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All Journal Narra J Annales Bogorienses
Prasetyoputri, Anggia
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Biochemistry, Genetics & Molecular Biology Health Professions Immunology & microbiology Medicine & Pharmacology Public Health

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SARS-CoV-2 lineages and naso-oropharyngeal bacterial communities in COVID-19 reinfection: A study in West Java, Indonesia Sativa, Alvira R.; Asyifa, Isnaini Z.; Adzdzakiy, Muhammad M.; Iryanto, Syam B.; Nugroho, Herjuno A.; Wulandari, Ari S.; Yanthi, Nova D.; Nasrulloh, Mukh F.; Rahmawati, Ema; Alamanda, Cut NC.; Ristandi, Ryan B.; Rachman, Rifky W.; Robiani, Rini; Agustiyani, Dian F.; Wisnuwardhani, Popi H.; Wardiana, Andri; Ningrum, Ratih A.; Dharmayanthi, Anik B.; Prasetyoputri, Anggia; Fibriani, Azzania; Saputra, Sugiyono
Narra J Vol. 5 No. 3 (2025): December 2025
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v5i3.2901

Abstract

Continuous emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants may influence viral transmission dynamics and alter interactions with the respiratory microbiota, potentially increasing the risks of reinfection. This study investigated cases of coronavirus disease 2019 (COVID-19) reinfection in West Java, Indonesia, with the aim of identifying the SARS-CoV-2 variants involved, characterizing their genomic mutations, and profiling the nasal and oropharyngeal microbiota associated with reinfection. Naso-oropharyngeal swab samples were collected from 42 COVID-19 reinfection cases and nine new infection cases. Whole genome sequencing was performed using Oxford Nanopore Technologies (ONT) MinION Mk1C and variant analysis was conducted using ARTIC workflow. Nexstrain and PANGOLIN were used to determine the lineages. Phylogenetic trees were constructed using IQ-tree and FigTree. Key mutations were identified by Cov-GLUE. Additionally, 16s rRNA amplicon sequencing was conducted on nine samples from each group to analyze bacterial communities using EPI2ME and MicrobiomeAnalyst. All identified SARS-CoV-2 strains in this study were Delta variant (B.1.617.2), predominantly lineage AY.23 (n=46, 90%), followed by AY.24 (n=3) and AY.109 (n=2). No differences in SARS-CoV-2 lineages were observed between reinfection and new infection cases. Unique hotspot mutations found only in COVID-19 reinfections included NSP3, V220A, S_T676I, ORF7a_V82A, and ORF7a_TI20I. Bacterial community analysis revealed no significant diversity differences (alpha and beta) between the two groups. While the most dominant phylum remained Terrabacteria in both groups, Streptococcus was dominant in COVID-19 reinfections, whereas Prevotella was dominant in new infection cases. Notably, Haemophilus parainfluenzae, Fusobacterium periodonticum, Fusobacterium nucleatum, and Leptotrichia buccalis had significant increases in reinfection cases. Despite the similarity in SARS-CoV-2 lineages causing both COVID-19 reinfection and new infection cases, the presence of distinct key mutations and bacterial species suggest their potential as biomarkers within this group.
The Development of A Bioassay Based on Heterologous Expression of M2 Ion-Channel Protein Prasetyoputri, Anggia; Yuliaty, Neti; Tuharea, Warda; Febyanti, Alisin; Sunarko, Bambang; Atmosukarto, Ines I. C.
Annales Bogorienses Vol. 14 No. 2 (2010): Annales Bogorienses
Publisher : BRIN

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Abstract

Emerging resistant viral strains combined with the limited availability of antivirals in a pandemic scenario highlight the need for the development of novel influenza antivirals. A bioassay based on the M2 protein of influenza virus - a potential target for antivirals - was developed to screen endophytic microbial extracts. M2 can be synthesized using PCR, thus eliminating the need for the handling of infectious specimen. Following cloning of the M2 gene into a pET backbone, the resultant plasmid was transformed into BL21 (DE3) pLyss E. coli cells. Cultures of these cells were set up at 37C following inoculation with a starter culture, to reach an OD at 600nm (OD600) of 0.4-0.6. Once at the required OD, the culture was split in two aliquots and expression of the M2 protein was induced in one of the duplicates with the addition of isopropyl β-D-thiogalactopyranoside (IPTG). Bacterial growth was monitored at 60-minute intervals. Exogenous expression of the M2 protein has been reported to decrease host cells viability, resulting in lower OD600 values. Our results suggest that the M2 protein was expressed and that overexpression of this protein resulted in consistently lower OD600 values of induced cultures compared with that of uninduced cultures. Based on this principle, extracts can be screened for their ability to block M2 function as identified by increased OD600 values.
Enhancing the Immunogenicity of Subunit Vaccines by Utilisation of Particulate Vaccine Delivery Systems Prasetyoputri, Anggia; Kusharyoto, Wien
Annales Bogorienses Vol. 17 No. 2 (2013): Annales Bogorienses
Publisher : BRIN

