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Gunadi, Hakim MS, Wibawa H, Vujira KA, Puspitarani DA, Supriyati E, Trisnawati I, Iskandar K, Khair RE, Afiahayati, Siswanto, Puspadewi Y, Irianingsih SH, Nugrahaningsih DAA, Eryvinka LS, Utami FDT, Devana EM, Aditama L, Kinasih NCP, Hediningsih Y, Ananda NR, Marcellus, Arguni E, Nuryastuti T, Wibawa T. Prognostic factors for the outcomes of COVID-19 patients infected with SARS-CoV-2 Omicron and Delta variants. BMC Med Genomics 2023; 16:205. [PMID: 37644458 PMCID: PMC10464379 DOI: 10.1186/s12920-023-01637-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 Omicron variant has replaced the previously dominant Delta variant because of high transmissibility. However, studies on the impact of the Omicron variant on the severity of COVID-19 are still limited in developing countries. Our study aimed to determine the prognostic factors for the outcomes of patients infected with SARS-CoV-2 Omicron and Delta variants, including age, sex, comorbidities, and smoking. METHODS In this retrospective cross-sectional study, we involved 352 patients with COVID-19 from Yogyakarta and Central Java provinces, Indonesia, from May 2021 to February 2022, consisting of 164 males and 188 females. We included all patients with the PCR's Ct value of less than 30 for further whole-genome sequencing. RESULTS Ct value and mean age of COVID-19 patients were not significantly different between both groups (p = 0.146 and 0.273, respectively). Patients infected with Omicron (n = 139) and Delta (n = 213) variants showed similar hospitalization (p = 0.396) and mortality rates (p = 0.565). Multivariate analysis of both groups showed that older age (≥ 65 years) had a higher risk for hospitalization (OR = 3.86 [95% CI = 1.29-11.5]; p = 0.015) and fatalities (OR = 3.91 [95% CI = 1.35-11.42]; p = 0.012). In both groups, patients with cardiovascular disease had a higher risk for hospitalization (OR = 5.36 [95% CI = 1.08-26.52]; p = 0.039), whereas patients with diabetes revealed a higher risk for fatalities (OR = 9.47 [95% CI = 3.23-27.01]; p = < 0.001). CONCLUSIONS Our study shows that patients infected with Omicron and Delta variants reveal similar clinical outcomes, including hospitalization and mortality. Our findings further confirm that older age, cardiovascular disease, and diabetes are substantial prognostic factors for the outcomes of COVID-19 patients. Our findings imply that COVID-19 patients with older age, cardiovascular disease, or diabetes should be treated comprehensively and cautiously to prevent further morbidity and mortality. Furthermore, incomplete data on vaccination status hampered us from analyzing further its impact on hospitalization and mortality in our patients.
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Affiliation(s)
- Gunadi
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hendra Wibawa
- Directorate General, and Livestock Services, Disease Investigation Center Wates (Balai Besar Veteriner Wates), Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Khanza Adzkia Vujira
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dyah Ayu Puspitarani
- Pediatric Surgery Division, Department of Surgery/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
| | - Ika Trisnawati
- Pulmonology Division, Department of Internal Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Kristy Iskandar
- Department of Child Health/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Riat El Khair
- Department of Clinical Pathology and Laboratory Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, 55281, Indonesia
| | - Afiahayati
- Department of Computer Science and Electronics Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Siswanto
- Department of Physiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Yunika Puspadewi
- Department of Child Health/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Sri Handayani Irianingsih
- Directorate General, and Livestock Services, Disease Investigation Center Wates (Balai Besar Veteriner Wates), Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Dwi Aris Agung Nugrahaningsih
- Department of Pharmacology and Therapy/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Laudria Stella Eryvinka
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Fadila Dyah Trie Utami
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edita Mayda Devana
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Lanang Aditama
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Nathania Christi Putri Kinasih
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Yekti Hediningsih
- Balai Laboratorium Kesehatan dan Pengujian Alat Kesehatan, Central Java, Semarang, Indonesia
| | - Nur Rahmi Ananda
- Pulmonology Division, Department of Internal Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Marcellus
- Pediatric Surgery Division, Department of Surgery/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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Shrestha L, Lin MJ, Xie H, Mills MG, Mohamed Bakhash SA, Gaur VP, Livingston RJ, Castor J, Bruce EA, Botten JW, Huang ML, Jerome KR, Greninger AL, Roychoudhury P. Clinical performance characteristics of the Swift Normalase Amplicon Panel for sensitive recovery of SARS-CoV-2 genomes. J Mol Diagn 2022; 24:963-976. [PMID: 35863699 PMCID: PMC9290336 DOI: 10.1016/j.jmoldx.2022.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/24/2022] [Accepted: 05/27/2022] [Indexed: 11/18/2022] Open
