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Publikasi Scopus 2024 per tanggal 31 Mei 2024 (409 artikel)
Publikasi Scopus 2024 per tanggal 31 Mei 2024 (409 artikel)
Adzdzakiy, Muhammad M. (58070801500); Sutarno, Sutarno (36940489100); Asyifa, Isnaini Z. (58070801600); Sativa, Alvira R. (58071432300); Fiqri, Ahmad R.A. (58643009400); Fibriani, Azzania (8429150200); Ristandi, Ryan B. (57222385672); Ningrum, Ratih A. (35976387300); Iryanto, Syam B. (57202874442); Prasetyoputri, Anggia (56309877800); Dharmayanthi, Anik B. (57193719895); Saputra, Sugiyono (57076979100)
SARS-CoV-2 genetic variation and bacterial communities of naso-oropharyngeal samples in middle-aged and elderly COVID-19 patients in West Java, Indonesia
2024
Journal of Taibah University Medical Sciences
19
1
70
81
11
0
https://www.scopus.com/inward/record.uri?eid=2-s2.0-85173963929&doi=10.1016%2fj.jtumed.2023.09.001&partnerID=40&md5=3ebd902ef2bf21e0718a04148473a320
Graduate School of Bioscience, Faculty of Mathematics and Natural Sciences, Universitas Sebelas Maret, Jl. Ir. Sutami 36A, Central Java, Surakarta, Indonesia; Master Program in Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jl. Salemba Raya No.6, Jakarta, Indonesia; School of Life Science and Technology, Institut Teknologi Bandung, Jl. Ganesa 10, West Java, Bandung, Indonesia; West Java Health Laboratory, Jl. Sederhana No. 3-5, Pasteur, Sukajadi, West Java, Bandung, Indonesia; Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, West Java, Bogor, Indonesia; Research Center for Computation, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, West Java, Bogor, Indonesia; Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, West Java, Bogor, Indonesia; Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, West Java, Bogor, Indonesia; Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, West Java, Bogor, Indonesia
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. © 2023 The Authors
coronavirus protein; coronavirus spike glycoprotein; nonstructural protein 12; nonstructural protein 15; nonstructural protein 3; RNA 16S; unclassified drug; virus RNA; Actinobacteria; adult; aged; amino acid substitution; Article; Bacilli; Bacteroidetes; coronavirus disease 2019; female; Firmicutes; gene sequence; genetic variability; genetic variation; Haemophilus parainfluenzae; human; human tissue; Indonesia; major clinical study; male; microbial community; middle aged; multiplex polymerase chain reaction; mutation rate; nasopharynx; oropharynx; Prevotella loescheii; Propionibacterium acnes; Proteobacteria; Pseudomonas aeruginosa; RNA gene; Severe acute respiratory syndrome coronavirus 2; Staphylococcus caprae; virus transmission
Educational Fund Management Institution; Riset Produktif dan Inovatif; Lembaga Pengelola Dana Pendidikan, LPDP; Kementerian Keuangan Republik Indonesia, (07/FI/P-19.2B3/X/2020); Kementerian Keuangan Republik Indonesia
This work was supported by the Riset Produktif dan Inovatif (RISPRO) by Educational Fund Management Institution (LPDP) Ministry of Finance of the Republic of Indonesia for COVID-19 Funding Program ( 07/FI/P-19.2B3/X/2020 ) under the project name “Surveilans Genom SARS-CoV-2” (VENOMCoV) LIPI/BRIN. The funders had no role in the study design, data collection and analysis, publication decisions, or m
Elsevier B.V.
16583612
Article
Q3
418
12080
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