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Koel BF, Vigeveno RM, Pater M, Koekkoek SM, Han AX, Tuan HM, Anh TTN, Hung NT, Thinh LQ, Hai LT, Ngoc HTB, Chau NVV, Ngoc NM, Chokephaibulkit K, Puthavathana P, Kinh NV, Trinh T, Lee RTC, Maurer-Stroh S, Eggink D, Thanh TT, Tan LV, van Doorn HR, de Jong MD. Longitudinal sampling is required to maximize detection of intrahost A/H3N2 virus variants. Virus Evol 2020; 6:veaa088. [PMID: 33343927 PMCID: PMC7733607 DOI: 10.1093/ve/veaa088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Seasonal human influenza viruses continually change antigenically to escape from neutralizing antibodies. It remains unclear how genetic variation in the intrahost virus population and selection at the level of individual hosts translates to the fast-paced evolution observed at the global level because emerging intrahost antigenic variants are rarely detected. We tracked intrahost variants in the hemagglutinin and neuraminidase surface proteins using longitudinally collected samples from 52 patients infected by A/H3N2 influenza virus, mostly young children, who received oseltamivir treatment. We identified emerging putative antigenic variants and oseltamivir-resistant variants, most of which remained detectable in samples collected at subsequent days, and identified variants that emerged intrahost immediately prior to increases in global rates. In contrast to most putative antigenic variants, oseltamivir-resistant variants rapidly increased to high frequencies in the virus population. Importantly, the majority of putative antigenic variants and oseltamivir-resistant variants were first detectable four or more days after onset of symptoms or start of treatment, respectively. Our observations demonstrate that de novo variants emerge, and may be positively selected, during the course of infection. Additionally, based on the 4–7 days post-treatment delay in emergence of oseltamivir-resistant variants in six out of the eight individuals with such variants, we find that limiting sample collection for routine surveillance and diagnostic testing to early timepoints after onset of symptoms can potentially preclude detection of emerging, positively selected variants.
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Affiliation(s)
- B F Koel
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - R M Vigeveno
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - M Pater
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - S M Koekkoek
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - A X Han
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | - N T Hung
- Children's Hospital 1, Ho Chi Minh City, Vietnam
| | - L Q Thinh
- Children's Hospital 1, Ho Chi Minh City, Vietnam
| | - L T Hai
- Vietnam National Children's Hospital, Hanoi, Vietnam
| | - H T B Ngoc
- Vietnam National Children's Hospital, Hanoi, Vietnam
| | - N V V Chau
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - N M Ngoc
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | | | - N V Kinh
- National Hospital of Tropical Diseases, Hanoi, Vietnam
| | - T Trinh
- National Hospital of Tropical Diseases, Hanoi, Vietnam
| | - R T C Lee
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore 138671 Singapore
| | - S Maurer-Stroh
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore 138671 Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore.,National Public Health Laboratory, National Centre for Infectious Diseases, Ministry of Health, Singapore 308442, Singapore
| | - D Eggink
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - T T Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - L V Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - H R van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam.,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - M D de Jong
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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