Abstract
Amplicon-based sequencing methods are central in characterizing the diversity, transmission, and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but need to be rigorously assessed for clinical utility. Herein, we validated the Swift Biosciences' SARS-CoV-2 Swift Normalase Amplicon Panels using remnant clinical specimens. High-quality genomes meeting our established library and sequence quality criteria were recovered from positive specimens, with 95% limit of detection of 40.08 SARS-CoV-2 copies/PCR. Breadth of genome recovery was evaluated across a range of CT values (11.3 to 36.7; median, 21.6). Of 428 positive samples, 413 (96.5%) generated genomes with <10% unknown bases, with a mean genome coverage of 13,545× ± SD 8382×. No genomes were recovered from PCR-negative specimens (n = 30) or from specimens positive for non–SARS-CoV-2 respiratory viruses (n = 20). Compared with whole-genome shotgun metagenomic sequencing (n = 14) or Sanger sequencing for the spike gene (n = 11), pairwise identity between consensus sequences was 100% in all cases, with highly concordant allele frequencies (R2 = 0.99) between Swift and shotgun libraries. When samples from different clades were mixed at varying ratios, expected variants were detected even in 1:99 mixtures. When deployed as a clinical test, 268 tests were performed in the first 23 weeks, with a median turnaround time of 11 days, ordered primarily for outbreak investigations and infection control.
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Affiliation(s)
- Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Michelle J Lin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Margaret G Mills
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | | | - Vinod P Gaur
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Robert J Livingston
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Jared Castor
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Emily A Bruce
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT
| | - Jason W Botten
- Department of Medicine, University of Vermont, Burlington, VT
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA.
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA.
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Li Y, Wang Z, Liu J, Han J, Yang L. A comparison of the protective effect of vaccination and clinical features between the SARS-CoV-2 wild-type strain and Delta (B.1.617.2) variant. Arch Med Sci 2022; 18:1678-1682. [PMID: 36457976 PMCID: PMC9710252 DOI: 10.5114/aoms/155114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/03/2022] [Indexed: 11/09/2022] Open
Abstract
INTRODUCTION This study aimed to investigate the clinical features and vaccine effectiveness of patients with the SARS-CoV-2 wild-type strain and the Delta variant. METHODS We retrospectively evaluated patients with the SARS-CoV-2 wild-type strain and the Delta variant. RESULTS The Delta-variant group showed a higher infection rate in minors, who had higher incidence of anosmia or dysgeusia and shorter incubation period. Unvaccinated patients had a 15.59-fold higher risk of severe classification than vaccinated patients. The viral clearance time was significantly shorter in the Delta-variant group. CONCLUSIONS The Delta-variant group show higher transmissibility, and vaccination reduces the incidence of severe classification and promotes viral clearance.
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Affiliation(s)
- Yanzi Li
- Department of Medical Administration, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Zhi Wang
- Department of Infectious surgery, Xi’an 8 Hospital, Xi’an, China
| | - Junhui Liu
- Department of Clinical Laboratory, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Jianfeng Han
- Department of Administrative Office, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Lin Yang
- Department of Administrative Office, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Vascular surgery, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
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4
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Handel AS, Muller WJ, Planet PJ. Metagenomic Next-Generation Sequencing (mNGS): SARS-CoV-2 as an Example of the Technology's Potential Pediatric Infectious Disease Applications. J Pediatric Infect Dis Soc 2021; 10:S69-S70. [PMID: 34951468 PMCID: PMC8755271 DOI: 10.1093/jpids/piab108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Metagenomic next-generation sequencing (mNGS) has emerged as a potentially powerful tool in clinical diagnosis, hospital epidemiology, microbial evolutionary biology, and studies of host-pathogen interaction. The SARS-CoV-2 pandemic provides a framework for demonstrating the applications of this technology in each of these areas. In this Supplement, we review applications of mNGS within the discipline of pediatric infectious diseases.
