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La Distia Nora R, Zahra SS, Riasanti M, Fatimah A, Ningtias RD, Ibrahim F, Bela B, Handayani RD, Yasmon A, Susiyanti M, Edwar L, Aziza Y, Sitompul R. Dry eye symptoms are prevalent in moderate-severe COVID-19, while SARS-COV-2 presence is higher in mild COVID-19: Possible ocular transmission risk of COVID-19. Heliyon 2024; 10:e28649. [PMID: 38586378 PMCID: PMC10998079 DOI: 10.1016/j.heliyon.2024.e28649] [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: 03/12/2023] [Revised: 03/17/2024] [Accepted: 03/21/2024] [Indexed: 04/09/2024] Open
Abstract
Purpose To evaluate the correlation between dry eye symptoms and coronavirus disease 2019 (COVID-19) infection and to assess the real-time reverse transcription-polymerase chain reaction (RT‒PCR) of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) from the conjunctival swab. Methods A prospective observational case series study was conducted of all suspected and confirmed COVID-19 patients from Dr. Cipto Mangunkusumo Hospital (RSCM) and the Universitas Indonesia Hospital (RSUI). On the first day of the visit (day 0), systemic clinical symptoms and naso-oropharyngeal (NO) RT‒PCR results will classify all subjects as non-, suspected, or confirmed (mild, moderate, and severe) COVID-19. In all patients, we determined the dry eye symptoms based on the Ocular Surface Disease Index (OSDI) and followed up 7(day 7) and 14 days (day 14) after the first visit. When it was technically possible, we also examined the objective dry eye measurements: tear meniscus height (TMH), noninvasive Keratograph® break-up time (NIKBUT), and ocular redness. Additionally, we took conjunctival swab samples for SARS-CoV-2 RT-PCR in all patients. Results The OSDI scores for 157 patients decreased across days 0, 7, and 14 (median (interquartile range): 2.3 (0-8), 0 (0-3), and 0 (0-0), p value < 0.0001 (D0 vs D14). The moderate-severe COVID-19 group had a higher OSDI score than the other groups at median D0 (15.6 vs 0-2.3), p value < 0.0001 and this pattern was consistently seen at follow-up D7 and D14. However, dry eye complaints were not correlated with the three objective dry eye measurements in mild-moderate COVID-19 patients. NO RT‒PCR results were positive in 32 (20.4%) patients, namely, 13 and 19 moderate-severe and mild COVID-19 patients, respectively. Positive RT‒PCR results were observed in 7/157 (4.5%) conjunctival swab samples from 1 in non-COVID-19 group and 6 in mild group. Conclusion In the early phase of infection, COVID-19 patients experience dry eye symptoms, which have no correlation with objective dry eye measurements. SARS-CoV-2 in conjunctival swab samples can be detected in patients with normal-to-mild COVID-19, which shows the risk of ocular transmission.
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Affiliation(s)
- Rina La Distia Nora
- Department of Ophthalmology, Faculty of Medicine, Universitas Indonesia – Cipto Mangunkusumo Kirana Eye Hospital, Jakarta, Indonesia
- Universitas Indonesia Hospital (RSUI), Depok, West Java, Indonesia
- Wisma Atlet COVID-19 Emergency Hospital, North Jakarta, Jakarta, Indonesia
| | | | - Mei Riasanti
- Department of Ophthalmology, Faculty of Medicine, Universitas Indonesia – Cipto Mangunkusumo Kirana Eye Hospital, Jakarta, Indonesia
| | - Aliya Fatimah
- Wisma Atlet COVID-19 Emergency Hospital, North Jakarta, Jakarta, Indonesia
| | - Rani Dwi Ningtias
- Wisma Atlet COVID-19 Emergency Hospital, North Jakarta, Jakarta, Indonesia
| | - Fera Ibrahim
- Universitas Indonesia Hospital (RSUI), Depok, West Java, Indonesia
- Department of Microbiology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia – Cipto Mangunkusumo, Jakarta, Indonesia
| | - Budiman Bela
