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Adzdzakiy MM, Sutarno S, Asyifa IZ, Sativa AR, Fiqri AR, Fibriani A, Ristandi RB, Ningrum RA, Iryanto SB, Prasetyoputri A, Dharmayanthi AB, Saputra S. SARS-CoV-2 genetic variation and bacterial communities of naso-oropharyngeal samples in middle-aged and elderly COVID-19 patients in West Java, Indonesia. J Taibah Univ Med Sci 2024; 19:70-81. [PMID: 37868100 PMCID: PMC10589881 DOI: 10.1016/j.jtumed.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 07/21/2023] [Accepted: 09/01/2023] [Indexed: 10/24/2023] Open
Abstract
Objective The number of COVID-19 cases in Indonesia reflects the disease severity and rapid dissemination. In response to the mounting threat, SARS-CoV-2 genomic surveillance and the investigation of naso-oropharyngeal bacterial communities in West Java were conducted, as dysbiosis of the upper respiratory tract microbiota might adversely affect the clinical condition of patients. Methods We utilized the Oxford Nanopore sequencing platform to analyze genetic variation of 43 samples of SARS-CoV-2 and 11 selected samples for 16S rRNA gene sequencing, using samples collected from May to August 2021. Results The prevalence of AY.23 (>82%) predominated among five virus lineages in the populations (AY.23, AY.24, AY.26, AY.42, B.1.1.7). The region in the SARS-CoV-2 genome found to have the highest number of mutations was the spike (S) protein (>20%). There was no association between SARS-CoV-2 lineages, mutation frequency, patient profile, and COVID-19 rapid spread-categorized cases. There was no association of bacterial relative abundance, alpha-beta diversity, and linear discriminant analysis effect size analysis with patient profile and rapid spread cases. MetagenomeSeq analysis showed eight differential abundance species in individual patient profiles, including Pseudomonas aeruginosa and Haemophilus parainfluenzae. Conclusions The data demonstrated relevant AY.23 dominance (the Delta variant) in West Java during that period supporting the importance of surveillance program in monitoring disease progression. The inconsistent results of the bacterial communities suggest that a complex multifactor process may contribute to the progression of bacterial-induced disease in each patient.
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Affiliation(s)
- Muhammad M. Adzdzakiy
- Graduate School of Bioscience, Faculty of Mathematics and Natural Sciences, Universitas Sebelas Maret, Jl. Ir. Sutami 36A Surakarta, Central Java, Indonesia
| | - Sutarno Sutarno
- Graduate School of Bioscience, Faculty of Mathematics and Natural Sciences, Universitas Sebelas Maret, Jl. Ir. Sutami 36A Surakarta, Central Java, Indonesia
| | - Isnaini Z. Asyifa
- Master Program in Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jl. Salemba Raya No.6, Jakarta, Indonesia
| | - Alvira R. Sativa
- School of Life Science and Technology, Institut Teknologi Bandung, Jl. Ganesa 10, Bandung, West Java, Indonesia
| | - Ahmad R.A. Fiqri
- Master Program in Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jl. Salemba Raya No.6, Jakarta, Indonesia
| | - Azzania Fibriani
- School of Life Science and Technology, Institut Teknologi Bandung, Jl. Ganesa 10, Bandung, West Java, Indonesia
| | - Ryan B. Ristandi
- West Java Health Laboratory, Jl. Sederhana No. 3-5, Pasteur, Sukajadi, Bandung, West Java, Indonesia
| | - Ratih A. Ningrum
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, Bogor, West Java, Indonesia
| | - Syam B. Iryanto
- Research Center for Computation, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, Bogor, West Java, Indonesia
| | - Anggia Prasetyoputri
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, Bogor, West Java, Indonesia
| | - Anik B. Dharmayanthi
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, Bogor, West Java, Indonesia
| | - Sugiyono Saputra
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, Bogor, West Java, Indonesia
- Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, Bogor, West Java, Indonesia