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Affiliation(s)
- Andrew S Handel
- Department of Pediatrics, Division of Infectious Diseases, Stony Brook Children’s Hospital, Stony Brook, New York, USA,Corresponding Author:> Andrew S. Handel, MD, Department of Pediatrics, Division of Infectious Diseases, Stony Brook Children’s Hospital, 101 Nicolls Road, HSC-T11, Stony Brook, NY 11794, USA. E-mail:
| | - William J Muller
- Department of Pediatrics, Northwestern University, Chicago, Illinois, USA,Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Paul J Planet
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA,Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA, and ,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
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5
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Gunadi, Hakim MS, Wibawa H, Marcellus, Setiawaty V, Slamet, Trisnawati I, Supriyati E, El Khair R, Iskandar K, Afiahayati, Siswanto, Irene, Anggorowati N, Daniwijaya EW, Nugrahaningsih DAA, Puspadewi Y, Puspitarani DA, Tania I, Vujira KA, Ardlyamustaqim MB, Gabriela GC, Eryvinka LS, Nirmala BC, Geometri ET, Darutama AA, Kuswandani AA, Lestari, Irianingsih SH, Khoiriyah S, Lestari I, Ananda NR, Arguni E, Nuryastuti T, Wibawa T. Is the Infection of the SARS-CoV-2 Delta Variant Associated With the Outcomes of COVID-19 Patients? Front Med (Lausanne) 2021; 8:780611. [PMID: 34957154 PMCID: PMC8695874 DOI: 10.3389/fmed.2021.780611] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) Delta variant (B.1.617.2) has been responsible for the current increase in Coronavirus disease 2019 (COVID-19) infectivity rate worldwide. We compared the impact of the Delta variant and non-Delta variant on the COVID-19 outcomes in patients from Yogyakarta and Central Java provinces, Indonesia. Methods: In this cross-sectional study, we ascertained 161 patients, 69 with the Delta variant and 92 with the non-Delta variant. The Illumina MiSeq next-generation sequencer was used to perform the whole-genome sequences of SARS-CoV-2. Results: The mean age of patients with the Delta variant and the non-Delta variant was 27.3 ± 20.0 and 43.0 ± 20.9 (p = 3 × 10-6). The patients with Delta variant consisted of 23 males and 46 females, while the patients with the non-Delta variant involved 56 males and 36 females (p = 0.001). The Ct value of the Delta variant (18.4 ± 2.9) was significantly lower than that of the non-Delta variant (19.5 ± 3.8) (p = 0.043). There was no significant difference in the hospitalization and mortality of patients with Delta and non-Delta variants (p = 0.80 and 0.29, respectively). None of the prognostic factors were associated with the hospitalization, except diabetes with an OR of 3.6 (95% CI = 1.02-12.5; p = 0.036). Moreover, the patients with the following factors have been associated with higher mortality rate than the patients without the factors: age ≥65 years, obesity, diabetes, hypertension, and cardiovascular disease with the OR of 11 (95% CI = 3.4-36; p = 8 × 10-5), 27 (95% CI = 6.1-118; p = 1 × 10-5), 15.6 (95% CI = 5.3-46; p = 6 × 10-7), 12 (95% CI = 4-35.3; p = 1.2 × 10-5), and 6.8 (95% CI = 2.1-22.1; p = 0.003), respectively. Multivariate analysis showed that age ≥65 years, obesity, diabetes, and hypertension were the strong prognostic factors for the mortality of COVID-19 patients with the OR of 3.6 (95% CI = 0.58-21.9; p = 0.028), 16.6 (95% CI = 2.5-107.1; p = 0.003), 5.5 (95% CI = 1.3-23.7; p = 0.021), and 5.8 (95% CI = 1.02-32.8; p = 0.047), respectively. Conclusions: We show that the patients infected by the SARS-CoV-2 Delta variant have a lower Ct value than the patients infected by the non-Delta variant, implying that the Delta variant has a higher viral load, which might cause a more transmissible virus among humans. However, the Delta variant does not affect the COVID-19 outcomes in our patients. Our study also confirms that older age and comorbidity increase the mortality rate of patients with COVID-19.