- Universitas Indonesia Hospital (RSUI), Depok, West Java, Indonesia
- Department of Microbiology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia – Cipto Mangunkusumo, Jakarta, Indonesia
| | - R.R. Diah Handayani
- Universitas Indonesia Hospital (RSUI), Depok, West Java, Indonesia
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia - Persahabatan Hospital, Jakarta, Indonesia
| | - Andi Yasmon
- Department of Microbiology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia – Cipto Mangunkusumo, Jakarta, Indonesia
| | - Made Susiyanti
- Department of Ophthalmology, Faculty of Medicine, Universitas Indonesia – Cipto Mangunkusumo Kirana Eye Hospital, Jakarta, Indonesia
| | - Lukman Edwar
- Department of Ophthalmology, Faculty of Medicine, Universitas Indonesia – Cipto Mangunkusumo Kirana Eye Hospital, Jakarta, Indonesia
| | - Yulia Aziza
- Department of Ophthalmology, Faculty of Medicine, Universitas Indonesia – Cipto Mangunkusumo Kirana Eye Hospital, Jakarta, Indonesia
| | - Ratna Sitompul
- Department of Ophthalmology, Faculty of Medicine, Universitas Indonesia – Cipto Mangunkusumo Kirana Eye Hospital, Jakarta, Indonesia
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Oktavianthi S, Lages AC, Kusuma R, Kurniasih TS, Trimarsanto H, Andriani F, Rustandi D, Meriyanti T, Yusuf I, Malik SG, Jo J, Suriapranata I. Whole-Genome Sequencing and Mutation Analyses of SARS-CoV-2 Isolates from Indonesia. Pathogens 2024; 13:279. [PMID: 38668234 PMCID: PMC11053823 DOI: 10.3390/pathogens13040279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/12/2024] [Accepted: 03/07/2024] [Indexed: 04/29/2024] Open
Abstract
The SARS-CoV-2 infection that caused the COVID-19 pandemic has become a significant public health concern. New variants with distinct mutations have emerged, potentially impacting its infectivity, immune evasion capacity, and vaccine response. A whole-genome sequencing study of 292 SARS-CoV-2 isolates collected from selected regions of Indonesia between January and October 2021 was performed to identify the distribution of SARS-CoV-2 variants and common mutations in Indonesia. During January-April 2021, Indonesian lineages B.1.466.2 and B.1.470 dominated, but from May 2021, Delta's AY.23 lineage outcompeted them. An analysis of 7515 published sequences from January 2021 to June 2022 revealed a decline in Delta in November 2021, followed by the emergence of Omicron variants in December 2021. We identified C241T (5'UTR), P314L (NSP12b), F106F (NSP3), and D614G (Spike) mutations in all sequences. The other common substitutions included P681R (76.4%) and T478K (60%) in Spike, D377Y in Nucleocapsid (61%), and I82T in Membrane (60%) proteins. Breakthrough infection and prolonged viral shedding cases were associated with Delta variants carrying the Spike T19R, G142D, L452R, T478K, D614G, P681R, D950N, and V1264L mutations. The dynamic of SARS-CoV-2 variants in Indonesia highlights the importance of continuous genomic surveillance in monitoring and identifying potential strains leading to disease outbreaks.
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Affiliation(s)
- Sukma Oktavianthi
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
| | - Aksar Chair Lages
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Rinaldy Kusuma
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Tri Shinta Kurniasih
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
- Menzies School of Health Research, Charles Darwin University, Darwin 0811, Australia
| | - Febi Andriani
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - David Rustandi
- Siloam Hospital Lippo Village, Tangerang 15810, Indonesia; (D.R.); (T.M.)
| | - Tandry Meriyanti
- Siloam Hospital Lippo Village, Tangerang 15810, Indonesia; (D.R.); (T.M.)
