Decision letter: A large effective population size for established within-host influenza virus infection

Strains of the influenza virus form coherent global populations, yet exist at the level of single infections in individual hosts. The relationship between these scales is a critical topic for understanding viral evolution. Here we investigate the within-host relationship between selection and the stochastic effects of genetic drift, estimating an effective population size of infection Ne for influenza infection. Examining whole-genome sequence data describing a chronic case of influenza B in a severely immunocompromised child we infer an Ne of 2.5 × 107 (95% confidence range 1.0 × 107 to 9.0 × 107) suggesting that genetic drift is of minimal importance during an established influenza infection. Our result, supported by data from influenza A infection, suggests that positive selection during within-host infection is primarily limited by the typically short period of infection. Atypically long infections may have a disproportionate influence upon global patterns of viral evolution.

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A large effective population size for within-host influenza virus infection

10.1101/2020.04.17.046250 ◽

2020 ◽

Cited By ~ 1

Author(s):

Casper K Lumby ◽

Lei Zhao ◽

Judy Breuer ◽

Christopher J R Illingworth

Keyword(s):

Influenza Virus ◽

Population Size ◽

Effective Population Size ◽

Genetic Drift ◽

Viral Evolution ◽

Influenza Virus Infection ◽

Whole Genome Sequence ◽

Influenza B ◽

Effective Population ◽

Short Period

Strains of the influenza virus form coherent global populations, yet exist at the level of single infections in individual hosts. The relationship between these scales is a critical topic for understanding viral evolution. Here we investigate the within-host relationship between selection and the stochastic effects of genetic drift, estimating an effective population size of infection Ne for influenza infection. Examining whole-genome sequence data describing a chronic case of influenza B in a severely immunocompromised child we infer an Ne of 2.5 × 107 (95% confidence range 1.0 × 107 to 9.0 × 107) suggesting the importance of genetic drift to be minimal. Our result, supported by the analysis of data from influenza A infection, suggests that positive selection during within-host infection is primarily limited by the typically short period of infection. Atypically long infections may have a disproportionate influence upon global patterns of viral evolution.

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Genomic Tools for the Conservation and Genetic Improvement of a Highly Fragmented Breed—The Ramo Grande Cattle from the Azores

Animals ◽

10.3390/ani10061089 ◽

2020 ◽

Vol 10 (6) ◽

pp. 1089

Author(s):

Andreia J. Amaral ◽

Ana L. Pavão ◽

Luis T. Gama

Keyword(s):

Population Size ◽

Effective Population Size ◽

Genome Wide Association Study ◽

Cattle Breed ◽

Production Traits ◽

Effective Population ◽

Age At First Calving ◽

Large Effective Population Size ◽

Genomic Inbreeding ◽

Genomic Regions

Ramo Grande is a local cattle breed raised in the archipelago of Azores, with a small and dispersed census, where inbreeding control is of utmost importance. A single nucleotide polymorphism (SNP) Beadchip array was used to assess inbreeding, by analysis of genomic regions harboring contiguous homozygous genotypes named runs of homozygosity (ROH), and to estimate past effective population size by analysis of linkage disequilibrium (LD). Genetic markers associated with production traits were also investigated, exploiting the unique genetic and adaptation features of this breed. A total of 639 ROH with length >4 Mb were identified, with mean length of 14.96 Mb. The mean genomic inbreeding was 0.09, and long segments of ROH were common, indicating recent inbred matings. The LD pattern indicates a large effective population size, suggesting the inflow of exotic germplasm in the past. The genome-wide association study identified novel markers significantly affecting longevity, age at first calving and direct genetic effects on calf weight. These results provide the first evidence of the association of longevity with genes related with DNA recognition and repair, and the association of age at first calving with aquaporin proteins, which are known to have a crucial role in reproduction.

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