An evolution-based high-fidelity method of epistasis measurement: Theory and application to influenza

Long-range linkage effects in adapting sexual populations

In sexual populations, closely-situated genes have linked evolutionary fates, while genes spaced far in genome are commonly thought to evolve independently due to recombination. In the case where evolution depends essentially on supply of new mutations, this assumption has been confirmed by mathematical modeling. Here I examine it in the case of pre-existing genetic variation, where mutation is not important. A haploid population with [Formula: see text] genomes, [Formula: see text] loci, a fixed selection coefficient, and a small initial frequency of beneficial alleles [Formula: see text] is simulated by a Monte-Carlo algorithm. When the number of loci, L, is larger than a critical value of [Formula: see text] simulation demonstrates a host of linkage effects that decrease neither with the distance between loci nor the number of recombination crossovers. Due to clonal interference, the beneficial alleles become extinct at a fraction of loci [Formula: see text]. Due to a genetic background effect, the substitution rate varies broadly between loci, with the fastest value exceeding the one-locus limit by the factor of [Formula: see text] Thus, the far-situated parts of a long genome in a sexual population do not evolve as independent blocks. A potential link between these findings and the emergence of new Variants of Concern of SARS-CoV-2 is discussed.

Evolutionary implications of SARS-CoV-2 vaccination for the future design of vaccination strategies

Once the first SARS-CoV-2 vaccine became available, mass vaccination was the main pillar of the public health response to the COVID-19 pandemic. It was very effective in reducing hospitalizations and deaths. Here, we discuss the possibility that mass vaccination might accelerate SARS-CoV-2 evolution in antibody-binding regions compared to natural infection at the population level. Using the evidence of strong genetic variation in antibody-binding regions and taking advantage of the similarity between the envelope proteins of SARS-CoV-2 and influenza, we assume that immune selection pressure acting on these regions of the two viruses is similar. We discuss the consequences of this assumption for SARS-CoV-2 evolution in light of mathematical models developed previously for influenza. We further outline the implications of this phenomenon, if our assumptions are confirmed, for the future design of SARS-CoV-2 vaccination strategies.

Measurement of selection coefficients from genomic samples of adapting populations by computer modeling

The existing protocols of measuring the selection coefficients of loci neglect linkage effects existing between loci. This protocol is free from this limitation. The protocol inputs a set of DNA sequences at three time points, removes conserved sites, and estimates selection coefficients. If the user wishes to test the accuracy, it can ask the protocol to generate mock data by computer simulation of evolution. The main limitation is the need for sequence samples isolated from 30-100 populations adapting in parallel. For complete details on the use and execution of this protocol, please refer to Barlukova and Rouzine (2021).

Temporal epistasis inference from more than 3 500 000 SARS-CoV-2 genomic sequences

We use direct coupling analysis (DCA) to determine epistatic interactions between loci of variability of the SARS-CoV-2 virus, segmenting genomes by month of sampling. We use full-length, high-quality genomes from the GISAID repository up to October 2021 for a total of over 3 500 000 genomes. We find that DCA terms are more stable over time than correlations but nevertheless change over time as mutations disappear from the global population or reach fixation. Correlations are enriched for phylogenetic effects, and in particularly statistical dependencies at short genomic distances, while DCA brings out links at longer genomic distance. We discuss the validity of a DCA analysis under these conditions in terms of a transient auasilinkage equilibrium state. We identify putative epistatic interaction mutations involving loci in spike.