| | - Irawan Yusuf
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Safarina G. Malik
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
| | - Juandy Jo
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Ivet Suriapranata
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
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Gupta S, Gupta D, Bhatnagar S. Analysis of SARS-CoV-2 genome evolutionary patterns. Microbiol Spectr 2024; 12:e0265423. [PMID: 38197644 PMCID: PMC10846092 DOI: 10.1128/spectrum.02654-23] [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: 06/26/2023] [Accepted: 11/20/2023] [Indexed: 01/11/2024] Open
Abstract
The spread of SARS-CoV-2 virus accompanied by public availability of abundant sequence data provides a window for the determination of viral evolutionary patterns. In this study, SARS-CoV-2 genome sequences were collected from seven countries in the period January 2020-December 2022. The sequences were classified into three phases, namely, pre-vaccination, post-vaccination, and recent period. Comparison was performed between these phases based on parameters like mutation rates, selection pressure (dN/dS ratio), and transition to transversion ratios (Ti/Tv). Similar comparisons were performed among SARS-CoV-2 variants. Statistical significance was tested using Graphpad unpaired t-test. The analysis showed an increase in the percent genomic mutation rates post-vaccination and in recent periods across all countries from the pre-vaccination sequences. Mutation rates were highest in NSP3, S, N, and NSP12b before and increased further after vaccination. NSP4 showed the largest change in mutation rates after vaccination. The dN/dS ratios showed purifying selection that shifted toward neutral selection after vaccination. N, ORF8, ORF3a, and ORF10 were under highest positive selection before vaccination. Shift toward neutral selection was driven by E, NSP3, and ORF7a in the after vaccination set. In recent sequences, the largest dN/dS change was observed in E, NSP1, and NSP13. The Ti/Tv ratios decreased with time. C→U and G→U were the most frequent transitions and transversions. However, U→G was the most frequent transversion in recent period. The Omicron variant had the highest genomic mutation rates, while Delta showed the highest dN/dS ratio. Protein-wise dN/dS ratio was also seen to vary across the different variants.IMPORTANCETo the best of our knowledge, there exists no other large-scale study of the genomic and protein-wise mutation patterns during the time course of evolution in different countries. Analyzing the SARS-CoV-2 evolutionary patterns in view of the varying spatial, temporal, and biological signals is important for diagnostics, therapeutics, and pharmacovigilance of SARS-CoV-2.
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Affiliation(s)
- Shubhangi Gupta
- Department of Biological Sciences and Engineering, Computational and Structural Biology Laboratory, Netaji Subhas University of Technology, Dwarka, New Delhi, India
| | - Deepanshu Gupta
- Division of Biotechnology, Computational and Structural Biology Laboratory, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
| | - Sonika Bhatnagar
- Department of Biological Sciences and Engineering, Computational and Structural Biology Laboratory, Netaji Subhas University of Technology, Dwarka, New Delhi, India
- Division of Biotechnology, Computational and Structural Biology Laboratory, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
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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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5
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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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Ahmadi AS, Shafiei-Jandaghi NZ, Sadeghi K, Nejati A, Zadheidar S, Mokhtari-Azad T, Yavarian J. Comparison of Circulating Variants during the Beginning, Middle and the End of the 4th Wave of COVID-19 in Tehran Province, Iran in 2021. IRANIAN JOURNAL OF PUBLIC HEALTH 2023; 52:2621-2629. [PMID: 38435775 PMCID: PMC10903313 DOI: 10.18502/ijph.v52i12.14323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/11/2023] [Indexed: 03/05/2024]
Abstract
Background Whole viral genome sequencing with next generation sequencing (NGS) technique is useful tool for determining the diversity of variants and mutations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study we have attempted to characterize the mutations and circulating variants of the SARSCoV-2 genome during the 4th wave of COVID-19 pandemic in Tehran, Iran in 2021. Methods We performed complete genome sequencing of 15 SARS-CoV-2 detected from 15 COVID-19 patients during the 4th wave of COVID-19 pandemic with NGS. Three groups of the patients at the beginning, middle and the end of the 4th wave were compared together. Results We detected alpha and delta variants during the 4th wave of the pandemic. The results illustrated a dominance of amino acid substitution D614G in spike, and the most frequent mutants were N-R203K, G204R, S235F, nsp12-P323L, nsp6-G106del, G107del and F108del. Conclusion The detection of the virus mutations is a useful procedure for identifying the virus behavior and its genetic evolution in order to improve the efficacy of the monitoring strategies and therapeutic measures.
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Affiliation(s)
- Akram Sadat Ahmadi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Kaveh Sadeghi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Nejati
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Sevrin Zadheidar
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Talat Mokhtari-Azad
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Jila Yavarian
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Antibiotic Stewardship and Antimicrobial Resistance, Tehran University of Medical Sciences, Tehran, Iran
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Oyola S. Characterization of SARS-CoV-2 genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population. RESEARCH SQUARE 2023:rs.3.rs-3457875. [PMID: 37961584 PMCID: PMC10635312 DOI: 10.21203/rs.3.rs-3457875/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Vaccination is a key control measure of COVID-19 by preventing severe effects of disease outcomes, reducing hospitalization rates and death, and increasing herd immunity. However, vaccination can affect the evolution and adaptation of SARS-CoV-2, largely through vaccine-induced immune pressure. Here we investigated the recombination events and single nucleotide polymorphisms (SNPs) on SARS-CoV-2 genome in non-vaccinated and vaccinated patients in the Kenyan population. We identified recombination hotspots in the S, N, and ORF1a/b genes and showed the genetic evolution landscape of SARS-CoV-2 by comparing within-wave and inter-wave recombination events from the beginning of the pandemic (June 2020) to (October 2022) in Kenya. An in-depth analysis of (SNPs) on the S, ORf1a/b, and N genes identified previously unreported mutations. We detected a minority variant in non-vaccinated patients in Kenya, that contained immune escape mutation S255F of the spike gene and showing a differential recombination pattern within the non-vaccinated patients. Detailed analysis of recombination between waves suggested an association between increased population immunity and declining risk of emergence of variants of concern. Overall, this work identified unique mutations in SARS-CoV-2 which could have significant implications for virus evolution, virulence, and immune escape.
