers using native Javanese language. Results Serum and swabs from 245 ducks were collected in total. For individual birds, 54.69% (134/245) of serum samples were H5 seropositive. Seroprevalence among nomadic ducks was 59.28% (95% CI: 0.48-0.61), which was higher than among intensively farmed ducks (48.57%, 95% CI: 0.38-0.58). Farm-level seroprevalence was 50% (95% CI: 0.30-0.69) for nomadic ducks but only 28.57% (95% CI: 0.11-0.51) for intensively farmed ducks. The farm-level virus prevalence (proportion of flocks with at least one bird positive for influenza Type A) was 17.85% (95% CI: 0.07-0.35) for nomadic ducks and 4.76% (1/21) for intensively farmed ducks (95% CI: 0.008-0.23). All influenza Type A positive samples were negative for the H5 subtype, indicating that another HA subtype AI viruses might have been circulating in ducks in the study area. A relationship between duck farms that were H5 seropositive and their maintenance system was present; however, this relationship was not significant, the nomadic duck system detected 2 times higher H5-seropositive ducks than the intensive farming system (OR: 2.16, 95% CI: 0.33-14.31). Conclusion This study found that the seroprevalence of HPAI in the duck population level in Purbalingga was 54.69% and demonstrated that the nomadic duck farming system was more likely to acquire HPAI H5 infection than the intensive farming duck system. Other risk factors should be further investigated as the diversity of the farming system is partially related to HPAI H5 infection.
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Affiliation(s)
- Imas Yuyun
- Magister Sain Veteriner, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Directorate of Animal Health, Directorate General of Livestock and Animal Health Services, Jakarta, Indonesia
| | - Hendra Wibawa
- Disease Investigation Center, Wates, Yogyakarta, Indonesia
| | - Gunawan Setiaji
- Directorate of Veterinary Public Health, Directorate General of Livestock and Animal Health Services, Jakarta, Indonesia
| | - Tri Anggraeni Kusumastuti
- Department of Socio Economic, Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Widagdo Sri Nugroho
- Departement of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Lestari, Wibawa H, Lubis EP, Dharmawan R, Rahayu RA, Mulyawan H, Charoenkul K, Nasamran C, Poermadjaja B, Amonsin A. Co-circulation and characterization of HPAI-H5N1 and LPAI-H9N2 recovered from a duck farm, Yogyakarta, Indonesia. Transbound Emerg Dis 2019; 67:994-1007. [PMID: 31770478 DOI: 10.1111/tbed.13434] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 06/12/2019] [Revised: 10/30/2019] [Accepted: 11/18/2019] [Indexed: 01/27/2023]
Abstract
In July 2016, an avian influenza outbreak in duck farms in Yogyakarta province was reported to Disease Investigation Center (DIC), Wates, Indonesia, with approximately 1,000 ducks died or culled. In this study, two avian influenza (AI) virus subtypes, A/duck/Bantul/04161291-OR/2016 (H5N1) and A/duck/Bantul/04161291-OP/2016 (H9N2) isolated from ducks in the same farm during an AI outbreak in Bantul district, Yogyakarta province, were sequenced and characterized. Our results showed that H5N1 virus was closely related to the highly pathogenic AI (HPAI) H5N1 of clade 2.3.2.1c, while the H9N2 virus was clustered with LPAI viruses from China, Vietnam and Indonesia H9N2 (CVI lineage). Genetic analysis revealed virulence characteristics for both in avian and in mammalian species. In summary, co-circulation of HPAI-H5N1 of clade 2.3.2.1c and LPAI-H9N2 was identified in a duck farm during an AI outbreak in Yogyakarta province, Indonesia. Our findings raise a concern of the potential risk of the viruses, which could increase viral transmission and/or threat to human health. Routine surveillance of avian influenza viruses should be continuously conducted to understand the dynamic and diversity of the viruses for influenza prevention and control in Indonesia and SEA region.