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Hakim MS, Gunadi, Rahayu A, Wibawa H, Eryvinka LS, Supriyati E, Vujira KA, Iskandar K, Afiahayati, Daniwijaya EW, Oktoviani FN, Annisa L, Utami FDT, Amadeus VC, Nurhidayah SS, Leksono TP, Halim FV, Arguni E, Nuryastuti T, Wibawa T. Sequence analysis of the Spike, RNA-dependent RNA polymerase, and protease genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia. Virus Genes 2024:10.1007/s11262-023-02048-1. [PMID: 38244104 DOI: 10.1007/s11262-023-02048-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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Agustina R, Rianda D, Lamuri A, Ekawidyani KR, Siregar DAS, Sari DS, Wulan PM, Devana ND, Syam AF, Rahyussalim AJ, Handayani DO, Widyastuti W, Shankar AH, Salama N. The impact of government pandemic policies on the vulnerability of healthcare workers to SARS-CoV-2 infection and mortality in Jakarta Province, Indonesia. Ann Med 2024; 55:2293306. [PMID: 38206905 PMCID: PMC10786428 DOI: 10.1080/07853890.2023.2293306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 11/30/2023] [Indexed: 01/13/2024] Open
Abstract
INTRODUCTION Healthcare workers (HCWs) are on the frontlines of the COVID-19 pandemic, putting them at a higher risk of infection and disease than non-HCWs. We analysed the effects of government policies for the public and for HCWs on the likelihood of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and mortality among HCWs during the first 8 months of the pandemic in Jakarta province, the capital city and COVID-19 hotspot in Indonesia. METHODS We conducted a retrospective cohort study using secondary data from the Jakarta provincial government from March to October 2020, which included sociodemographic characteristics, symptoms, comorbidities and COVID-19 diagnosis history for all cases. A generalized linear mixed-effect regression model was used to determine the effect of each month on the odds ratio (OR) of COVID-19 cases and deaths for HCW compared with non-HCW, assuming that monthly trends were influenced by varying government policies. RESULTS A total of 894,487 suspected and confirmed COVID-19 cases in health facilities in Jakarta province were analysed. The OR of confirmed cases for HCW was 2.04 (95% CI 2.00-2.08; p < .001) compared to non-HCW. Despite this higher OR for infection, the case fatality rate (2.32 per 100) and OR (1.02, 95% CI 0.93-1.11; p = .65) of COVID-19 deaths for HCW were similar to those of non-HCW. We observed a trend towards a lower number of COVID-19 patients in hospitals and lower odds of COVID-19 cases among HCWs during the April-to-July 2020 phase compared to the August-to-October phase. This chronologically aligned with more extensive policies to support hospital-based, community-based and well-being-related actions to protect HCW. CONCLUSIONS HCW had higher odds of having SARS-CoV-2 infection, yet similar odds of death from COVID-19, as compared to non-HCW. Government policies with collective efforts to prevent hospital overcapacity during high transmission and burden periods of the pandemic should be prioritized.
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Affiliation(s)
- Rina Agustina
- Department of Nutrition, Faculty of Medicine, Universitas Indonesia – Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Human Nutrition Research Center, Indonesian Medical Education and Research Institute (HNRC-IMERI), Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Davrina Rianda
- Human Nutrition Research Center, Indonesian Medical Education and Research Institute (HNRC-IMERI), Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Nutrition, University of California at Davis, Davis, CA, USA
| | - Aly Lamuri
- Big Data Center, Indonesian Medical Education and Research Institute (BDC-IMERI), Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Karina Rahmadia Ekawidyani
- Department of Nutrition, Faculty of Medicine, Universitas Indonesia – Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Department of Community Nutrition, Faculty of Human Ecology, IPB University, Bogor, Indonesia
| | - Deviana Ayushinta Sani Siregar
- Human Nutrition Research Center, Indonesian Medical Education and Research Institute (HNRC-IMERI), Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Dyana Santika Sari
- Human Nutrition Research Center, Indonesian Medical Education and Research Institute (HNRC-IMERI), Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Prashti Mutia Wulan
- Human Nutrition Research Center, Indonesian Medical Education and Research Institute (HNRC-IMERI), Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Natasha Dianasari Devana
- Department of Nutrition, Faculty of Medicine, Universitas Indonesia – Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | - Ari Fahrial Syam
- Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia – Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | - Ahmad Jabir Rahyussalim