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8
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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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9
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Artika IM, Dewi YP, Nainggolan IM, Siregar JE, Antonjaya U. Real-Time Polymerase Chain Reaction: Current Techniques, Applications, and Role in COVID-19 Diagnosis. Genes (Basel) 2022; 13:genes13122387. [PMID: 36553654 PMCID: PMC9778061 DOI: 10.3390/genes13122387] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Successful detection of the first SARS-CoV-2 cases using the real-time polymerase chain reaction (real-time PCR) method reflects the power and usefulness of this technique. Real-time PCR is a variation of the PCR assay to allow monitoring of the PCR progress in actual time. PCR itself is a molecular process used to enzymatically synthesize copies in multiple amounts of a selected DNA region for various purposes. Real-time PCR is currently one of the most powerful molecular approaches and is widely used in biological sciences and medicine because it is quantitative, accurate, sensitive, and rapid. Current applications of real-time PCR include gene expression analysis, mutation detection, detection and quantification of pathogens, detection of genetically modified organisms, detection of allergens, monitoring of microbial degradation, species identification, and determination of parasite fitness. The technique has been used as a gold standard for COVID-19 diagnosis. Modifications of the standard real-time PCR methods have also been developed for particular applications. This review aims to provide an overview of the current applications of the real-time PCR technique, including its role in detecting emerging viruses such as SARS-CoV-2.
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Affiliation(s)
- I Made Artika
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Bogor 16680, Indonesia
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Bogor 16911, Indonesia
- Correspondence:
| | - Yora Permata Dewi
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
| | - Ita Margaretha Nainggolan
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Bogor 16911, Indonesia
| | - Josephine Elizabeth Siregar
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Bogor 16911, Indonesia
| | - Ungke Antonjaya
- Eijkman Oxford Clinical Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
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10
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Isnaini N, Mardian Y, Lokida D, Budiono F, Butar-Butar DP, Arlinda D, Salim G, Kosasih H, Wulan WN, Perodin J, Neal A, Lane HC, Karyana M. Mild reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant: First case report from Indonesia. Front Med (Lausanne) 2022; 9:906469. [PMID: 35935779 PMCID: PMC9355687 DOI: 10.3389/fmed.2022.906469] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/27/2022] [Indexed: 12/21/2022] Open
Abstract
Background Reinfection with SARS-CoV-2 has been well documented, yet little is known about the degree of protection a previous infection provides against reinfection, especially against Variants of Concern (VOC). Case presentation Here we describe a case of an unvaccinated 49-year-old man who experienced two sequential SARS-CoV-2 infections with two different variants, as evidenced by genomic sequencing. The first episode was caused by the Pango lineage B.1.466.2 and resulted in severe COVID-19 with 5 days in an intensive care unit (ICU). The second episode occurred approximately 6 months later, during the Delta surge in Indonesia. Genomic analysis showed that the second infection was caused by the Delta variant (Pango lineage B.1.617.2) and resulted in mild disease that did not require hospitalization. No SARS-CoV-2 nucleic acid was detected between the two episodes, but both binding and neutralizing antibodies to SARS-CoV-2 were detected prior to the reinfection, with the second infection leading to an increase in the levels of antibody. Conclusion We confirmed that the patient experienced a reinfection instead of persistent viral shedding from the first infection based on epidemiological, clinical, serological, and genomic analyses. Our case supports the hypothesis that SARS-CoV-2 reinfection may occur once antibody titers decrease or following the emergence of a new variant. The milder presentation in the patient’s second infection deserves further investigation to provide a clear picture of the role of post-infection immunity in altering the course of subsequent disease.
