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El-Haddad K, Adhikari TM, Tu ZJ, Cheng YW, Leng X, Zhang X, Rhoads D, Ko JS, Worley S, Li J, Rubin BP, Esper FP. Intra-host mutation rate of acute SARS-CoV-2 infection during the initial pandemic wave. Virus Genes 2023; 59:653-661. [PMID: 37310519 DOI: 10.1007/s11262-023-02011-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/22/2023] [Indexed: 06/14/2023]
Abstract
SARS-CoV-2 mutation is minimized through a proofreading function encoded by NSP-14. Most estimates of the SARS-CoV-2 mutation rate are derived from population based sequence data. Our understanding of SARS-CoV-2 evolution might be enhanced through analysis of intra-host viral mutation rates in specific populations. Viral genome analysis was performed between paired samples and mutations quantified at allele frequencies (AF) ≥ 0.25, ≥ 0.5 and ≥ 0.75. Mutation rate was determined employing F81 and JC69 evolution models and compared between isolates with (ΔNSP-14) and without (wtNSP-14) non-synonymous mutations in NSP-14 and by patient comorbidity. Forty paired samples with median interval of 13 days [IQR 8.5-20] were analyzed. The estimated mutation rate by F81 modeling was 93.6 (95%CI 90.8-96.4], 40.7 (95%CI 38.9-42.6) and 34.7 (95%CI 33.0-36.4) substitutions/genome/year at AF ≥ 0.25, ≥ 0.5, ≥ 0.75 respectively. Mutation rate in ΔNSP-14 were significantly elevated at AF ≥ 0.25 vs wtNSP-14. Patients with immune comorbidities had higher mutation rate at all allele frequencies. Intra-host SARS-CoV-2 mutation rates are substantially higher than those reported through population analysis. Virus strains with altered NSP-14 have accelerated mutation rate at low AF. Immunosuppressed patients have elevated mutation rate at all AF. Understanding intra-host virus evolution will aid in current and future pandemic modeling.
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Affiliation(s)
- Kim El-Haddad
- Center for Pediatric Infectious Disease, Cleveland Clinic Children's, R3, 9500 Euclid Avenue, Cleveland, 44195 , OH, USA.
| | - Thamali M Adhikari
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Zheng Jin Tu
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yu-Wei Cheng
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Xiaoyi Leng
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Xiangyi Zhang
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Daniel Rhoads
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jennifer S Ko
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Sarah Worley
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Jing Li
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Brian P Rubin
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Frank P Esper
- Center for Pediatric Infectious Disease, Cleveland Clinic Children's, R3, 9500 Euclid Avenue, Cleveland, 44195 , OH, USA.
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Esper FP, Adhikari TM, Tu ZJ, Cheng YW, El-Haddad K, Farkas DH, Bosler D, Rhoads D, Procop GW, Ko JS, Jehi L, Li J, Rubin BP. Alpha to Omicron: Disease Severity and Clinical Outcomes of Major SARS-CoV-2 Variants. J Infect Dis 2022. [DOI: 10.1093/infdis/jiac411
https://www.uptodate.com/contents/covid-19-clinical-manifestations-and-diagnosis-in-children/abstract/140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Abstract
Background
Four severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants predominated in the United States since 2021. Understanding disease severity related to different SARS-CoV-2 variants remains limited.
Method
Viral genome analysis was performed on SARS-CoV-2 clinical isolates circulating March 2021 through March 2022 in Cleveland, Ohio. Major variants were correlated with disease severity and patient outcomes.
Results
In total 2779 patients identified with either Alpha (n = 1153), Gamma (n = 122), Delta (n = 808), or Omicron variants (n = 696) were selected for analysis. No difference in frequency of hospitalization, intensive care unit (ICU) admission, and death were found among Alpha, Gamma, and Delta variants. However, patients with Omicron infection were significantly less likely to be admitted to the hospital, require oxygen, or admission to the ICU (χ2 = 12.8, P < .001; χ2 = 21.6, P < .002; χ2 = 9.6, P = .01, respectively). In patients whose vaccination status was known, a substantial number had breakthrough infections with Delta or Omicron variants (218/808 [26.9%] and 513/696 [73.7%], respectively). In breakthrough infections, hospitalization rate was similar regardless of variant by multivariate analysis. No difference in disease severity was identified between Omicron subvariants BA.1 and BA.2.
