Rapid Emergence and Evolution of SARS-CoV-2 Intrahost Variants among COVID-19 Patients with Prolonged Infections, Singapore
The evolution and spread of SARS-CoV-2 variants have driven successive waves of global COVID-19 outbreaks, yet the longitudinal dynamics of intrahost variation within the same patient remain less clear. We conducted a longitudinal cohort study by deep sequencing 198 swab samples collected from COVI...
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| Format: | Article |
| Language: | English |
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Centers for Disease Control and Prevention
2025-08-01
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| Series: | Emerging Infectious Diseases |
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| Online Access: | https://wwwnc.cdc.gov/eid/article/31/8/24-1419_article |
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| _version_ | 1849251784343683072 |
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| author | Yvonne C.F. Su Michael A. Zeller Peter Cronin Rong Zhang Yan Zhuang Jordan Ma Foong Ying Wong Giselle G.K. Ng Áine O’Toole Andrew Rambaut Jenny G. Low Gavin J.D. Smith |
| author_facet | Yvonne C.F. Su Michael A. Zeller Peter Cronin Rong Zhang Yan Zhuang Jordan Ma Foong Ying Wong Giselle G.K. Ng Áine O’Toole Andrew Rambaut Jenny G. Low Gavin J.D. Smith |
| author_sort | Yvonne C.F. Su |
| collection | DOAJ |
| description |
The evolution and spread of SARS-CoV-2 variants have driven successive waves of global COVID-19 outbreaks, yet the longitudinal dynamics of intrahost variation within the same patient remain less clear. We conducted a longitudinal cohort study by deep sequencing 198 swab samples collected from COVID-19 patients with varying infection durations. Our analysis showed that prolonged infections enhanced viral genomic diversity, leading to emergence of co-occurring variants that maintained high (>20%) frequency and became dominant in virus populations. We observed heterogeneous intrahost dynamics among individual patients, 2 of whom exhibited a minor variant of the spike D614G substitution over the course of infection. The increase in intrahost variants strongly correlated with prolonged infections, highlighting the complex interplay between viral diversity and host factors. This study revealed the intricate evolutionary mechanisms driving the emergence of de novo variants and lineage dominance, which could inform development of effective vaccine candidates and strategies to protect public health.
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| format | Article |
| id | doaj-art-8b439eb7aecf463899e041cbce41f455 |
| institution | Kabale University |
| issn | 1080-6040 1080-6059 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Centers for Disease Control and Prevention |
| record_format | Article |
| series | Emerging Infectious Diseases |
| spelling | doaj-art-8b439eb7aecf463899e041cbce41f4552025-08-20T03:56:49ZengCenters for Disease Control and PreventionEmerging Infectious Diseases1080-60401080-60592025-08-013181537154910.3201/eid3108.241419Rapid Emergence and Evolution of SARS-CoV-2 Intrahost Variants among COVID-19 Patients with Prolonged Infections, SingaporeYvonne C.F. SuMichael A. ZellerPeter CroninRong ZhangYan ZhuangJordan MaFoong Ying WongGiselle G.K. NgÁine O’TooleAndrew RambautJenny G. LowGavin J.D. Smith The evolution and spread of SARS-CoV-2 variants have driven successive waves of global COVID-19 outbreaks, yet the longitudinal dynamics of intrahost variation within the same patient remain less clear. We conducted a longitudinal cohort study by deep sequencing 198 swab samples collected from COVID-19 patients with varying infection durations. Our analysis showed that prolonged infections enhanced viral genomic diversity, leading to emergence of co-occurring variants that maintained high (>20%) frequency and became dominant in virus populations. We observed heterogeneous intrahost dynamics among individual patients, 2 of whom exhibited a minor variant of the spike D614G substitution over the course of infection. The increase in intrahost variants strongly correlated with prolonged infections, highlighting the complex interplay between viral diversity and host factors. This study revealed the intricate evolutionary mechanisms driving the emergence of de novo variants and lineage dominance, which could inform development of effective vaccine candidates and strategies to protect public health. https://wwwnc.cdc.gov/eid/article/31/8/24-1419_articleCOVID-19respiratory infectionssevere acute respiratory syndrome coronavirus 2SARS-CoV-2SARScoronavirus disease |
| spellingShingle | Yvonne C.F. Su Michael A. Zeller Peter Cronin Rong Zhang Yan Zhuang Jordan Ma Foong Ying Wong Giselle G.K. Ng Áine O’Toole Andrew Rambaut Jenny G. Low Gavin J.D. Smith Rapid Emergence and Evolution of SARS-CoV-2 Intrahost Variants among COVID-19 Patients with Prolonged Infections, Singapore Emerging Infectious Diseases COVID-19 respiratory infections severe acute respiratory syndrome coronavirus 2 SARS-CoV-2 SARS coronavirus disease |
| title | Rapid Emergence and Evolution of SARS-CoV-2 Intrahost Variants among COVID-19 Patients with Prolonged Infections, Singapore |
| title_full | Rapid Emergence and Evolution of SARS-CoV-2 Intrahost Variants among COVID-19 Patients with Prolonged Infections, Singapore |
| title_fullStr | Rapid Emergence and Evolution of SARS-CoV-2 Intrahost Variants among COVID-19 Patients with Prolonged Infections, Singapore |
| title_full_unstemmed | Rapid Emergence and Evolution of SARS-CoV-2 Intrahost Variants among COVID-19 Patients with Prolonged Infections, Singapore |
| title_short | Rapid Emergence and Evolution of SARS-CoV-2 Intrahost Variants among COVID-19 Patients with Prolonged Infections, Singapore |
| title_sort | rapid emergence and evolution of sars cov 2 intrahost variants among covid 19 patients with prolonged infections singapore |
| topic | COVID-19 respiratory infections severe acute respiratory syndrome coronavirus 2 SARS-CoV-2 SARS coronavirus disease |
| url | https://wwwnc.cdc.gov/eid/article/31/8/24-1419_article |
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