An interesting preprint in BioRxiv by Souilmi and others investigated this interesting thought.
The current SARS-CoV-2 pandemic has emphasised the vulnerability of human populations to novel viral pressures, despite the vast array of epidemiological and biomedical tools now available.
Notably, modern human genomes contain evolutionary information tracing back 10s of 1000s of years, which may help identify the viruses that have impacted our ancestors – pointing to which viruses have future pandemic potential.
Here in this study, they applied evolutionarily analysis to human genomic datasets to recover selection events including 10s of human genes that interacted with coronaviruses, including SARS-CoV-2 that likely started more than 20,000 years ago.
These adaptive events were limited to the population ancestral to East Asian populations.
Multiple lines of functional evidence support an ancient viral selective pressure, and East Asia is the geographical origin of several modern coronavirus epidemics.
An arms race with an ancient coronavirus, or with a different virus that happened to use similar interactions of coronaviruses with human hosts, made thus have taken place in ancestral East Asian populations.
By learning more about our ancient viral foes, this study highlighted the promise of evolutionary information to better predict the pandemics of the future.
Importantly, adaptation to ancient viral epidemics in specific human populations does not necessarily imply any difference in genetic susceptibility between different human populations, and the current evidence points towards an overwhelming impact of socioeconomic factors in the case of COVID-19.
In this study, by scanning 26 diverse human populations from five continental regions for evidence of strong selection acting on genes that interact with the coronavirus strains, they identified a set of 42 CoV-VIPs exhibiting a coordinated adaptive response that likely emerged more than 20,000 years ago.
This pattern was unique to the ancestors of East Asian populations, being absent from any of the 21 non-East Asian human populations that were tested.
By using reconstructive methods, they identified the trajectories of selected alleles and showed that this selection process produced a strong response across the 42 CoV-VIP genes that gradually waned and resulted in the selected loci plateauing at intermediate frequencies.
They demonstrated that this adaptive response was likely to be the outcome of a multigenerational viral epidemic, as attested by the clustering of putatively selected loci around variants that regulated tissues known to exhibit COVID-19 related pathologies.
The net result of this ancient selection patterns on the CoV-VIPs in ancient human populations is the creation of genetic differences amongst individuals now living in East Asia and between East Asians and populations distributed across the rest of the world.
By leveraging the evolutionary information contained in publicly available human genomic datasets, they were able to infer ancient viral epidemics impacting the ancestors of contemporary East Asian populations, which initially arose likely more than 20,000 years ago. This resulted in coordinated adaptive changes across 42 genes.
Importantly, their evolutionary genomic analysis has identified several new candidate genes that might benefit current efforts to combat COVID-19, either by providing novel drug targets or by repurposing currently available drugs that target these candidate genes.
More broadly, their findings highlighted the utility of thinking about the possible contribution of evolutionary genomic approaches into standard medical research protocols.
Indeed, by revealing the identity of ancient pathogenic foes, evolutionary genomic methods may ultimately improve the ability to predict and thus prevent the epidemics of the future.
Dr Paul Ettlinger
BM, DRCOG, FRCGP, FRIPH, DOccMed