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Affiliation(s)
- Gunadi
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hendra Wibawa
- Disease Investigation Center, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Marcellus
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Vivi Setiawaty
- National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Slamet
- National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Ika Trisnawati
- Pulmonology Division, Department of Internal Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Riat El Khair
- Department of Clinical Pathology and Laboratory Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Kristy Iskandar
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Afiahayati
- Department of Computer Science and Electronics Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Siswanto
- Department of Physiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Irene
- Balai Besar Teknik Kesehatan Lingkungan dan Pengendalian Penyakit, Yogyakarta, Indonesia
| | - Nungki Anggorowati
- Department of Anatomical Pathology/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edwin Widyanto Daniwijaya
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dwi Aris Agung Nugrahaningsih
- Department of Pharmacology and Therapy/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Yunika Puspadewi
- Department of Clinical Pathology and Laboratory Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Dyah Ayu Puspitarani
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Irene Tania
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Khanza Adzkia Vujira
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Muhammad Buston Ardlyamustaqim
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Gita Christy Gabriela
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Laudria Stella Eryvinka
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Bunga Citta Nirmala
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Esensi Tarian Geometri
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Abirafdi Amajida Darutama
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Anisa Adityarini Kuswandani
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Lestari
- Disease Investigation Center, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | | | | | | | - Nur Rahmi Ananda
- Pulmonology Division, Department of Internal Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, 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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Laubscher F, Cordey S, Friedlaender A, Schweblin C, Noetzlin S, Simand PF, Bordry N, De Sousa F, Pigny F, Baggio S, Getaz L, Dietrich PY, Kaiser L, Vu DL. SARS-CoV-2 Evolution among Oncological Population: In-Depth Virological Analysis of a Clinical Cohort. Microorganisms 2021; 9:2145. [PMID: 34683466 PMCID: PMC8540785 DOI: 10.3390/microorganisms9102145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/30/2021] [Accepted: 10/06/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Oncological patients have a higher risk of prolonged SARS-CoV-2 shedding, which, in turn, can lead to evolutionary mutations and emergence of novel viral variants. The aim of this study was to analyze biological samples of a cohort of oncological patients by deep sequencing to detect any significant viral mutations. METHODS High-throughput sequencing was performed on selected samples from a SARS-CoV-2-positive oncological patient cohort. Analysis of variants and minority variants was performed using a validated bioinformatics pipeline. RESULTS Among 54 oncological patients, we analyzed 12 samples of 6 patients, either serial nasopharyngeal swab samples or samples from the upper and lower respiratory tracts, by high-throughput sequencing. We identified amino acid changes D614G and P4715L as well as mutations at nucleotide positions 241 and 3037 in all samples. There were no other significant mutations, but we observed intra-host evolution in some minority variants, mainly in the ORF1ab gene. There was no significant mutation identified in the spike region and no minority variants common to several hosts. CONCLUSIONS There was no major and rapid evolution of viral strains in this oncological patient cohort, but there was minority variant evolution, reflecting a dynamic pattern of quasi-species replication.
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Affiliation(s)
- Florian Laubscher
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (C.S.); (F.P.); (L.K.)
| | - Samuel Cordey
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (C.S.); (F.P.); (L.K.)
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (S.B.); (L.G.); (P.-Y.D.)
| | - Alex Friedlaender
- Department of Oncology, Geneva University Hospitals, 1205 Geneva, Switzerland; (A.F.); (S.N.); (P.-F.S.); (N.B.); (F.D.S.)
| | - Cecilia Schweblin
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (C.S.); (F.P.); (L.K.)
| | - Sarah Noetzlin
- Department of Oncology, Geneva University Hospitals, 1205 Geneva, Switzerland; (A.F.); (S.N.); (P.-F.S.); (N.B.); (F.D.S.)
| | - Pierre-François Simand
- Department of Oncology, Geneva University Hospitals, 1205 Geneva, Switzerland; (A.F.); (S.N.); (P.-F.S.); (N.B.); (F.D.S.)
| | - Natacha Bordry
- Department of Oncology, Geneva University Hospitals, 1205 Geneva, Switzerland; (A.F.); (S.N.); (P.-F.S.); (N.B.); (F.D.S.)
| | - Filipe De Sousa
- Department of Oncology, Geneva University Hospitals, 1205 Geneva, Switzerland; (A.F.); (S.N.); (P.-F.S.); (N.B.); (F.D.S.)
| | - Fiona Pigny
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (C.S.); (F.P.); (L.K.)
| | - Stephanie Baggio
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (S.B.); (L.G.); (P.-Y.D.)
- Division of Prison Health, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Laurent Getaz
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (S.B.); (L.G.); (P.-Y.D.)
- Division of Prison Health, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Pierre-Yves Dietrich
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (S.B.); (L.G.); (P.-Y.D.)
- Department of Oncology, Geneva University Hospitals, 1205 Geneva, Switzerland; (A.F.); (S.N.); (P.-F.S.); (N.B.); (F.D.S.)
| | - Laurent Kaiser
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (C.S.); (F.P.); (L.K.)
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (S.B.); (L.G.); (P.-Y.D.)
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
- Center for Emerging Viruses, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Diem-Lan Vu
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (C.S.); (F.P.); (L.K.)
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (S.B.); (L.G.); (P.-Y.D.)
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
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