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Affiliation(s)
- Lestari
- Department of Veterinary Public Health, Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Disease Investigation Center Wates Yogyakarta, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Hendra Wibawa
- Disease Investigation Center Wates Yogyakarta, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Elly Puspasari Lubis
- Disease Investigation Center Wates Yogyakarta, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Rama Dharmawan
- Disease Investigation Center Wates Yogyakarta, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Rina Astuti Rahayu
- Disease Investigation Center Wates Yogyakarta, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Herdiyanto Mulyawan
- Disease Investigation Center Wates Yogyakarta, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Kamonpan Charoenkul
- Department of Veterinary Public Health, Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Chanakarn Nasamran
- Department of Veterinary Public Health, Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Bagoes Poermadjaja
- Disease Investigation Center Wates Yogyakarta, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Alongkorn Amonsin
- Department of Veterinary Public Health, Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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16
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Karo-Karo D, Bodewes R, Wibawa H, Artika M, Pribadi ES, Diyantoro D, Pratomo W, Sugama A, Hendrayani N, Indasari I, Wibowo MH, Muljono DH, Stegeman JA, Koch G. Reassortments among Avian Influenza A(H5N1) Viruses Circulating in Indonesia, 2015-2016. Emerg Infect Dis 2019; 25:465-472. [PMID: 30789142 PMCID: PMC6390736 DOI: 10.3201/eid2503.180167] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Highly pathogenic avian influenza (HPAI) A(H5N1) viruses have been circulating since 2003 in Indonesia, with major impacts on poultry health, severe economic losses, and 168 fatal laboratory-confirmed human cases. We performed phylogenetic analysis on 39 full-genome H5N1 virus samples collected during outbreaks among poultry in 2015-2016 in West Java and compared them with recently published sequences from Indonesia. Phylogenetic analysis revealed that the hemagglutinin gene of all samples belonged to 2 genetic groups in clade 2.3.2.1c. We also observed these groups for the neuraminidase, nucleoprotein, polymerase, and polymerase basic 1 genes. Matrix, nonstructural protein, and polymerase basic 2 genes of some HPAI were most closely related to clade 2.1.3 instead of clade 2.3.2.1c, and a polymerase basic 2 gene was most closely related to Eurasian low pathogenicity avian influenza. Our results detected a total of 13 reassortment types among HPAI in Indonesia, mostly in backyard chickens in Indramayu.
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Irianingsih SH, Wuryastuty H, Wasito R, Wibawa H, Rasa FST, Poermadjaja B. Genetic analysis of NS5B gene from bovine viral diarrhea virus-infected cattle in Central and East Java, Indonesia. Vet World 2019; 12:1108-1115. [PMID: 31528040 PMCID: PMC6702556 DOI: 10.14202/vetworld.2019.1108-1115] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/13/2019] [Indexed: 01/16/2023] Open
Abstract
Background and Aim: A previous study divided Indonesian bovine viral diarrhea virus (BVDV)-1 into subgenotypes BVDV-1a to BVDV-1d based on the partial NS5B gene using strain Bega as reference for BVDV-1a. In fact, it is clustered into BVDV-1c with strain Bega-like Australia. BVDV genotyping has been done on isolates from Jakarta, West and Central Java, but East Java isolates have not been genotyped. This study aimed to analyze genetic variability and amino acid residues in the nucleotide-binding pocket of the NS5B gene from infected cattle. Materials and Methods: Samples were obtained from the Sera Bank originating from active and passive surveillance of cattle that had been tested for BVDV antigen from 2013 to 2017. Detection of the p80 antibody and BVDV genotyping was carried out using ELISA and nested-multiplex-polymerase chain reaction (PCR), respectively. We defined 15 nested PCR products for partial sequencing of NS5B. Those field samples were selected from each location and year using proportional calculation as a representative sample. Homological and phylogenetic analyses of the partial NS5B gene were performed using BLAST and MEGA version 6. Results: Based on the phylogenetic tree analysis using 360 nucleotides as the partial NS5B gene, Indonesian BVDV-1 isolates from Central and East Java were subdivided to BVDV-1a (n=9), BVDV-1b (n=1), and BVDV-1c (n=5). In the present study, the homology of BVDV subgenotype -1a, -1b, and -1c was compared to the BVDV GenBank data and found 90-93%, 93%, and 92-95% respectively with the average pairwise distance of 0.207. A point mutation was shown at R283K of all BVDV isolates based on the sequence of three amino acid residues R283, R285, and I287 in the nucleotide-binding pocket as a part of the encoded RNA-dependent RNA polymerase. Conclusion: This study revealed the genetic variability of BVDV infecting cattle in Central Java and East Java, Indonesia, the subtypes BVDV-1a, BVDV-1b, BVDV-1c, and a point mutation at the R283K residue.
