Genetic Diversity and Evolution of the Biological Features of the Pandemic SARS-CoV-2

Nikonova, Alexandra; Файзулоев, Е. Б.; Gracheva, A. V.; Zverev,

doi:10.32607/actanaturae.11337

Cited by 9 publications

(4 citation statements)

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“…There are many published reports available describing the comparative study of genetic determinants with high-and low-virulence properties and mortality rates caused by HCoVs like SARS-CoV-1, SARS-CoV-2, and MERS-CoV in comparison to other HCoVs like HCoV-NL63, -229E, -OC43, and -HKU1 [53]. Global viromics studies of more than 3000 viral genomes collected from both humans and animals (SARS-CoV-1, MERS-CoV, and SARS-CoV-2) confirmed variations in four locations situated in the nucleoprotein gene (N) and S protein gene as compared to HCoV-NL63, -229E, -OC43, and -HKU1 [47,53]. The WHO has kept MERS-CoV on the priority list for performing detailed studies because of its continuous infection and spread to humans and camels in different locations [22].…”

Section: Discussionmentioning

confidence: 78%

“…The monitoring of HCoV infections at a molecular level with an emphasis on the genome and phylogeny enables us to elucidate the emergence of new variants/strains that may infect and cause diseases to new hosts, including animals and humans at different geographic locations. Seasonal HCoVs such as HCoV-NL63, -229E, -OC43, and -HKU1 cause only seasonal infections, while SARS-CoV-1, MERS-CoV, and SARS-CoV-2 are known to cause respiratory illnesses throughout the year [2,22,47,48]. Genetic changes in the viral genomes lead to disruption of the virus-and-host cell interactions, as well as changes in virus reproduction, virulence, pathogenicity, gene expression, and ultimately determine the outcome of the severe infection [47].…”

Section: Discussionmentioning

confidence: 99%

“…Seasonal HCoVs such as HCoV-NL63, -229E, -OC43, and -HKU1 cause only seasonal infections, while SARS-CoV-1, MERS-CoV, and SARS-CoV-2 are known to cause respiratory illnesses throughout the year [2,22,47,48]. Genetic changes in the viral genomes lead to disruption of the virus-and-host cell interactions, as well as changes in virus reproduction, virulence, pathogenicity, gene expression, and ultimately determine the outcome of the severe infection [47]. Due to the favorable climatic conditions, frequent recombination and mutation occurs in the coronavirus genome and new virus variants/strains and isolates emerge, which results in interspecies transmission and infection.…”

Section: Discussionmentioning

confidence: 99%

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Genomic Diversity and Recombination Analysis of the Spike Protein Gene from Selected Human Coronaviruses

Sohrab,

Alsaqaf,

Hassan

et al. 2024

Biology

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Human coronaviruses (HCoVs) are seriously associated with respiratory diseases in humans and animals. The first human pathogenic SARS-CoV emerged in 2002–2003. The second was MERS-CoV, reported from Jeddah, the Kingdom of Saudi Arabia, in 2012, and the third one was SARS-CoV-2, identified from Wuhan City, China, in late December 2019. The HCoV-Spike (S) gene has the highest mutation/insertion/deletion rate and has been the most utilized target for vaccine/antiviral development. In this manuscript, we discuss the genetic diversity, phylogenetic relationships, and recombination patterns of selected HCoVs with emphasis on the S protein gene of MERS-CoV and SARS-CoV-2 to elucidate the possible emergence of new variants/strains of coronavirus in the near future. The findings showed that MERS-CoV and SARS-CoV-2 have significant sequence identity with the selected HCoVs. The phylogenetic tree analysis formed a separate cluster for each HCoV. The recombination pattern analysis showed that the HCoV-NL63-Japan was a probable recombinant. The HCoV-NL63-USA was identified as a major parent while the HCoV-NL63-Netherland was identified as a minor parent. The recombination breakpoints start in the viral genome at the 142 nucleotide position and end at the 1082 nucleotide position with a 99% CI and Bonferroni-corrected p-value of 0.05. The findings of this study provide insightful information about HCoV-S gene diversity, recombination, and evolutionary patterns. Based on these data, it can be concluded that the possible emergence of new strains/variants of HCoV is imminent.

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Section: Discussionmentioning

confidence: 78%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Genomic Diversity and Recombination Analysis of the Spike Protein Gene from Selected Human Coronaviruses

Sohrab,

Alsaqaf,

Hassan

et al. 2024

Biology

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“…Thus, it turns out that the space of variants available to the SARS-CoV-2 coronavirus is quite narrow, and the trajectories of its development may be determined to some extent. Indeed, the SARS-CoV-2 genome has been shown to have a much lower mutation rate and genetic diversity compared to the SARS-CoV virus that caused the atypical pneumonia outbreak in 2002-2003(Jia et al, 2020Zhou et al, 2020;Nikonova et al, 2021). Thus, for example, for the SARS-CoV-2 S-protein, the d N and d S values appeared to be approximately 12 and 7 times lower than those for SARS-CoV (where d N is the fraction of sequences in a sample of genomes that contain non-synonymous mutations in a particular gene; d S is a similar value, but for synonymous mutations).…”

Section: Discussionmentioning

confidence: 99%

On the space of SARS-CoV-2 genetic sequence variants

Palyanov,

Palyanova

2023

Vestn. VOGiS

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The coronavirus pandemic caused by the SARS-CoV-2 virus, which humanity resisted using the latest advances in science, left behind, among other things, extensive genetic data. Every day since the end of 2019, samples of the virus genomes have been collected around the world, which makes it possible to trace its evolution in detail from its emergence to the present. The accumulated statistics of testing results showed that the number of confirmed cases of SARS-CoV-2 infection was at least 767.5 million (9.5 % of the current world population, excluding asymptomatic people), and the number of sequenced virus genomes is more than 15.7 million (which is over 2 % of the total number of infected people). These new data potentially contain information about the mechanisms of the variability and spread of the virus, its interaction with the human immune system, the main parameters characterizing the mechanisms of the development of a pandemic, and much more. In this article, we analyze the space of possible variants of SARS-CoV-2 genetic sequences both from a mathematical point of view and taking into account the biological limitations inherent in this system, known both from general biological knowledge and from the consideration of the characteristics of this particular virus. We have developed software capable of loading and analyzing SARS-CoV-2 nucleotide sequences in FASTA format, determining the 5’ and 3’ UTR positions, the number and location of unidentified nucleotides (“N”), performing alignment with the reference sequence by calling the program designed for this, determining mutations, deletions and insertions, as well as calculating various characteris tics of virus genomes with a given time step (days, weeks, months, etc.). The data obtained indicate that, despite the apparent mathematical diversity of possible options for changing the virus over time, the corridor of the evolutionary trajectory that the coronavirus has passed through seems to be quite narrow. Thus it can be assumed that it is determined to some extent, which allows us to hope for a possibility of modeling the evolution of the coronavirus.

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