- Department of Orthopaedic and Traumatology, Faculty of Medicine, Universitas Indonesia – Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | | | | | - Anuraj Harish Shankar
- Oxford University Clinical Research Unit – Indonesia, Jakarta, Indonesia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ngabila Salama
- Health Office, Government of Jakarta Province, Jakarta, Indonesia
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Erendereg M, Tumurbaatar S, Byambaa O, Enebish G, Burged N, Khurelsukh T, Baatar N, Munkhjin B, Ulziijargal J, Gantumur A, Altanbayar O, Batjargal O, Altangerel D, Tulgaa K, Ganbold S, Tundev O, Jigjidsuren S, Nyamdorj T, Tsedenbal N, Batmunkh B, Jantsansengee B, Lkhagvaa B, Tsolmon B, Enebish O, Tsevegmid E, Sereejav E, Nyamdavaa K, Erkhembayar R, Chimeddorj B. Molecular epidemiology of SARS-CoV-2 in Mongolia, first experience with nanopore sequencing in lower- and middle-income countries setting. Immun Inflamm Dis 2023; 11:e1095. [PMID: 38156392 PMCID: PMC10716720 DOI: 10.1002/iid3.1095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/30/2023] [Accepted: 11/09/2023] [Indexed: 12/30/2023] Open
Abstract
BACKGROUND Coronavirus disease (COVID-19) has had a significant impact globally, and extensive genomic research has been conducted on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage patterns and its variants. Mongolia's effective response resulted in low prevalence until vaccinations became available. However, due to the lack of systematically collected data and absence of whole genome sequencing capabilities, we conducted a two-stepped, nationally representative molecular epidemiologic study of SARS-CoV-2 in Mongolia for 2020 and 2021. METHODS We used retrospective analysis of stored biological samples from November 2020 to October 2021 and a variant-specific real-time reverse transcription polymerase chain reaction (RT-PCR) test to detect SARS-CoV-2 variants, followed by whole genome sequencing by Nanopore technology. Samples were retrieved from different sites and stored at -70°C deep freezer, and tests were performed on samples with cycle threshold <30. RESULTS Out of 4879 nucleic acid tests, 799 whole genome sequencing had been carried out. Among the stored samples of earlier local transmission, we found the 20B (B.1.1.46) variant predominated in the earlier local transmission period. A slower introduction and circulation of alpha and delta variants were observed compared to global dynamics in 2020 and 2021. Beta or Gamma variants were not detected between November 2020 and September 2021 in Mongolia. CONCLUSIONS SARS-CoV-2 variants of concerns including alpha and delta were delayed in circulation potentially due to public health stringencies in Mongolia. We are sharing our initial experience with whole genome sequencing of SARS-CoV-2 from Mongolia, where sequencing data is sparse.
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Affiliation(s)
- Munkhtuya Erendereg
- Department of Microbiology and Infection Prevention Control, School of BiomedicineMongolian National University of Medical SciencesUlaanbaatarMongolia
- Intermed HospitalUlaanbaatarMongolia
| | - Suvd Tumurbaatar
- Institute of Biomedical SciencesMongolian National University of Medical SciencesUlaanbaatarMongolia
| | - Otgonjargal Byambaa
- Department of Microbiology and Infection Prevention Control, School of BiomedicineMongolian National University of Medical SciencesUlaanbaatarMongolia
| | - Gerelmaa Enebish
- Department of Microbiology and Infection Prevention Control, School of BiomedicineMongolian National University of Medical SciencesUlaanbaatarMongolia
| | | | | | | | - Badmaarag Munkhjin
- Division for Science and TechnologyMongolian National University of Medical SciencesUlaanbaatarMongolia
| | | | - Anuujin Gantumur
- Department of Microbiology and Infection Prevention Control, School of BiomedicineMongolian National University of Medical SciencesUlaanbaatarMongolia
| | - Oyunbaatar Altanbayar
- Department of Microbiology and Infection Prevention Control, School of BiomedicineMongolian National University of Medical SciencesUlaanbaatarMongolia
| | - Ochbadrakh Batjargal
- Institute of Biomedical SciencesMongolian National University of Medical SciencesUlaanbaatarMongolia
| | | | - Khosbayar Tulgaa
- Institute of Biomedical SciencesMongolian National University of Medical SciencesUlaanbaatarMongolia
| | | | - Odgerel Tundev
- National Center for Communicable DiseasesUlaanbaatarMongolia
| | | | | | | | | | | | - Battur Lkhagvaa
