Ecological and Evolutionary Processes Shaping Viral Genetic Diversity

Abstract

The contemporary genomic diversity of viruses is a result of the continuous and dynamic interaction of past ecological and evolutionary processes. Thus, genome sequences of viruses can be a valuable source of information about these processes. In this review, we first describe the relevant processes shaping viral genomic variation, with a focus on the role of host–virus coevolution and its potential to give rise to eco-evolutionary feedback loops. We further give a brief overview of available methodology designed to extract information about these processes from genomic data. Short generation times and small genomes make viruses ideal model systems to study the joint effect of complex coevolutionary and eco-evolutionary interactions on genetic evolution. This complexity, together with the diverse array of lifetime and reproductive strategies in viruses ask for extensions of existing inference methods, for example by integrating multiple information sources. Such integration can broaden the applicability of genetic inference methods and thus further improve our understanding of the role viruses play in biological communities.

Genomic Study of COVID-19 Corona Virus Excludes Its Origin from Recombination or Characterized Biological Sources and Suggests a Role for HERVS in Its Wide Range Symptoms

“…This is very difficult to determine because it is not known how many generations (infections) these isolates have gone before they had been sequenced, therefore this number is overestimation of SNPs rate in the studied strains because they should have gone through huge number of infections from being isolated from patients with symptoms. RNA viruses have mutation rate from 1 × 10 -6 to 1 × 10 -4 [22][23][24]. Our overestimated mutation rate of COVID-19 is still in the range of RNA viruses' mutation rate indicating that COVID-19 is a new viral strain.…”

Reservoir population dynamics and pathogen epidemiology drive pathogen genetic diversity, spillover, and emergence

“…Many factors affect pathogen genetic diversity, and thus the likelihood that strains capable of human spillover and emergence circulate within the population [11]. For instance, high mutation rates and short generation times allow pathogenic viruses to rapidly increase genetic diversity, whereas bottlenecks at transmission can result in the stochastic loss of genetic variation [12–16].…”

Evolution of pathogen tolerance and emerging infections: A missing experimental paradigm

“…Increased strain diversity might be particularly useful here to improve the pathogen's prospect of jumping across species barrier by harbouring the pool of useful mutations to establish infection in a new host. For instance, changes in genetic diversity of the pathogen pool by mutations or genetic exchanges can lead to alterations in the kinetics of viral replication within the natural hosts (Simmonds et al, 2019), modulating their ability to detect antigens and initiate counter-effective immune responses (Burmeister et al, 2016;Retel et al, 2019). Such alterations are perhaps also useful to evade immune responses and establish infection in a new host.…”

“…While the role of host immune responses in shaping heterogeneous infection outcomes (Duneau et al, 2017) and pathogen evolution (Retel et al, 2019) is unquestionable, their importance in driving naturally-occurring variations in pathogen prevalence should gain more importance. Tracing the link between variations in inflammatory responses, pathogen abundance and diversity, and the ability to tolerate infections can provide insightful evidence about how the infection outcomes and their downstream effects on pathogen transmission by potential reservoirs vary across populations.…”