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Comment
. 2019 Sep;51(9):1298-1301.
doi: 10.1038/s41588-019-0349-3.

Reconciling disparate estimates of viral genetic diversity during human influenza infections

Katherine S Xue  1   2   3 , Jesse D Bloom  4   5   6   7
Affiliations
Comment

Reconciling disparate estimates of viral genetic diversity during human influenza infections

Katherine S Xue et al. Nat Genet. 2019 Sep.
No abstract available

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Conflict of interest statement

Competing Interests Statement

The authors declare no competing financial interests.

Figures

Figure 1.
Figure 1.. Comparison of shared within-host viral genetic diversity in four large-scale deep-sequencing studies of human influenza virus.
Proportion of samples in each study in which we identified within-host variation at each genome site. For each sample, we identified within-host variants that were present at a frequency of at least 3% at sites with minimum sequencing coverage of 200 reads. Our re-analysis is consistent with the previously reported results of each study: we find little shared genetic diversity in the data from the Dinis et al. (2016), Debbink et al. (2017), and McCrone et al. (2018) studies, but we observe high shared genetic diversity in the data from the Poon et al study.
Figure 2.
Figure 2.. Paired-end sequencing reads are frequently split between samples that were run on the same sequencing lane.
(A) Paired-end sequencing reads are derived from the same physical DNA molecule. (B) The FASTQ header for each sequencing read provides information about the sequencing instrument, flowcell lane, tile, cluster coordinates, and sequencing index for each read, as well as whether the read is the first or second member of a read pair. (C) Sequencing reads from the Hong Kong dataset are frequently split between distinct biological samples. (D) Hierarchical clustering of the number of read pairs split between each pair of samples in the Hong Kong study. Sequencing reads from the Hong Kong dataset are split between four distinct clusters of samples. All sequencing reads in each cluster are derived from the same flowcell lane and correspond to one set of replicate samples for one of the two influenza subtypes sequenced in the study. (E) Proportion of samples for which we identified within-host variation at each genome site when analyzing both reads for a pair, just read 1, or just read 2. For each sample, we identified within-host variants that were present at a frequency of at least 3% at sites with minimum sequencing coverage of 200 reads.
See this image and copyright information in PMC

Comment in

Comment on

  • Quantifying influenza virus diversity and transmission in humans.
    Poon LL, Song T, Rosenfeld R, Lin X, Rogers MB, Zhou B, Sebra R, Halpin RA, Guan Y, Twaddle A, DePasse JV, Stockwell TB, Wentworth DE, Holmes EC, Greenbaum B, Peiris JS, Cowling BJ, Ghedin E. Poon LL, et al. Nat Genet. 2016 Feb;48(2):195-200. doi: 10.1038/ng.3479. Epub 2016 Jan 4. Nat Genet. 2016. PMID: 26727660 Free PMC article.

References

    1. Xue KS, Moncla LH, Bedford T & Bloom JD Within-Host Evolution of Human Influenza Virus. Trends Microbiol. (2018). doi: 10.1016/J.TIM.2018.02.007 - DOI - PMC - PubMed
    1. McCrone JT & Lauring AS Genetic bottlenecks in intraspecies virus transmission. Curr. Opin. Virol 28, 20–25 (2018). - PMC - PubMed
    1. Dinis JM et al. Deep Sequencing Reveals Potential Antigenic Variants at Low Frequencies in Influenza A Virus-Infected Humans. J. Virol 90, 3355–65 (2016). - PMC - PubMed
    1. Poon LLM et al. Quantifying influenza virus diversity and transmission in humans. Nat. Genet 48, 195–200 (2016). - PMC - PubMed
    1. Debbink K et al. Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses. PLOS Pathog. 13, e1006194 (2017). - PMC - PubMed