- National Center for Communicable DiseasesUlaanbaatarMongolia
| | - Bilegtsaikhan Tsolmon
- Institute of Biomedical SciencesMongolian National University of Medical SciencesUlaanbaatarMongolia
- National Center for Communicable DiseasesUlaanbaatarMongolia
| | | | | | | | | | - Ryenchindorj Erkhembayar
- International Cyber Education Center, Graduate SchoolMongolian National University of Medical SciencesUlaanbaatarMongolia
- Department of Global Health and PopulationHarvard T.H. Chan School of Public HealthBostonMassachusettsUSA
| | - Battogtokh Chimeddorj
- Department of Microbiology and Infection Prevention Control, School of BiomedicineMongolian National University of Medical SciencesUlaanbaatarMongolia
- Institute of Biomedical SciencesMongolian National University of Medical SciencesUlaanbaatarMongolia
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Harapan BN, Harapan T, Theodora L, Anantama NA. From Archipelago to Pandemic Battleground: Unveiling Indonesia's COVID-19 Crisis. J Epidemiol Glob Health 2023; 13:591-603. [PMID: 37707715 PMCID: PMC10686963 DOI: 10.1007/s44197-023-00148-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/25/2023] [Indexed: 09/15/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has posed unprecedented challenges to countries worldwide, including Indonesia. With its unique archipelagic geography consisting of more than 17,000 thousand islands, Indonesia faces unique complexities in managing the spread of the virus. Based on existing literature, this review article elaborates on key issues that have shaped Indonesia's COVID-19 response. The article begins by examining the early stages of the COVID-19 pandemic in Indonesia, along with the implementation of various preventive measures and the impact of the virus on public health. This article examines how Indonesia's socio-economic factors have generally influenced its healthcare system and further delves into the COVID-19 response strategies implemented by the Indonesian government and public health authorities as well as overall crisis preparedness. It discusses the actions taken to control the spread of the virus, including testing strategies and vaccination efforts. The difficulties encountered in implementing these measures are presented. In conclusion, this review article provides a comprehensive understanding of the COVID-19 crisis in Indonesia, covering facts on multiple dimensions ranging from the timeline of the pandemic to vaccination efforts, epidemiology, socio-economic implications, testing strategies, mobility patterns, public holidays, the impact of working from home, and the utilization of complementary and alternative medicine in addition to the standard of care for COVID-19. The insights gained from this article can complement future strategies for pandemic management and response in Indonesia and other countries facing similar challenges.
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Affiliation(s)
| | - Triswan Harapan
- Complementary Cardiovascular Clinic (CCV Clinic), Tangerang Selatan, Indonesia
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Bestari R, Nainggolan IRA, Hasibuan M, Ratnanggana R, Rahardjo K, Nastri AM, Dewantari JR, Soetjipto S, Lusida MI, Mori Y, Shimizu K, Kusumawati RL, Ichwan M, Lubis IND. SARS-CoV-2 lineages circulating during the first wave of the pandemic in North Sumatra, Indonesia. IJID REGIONS 2023; 8:S1-S7. [PMID: 37799539 PMCID: PMC10548867 DOI: 10.1016/j.ijregi.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 07/12/2023] [Accepted: 07/16/2023] [Indexed: 10/07/2023]
Abstract
Objectives To determine the lineage distribution of the virus during the first wave of the pandemic in North Sumatra, Indonesia. Methods A total of 20 samples with positive results based on reverse transcription-polymerase chain reaction were selected for virus culture and then performed whole-genome sequence analysis using next-generation sequencing which was applied by the Illumina MiSeq instrument. Results Whole-genome sequence analysis revealed that the majority of our samples belong to lineages B.1.468 (n = 10), B.1 (n = 5), B.1.1 (n = 2), B.1.1.398 (n = 2), and B.6 (n = 1). Other unique amino acid mutations found in our samples were present in A58T on non-structural protein (NSP3) (70%), P323L on NSP12 (95%), Q57H on NS3 protein (75%), and D614G on S (100%). Conclusion The SARS-CoV-2 lineage B.1.468 may be the main virus variant circulating in North Sumatra at the beginning of the emergence of COVID-19 cases in this province.
