Reply to: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data-Reference-Cited by-同舟云学术

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Reply to: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data

Published:2024-04-16 Issue:1 Volume:15 Page:
ISSN:2041-1723
Container-title:Nature Communications
language:en
Short-container-title:Nat Commun

Author:

Nelson Chase W.^ORCID,Poon Leo L. M.^ORCID,Gu Haogao^ORCID

Funder

Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund

Research Grants Council, University Grants Committee

U.S. Department of Energy

Publisher

Springer Science and Business Media LLC

Link

https://www.nature.com/articles/s41467-024-46262-3.pdf

Reference25 articles.

1. Nei, M. & Li, W.-H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl Acad. Sci. USA 76, 5269–5273 (1979).

2. Lauring, A. S. Within-host viral diversity: a window into viral evolution. Annu. Rev. Virol. 7, 63–81 (2020).

3. Nelson, C. W. & Hughes, A. L. Within-host nucleotide diversity of virus populations: Insights from next-generation sequencing. Infection Genet. Evol. 30, 1–7 (2015).

4. Nelson, C. W., Moncla, L. H. & Hughes, A. L. SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data. Bioinformatics 31, 3709–3711 (2015).

5. Moncla, L. H. et al. Selective bottlenecks shape evolutionary pathways taken during mammalian adaptation of a 1918-like avian influenza virus. Cell Host Microbe 19, 169–180 (2016).

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