Viruses and viral epidemics in the metabolic theory of evolution

Using Chaos-Game-Representation for Analysing the SARS-CoV-2 Lineages, Newly Emerging Strains and Recombinants

Background

Viruses have high mutation rates, facilitating rapid evolution and the emergence of new species, subspecies, strains and recombinant forms. Accurate classification of these forms is crucial for understanding viral evolution and developing therapeutic applications. Phylogenetic classification is typically performed by analyzing molecular differences at the genomic and sub-genomic levels. This involves aligning homologous proteins or genes. However, there is growing interest in developing alignment-free methods for whole-genome comparisons that are computationally efficient.

Methods

Here we elaborate on the Chaos Game Representation (CGR) method, based on concepts of statistical physics and free of sequence alignment assumptions. We adopt the CGR method for classification of the closely related clades/lineages A and B of the SARS-Corona virus 2019 (SARS-CoV-2), which is one of the fastest evolving viruses.

Results

Our study shows that the CGR approach can easily yield the SARS-CoV-2 phylogeny from the available whole genomes of lineage A and lineage B sequences. It also shows an accurate classification of eight different strains and the newly evolved XBB variant from its parental strains. Compared to alignment-based methods (Neighbour-Joining and Maximum Likelihood), the CGR method requires low computational resources, is fast and accurate for long sequences, and, being a K-mer based approach, allows simultaneous comparison of a large number of closely-related sequences of different sizes. Further, we developed an R pipeline CGRphylo, available on GitHub, which integrates the CGR module with various other R packages to create phylogenetic trees and visualize them.

Conclusion

Our findings demonstrate the efficacy of the CGR method for accurate classification and tracking of rapidly evolving viruses, offering valuable insights into the evolution and emergence of new SARS-CoV-2 strains and recombinants.

Prevalence and Characteristics of Altered Sense of Smell/Taste During Covid-19 first wave: A French Nationwide Cross-sectional Study

AIM

Altered sense of smell and/or taste is a leading symptom of SARS-CoV-2 infection, but its prevalence at a population-level is unknown.

METHODS

From a questionnaire addressed to a representative subset of the French general adult (≥18-year) population over a 6-week period during the first French lockdown (April 7 to May 19 2020), self-reported new cases of altered sense of smell and/or taste were collected.

RESULTS

From 29,660 participants, new altered sense of smell and/or taste was 2.18% and 2.11% after direct standardization on the French population representing more than 1,110,000 subjects in France. Moreover, 0.5% of participants reported a positive SARS-CoV-2 test, among which 47.4% reported a newly altered sense of smell and/or taste. Male participants, younger ones together with those presenting with chronic condition had higher odds of reporting a newly altered sense of smell and/or taste.

CONCLUSION

This study provides an accurate estimate of new cases of altered sense of smell and/or taste in the general population at a nationwide level during the Covid-19 first wave.

Virtual 2D mapping of the viral proteome reveals host-specific modality distribution of molecular weight and isoelectric point

A proteome-wide study of the virus kingdom based on 1.713 million protein sequences from 19,128 virus proteomes was conducted to construct an overall proteome map of the virus kingdom. Viral proteomes encode an average of 386.214 amino acids per protein with the variation in the number of protein-coding sequences being host-specific. The proteomes of viruses of fungi hosts (882.464) encoded the greatest number of amino acids, while the viral proteome of bacterial host (210.912) encoded the smallest number of amino acids. Viral proteomes were found to have a host-specific amino acid composition. Leu (8.556%) was the most abundant and Trp (1.274%) the least abundant amino acid in the collective proteome of viruses. Viruses were found to exhibit a host-dependent molecular weight and isoelectric point of encoded proteins. The isoelectric point (pI) of viral proteins was found in the acidic range, having an average pI of 6.89. However, the pI of viral proteins of algal (pI 7.08) and vertebrate (pI 7.09) hosts was in the basic range. The virtual 2D map of the viral proteome from different hosts exhibited host-dependent modalities. The virus proteome from algal hosts and archaea exhibited a bimodal distribution of molecular weight and pI, while the virus proteome of bacterial host exhibited a trimodal distribution, and the virus proteome of fungal, human, land plants, invertebrate, protozoa, and vertebrate hosts exhibited a unimodal distribution.