Observing micro-evolutionary processes of viral populations at multiple scales

Abstract

Advances in sequencing technology coupled with new integrative approaches to data analysis provide a potentially transformative opportunity to use pathogen genome data to advance our understanding of transmission. However, to maximize the insights such genetic data can provide, we need to understand more about how the microevolution of pathogens is observed at different scales of biological organization. Here, we examine the evolutionary processes in foot-and-mouth disease virus observed at different scales, ranging from the tissue, animal, herd and region. At each scale, we observe analogous processes of population expansion, mutation and selection resulting in the accumulation of mutations over increasing time scales. While the current data are limited, rates of nucleotide substitution appear to be faster over individual-to-individual transmission events compared with those observed at a within-individual scale suggesting that viral population bottlenecks between individuals facilitate the fixation of polymorphisms. Longer-term rates of nucleotide substitution were found to be equivalent in individual-to-individual transmission compared with herd-to-herd transmission indicating that viral diversification at the herd level is not retained at a regional scale.

Figure 1.

Multiple scales at which FMDV evolution can be observed. (a) Virions containing the FMDV genome infect cells, where all viral replication occurs; higher scales at which the evolutionary process can be observed are the tissue (a set of cells), the host animal (a set of tissues), the herd (a set of animals), a country (a set of herds) and the globe. (b) The fundamental processes of population expansion, transmission and selection, which occur at each scale, illustrated for the cell and tissue scales.

Figure 2.

Mutation spectrum of a lesion. The black line represents the mutation spectrum generated from NGS sequence data from a cow foot lesion.

Figure 3.

Genetic network of intra-host tissue samples. (a) Genealogy of nine samples from cow number 2 in the cow-to-cow infection chain in [26]. A consensus sequence was generated for each sample from the NGS data and a statistical parsimony tree using the software package TCS [37]. Samples are labelled according to the animal number (A2), followed by the number of DPFC, and then the tissue type (probang, PB; serum, SR; or foot: BRF, back right foot; FLF, front left foot; FRF, front right foot). The original O1/BFS 1860 FMDV inoculum is also shown in tree. Samples located within the same box share the same sequence, links between boxes represent single mutations, with additional unsampled genomes represented with open circles; the genome position at which changes distinguish the different genotypes is indicated next to each link. The box shaded in grey represents the animals overall consensus sequence. (b) Mutation frequency (y-axis) of genome positions 1087 (straight line) and 7355 (dotted line) across all samples; the bottom x-axis represents the number of DPFC followed by the sample type.

Figure 4.

Statistical parsimony trees of FMD transmission between cows and herds: UK2007 and UK2001 represent the between-herd transmission tree from the full 2007 FMD epidemic [12] and the largest chain from the 2001 epidemic [11], respectively. Chain A and Chain B represent two between cow transmission chains from the study of Juleff et al. [38]. In all cases, solid black circles represent samples from different cows or herds, open circles represent unsampled genomes and the connecting lines represent single nucleotide differences between genomes.

Figure 5.

Distribution of the number of variant nucleotides between viruses recovered from consecutively infected herds and cows. The number of variant nucleotides between herds (grey) and cows (black) was calculated from their respective herd-to-herd and cow-to-cow transmission chains. The number of variant nucleotides was determined from the common ancestor of source and daughter herd if not directly linked.

Figure 6.

Comparison of within and between nucleotide variations. The solid grey and black lines represent the accumulated number of variant nucleotides over time between consensus sequences along the A1 → A5 and B1 → B5 chains (figure 5), respectively. The dashed grey (A chain) and black (B chain) lines represent the number of variant nucleotides observed in animal number 2 of the chain in the sample taken 32 DPFC.