The Take Away: Paper explores the origin and evolution of SARS-CoV-2

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This is only a bullet point summary of a longer and more in-depth paper in the National Science Review, “On the origin and continuing evolution of SARS-CoV-2”. We suggest reading the paper in full on the publisher’s website for a better understanding of the points made here.

  • Coronaviruses are naturally hosted and evolutionarily shaped by bats.
  • The whole-genome sequence identity of the novel virus has 96.2% similarity to a bat.
  • SARS-related coronavirus (SARSr-CoV; RaTG13) collected in Yunnan province, China, but is not very similar to the genomes of SARS-CoV (about 79%) or MERS-CoV (about 50%).
  • We found that the nucleotide divergence at synonymous sites between SARS-CoV-2 and other viruses was much higher than previously anticipated.
  • Both SARS-CoV and SARS-CoV-2 bind to ACE2 through the RBD of spike protein in order to initiate membrane fusion and enter human cells
  • Although several ancient recombination events have been described in spike [27, 28], it also seems likely that the identical functional sites in SARS-CoV-2 and GD Pangolin-CoV may actually the result of coincidental convergent evolution.
  • It seems very unlikely that SARS-CoV-2 originated from the GD Pangolin-CoV due to a very recent recombination event.
  • Although we defined the L and S types based on two tightly linked SNPs, strikingly, the separation between the L (blue) and S (red) types was maintained when we reconstructed the haplotype networks using all the SNPs in the SARS-CoV-2 genomes.
  • We propose that, although the L type newly evolved from the ancient S type, it transmits faster or replicates faster in human populations, causing it to accumulate more mutations than the S type.
  • Thus, our results suggest the L might be more aggressive than the S type due to the potentially higher transmission and/or replication rates.
  • One possible explanation [of the prevalence of S type] is that, since January 2020, the Chinese central and local governments have taken rapid and comprehensive prevention and control measures.
  • Our analyses of molecular evolution and population genetics suggested that some amino acid changes might be favored by natural selection during the evolution of SARS-CoV-2 and other related viruses.
  • In summary, our analyses of 103 sequenced SARS-CoV-2 genomes suggest that the L type is more aggressive than the S type and that human interference may have shifted the relative abundance of L and S type soon after the SARS-CoV-2 outbreak.

Read the study in full here.

IMAGE SOURCE: Creative Commons

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