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Affiliation(s)
- S H Irianingsih
- Doctoral Study Program, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Disease Investigation Centre Wates, Yogyakarta, Indonesia
| | - H Wuryastuty
- Department of Veterinary Internal Medicine, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - R Wasito
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - H Wibawa
- Disease Investigation Centre Wates, Yogyakarta, Indonesia
| | - F S Tjatur Rasa
- Directorate of Animal Health, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, The Republic of Indonesia, Jakarta, Indonesia
| | - B Poermadjaja
- Disease Investigation Centre Wates, Yogyakarta, Indonesia
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Abstract
H5N1 highly pathogenic avian influenza (HPAI) virus causes high mortality of infected birds, with infection in multiple organs, including in feathers. Feathers have been proposed as samples for diagnosis of HPAI infection in birds, and this study is part of a broader investigation validating the use of feathers for diagnostic purposes. To understand and characterize the morphological basis for feather infection, sections from 7 different skin tracts of ducks and chickens infected with 3 different clades of H5N1 HPAI virus from Indonesia and Vietnam were examined histologically. Results showed that in ducks, lesions and viral antigen were mainly detected in the epidermis of feathers and follicles, whereas in chickens, they were mostly found in the dermis of these structures. Abundant viral antigen was found in nearly all the feathers examined from chickens, and there was no apparent difference between virus isolates or skin tracts in the proportion of feathers that were antigen positive. By immunohistochemistry, the majority of feathers from most skin tracts from ducks infected with a Vietnamese H5N1 HPAI virus contained abundant levels of viral antigen, while few feathers were antigen positive from ducks infected with 2 Indonesian viruses. These results support and inform the use of feathers for diagnostic detection of H5N1 HPAI virus in birds.
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Affiliation(s)
- H Nuradji
- 1 CSIRO-Australian Animal Health Laboratory, Geelong, Victoria, Australia.,2 School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia.,3 Indonesian Research Center for Veterinary Science, Bogor, West Java, Indonesia
| | - J Bingham
- 1 CSIRO-Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - J Payne
- 1 CSIRO-Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - J Harper
- 1 CSIRO-Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - S Lowther
- 1 CSIRO-Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - H Wibawa
- 1 CSIRO-Australian Animal Health Laboratory, Geelong, Victoria, Australia.,2 School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia.,4 Disease Investigation Centre Region IV Wates, Yogyakarta, Indonesia
| | - N T Long
- 5 Center for Veterinary Diagnostics, Regional Animal Health Office No. 6, Ho Chi Minh City, Viet Nam
| | - J Meers
- 2 School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
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19
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Nuradji H, Bingham J, Lowther S, Wibawa H, Colling A, Long NT, Meers J. A comparative evaluation of feathers, oropharyngeal swabs, and cloacal swabs for the detection of H5N1 highly pathogenic avian influenza virus infection in experimentally infected chickens and ducks. J Vet Diagn Invest 2015; 27:704-15. [PMID: 26462759 DOI: 10.1177/1040638715611443] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Oropharyngeal and cloacal swabs have been widely used for the detection of H5N1 highly pathogenic avian Influenza A virus (HPAI virus) in birds. Previous studies have shown that the feather calamus is a site of H5N1 virus replication and therefore has potential for diagnosis of avian influenza. However, studies characterizing the value of feathers for this purpose are not available, to our knowledge; herein