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Affiliation(s)
- Ramadhan Bestari
- Faculty of Medicine, Universitas Islam Sumatera Utara, Medan, Indonesia
| | | | - Mirzan Hasibuan
- Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
| | - Rima Ratnanggana
- Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Krisnoadi Rahardjo
- Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | | | | | | | - Maria Inge Lusida
- Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Yasuko Mori
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Chuo-ku, Japan
| | - Kazufumi Shimizu
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Chuo-ku, Japan
| | - R Lia Kusumawati
- Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
| | - Muhammad Ichwan
- Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
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Zheng P, Zhou C, Ding Y, Liu B, Lu L, Zhu F, Duan S. Nanopore sequencing technology and its applications. MedComm (Beijing) 2023; 4:e316. [PMID: 37441463 PMCID: PMC10333861 DOI: 10.1002/mco2.316] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third-generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID-19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus-2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID-19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID-19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.
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Affiliation(s)
- Peijie Zheng
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Chuntao Zhou
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Yuemin Ding
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
| | - Bin Liu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Liuyi Lu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Feng Zhu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Shiwei Duan
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
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Marascio N, Cilburunoglu M, Torun EG, Centofanti F, Mataj E, Equestre M, Bruni R, Quirino A, Matera G, Ciccaglione AR, Yalcinkaya KT. Molecular Characterization and Cluster Analysis of SARS-CoV-2 Viral Isolates in Kahramanmaraş City, Turkey: The Delta VOC Wave within One Month. Viruses 2023; 15:v15030802. [PMID: 36992510 PMCID: PMC10054778 DOI: 10.3390/v15030802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/13/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
The SARS-CoV-2 pandemic has seriously affected the population in Turkey. Since the beginning, phylogenetic analysis has been necessary to monitor public health measures against COVID-19 disease. In any case, the analysis of spike (S) and nucleocapsid (N) gene mutations was crucial in determining their potential impact on viral spread. We screened S and N regions to detect usual and unusual substitutions, whilst also investigating the clusters among a patient cohort resident in Kahramanmaraş city, in a restricted time span. Sequences were obtained by Sanger methods and genotyped by the PANGO Lineage tool. Amino acid substitutions were annotated comparing newly generated sequences to the NC_045512.2 reference sequence. Clusters were defined using phylogenetic analysis with a 70% cut-off. All sequences were classified as Delta. Eight isolates carried unusual mutations on the S protein, some of them located in the S2 key domain. One isolate displayed the unusual L139S on the N protein, while few isolates carried the T24I and A359S N substitutions able to destabilize the protein. Phylogeny identified nine monophyletic clusters. This study provided additional information about SARS-CoV-2 epidemiology in Turkey, suggesting local transmission of infection in the city by several transmission routes, and highlighting the necessity to improve the power of sequencing worldwide.
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Affiliation(s)
- Nadia Marascio
- Department of Health Sciences, Institute of Microbiology, "Magna Grecia" University, 88100 Catanzaro, Italy
| | - Merve Cilburunoglu
- Microbiology Department, Faculty of Medicine, Kahramanmaras Sutcü Imam University, 46050 Kahramanmaras, Turkey
| | - Elif Gulsum Torun
- Microbiology Department, Faculty of Medicine, Kahramanmaras Sutcü Imam University, 46050 Kahramanmaras, Turkey
| | - Federica Centofanti
- Department of Applied Clinical Sciences and Biotechnology, University of Aquila, 67100 L'Aquila, Italy
| | - Elida Mataj
- Instituti i Shendetit Publik (ISHP), 1000 Tirana, Albania
| | - Michele Equestre
- Department of Neurosciences, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Roberto Bruni
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Angela Quirino
- Department of Health Sciences, Institute of Microbiology, "Magna Grecia" University, 88100 Catanzaro, Italy
| | - Giovanni Matera
- Department of Health Sciences, Institute of Microbiology, "Magna Grecia" University, 88100 Catanzaro, Italy
| | | | - Kezban Tulay Yalcinkaya
- Microbiology Department, Faculty of Medicine, Kahramanmaras Sutcü Imam University, 46050 Kahramanmaras, Turkey
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