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Full Vaccination Suppresses SARS-CoV-2 Delta Variant Mutation Frequency | medRxiv | Virus World | Scoop.it

From www.medrxiv.org - August 12, 2021 12:29 PM

This study presents the first evidence that full vaccination against COVID-19 suppresses emergent mutations of SARS-CoV-2 delta variants. An evolution algorithm, Tajima’s D test with a threshold value as -2.50, can provide a promising tool to forecast new COVID-19 outbreaks.

Question It remains unclear how human interventions (vaccinations, lockdowns, etc.) affect viral mutation or generate selection pressure of SARS-CoV-2. It has also been obscure if there are differences in various geographic populations.

Findings The vaccination coverage rate is inversely correlated to the mutation frequency of the SARS-CoV-2 delta variants in 16 countries of 20 countries studied. We also discovered delta variants evolved differently under the positive selection pressure in the United Kingdom and India.

Meaning Full vaccination against COVID-19 is critical to suppress emergent mutations. Tajima’s D test score, with a threshold value as -2.50, can provide a promising tool to forecast new COVID-19 outbreaks.

Available as preprint in medRxiv (August 10, 2021):

https://doi.org/10.1101/2021.08.08.21261768

Genomic Diversity of SARS-CoV-2 Can Be Accelerated by a Mutation in the Nsp14 Gene | bioRxiv | Virus World | Scoop.it

From www.biorxiv.org - December 26, 2020 11:43 AM

Nucleotide substitution rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is relatively low compared to the other RNA viruses because coronaviruses including SARS-CoV-2 encode non-structural protein 14 (nsp14) that is an error-correcting exonuclease protein. In this study, to understand genome evolution of SARS-CoV-2 in the current pandemic, we examined mutations of SARS-CoV-2 nsp14 which could inhibit its error-correcting function. First, to obtain functionally important sites of nsp14, we examined 62 representative coronaviruses belonging to alpha, beta, gamma, delta, and unclassified coronaviruses. As a result, 99 out of 527 amino acid sites of nsp14 were evolutionarily conserved. We then examined nsp14 sequences obtained from 28,082 SARS-CoV-2 genomes and identified 6 amino acid changes in nsp14 mutants that were not detected in the 62 representative coronaviruses. We examined genome substitution rates of these mutants and found that an nsp14 mutant with a proline to leucine change at position 203 (P203L) showed a higher substitution rate (35.9 substitutions/year) than SARS-CoV-2 possessing wild-type nsp14 (19.8 substitutions/year).

We confirmed that the substitution rate of the P203L is significantly higher than those of other variants containing mutations in structural proteins. Although the number of SARS-CoV-2 variants containing P203L mutation of nsp14 is limited (26), these mutants appeared at least 10 times independently in the current pandemic. These results indicated that the molecular function of nsp14 is important for survival of various coronaviruses including SARS-CoV-2 and that some mutations such as P203L of nsp14 inhibiting its error-correcting function are removed rapidly due to their deleterious effects.

Preprint available in bioRxiv (Dec. 26, 2020):

https://doi.org/10.1101/2020.12.23.424231

Full Vaccination Suppresses SARS-CoV-2 Delta Variant Mutation Frequency | medRxiv

Genomic Diversity of SARS-CoV-2 Can Be Accelerated by a Mutation in the Nsp14 Gene | bioRxiv