we present a study investigating feathers for detection of H5N1 virus. Ducks and chickens were experimentally infected with H5N1 HPAI virus belonging to 1 of 3 clades (Indonesian clades 2.1.1 and 2.1.3, Vietnamese clade 1). Different types of feathers and oropharyngeal and cloacal swab samples were compared by virus isolation. In chickens, virus was detected from all sample types: oral and cloacal swabs, and immature pectorosternal, flight, and tail feathers. During clinical disease, the viral titers were higher in feathers than swabs. In ducks, the proportion of virus-positive samples was variable depending on viral strain and time from challenge; cloacal swabs and mature pectorosternal feathers were clearly inferior to oral swabs and immature pectorosternal, tail, and flight feathers. In ducks infected with Indonesian strains, in which most birds did not develop clinical signs, all sampling methods gave intermittent positive results; 3-23% of immature pectorosternal feathers were positive during the acute infection period; oropharyngeal swabs had slightly higher positivity during early infection, while feathers performed better during late infection. Our results indicate that immature feathers are an alternative sample for the diagnosis of HPAI in chickens and ducks.
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Affiliation(s)
- Harimurti Nuradji
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)-Australian Animal Health Laboratory, Geelong, Victoria, Australia (Nuradji, Bingham, Lowther, Wibawa, Colling)School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia (Nuradji, Wibawa, Meers)Indonesian Research Centre for Veterinary Science, Bogor, West Java, Indonesia (Nuradji)Disease Investigation Centre Region IV Wates, Yogyakarta, Indonesia (Wibawa)Centre for Veterinary Diagnostics, Regional Animal Health Office No. 6, Ho Chi Minh City, Vietnam (Long)
| | - John Bingham
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)-Australian Animal Health Laboratory, Geelong, Victoria, Australia (Nuradji, Bingham, Lowther, Wibawa, Colling)School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia (Nuradji, Wibawa, Meers)Indonesian Research Centre for Veterinary Science, Bogor, West Java, Indonesia (Nuradji)Disease Investigation Centre Region IV Wates, Yogyakarta, Indonesia (Wibawa)Centre for Veterinary Diagnostics, Regional Animal Health Office No. 6, Ho Chi Minh City, Vietnam (Long)
| | - Sue Lowther
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)-Australian Animal Health Laboratory, Geelong, Victoria, Australia (Nuradji, Bingham, Lowther, Wibawa, Colling)School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia (Nuradji, Wibawa, Meers)Indonesian Research Centre for Veterinary Science, Bogor, West Java, Indonesia (Nuradji)Disease Investigation Centre Region IV Wates, Yogyakarta, Indonesia (Wibawa)Centre for Veterinary Diagnostics, Regional Animal Health Office No. 6, Ho Chi Minh City, Vietnam (Long)
| | - Hendra Wibawa
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)-Australian Animal Health Laboratory, Geelong, Victoria, Australia (Nuradji, Bingham, Lowther, Wibawa, Colling)School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia (Nuradji, Wibawa, Meers)Indonesian Research Centre for Veterinary Science, Bogor, West Java, Indonesia (Nuradji)Disease Investigation Centre Region IV Wates, Yogyakarta, Indonesia (Wibawa)Centre for Veterinary Diagnostics, Regional Animal Health Office No. 6, Ho Chi Minh City, Vietnam (Long)
| | - Axel Colling
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)-Australian Animal Health Laboratory, Geelong, Victoria, Australia (Nuradji, Bingham, Lowther, Wibawa, Colling)School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia (Nuradji, Wibawa, Meers)Indonesian Research Centre for Veterinary Science, Bogor, West Java, Indonesia (Nuradji)Disease Investigation Centre Region IV Wates, Yogyakarta, Indonesia (Wibawa)Centre for Veterinary Diagnostics, Regional Animal Health Office No. 6, Ho Chi Minh City, Vietnam (Long)
| | - Ngo Thanh Long