Conclusions
Disease severity associated with Alpha, Gamma, and Delta variants is comparable while Omicron infections are significantly less severe. Breakthrough disease is significantly more common in patients with Omicron infection.
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Affiliation(s)
- Frank P Esper
- Center for Pediatric Infectious Disease, Cleveland Clinic Children’s , Cleveland, Ohio , USA
| | - Thamali M Adhikari
- Department of Computer and Data Sciences, Case Western Reserve University , Cleveland, Ohio , USA
| | - Zheng Jin Tu
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic , Cleveland, Ohio , USA
| | - Yu-Wei Cheng
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic , Cleveland, Ohio , USA
| | - Kim El-Haddad
- Center for Pediatric Infectious Disease, Cleveland Clinic Children’s , Cleveland, Ohio , USA
| | - Daniel H Farkas
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic , Cleveland, Ohio , USA
| | - David Bosler
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic , Cleveland, Ohio , USA
| | - Daniel Rhoads
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic , Cleveland, Ohio , USA
| | | | - Jennifer S Ko
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic , Cleveland, Ohio , USA
| | - Lara Jehi
- Lerner Research Institute, Cleveland Clinic , Cleveland, Ohio , USA
| | - Jing Li
- Department of Computer and Data Sciences, Case Western Reserve University , Cleveland, Ohio , USA
| | - Brian P Rubin
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic , Cleveland, Ohio , USA
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Esper FP, Adhikari TM, Tu ZJ, Cheng YW, El-Haddad K, Farkas DH, Bosler D, Rhoads D, Procop GW, Ko JS, Jehi L, Li J, Rubin BP. Alpha to Omicron: Disease Severity and Clinical Outcomes of Major SARS-CoV-2 Variants. J Infect Dis 2022; 227:344-352. [PMID: 36214810 PMCID: PMC9619650 DOI: 10.1093/infdis/jiac411] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 09/29/2022] [Accepted: 10/06/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Four severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants predominated in the United States since 2021. Understanding disease severity related to different SARS-CoV-2 variants remains limited. METHOD Viral genome analysis was performed on SARS-CoV-2 clinical isolates circulating March 2021 through March 2022 in Cleveland, Ohio. Major variants were correlated with disease severity and patient outcomes. RESULTS In total 2779 patients identified with either Alpha (n 1153), Gamma (n 122), Delta (n 808), or Omicron variants (n 696) were selected for analysis. No difference in frequency of hospitalization, intensive care unit (ICU) admission, and death were found among Alpha, Gamma, and Delta variants. However, patients with Omicron infection were significantly less likely to be admitted to the hospital, require oxygen, or admission to the ICU (2 12.8, P .001; 2 21.6, P .002; 2 9.6, P .01, respectively). In patients whose vaccination status was known, a substantial number had breakthrough infections with Delta or Omicron variants (218/808 [26.9] and 513/696 [73.7], respectively). In breakthrough infections, hospitalization rate was similar regardless of variant by multivariate analysis. No difference in disease severity was identified between Omicron subvariants BA.1 and BA.2. CONCLUSIONS Disease severity associated with Alpha, Gamma, and Delta variants is comparable while Omicron infections are significantly less severe. Breakthrough disease is significantly more common in patients with Omicron infection.
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Affiliation(s)
- Frank P Esper
- Correspondence: F. Esper, MD, Center for Pediatric Infectious Diseases, Cleveland Clinic Children's, 9500 Euclid Avenue, Cleveland, OH 44195 ()
| | - Thamali M Adhikari
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Zheng Jin Tu
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Yu-Wei Cheng
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Kim El-Haddad
- Center for Pediatric Infectious Disease, Cleveland Clinic Children’s, Cleveland, Ohio, USA
| | - Daniel H Farkas
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - David Bosler
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Daniel Rhoads
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Jennifer S Ko
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Lara Jehi
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jing Li
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, Ohio, USA
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El-Haddad K, Buscombe JR, Caplin ME, Watkinson AJ, Hilson AJ. 10. Imaging disseminated NETs: What is the best scintigraphic method? Nucl Med Commun 2000. [DOI: 10.1097/00006231-200004000-00022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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