An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia

Souilmi, Yassine; Lauterbur, M. Elise; Tobler, Ray; Johar, Angad; Enard, David

doi:10.1101/2020.11.16.385401

Cited by 25 publications

(36 citation statements)

References 64 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Our results indicate that humanity may have been exposed to these viruses since the Paleolithic if they had come into contact with their natural hosts. Also, our date estimates of the origin of the sarbecovirus lineage are in remarkable concordance with signatures of selection on human genomic datasets that indicate an arms race with corona-like viruses dating back 25,000 years 50 , providing an external comparator for our methodology.…”

Section: Mainsupporting

confidence: 67%

Prisoner of War dynamics explains the time-dependent pattern of substitution rates in viruses

Ghafari

Simmonds

2021

Preprint

View full text Add to dashboard Cite

Molecular clock dating is widely used to estimate timescales of phylogenetic histories and to infer rates at which species evolve. One of the major challenges with inferring rates of molecular evolution is the observation of a strong correlation between estimated rates and the timeframe of their measurements. Recent empirical analysis of virus evolutionary rates suggest that a power-law rate decay best explains the time-dependent pattern of substitution rates and that the same pattern is observed regardless of virus type (e.g. groups I-VII in the Baltimore classification). However there exists no explanation for this trend based on molecular evolutionary mechanisms. We provide a simple predictive mechanistic model of the time-dependent rate phenomenon, incorporating saturation and host constraints on the evolution of some sites. Our model recapitulates the ubiquitous power-law rate decay with a slope of -0.65 (95% HPD: -0.72, -0.52) and can satisfactorily account for the variation in inferred molecular evolutionary rates over a wide range of timeframes. We show that once the saturation of sites starts - typically after hundreds of years in RNA viruses and thousands of years in DNA viruses - standard substitution models fail to correctly estimate divergence times among species, while our model successfully re-creates the observed pattern of rate decay. We apply our model to re-date the diversification of genotypes of hepatitis C virus (HCV) to 396,000 (95% HPD: 326,000 - 425,000) years before present, a time preceding the dispersal of modern humans out of Africa, and also showed that the most recent common ancestor of sarbecoviruses dates back to 23,500 (95% HPD: 21,100 - 25,300) years ago, nearly thirty times older than previous estimates. This not only creates a radical new perspective for our understanding the origins of HCV but also suggests a substantial revision of evolutionary timescales of other viruses can be similarly achieved.

show abstract

Section: Mainsupporting

confidence: 67%

Prisoner of War dynamics explains the time-dependent pattern of substitution rates in viruses

Ghafari

Simmonds

2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Our findings thus suggest that persisting archaic introgressed haplotypes provided a reservoir of functional variation to the ancestors of CDX and KHV that proved adaptive during a period of environmental change, for example in response to local pathogens (Rasmussen et al, 2015). Recent reports that Neanderthal-introgressed sequences mediate individual outcomes of SARS-CoV-2 infections to this day lend plausibility to this hypothesis Pääbo, 2020a, 2020b) (Zhou et al, 2020), as does polygenic evidence of adaptation in response to ancient viral epidemics, including in East Asia (Souilmi et al, 2021).…”

Section: Discussionmentioning

confidence: 95%

Local adaptation and archaic introgression shape global diversity at human structural variant loci

Shu

Sherman

Taylor

et al. 2021

Preprint

View full text Add to dashboard Cite

Large genomic insertions, deletions, and inversions are a potent source of functional and fitness-altering variation, but are challenging to resolve with short-read DNA sequencing alone. While recent long-read sequencing technologies have greatly expanded the catalog of structural variants (SVs), their costs have so far precluded their application at population scales. Given these limitations, the role of SVs in human adaptation remains poorly characterized. Here, we used a graph-based approach to genotype 107,866 long-read-discovered SVs in short-read sequencing data from diverse human populations. We then applied an admixture-aware method to scan these SVs for patterns of population-specific frequency differentiation—a signature of local adaptation. We identified 220 SVs exhibiting extreme frequency differentiation, including several SVs that were among the lead variants at their corresponding loci. The top two signatures traced to separate insertion and deletion polymorphisms at the immunoglobulin heavy chain locus, together tagging a 325 Kbp haplotype that swept to high frequency and was subsequently fragmented by recombination. Alleles defining this haplotype are nearly fixed (60-95%) in certain Southeast Asian populations, but are rare or absent from other global populations composing the 1000 Genomes Project. Further investigation revealed that the haplotype closely matches with sequences observed in two of three high-coverage Neanderthal genomes, providing strong evidence of a Neanderthal-introgressed origin. This extraordinary episode of positive selection, which we infer to have occurred between 1700 and 8400 years ago, corroborates the role of immune-related genes as prominent targets of adaptive archaic introgression. Our study demonstrates how combining recent advances in genome sequencing, genotyping algorithms, and population genetic methods can reveal signatures of key evolutionary events that remained hidden within poorly resolved regions of the genome.

show abstract

“…The risk of negative disease outcome strongly correlates with Asian ethnicity has been the research subject since the beginning of 2020. In particular, the level of ACE2 expression in the lung tissues of Asians [13] and the found genetic predisposition to coronaviruses in Asians [14] are mentioned. In Supplementary Materials, attached a dataset of 525 embeddings of COVID-19 patients to verify the results indicated here.…”

Section: Resultsmentioning

confidence: 99%

Face Biometrics as a Potential Predictor for COVID-19 Susceptibility

O¹

2021

Preprint

View full text Add to dashboard Cite

Fighting against the COVID-19 pandemic caused by the SARS-CoV-2 virus is one of the most critical challenges facing the global health system today. The possibility to identify the group of persons in the cohort of people under 50 years old, who are sensitive to the COVID-disease by non-invasive methods, is a very perspective approach for estimating the epidemiological state of the human population. The study aimed to identify the features of people's faces with COVID-19 that the most correlate with disease severity could serve as one of these approaches. For this aim, 525 photos of patients' faces with different outcomes of COVID-19 disease were analyzed using the Dlib face recognition convolutional neural network pre-trained for face recognition. Face descriptor vectors were obtained using the convolutional neural network. Facial features were found that predict a person's sensitivity to the SARS-CoV-2 virus (disease severity), and the contribution of each of the features to the risk of developing a severe form of COVID in a person was found. The accuracy of the binary classification of the individual severity of the COVID-19 course using the k-nearest neighbors algorithm on the test dataset was accuracy - 84%, AUC - 0.90.

show abstract

An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia

Cited by 25 publications

References 64 publications

Prisoner of War dynamics explains the time-dependent pattern of substitution rates in viruses

Prisoner of War dynamics explains the time-dependent pattern of substitution rates in viruses

Local adaptation and archaic introgression shape global diversity at human structural variant loci

Face Biometrics as a Potential Predictor for COVID-19 Susceptibility

Contact Info

Product

Resources

About