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Affiliation(s)
| | - Yan Mardian
- Indonesia Research Partnership on Infectious Disease, Jakarta, Indonesia
| | - Dewi Lokida
- Tangerang District Hospital, Tangerang, Indonesia.,Indonesia Research Partnership on Infectious Disease, Jakarta, Indonesia
| | | | - Deni P Butar-Butar
- Indonesia Research Partnership on Infectious Disease, Jakarta, Indonesia
| | - Dona Arlinda
- Indonesia Research Partnership on Infectious Disease, Jakarta, Indonesia.,National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Gustiani Salim
- Indonesia Research Partnership on Infectious Disease, Jakarta, Indonesia
| | - Herman Kosasih
- Indonesia Research Partnership on Infectious Disease, Jakarta, Indonesia
| | - Wahyu Nawang Wulan
- Indonesia Research Partnership on Infectious Disease, Jakarta, Indonesia
| | | | - Aaron Neal
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - H Clifford Lane
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Muhammad Karyana
- Indonesia Research Partnership on Infectious Disease, Jakarta, Indonesia.,National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
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11
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Zhu M, Zeng Q, Saputro BIL, Chew SP, Chew I, Frendy H, Tan JW, Li L. Tracking the molecular evolution and transmission patterns of SARS-CoV-2 lineage B.1.466.2 in Indonesia based on genomic surveillance data. Virol J 2022; 19:103. [PMID: 35710544 PMCID: PMC9202327 DOI: 10.1186/s12985-022-01830-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/02/2022] [Indexed: 12/22/2022] Open
Abstract
Background As a new epi-center of COVID-19 in Asia and a densely populated developing country, Indonesia is facing unprecedented challenges in public health. SARS-CoV-2 lineage B.1.466.2 was reported to be an indigenous dominant strain in Indonesia (once second only to the Delta variant). However, it remains unclear how this variant evolved and spread within such an archipelagic nation. Methods For statistical description, the spatiotemporal distributions of the B.1.466.2 variant were plotted using the publicly accessible metadata in GISAID. A total of 1302 complete genome sequences of Indonesian B.1.466.2 strains with high coverage were downloaded from the GISAID’s EpiCoV database on 28 August 2021. To determine the molecular evolutionary characteristics, we performed a time-scaled phylogenetic analysis using the maximum likelihood algorithm and called the single nucleotide variants taking the Wuhan-Hu-1 sequence as reference. To investigate the spatiotemporal transmission patterns, we estimated two dynamic parameters (effective population size and effective reproduction number) and reconstructed the phylogeography among different islands. Results As of the end of August 2021, nearly 85% of the global SARS-CoV-2 lineage B.1.466.2 sequences (including the first one) were obtained from Indonesia. This variant was estimated to account for over 50% of Indonesia’s daily infections during the period of March–May 2021. The time-scaled phylogeny suggested that SARS-CoV-2 lineage B.1.466.2 circulating in Indonesia might have originated from Java Island in mid-June 2020 and had evolved into two disproportional and distinct sub-lineages. High-frequency non-synonymous mutations were mostly found in the spike and NSP3; the S-D614G/N439K/P681R co-mutations were identified in its larger sub-lineage. The demographic history was inferred to have experienced four phases, with an exponential growth from October 2020 to February 2021. The effective reproduction number was estimated to have reached its peak (11.18) in late December 2020 and dropped to be less than one after early May 2021. The relevant phylogeography showed that Java and Sumatra might successively act as epi-centers and form a stable transmission loop. Additionally, several long-distance transmission links across seas were revealed. Conclusions SARS-CoV-2 variants circulating in the tropical archipelago may follow unique patterns of evolution and transmission. Continuous, extensive and targeted genomic surveillance is essential. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01830-1.