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)-Australian Animal Health Laboratory, Geelong, Victoria, Australia (Nuradji, Bingham, Lowther, Wibawa, Colling)School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia (Nuradji, Wibawa, Meers)Indonesian Research Centre for Veterinary Science, Bogor, West Java, Indonesia (Nuradji)Disease Investigation Centre Region IV Wates, Yogyakarta, Indonesia (Wibawa)Centre for Veterinary Diagnostics, Regional Animal Health Office No. 6, Ho Chi Minh City, Vietnam (Long)
| | - Joanne Meers
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)-Australian Animal Health Laboratory, Geelong, Victoria, Australia (Nuradji, Bingham, Lowther, Wibawa, Colling)School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia (Nuradji, Wibawa, Meers)Indonesian Research Centre for Veterinary Science, Bogor, West Java, Indonesia (Nuradji)Disease Investigation Centre Region IV Wates, Yogyakarta, Indonesia (Wibawa)Centre for Veterinary Diagnostics, Regional Animal Health Office No. 6, Ho Chi Minh City, Vietnam (Long)
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Dharmayanti NLPI, Hartawan R, Wibawa H, Balish A, Donis R, Davis CT, Samaan G. Genetic characterization of clade 2.3.2.1 avian influenza A(H5N1) viruses, Indonesia, 2012. Emerg Infect Dis 2014; 20:671-4. [PMID: 24656213 PMCID: PMC3966381 DOI: 10.3201/eid2004.130517] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
After reports of unusually high mortality rates among ducks on farms in Java Island, Indonesia, in September 2012, influenza A(H5N1) viruses were detected and characterized. Sequence analyses revealed all genes clustered with contemporary clade 2.3.2.1 viruses, rather than enzootic clade 2.1.3 viruses, indicating the introduction of an exotic H5N1 clade into Indonesia.
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Wibawa H, Bingham J, Nuradji H, Lowther S, Payne J, Harper J, Junaidi A, Middleton D, Meers J. Experimentally infected domestic ducks show efficient transmission of Indonesian H5N1 highly pathogenic avian influenza virus, but lack persistent viral shedding. PLoS One 2014; 9:e83417. [PMID: 24392085 PMCID: PMC3879242 DOI: 10.1371/journal.pone.0083417] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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: 06/22/2013] [Accepted: 11/05/2013] [Indexed: 11/26/2022] Open
Abstract
Ducks are important maintenance hosts for avian influenza, including H5N1 highly pathogenic avian influenza viruses. A previous study indicated that persistence of H5N1 viruses in ducks after the development of humoral immunity may drive viral evolution following immune selection. As H5N1 HPAI is endemic in Indonesia, this mechanism may be important in understanding H5N1 evolution in that region. To determine the capability of domestic ducks to maintain prolonged shedding of Indonesian clade 2.1 H5N1 virus, two groups of Pekin ducks were inoculated through the eyes, nostrils and oropharynx and viral shedding and transmission investigated. Inoculated ducks (n = 15), which were mostly asymptomatic, shed infectious virus from the oral route from 1 to 8 days post inoculation, and from the cloacal route from 2–8 dpi. Viral ribonucleic acid was detected from 1–15 days post inoculation from the oral route and 1–24 days post inoculation from the cloacal route (cycle threshold <40). Most ducks seroconverted in a range of serological tests by 15 days post inoculation. Virus was efficiently transmitted during acute infection (5 inoculation-infected to all 5 contact ducks). However, no evidence for transmission, as determined by seroconversion and viral shedding, was found between an inoculation-infected group (n = 10) and contact ducks (n = 9) when the two groups only had contact after 10 days post inoculation. Clinical disease was more frequent and more severe in contact-infected (2 of 5) than inoculation-infected ducks (1 of 15). We conclude that Indonesian clade 2.1 H5N1 highly pathogenic avian influenza virus does not persist in individual ducks after acute infection.
