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Agustus Sani Nugroho & Ema Rahmawati Heryaman, Agustus Sani Nugroho &
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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.
Co-Authors Aam Suryamah Adinda, Fadhel Arjuna Adzdzakiy, Muhammad M. Afriana, Anita Agus Pratiwi Agustinus Pandiangan, Lumiere Rejeki Agustiyani, Dian F. Alamanda, Cut NC. Andri Wardiana, Andri Anita Afriana Anita Afriana Are, Robert La Asep Syaiful Bahri, Asep Syaiful Asyifa, Isnaini Z. Bambang Suseno Bambang Sutiyoso Chandra, Muliyadi Damayanti, Elok Deviana Yuanitasari Dewi Rokhmah Dharmayanthi, Anik B. Dhian Anggraini, Fera Disyon, Huta Diva Davina, Nathania Elisatris Gultom Elly Nurus Shakinah Eman Suparman Ezzerouali, Souad Fajar Pradapa, Sri Yulianto Fera Dhian Anggraini Fibriani, Azzania Fidel, Yohanes Fiona Chrisanta Gagih Pradini Galih Dani Septiyan Rahayu Haikal Yushendri, Muhammad Hamzah, Rosyidi Hendratono, Tonny Hetharie, Yosia Holyness Nurdin Singadimedja Holyness Singadimeja Husna, Anisatul Ihalau, John JOI Iryanto, Syam B. Isis Ikhwansyah Karsona , H. Agus Mulya Karsona, H. Agus Mulya Kartika Eka Pertiwi Kasmin Khoiron Khoiron Kris Cahyani Ermawati Kusumaningrum, Anisa Putri Lastuti Abubakar Lastuti Abubakar Lastuti Abubakar Lastuti Abubakar Linda Rachmainy Muhamad Amirulloh, Muhamad MUHAMMAD BAKRI Nasrulloh, Mukh F. Ndaru Prasastono Ningrum, Ratih A. Noviastuti, Nina Nugrahani Primary Putri Nugroho, Herjuno A. Nyulistiowati Suryanti Pangihutan, Kaiji Natanael Pertiwi, Hana Febrianti Pradini, Gagih Prasastono, Ndaru Prasetyoputri, Anggia Putri, Fraya Anggraini Putri, Rahmi Adriani Rachman, Rifky W. Rafika Annisa Sari Rahmaniah, Rahmaniah Rahmawati, Diah Ayu Rai Mantili Ratnawati, Indah Raysa Mayasonda Ridwan Arifin Ristandi, Ryan B. Robiani, Rini Saputra, Sugiyono Sativa, Alvira R. Setiawan, Muhammad Vikri Sherly Ayuna Putri Soerjati , Enni Sony Heru Priyanto Soplantila, Valentino Dinatra Sudaryat Sudaryat Sudaryat Sugiarto S Suntari, Yustia Trianto, Rachmad Rizky Wisnuwardhani, Popi H. Woodward, John Wulandari, Ari S. Yanthi, Nova D. Yushendri , Muhammad Haikal