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Affiliation(s)
- Mingjian Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianli Zeng
- Shanghai Institute of Biological Products, Shanghai, China
| | | | - Sien Ping Chew
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ian Chew
- Zhejiang University School of Medicine, Hangzhou, China
| | - Holie Frendy
- Faculty of Medicine and Health Sciences, Krida Wacana Christian University, Jakarta, Indonesia
| | - Joanna Weihui Tan
- Faculty of Arts and Social Sciences, National University of Singapore, Singapore, Singapore
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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12
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Massi MN, Abidin RS, Farouk AE, Halik H, Soraya GV, Hidayah N, Sjahril R, Handayani I, Hakim MS, Gazali FM, Setiawaty V, Wibawa T. Full-genome sequencing and mutation analysis of SARS-CoV-2 isolated from Makassar, South Sulawesi, Indonesia. PeerJ 2022; 10:e13522. [PMID: 35707124 PMCID: PMC9190667 DOI: 10.7717/peerj.13522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 05/10/2022] [Indexed: 01/17/2023] Open
Abstract
Introduction A global surge in SARS-CoV-2 cases is occurring due to the emergence of new disease variants, and requires continuous adjustment of public health measures. This study aims to continuously monitor and mitigate the impact of SARS-CoV-2 through genomic surveillance, to determine the emergence of variants and their impact on public health. Methods Data were collected from 50 full-genome sequences of SARS-CoV-2 isolates from Makassar, South Sulawesi, Indonesia. Mutation and phylogenetic analysis was performed of SARS-CoV-2 from Makassar, South Sulawesi, Indonesia. Results Phylogenetic analysis showed that two samples (4%) were of the B.1.319 lineage, while the others (96%) were of the B.1.466.2 lineage. Mutation analysis of the spike (S) protein region showed that the most common mutation was D614G (found in 100% of the sequenced isolates), followed by N439K (98%) and P681R (76%). Several mutations were also identified in other genomes with a high frequency, including P323L (nsp12), Q57H (ns3-orf3a), and T205I (nucleoprotein). Conclusion Our findings highlight the importance of continuous genomic surveillance to identify new viral mutations and variants with possible impacts on public health.
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Affiliation(s)
- Muhammad Nasrum Massi
- Department of Clinical Microbiology, Hasanuddin University, Makassar, South Sulawesi, Indonesia,Microbiology Laboratory, Hasanuddin University Hospital, Makassar, South Sulawesi, Indonesia,Hasanuddin University Medical Research Center Laboratory, Faculty of Medicine, Hasanuddin University, Makassar, South Sulawesi, Indonesia
| | - Rufika Shari Abidin
- Hasanuddin University Medical Research Center Laboratory, Faculty of Medicine, Hasanuddin University, Makassar, South Sulawesi, Indonesia
| | - Abd-ElAziem Farouk
- Department of Biotechnology, Faculty of Science, Taif University, Taif City, Al-Hawiyya, Saudi Arabia
| | - Handayani Halik
- Hasanuddin University Medical Research Center Laboratory, Faculty of Medicine, Hasanuddin University, Makassar, South Sulawesi, Indonesia,Mega Rezky University, Makassar, South Sulawesi, Indonesia
| | - Gita Vita Soraya
- Department of Biochemistry, Faculty of Medicine, Hasanuddin University, Makassar, South Sulawesi, Indonesia
| | - Najdah Hidayah
- Hasanuddin University Medical Research Center Laboratory, Faculty of Medicine, Hasanuddin University, Makassar, South Sulawesi, Indonesia
| | - Rizalinda Sjahril
- Department of Clinical Microbiology, Hasanuddin University, Makassar, South Sulawesi, Indonesia,Microbiology Laboratory, Hasanuddin University Hospital, Makassar, South Sulawesi, Indonesia
| | - Irda Handayani
- Clinical Pathology Laboratory, Wahidin Sudirohusodo Hospital, Makassar, South Sulawesi, Indonesia
| | - Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Gadjah Mada University, Yogyakarta, Indonesia
| | - Faris Muhammad Gazali
- Master Program in Biotechnology, Postgraduate School, Gadjah Mada University, Yogyakarta, Indonesia
| | - Vivi Setiawaty
- National Institute for Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Gadjah Mada University, Yogyakarta, Indonesia
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13
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Zhou H, Ni WJ, Huang W, Wang Z, Cai M, Sun YC. Advances in Pathogenesis, Progression, Potential Targets and Targeted Therapeutic Strategies in SARS-CoV-2-Induced COVID-19. Front Immunol 2022; 13:834942. [PMID: 35450063 PMCID: PMC9016159 DOI: 10.3389/fimmu.2022.834942] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/07/2022] [Indexed: 01/18/2023] Open
Abstract
As the new year of 2020 approaches, an acute respiratory disease quietly caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as coronavirus disease 2019 (COVID-19) was reported in Wuhan, China. Subsequently, COVID-19 broke out on a global scale and formed a global public health emergency. To date, the destruction that has lasted for more than two years has not stopped and has caused the virus to continuously evolve new mutant strains. SARS-CoV-2 infection has been shown to cause multiple complications and lead to severe disability and death, which has dealt a heavy blow to global development, not only in the medical field but also in social security, economic development, global cooperation and communication. To date, studies on the epidemiology, pathogenic mechanism and pathological characteristics of SARS-CoV-2-induced COVID-19, as well as target confirmation, drug screening, and clinical intervention have achieved remarkable effects. With the continuous efforts of the WHO, governments of various countries, and scientific research and medical personnel, the public’s awareness of COVID-19 is gradually deepening, a variety of prevention methods and detection methods have been implemented, and multiple vaccines and drugs have been developed and urgently marketed. However, these do not appear to have completely stopped the pandemic and ravages of this virus. Meanwhile, research on SARS-CoV-2-induced COVID-19 has also seen some twists and controversies, such as potential drugs and the role of vaccines. In view of the fact that research on SARS-CoV-2 and COVID-19 has been extensive and in depth, this review will systematically update the current understanding of the epidemiology, transmission mechanism, pathological features, potential targets, promising drugs and ongoing clinical trials, which will provide important references and new directions for SARS-CoV-2 and COVID-19 research.