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Affiliation(s)
- Hendra Wibawa
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Animal Health Laboratory, Geelong, Australia
- School of Veterinary Science, The University of Queensland, Brisbane, Australia
- Disease Investigation Centre Regional IV Wates, Yogyakarta, Indonesia
| | - John Bingham
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Animal Health Laboratory, Geelong, Australia
- * E-mail:
| | - Harimurti Nuradji
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Animal Health Laboratory, Geelong, Australia
- School of Veterinary Science, The University of Queensland, Brisbane, Australia
- Indonesian Research Center for Veterinary Science, Bogor, West Java, Indonesia
| | - Sue Lowther
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Animal Health Laboratory, Geelong, Australia
| | - Jean Payne
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Animal Health Laboratory, Geelong, Australia
| | - Jenni Harper
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Animal Health Laboratory, Geelong, Australia
| | - Akhmad Junaidi
- Disease Investigation Centre Regional IV Wates, Yogyakarta, Indonesia
| | - Deborah Middleton
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Animal Health Laboratory, Geelong, Australia
| | - Joanne Meers
- School of Veterinary Science, The University of Queensland, Brisbane, Australia
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Wibawa H, Henning J, Waluyati DE, Usman TB, Lowther S, Bingham J, Junaidi A, Meers J. Comparison of serological assays for detecting antibodies in ducks exposed to H5 subtype avian influenza virus. BMC Vet Res 2012; 8:117. [PMID: 22823985 PMCID: PMC3546307 DOI: 10.1186/1746-6148-8-117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 06/29/2012] [Indexed: 12/03/2022] Open
Abstract
Background Chicken red blood cells (RBCs) are commonly used in hemagglutination inhibition (HI) tests to measure hemagglutinating antibodies against influenza viruses. The use of horse RBCs in the HI test can reportedly increase its sensitivity when testing human sera for avian influenza antibodies. This study aims to compare the proportion of positives detected and the agreement between two HI tests using either chicken or horse red blood cells for antibody detection in sera of ducks experimentally infected or naturally exposed to Indonesian H5 subtype avian influenza virus. In addition, comparison with a virus neutralisation (VN) test was conducted with the experimental sera. Results In the experimental study, the proportion of HI antibody-positive ducks increased slightly, from 0.57 when using chicken RBCs to 0.60 when using horse RBCs. The HI tests indicated almost perfect agreement (kappa = 0.86) when results were dichotomised (titre ≥ 4 log2), and substantial agreement (weighted kappa = 0.80) for log titres. Overall agreements between the two HI tests were greater than between either of the HI tests and the VN test. The use of horse RBCs also identified a higher proportion of antibody positives in field duck sera (0.08, compared to chicken RBCs 0.02), with also almost perfect agreements for dichotomized results (Prevalence and bias adjusted Kappa (PABAK) = 0.88) and for log titres (weighted PABAK = 0.93), respectively. Factors that might explain observed differences in the proportion of antibody-positive ducks and in the agreements between HI tests are discussed. Conclusion In conclusion, we identified a good agreement between HI tests. However, when horse RBCs were used, a higher proportion of sera was positive (titre ≥ 4 log2) than using chicken RBCs, especially during the early response against H5N1 virus. The HRBC-HI might be more responsive in identifying early H5N1 HPAI serological response and could be a recommended assay for avian influenza sero-surveillance in both wild and domestic birds.