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Abstract

Control and eradication of a number of infectious diseases are primarily attributed to effective vaccination programs. A concerted effort is still imperative to develop novel vaccines and improve the immunogenicity of existing ones with regards to efficacy, immunogenicity and safety. Rational design of vaccines using subunit vaccines is a potentially safer alternative to conventional vaccines, yet they are poorly immunogenic without additional adjuvant. Using antigen carriers to enhance their immunogenicity in the forms of adsorption or encapsulation with a delivery system has been widely investigated as an alternative to currently available adjuvants. This review aims to elaborate on the existing nanotechnology being used to develop more immunogenic subunit vaccines, with focus on particulate delivery systems for development of prophylactic vaccine candidates. 
A Preliminary Report on The Syntheses of Oligonucleotide Primers in The National Research and Innovation Agency (NRIA) Atikana, Akhirta; Prasetyoputri, Anggia; Rubiyana, Yana; Herawati, Neng; Desriani, Desriani; Pratiwi, Riyona Desvy; Wulandari, Dwi; Sukmarini, Linda; Kusharyoto, Wien; Santoso, Adi; Putra, Masteria Yunovilsa; Lisdiyanti, Puspita
Annales Bogorienses Vol. 26 No. 1 (2022): Annales Bogorienses
Publisher : BRIN

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/ann.bogor.2022.v26.n1.21-27

Abstract

A PolyGen DNA Synthesizer is equipment that is used for synthesizing oligonucleotide primers for any amplification targets. Oligonucleotide primers are indispensable components for any Polymerase Chain Reaction (PCR)-based detections. In the present study a number of oligonucleotide primer sets were synthesized to target (1) the Human Insuline Glargin (HIG) and (2) the Human Erythropoietin (EPO), as well as (3) the RNA-dependent RNA Polymerase (RdRp) and (4) the Nucleocapsid (N) genes of the severe acute respiratory syndrome virus 2 (SARS-CoV-2). A solid-phase oligonucleotide synthesis method was used according to the default protocol of the Polygen’s instrument to synthesize primers at a 40 nmol scale. The synthesized primers in this study were compared to commercially produced primers in their ability to amplify the gene target(s) in PCR and quantitative real-time PCR (qPCR) reactions. The first two sets of primers showed similar results in PCR compared to commercial primers; however, these primers were not tested for qPCR due to sample limitation. In contrast, the primer sets 3 and 4 were not able to produce amplicons in PCR reactions and only the primer set 4 successfully amplified the gene target in qPCR. These results indicate that the crude primers synthesized in this study are promising candidates for molecular detection and diagnostics, but these primers would benefit from further optimization for routine applications.
Co-Authors Adi Santoso Adzdzakiy, Muhammad M. Agustiyani, Dian F. Alamanda, Cut NC. Andri Wardiana, Andri Asyifa, Isnaini Z. Atikana, Akhirta Atmosukarto, Ines I. C. BAMBANG SUNARKO Desriani Desriani Dharmayanthi, Anik B. Dwi Wulandari Ema Rahmawati Febyanti, Alisin Fibriani, Azzania Iryanto, Syam B. Kusharyoto, Wien LINDA SUKMARINI Nasrulloh, Mukh F. Neng Herawati, Neng Ningrum, Ratih A. Nugroho, Herjuno A. PUSPITA LISDIYANTI Putra, Masteria Yunovilsa Rachman, Rifky W. Ristandi, Ryan B. Riyona Desvy Pratiwi, Riyona Desvy Robiani, Rini Saputra, Sugiyono Sativa, Alvira R. Tuharea, Warda Wisnuwardhani, Popi H. Wulandari, Ari S. Yana Rubiyana, Yana Yanthi, Nova D. Yuliaty, Neti