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Review
. 2018 Feb:28:20-25.
doi: 10.1016/j.coviro.2017.10.008. Epub 2017 Nov 3.

Genetic bottlenecks in intraspecies virus transmission

John T McCrone  1 , Adam S Lauring  2
Affiliations
Review

Genetic bottlenecks in intraspecies virus transmission

John T McCrone et al. Curr Opin Virol. 2018 Feb.

Abstract

Ultimately, viral evolution is a consequence of mutations that arise within and spread between infected hosts. The transmission bottleneck determines how much of the viral diversity generated in one host passes to another during transmission. It therefore plays a vital role in linking within-host processes to larger evolutionary trends. Although many studies suggest that transmission severely restricts the amount of genetic diversity that passes between individuals, there are important exceptions to this rule. In many cases, the factors that determine the size of the transmission bottleneck are only beginning to be understood. Here, we review how transmission bottlenecks are measured, how they arise, and their consequences for viral evolution.

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Figures

Figure 1
Figure 1
The effect of transmission bottlenecks on viral diversity. In a variety of hosts (e.g. humans, pigs, plant shown here), stringent bottlenecks (top) limit the size and diversity of a population and drastically alter their composition. The large populations that pass through loose bottlenecks (bottom) allow for transmission of rare variants. As a result the diversity of the population in the recipient approximates that of the donor.
Figure 2
Figure 2
Measuring transmission bottlenecks. (A) The number of donor-derived, neutral markers detected in the recipient is an indication of the stringency of the transmission bottleneck. Here, 3 of the 6 markers were transmitted suggesting a stringent bottleneck. (B) Shared diversity data from natural systems can be used to estimate a bottleneck. In the example, only two donor genotypes, denoted with *, were transmitted to the recipient suggesting a stringent bottleneck. Other de novo mutations arise on these backgrounds after transmission. (C) Coalescent models allow one to work backward from the time of sampling and estimate the number of genotypes that could plausibly give rise to the observed diversity. In this case, the two lineages are traced back to two genetically distinct variants present at transmission.
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