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Affiliation(s)
- Hong Zhou
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wei-Jian Ni
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China.,Anhui Provincial Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wei Huang
- The Third People's Hospital of Hefei, The Third Clinical College of Anhui Medical University, Hefei, China
| | - Zhen Wang
- Anhui Provincial Children's Hospital, Children's Hospital of Fudan University-Anhui Campus, Hefei, China
| | - Ming Cai
- Department of Pharmacy, The Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.,School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Yan-Cai Sun
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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14
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Anwar MZ, Lodhi MS, Khan MT, Khan MI, Sharif S. Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Genes (Basel) 2022; 13:552. [PMID: 35328105 PMCID: PMC8951394 DOI: 10.3390/genes13030552] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/10/2022] [Accepted: 03/18/2022] [Indexed: 12/15/2022] Open
Abstract
Genomic epidemiology of SARS-CoV-2 is imperative to explore the transmission, evolution, and also pathogenicity of viruses. The emergence of SARS-CoV-2 variants of concern posed a severe threat to the global public health efforts. To assess the potential consequence of these emerging variants on public health, continuous molecular epidemiology is of vital importance. The current study has been designed to investigate the major SARS-CoV-2 variants and emerging mutations in virus structural and non-structural proteins (NSP) during the fourth wave in September 2021 from the Punjab province of Pakistan. Twenty SARS-CoV-2 positive samples have been collected from major cities were subjected to next-generation sequencing. Among the 20 whole genomes (GenBank Accession SRR16294858-SRR16294877), 2 samples failed to be completely sequenced. These genome sequences harbored 207 non-synonymous mutations, among which 19 were unique to GISAID. The genome sequences were detected: Delta 21I, 21J variants (B.1.617.2). Mutation's spike_F157del, spike_P681R, spike_T478K, spike_T19R, spike_L452R, spike_D614G, spike_G142D, spike_E156G, and spike_R158del have been detected in all samples where K1086Q, E554K, and C1250W were unique in spike protein. These genomic sequences also harbored 129 non-synonymous mutations in NSP. The most common were NSP3_P1469S (N = 17), NSP3_A488S (N = 17), NSP3_P1228L (N = 17), NSP4_V167L (N = 17), NSP4_T492I (N = 17), NSP6_T77A (N = 17), NSP14_A394V (N = 17), NSP12_G671S (N = 18), and NSP13_P77L (N = 18). The mutation, F313Y in NSP12, detected in the current study, was found in a single isolate from Belgium. Numerous other unique mutations have been detected in the virus papain-like protease (NSP3), main protease (NSP5), and RNA-dependent RNA polymerase (NSP12). The most common non-synonymous mutations in the spike protein were subjected to stability analysis, exhibiting a stabilizing effect on structures. The presence of Delta variants may affect therapeutic efforts and vaccine efficacy. Continuous genomic epidemiology of SARS-CoV-2 in Pakistan may be useful for better management of SARS-CoV-2 infections.
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Affiliation(s)
| | - Madeeha Shahzad Lodhi
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, 1 KM Defence Road, Lahore 58 810, Pakistan; (M.Z.A.); (M.T.K.); (M.I.K.); (S.S.)
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