Time dependence of evolutionary metrics during the 2009 pandemic influenza virus outbreak

Virus Evolution
Austin G MeyerClaus O Wilke

Abstract

With the expansion of DNA sequencing technology, quantifying evolution in emerging viral outbreaks has become an important tool for scientists and public health officials. Although it is known that the degree of sequence divergence significantly affects the calculation of evolutionary metrics in viral outbreaks, the extent and duration of this effect during an actual outbreak remains unclear. We have analyzed how limited divergence time during an early viral outbreak affects the accuracy of molecular evolutionary metrics. Using sequence data from the first 25 months of the 2009 pandemic H1N1 (pH1N1) outbreak, we calculated each of three different standard evolutionary metrics-molecular clock rate (i.e., evolutionary rate), whole gene dN/dS, and site-wise dN/dS-for hemagglutinin and neuraminidase, using increasingly longer time windows, from 1 month to 25 months. For the molecular clock rate, we found that at least three to four months of temporal divergence from the start of sampling was required to make precise estimates that also agreed with long-term values. For whole gene dN/dS, we found that at least two months of data were required to generate precise estimates, but six to nine months were required for estimates to approa...Continue Reading

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Citations

Jan 20, 2016·Nature Reviews. Genetics·Julian EchaveClaus O Wilke
Oct 16, 2015·Journal of the Royal Society, Interface·Austin G Meyer, Claus O Wilke
Mar 26, 2016·Science·Nuno Rodrigues FariaPedro F C Vasconcelos
Oct 13, 2017·Viruses·María José Benítez-GaleanoRodney Colina
Oct 11, 2019·Archives of Virology·Lucia P Barzilai, Carlos G Schrago
Apr 15, 2020·Scientific Reports·Wanhong XuYohannes Berhane
Jun 27, 2018·Virus Evolution·Juan Ángel Patiño-Galindo, Fernando González-Candelas
Jan 23, 2021·Briefings in Bioinformatics·Roberto Del AmparoMiguel Arenas
Aug 17, 2020·Current Biology : CB·Kerttu MajanderVerena J Schuenemann

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Methods Mentioned

BETA
RSA

Software Mentioned

R
PyMOL
Tracer
FastTree
MAFFT
HyPhy
BEAST
ggplot2 R package

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