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Affiliation(s)
- Hendra Wibawa
- School of Veterinary Science, The University of Queensland, Gatton Campus, Gatton, QLD, Australia.
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Wibawa H, Henning J, Wong F, Selleck P, Junaidi A, Bingham J, Daniels P, Meers J. A molecular and antigenic survey of H5N1 highly pathogenic avian influenza virus isolates from smallholder duck farms in Central Java, Indonesia during 2007-2008. Virol J 2011; 8:425. [PMID: 21896207 PMCID: PMC3179459 DOI: 10.1186/1743-422x-8-425] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 09/07/2011] [Indexed: 12/29/2022] Open
Abstract
Background Indonesia is one of the countries most severely affected by H5N1 highly pathogenic avian influenza (HPAI) virus in terms of poultry and human health. However, there is little information on the diversity of H5N1 viruses circulating in backyard farms, where chickens and ducks often intermingle. In this study, H5N1 virus infection occurring in 96 smallholder duck farms in central Java, Indonesia from 2007-2008 was investigated and the molecular and antigenic characteristics of H5N1 viruses isolated from these farms were analysed. Results All 84 characterised viruses belonged to H5N1 clade 2.1 with three virus sublineages being identified: clade 2.1.1 (1), clade 2.1.3 (80), and IDN/6/05-like viruses (3) that did not belong to any of the present clades. All three clades were found in ducks, while only clade 2.1.3 was isolated from chickens. There were no significant amino acid mutations of the hemagglutinin (HA) and neuraminidase (NA) sites of the viruses, including the receptor binding, glycosylation, antigenic and catalytic sites and NA inhibitor targets. All the viruses had polybasic amino acids at the HA cleavage site. No evidence of major antigenic variants was detected. Based on the HA gene, identical virus variants could be found on different farms across the study sites and multiple genetic variants could be isolated from HPAI outbreaks simultaneously or at different time points from single farms. HPAI virus was isolated from both ducks and chickens; however, the proportion of surviving duck cases was considerably higher than in chickens. Conclusions The 2.1.3 clade was the most common lineage found in this study. All the viruses had sequence characteristic of HPAI, but negligible variations in other recognized amino acids at the HA and NA proteins which determine virus phenotypes. Multiple genetic variants appeared to be circulating simultaneously within poultry communities. The high proportion of live duck cases compared to chickens over the study period suggests that ducks are more likely to survive infection and they may better suit the role of long-term maintenance host for H5N1. As some viruses were isolated from dead birds, there was no clear correlation between genetic variations and pathogenicity of these viruses.
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Affiliation(s)
- Hendra Wibawa
- CSIRO-Australian Animal Health Laboratory, Geelong, Victoria, Australia.
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Henning J, Wibawa H, Morton J, Usman TB, Junaidi A, Meers J. Scavenging ducks and transmission of highly pathogenic avian influenza, Java, Indonesia. Emerg Infect Dis 2010; 16:1244-50. [PMID: 20678318 PMCID: PMC3298304 DOI: 10.3201/eid1608.091540] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [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: 11/19/2022] Open
Abstract
In Java, Indonesia, during March 2007-March 2008, 96 farms with scavenging ducks that were not vaccinated against highly pathogenic avian influenza (HPAI) were monitored bimonthly. Bird-level (prevalence among individual birds) H5 seroprevalence was 2.6% for ducks and 0.5% for chickens in contact with ducks. At least 1 seropositive bird was detected during 19.5% and 2.0% of duck- and chicken-flock visits, respectively. Duck flocks were 12.4x more likely than chicken flocks to have seropositive birds. During 21.4% of farm visits, <or=1 sampled duck was H5 seropositive when all sampled in-contact chickens were seronegative. Subtype H5 virus was detected during 2.5% of duck-flock visits and 1.5% of chicken-flock visits. When deaths from HPAI infection occurred, H5 virus shedding occurred in apparently healthy birds on 68.8% of farms. Of 180 poultry deaths investigated, 43.9% were attributed to H5 virus. These longitudinal study results indicate that ducks are a source of infection for chickens and, potentially, for humans.
