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Elife
. 2021 Aug 3;10:e68917.
doi: 10.7554/eLife.68917. Online ahead of print.
Within-host evolutionary dynamics of seasonal and pandemic human influenza A viruses in young children
Alvin X Han 1 , Zandra C Felix Garza 1 , Matthijs Ra Welkers 2 , René M Vigeveno 2 , Nhu Duong Tran 3 , Thi Quynh Mai Le 3 , Thai Pham Quang 4 , Dinh Thoang Dang 5 , Thi Ngoc Anh Tran 6 , Manh Tuan Ha 6 , Thanh **** Nguyen 7 , Quoc Thinh Le 7 , Thanh Hai Le 8 , Thi Bich Ngoc Hoang 8 , Kulkanya Chokephaibulkit 9 , Pilaipan Puthavathana 9 , Van Vinh Chau Nguyen 10 , My Ngoc Nghiem 10 , Van Kinh Nguyen 11 , Tuyet Trinh Dao 11 , Tinh Hien Tran 10 , Heiman Fl Wertheim 12 , Peter W Horby 13 , Annette Fox 14 , H Rogier van Doorn 15 , Dirk Eggink 2 , Menno D de Jong 2 , Colin A Russell 1
Affiliations
- PMID: 34342576
- DOI: 10.7554/eLife.68917
Abstract
The evolution of influenza viruses is fundamentally shaped by within-host processes. However, the within-host evolutionary dynamics of influenza viruses remain incompletely understood, in part because most studies have focused on infections in healthy adults based on single timepoint data. Here, we analysed the within-host evolution of 82 longitudinally-sampled individuals, mostly young children, infected with A/H1N1pdm09 or A/H3N2 viruses between 2007 and 2009. For A/H1N1pdm09 infections during the 2009 pandemic, nonsynonymous minority variants were more prevalent than synonymous ones. For A/H3N2 viruses in young children, early infection was dominated by purifying selection. As these infections progressed, nonsynonymous variants typically increased in frequency even when within-host virus titres decreased. Unlike the short-lived infections of adults where de novo within-host variants are rare, longer infections in young children allow for the maintenance of virus diversity via mutation-selection balance creating potentially important opportunities for within-host virus evolution.
Keywords: evolutionary biology; human; infectious disease; microbiology; viruses.