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Affiliation(s)
- Joerg Henning
- The University of Queensland, Brisbane, Queensland, Australia.
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Bingham J, Green DJ, Lowther S, Klippel J, Burggraaf S, Anderson DE, Wibawa H, Hoa DM, Long NT, Vu PP, Middleton DJ, Daniels PW. Infection studies with two highly pathogenic avian influenza strains (Vietnamese and Indonesian) in Pekin ducks (Anas platyrhynchos), with particular reference to clinical disease, tissue tropism and viral shedding. Avian Pathol 2009; 38:267-78. [DOI: 10.1080/03079450903055371] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Loth L, Prijono WB, Wibawa H, Usman TB. Evaluation of two avian influenza type A rapid antigen tests under Indonesian field conditions. J Vet Diagn Invest 2008; 20:642-4. [PMID: 18776101 DOI: 10.1177/104063870802000519] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The current study evaluated the test characteristics of 2 commercially available rapid antigen tests for highly pathogenic avian influenza. Diagnostic specimens were collected from free-ranging village chickens in Indonesia. A total of 174 healthy, sick, and dead birds were included in the study. The relative diagnostic test sensitivity and the relative diagnostic test specificity were calculated by using real-time reverse transcription polymerase chain reaction (RT-PCR) as the confirmatory diagnosis. The AnigenR Rapid AIV Ag test had a relative diagnostic sensitivity of 0.69 (95% confidence interval [CI]: 0.56-0.80) and a relative diagnostic specificity of 0.98 (95% CI: 0.93-0.99). The Flu Detect(TM) Antigen Capture test strip had a relative diagnostic sensitivity of 0.71 (95% CI: 0.58-0.82) and a relative diagnostic specificity of 0.98 (95% CI: 0.93-0.99). These tests are a valuable tool for the Indonesian avian influenza control program by reliably and quickly detecting Influenza A virus from oropharyngeal swabs from sick or dying chickens.
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Affiliation(s)
- Leo Loth
- Food and Agricultural Organization of the United Nations, Jakarta, Indonesia.
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Wibawa H, Noviana D, Tsuchiya K, Satruja F, Horii Y. Resistance of cotton rats, Sigmodon hispidus, to primary infection by Nippostrongylus brasiliensis. J Vet Med Sci 2002; 64:423-6. [PMID: 12069075 DOI: 10.1292/jvms.64.423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The resistance of cotton rats, Sigmodon hispidus to Nippostrongylus brasiliensis infection was examined and compared the response to that of the susceptible Indian soft-furred rat, Millardia meltada. After a primary infection with infective third-stage N. brasiliensis larvae (L3), the number of eggs in feces and adult worm recovery rates from the small intestine of cotton rats were significantly lower than in the controls. To determine whether cotton rat resistance was observed during the migratory phase or the intestinal phase, cotton rats and control animals were challenged subcutaneously with L3 or intraduodenally with adult worms, and larval recovery from lungs and adult worm burden were evaluated. The recovery rate of larvae from the lungs of cotton rats was about five-fold lower than from controls. Adult worm recovery from the small intestine of cotton rats was also lower than that from the controls, but the difference (two-fold lower) was smaller than that observed for lung recovery. Carbon treatment at a dose of 250-500 mg/kg effectively increased larval worm recovery from the lungs of cotton rats. However, this treatment had no effect on worm recovery from the intestine after intraduodenal implantation of adult N. brasiliensis. These results suggest that macrophage function have important role in the expression of strong resistance during the migratory phase of N. brasiliensis infection in cotton rats.
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Affiliation(s)
- Hendra Wibawa
- Veterinary Teaching Hospital and Internal Medicine, Faculty of Agriculture, Miyazaki University, Gakuen-Kibanadai, Japan
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